Tofogliflozin

Tofogliflozin (INN, USAN, codenamed CSG452) is an experimental drug for the treatment of diabetes mellitus and is being developed by Chugai Pharma in collaboration with Kowa and Sanofi. It is an inhibitor of subtype 2 sodium-glucose transport protein (SGLT2), which is responsible for at least 90% of the glucose reabsorption in the kidney. , the drug is in Phase III clinical trials.
Chemistry.
The active moiety or anhydrous form (ChemSpider ID: 28530778, CHEMBL2110731) has the chemical formula C22H26O6 and a molecular mass of 386.44 g/mol.
The United States Adopted Name "tofogliflozin" applies to the monohydrate, which is the form used as a drug. The International Nonproprietary Name "tofogliflozin" applies to the anhydrous compound and the drug form is referred to as "tofogliflozin hydrate".


Skor

Skor is a chocolate toffee bar produced by The Hershey Company. It was first marketed in the United States in 1981 and later launched in Canada in 1983. The Skor bar consists of a thin slab of butter toffee covered in a milk chocolate coating. It was created to compete with the Heath bar, and is similar in style to both Heath and a Daim bar. Skor is available from retail stores as a single- or king size-wrapped candy bar in a 1.4 oz (39 gram) portion
Heath Bar Comparison.
The Skor bar was originally created to compete with the Heath bar, produced by the Heath Company and later the Leaf Candy Company. Hershey eventually acquired the Leaf, Inc. company in 1996 and currently manufactures the Heath bar under the Hershey name. However, the Hershey company continues to market the Skor bar as well.
The Skor bar is very similar to its former competitor, the Heath bar. However, there are differences between the two, such as the Skor bar being slightly thinner than the Heath bar.
Name.
"Skör" (with umlaut dots over the "o") is Swedish for "brittle", and the crown that appears in the product's logo is identical to that found in the Swedish national emblem of "Tre Kronor" ("Three Crowns"). However, if one ignores the umlaut, the name becomes "Skor", which means "shoes" in Swedish.


CD20-like family

In molecular biology, the CD20-like family of proteins includes the CD20 protein and the beta subunit of the high affinity receptor for IgE Fc, MS4A2. MS4A2 has a tetrameric structure consisting of a single IgE-binding alpha subunit, a single beta subunit, and two disulfide-linked gamma subunits. It has four putative transmembrane segments and a probable topology where both amino- and carboxy termini protrude into the cytoplasm. This family also includes LR8 like proteins from humans (TMEM176B), mice and rats. The function of the human LR8 protein is unknown although it is known to be strongly expressed in the lung fibroblasts. This family also includes sarcospan, a transmembrane component of dystrophin-associated glycoprotein. Loss of the sarcoglycan complex and sarcospan alone is sufficient to cause muscular dystrophy. The role of the sarcoglycan complex and sarcospan is thought to be to strengthen the dystrophin axis connecting the basement membrane with the cytoskeleton.


6-oxocineole dehydrogenase

In enzymology, a 6-oxocineole dehydrogenase () is an enzyme that catalyzes the chemical reaction
The 4 substrates of this enzyme are 6-oxocineole, NADPH, H+, and O2, whereas its 3 products are 1,6,6-trimethyl-2,7-dioxabicyclo[3.2.2]nonan-3-one, NADP+, and H2O.
This enzyme belongs to the family of oxidoreductases, specifically those acting on paired donors, with O2 as oxidant and incorporation or reduction of oxygen. The oxygen incorporated need not be derived from O2 with NADH or NADPH as one donor, and incorporation of one atom o oxygen into the other donor. The systematic name of this enzyme class is 6-oxocineole,NADPH:oxygen oxidoreductase. This enzyme is also called 6-oxocineole oxygenase. This enzyme participates in terpenoid biosynthesis.


Agnuside

Agnuside is a chemical compound found in "Vitex agnus-castus". Agnuside is the ester of aucubin and "p"-hydroxybenzoic acid.


Cortisone alpha-reductase

In enzymology, a cortisone alpha-reductase () is an enzyme that catalyzes the chemical reaction
Thus, the two substrates of this enzyme are 4,5alpha-dihydrocortisone and NADP+, whereas its 3 products are cortisone, NADPH, and H+.
This enzyme belongs to the family of oxidoreductases, specifically those acting on the CH-CH group of donor with NAD+ or NADP+ as acceptor. The systematic name of this enzyme class is 4,5alpha-dihydrocortisone:NADP+ Delta4-oxidoreductase. Other names in common use include cortisone Delta4-5alpha-reductase, microsomal steroid reductase (5alpha), Delta4-3-ketosteroid reductase (5alpha), Delta4-3-oxosteroid-5alpha-reductase, NADPH:Delta4-3-oxosteroid-5alpha-oxidoreductase, and Delta4-5alpha-reductase.


N-Acetylmannosamine

"N"-Acetylmannosamine is a hexosamine monosaccharide. It is a neutral, stable naturally occurring compound. N-Acetylmannosamine is also known as N-Acetyl-D-mannosamine monohydrate, (which has the CAS Registry Number: 676347-48-1), N-Acetyl-D-mannosamine which can be abbreviated to ManNAc or, less commonly, NAM).
ManNAc is the first committed biological precursor of N-acetylneuraminic acid (Neu5Ac, sialic acid) (Figure 1). Sialic acids are the negatively charged, terminal monosaccharides of carbohydrate chains that are attached to glycoproteins and glycolipids (glycans).
Biological role of ManNAc.
ManNAc is the first committed biological precursor of Neu5Ac.
The initiation of sialic acid biosynthesis occurs in the cytoplasm. The main substrate for this pathway is UDP-GlcNAc, which is derived from glucose. In the rate-limiting step of the pathway, UDP-GlcNAc is converted into ManNAc by UDP-GlcNAc 2-epimerase, encoded by the epimerase domain of GNE. ManNAc is phosphorylated by ManNAc kinase encoded by the kinase domain of GNE. Sialic acid becomes “activated” by CMP-sialic acid synthetase in the nucleus. CMP-sialic acid acts as a sialic acid donor to sialylate glycans on nascent glycoproteins and glycolipids in the Golgi apparatus; it also acts as a cytoplasmic feedback inhibitor of the UDP-GlcNAc 2-epimerase enzyme by binding to its allosteric site.
The UDP-GlcNAc 2-epimerase kinase is the rate limiting step in sialic acid biosynthesis. If the enzyme does not work efficiently the organism cannot function correctly.
Synthesis.
There are several ways in which ManNAc can be synthesised and three examples follow.
ManNAc is now manufactured in large quantities by New Zealand Pharmaceuticals Ltd, in a commercial process from N-acetylglucosamine.
Uses.
Sialylation of recombinant proteins.
There is normally some level of glycan sialylation within a glycoprotein, but with the observation that incomplete sialylation can lead to reduced therapeutic activity, it becomes relevant to assess the cell-lines and culture media to “humanise” the glycoprotein to improve performance and yield and reduce manufacturing costs. Keppler et al. demonstrated that the GNE enzyme was rate limiting in human hematopoietic cell lines and affected efficiency in cell surface sialylation. The activity of the GNE enzyme is now recognised as one of the defining features in the efficient production of sialylated recombinant glycoprotein therapeutic drugs. Improved sialylation after the addition of ManNAc and other supporting ingredients to the culture medium not only increases manufacturing yield, but also improves therapeutic efficacy by increasing solubility, increasing half-life and reducing immunogenicity by reducing the formation of antibodies to the therapeutic glycoprotein
Therapeutic potential.
When the GNE epimerase kinase does not function correctly in the human body thereby reducing the available ManNAc, it is reasonable to assume that treatment with ManNAc could assist with improving health benefits. The therapeutic potential for ManNAc is currently being assessed in several diseases in which therapy could benefit from its ability to enhance the biosynthesis of sialic acid.
GNE myopathy.
The disease GNE myopathy [formerly known as hereditary Inclusion Body Myopathy (HIBM), and Distal Myopathy with Rimmed Vacuoles (DMRV)] is manifested as progressive muscle weakness. GNE myopathy is a rare genetic disorder caused by hyposialylated muscle proteins and glycosphingolipids because there is insufficient metabolic ManNAc to form the Neu5Ac terminal sugar. There is no available therapy to treat GNE myopathy.
Kidney diseases.
There is a growing body of evidence that reduced activity of the GNE enzyme in the sialylation pathway in kidney tissue could contribute to several glomerular kidney diseases, due to the lack of the Neu5Ac terminal sugar on several kidney glycoproteins.
Three kidney diseases that affect both children and adults are minimal change disease (MCD), focal segmental glomerulosclerosis (FSGS) and membranous nephropathy (MN). These diseases are characterized by proteinuria (protein in the urine) and in the case of FSGS, a tendency to progressive scarring of the glomerulus (the filtering units of the kidneys) that leads to end-stage kidney disease. Several therapies are available for these diseases, but these therapies do not provide lasting reduction in proteinuria for many subjects and there can be severe side-effects.
There is now substantial pre-clinical evident correlating with human kidney biopsy samples, that some patients with MCD, FSGS or MN have kidney sialic acid insufficiency on their glomerular proteins. ManNAc therapy may increase sialic acid production and subsequently increase sialylation of glomerular proteins.


Talopeptin

Talopeptin is a chemical compound derived from cultures of "Streptomyces". It is a known reversible inhibitor of thermolysin and is expected to inhibit other metalloproteinases. Chemically, talopeptin differs from its closely related peptidase inhibitor phosphoramidon by a single stereocenter.


DNA-3-methyladenine glycosylase II

DNA-3-methyladenine glycosylase II () is an enzyme that catalyses the following chemical reaction:
Involved in the removal of alkylated bases from DNA in "Escherichia coli".
Evolution.
Through the process of convergent evolution, there are at least two unrelated protein folds that share the same DNA-3-methyladenine glycosylase activity. The first, the AlkA N-terminal domain, is found in bacteria . The second, methylpurine-DNA glycosylase (MPG) is found in vertebrates including humans.
Nomenclature.
DNA-3-methyladenine glycosylase II is also known as


4-Thiouridine

4-Thiouridine is an atypical nucleotide formed with the 4-thiouracil base found in transfer RNA (tRNA).


Neuroglobin

Neuroglobin is a member of the vertebrate globin family involved in cellular oxygen homeostasis and reactive oxygen/nitrogen scavenging. It is an intracellular hemoprotein expressed in the central and peripheral nervous system, cerebrospinal fluid, retina and endocrine tissues. Neuroglobin is a monomer that reversibly binds oxygen with an affinity higher than that of hemoglobin. It also increases oxygen availability to brain tissue and provides protection under hypoxic or ischemic conditions, potentially limiting brain damage. Neuroglobin were in the past found only in vertebrate neurons, but recently in 2013, were found in the neurons of unrelated protostomes, like photosynthesis acoel as well as radiata such as jelly fish. In addition to neurons, neuroglobin is present in astrocytes in certain pathologies of the rodent brain and in the physiological seal brain. This is thought to be due to convergent evolution. It is of ancient evolutionary origin, and is homologous to nerve globins of invertebrates. Recent research confirmed the presence of human neuroglobin protein in cerebrospinal fluid (CSF).
Neuroglobin was first identified by Thorsten Burmester "et al." in 2000.
The 3D structure of human neuroglobin was determined in 2003. The next year, murine neuroglobin was determined at a higher resolution.
A practical treatment for carbon monoxide poisoning based on binding of CO by neuroglobin (Ngb) with a mutated distal histidine (H64Q) appears to be possible.


Cinnamoyl-CoA reductase

Cinnamoyl-CoA reductase (), systematically named cinnamaldehyde:NADP+ oxidoreductase (CoA-cinnamoylating) but commonly referred to by the acronym CCR, is an enzyme that catalyzes the reduction of a substituted cinnamoyl-CoA to its corresponding cinnamaldehyde, utilizing NADPH and H+ and releasing free CoA and NADP+ in the process. Common biologically relevant cinnamoyl-CoA substrates for CCR include "p"-coumaroyl-CoA and feruloyl-CoA, which are converted into "p"-coumaraldehyde and coniferaldehyde, respectively, though most CCRs show activity toward a variety of other substituted cinnamoyl-CoA's as well. Catalyzing the first committed step in monolignol biosynthesis, this enzyme plays a critical role in lignin formation, a process important in plants both for structural development and defense response.
Structure.
The first confirmed CCR was isolated from soybean ("Glycine max") in 1976. However, crystal structures have so far been reported for just three CCR homologs: "Petunia x hybrida" CCR1, "Medicago truncatula" CCR2, and "Sorghum bicolor" CCR1. While the enzyme crystallizes as an asymmetric dimer, it is thought to exist as a monomer in the cytoplasm, with each individual protein having a bilobal structure consisting of two domains surrounding a large, empty inner cleft for substrate binding. Typical CCRs have a molecular weight of around 36-38 kDa.
The domain containing the enzyme's N-terminus consists of several alpha helices and six beta strands that, in addition to a seventh strand connected to the C-terminus side of the enzyme, form a parallel beta sheet structure known as a Rossmann fold. In CCR, this fold structure, a common motif amongst proteins, serves as a binding domain for NADPH. The second domain, which consists of several alpha helices, beta strands, and extended loops, is responsible for binding the cinnamoyl-CoA substrate. These two domains are situated in such a way that the binding sites for NADPH and cinnamoyl-CoA are positioned closely to one another at the lobes' interface.
Though attempts to cocrystallize the enzyme with a bound cinnamoyl-CoA have thus far been unsuccessful, molecular docking studies indicate that the CoA segment of these molecules folds around to bind along the outer part of the inter-domain cleft, while the phenyl-containing portion of these substrates likely binds in the deepest part of the cleft. This inner part of the pocket contains several amino acids with nonpolar side chains necessary for stabilization of the hydrophobic phenyl ring in addition to a tyrosine residue important for hydrogen bond formation with the ring's 4-hydroxyl group. The particular identities of the nonpolar residues are believed to play a critical role in determining substrate specificity.
Mechanism.
The mechanism for the reduction of the CoA thioester to the aldehyde involves a hydride transfer to the carbonyl carbon from NADPH, forming a tetrahedral intermediate with a formal negative charge on the oxygen atom. This negative charge is thought to be stabilized partially via hydrogen bonding with the hydrogen atoms of nearby tyrosine and serine side chains. The serine and tyrosine residues are conserved across all CCRs as part of a catalytic triad along with lysine, which is thought to control the pKa of the tyrosine via electrostatic interactions with the ribose group of the NADPH.
The tetrahedral intermediate then collapses, kicking out the CoA and forming an aldehyde as the final product. The thiolate of the CoA is protonated either as it leaves by a nearby residue or after it is free from the binding pocket and out of the enzyme all-together; the exact mechanism is currently unclear, but evidence suggests that a cysteine residue may play the role of thiolate proton donor.
Biological Function.
Phylogenomic analysis indicates that enzymes with true CCR activity first evolved in the of land plants. Most if not all modern land plants and all vascular plants are believed to have at least one functional CCR, an absolute requirement for any plant species with lignified tissues. Most CCR homologs are highly expressed during development, especially in stem, root, and xylem cells which require the enhanced structural support provided by lignin. However, certain CCRs are not constitutively expressed throughout development and are only up-regulated during enhanced lignification in response to stressors such as pathogen attack. CCR is especially important because it acts as a final control point for regulation of metabolic flux toward the monolignols and therefore toward lignin as well; prior to this reduction step, the cinnamoyl-CoA's can still enter into other expansive specialized metabolic pathways. For example, feruloyl-CoA is a precursor of the coumarin scopoletin, a compound believed to play an important role in plant pathogen response. CCR also plays a role in determining lignin composition by regulating levels of the different monomers according to its specific activity toward particular cinnamoyl-CoA's. Monocots and dicots, for example, tend to have very different lignin patterns: lignin found in monocots typically has a higher percentage of "p"-coumaroyl alcohol-derived subunits, while lignin found in dicots is typically composed of almost entirely coniferyl alcohol and sinapyl alcohol subunits. As can be seen in the diagram shown to the right, these monolignols are derived directly from their corresponding aldehydes, except in the case of sinapyl alcohol - while several CCR homologs have been shown to act on sinapoyl-CoA "in vitro", it is unclear whether this activity is biologically relevant and most current models of the lignin pathway do not include this reaction as a valid step.
Recent studies indicate that many plant species have two distinct homologs of CCR with differential activity "in planta". In some plants the two homologs vary primarily by substrate specificity. For example, CCR1 of the model legume "Medicago truncatula" shows strong preference toward feruloyl-CoA (typical of most CCRs), while the plant's CCR2 exhibits a clear preference for both "p"-coumaroyl- and caffeoyl-CoA. This second CCR, which is allosterically activated by its preferred substrates but inhibited by feruloyl-CoA, is thought to act as part of a shunt pathway toward coniferaldehyde that enhances the pathway's overall flexibility and robustness in different conditions. In other cases though, the two homologs vary primarily by expression pattern. In the model plant "Arabidopsis thaliana", for instance, the CCR1 and CCR2 homologs both display higher activity toward feruloyl-CoA than other substrates, but CCR2 is only expressed transiently during bacterial infection. The homolog pair in switchgrass ("Panicum virgatum") differs in both ways: CCR2 prefers "p"-coumaroyl- and caffeoyl-CoA and is only expressed under specifically induced conditions, while CCR1 prefers feruloyl-CoA and is expressed constitutively in lignifying tissue.
Regulation of CCR expression is thought to occur primarily at the transcriptional level. In "Arabidopsis thaliana", several of the required transcription factors for CCR expression have actually been identified, including MYB58 and MYB63, both of which are implicated generally in secondary cell wall formation. It has been shown that over-expression of these two transcription factors results in a 2- to 3-fold increase in CCR mRNA transcripts, though intriguingly, the up-regulation of genes further upstream in the monolignol pathway is even greater. Non-transcriptional regulation of CCR, however, can be important as well. In rice ("Oryza sativa"), for example, evidence suggests that the CCR1 homolog is an effector of Rac1, a small GTPase important for plant defense response. In this case, the Rac1 protein is proposed to activate CCR upon binding, leading to enhanced monolignol biosynthesis. Because Rac1 also activates NADPH oxidase, which produces peroxides critical for monolignol polymerization, overall lignin biosynthesis is enhanced as well.
Biotechnological significance.
Efforts to engineer plant cell wall formation for enhanced biofuel production commonly target lignin biosynthesis in order to reduce lignin content and thereby improve yields of ethanol from cellulose, a complex polysaccharide important for cell wall structure. Lignin is troublesome for biofuel production because it is the main contributor to plant biomass recalcitrance due to its toughness and heterogeneity. By reducing lignin content, the cellulose is more easily accessible to the chemical and biological reagents used to break it down. Lowering the expression level of CCR in particular has emerged as a common strategy for accomplishing this goal, and this strategy has resulted in successful lignin content reduction and increased ethanol production from several plant species including tobacco ("Nicotiana tabacum") and poplar ("Populus tremula x Populus alba"). Challenges with this strategy include the wide variation in expression levels associated with current plant genetic transformation technologies in addition to the dramatic decrease in overall growth and biomass that typically accompanies low lignin production. However, it has been shown that by targeting CCR down-regulation to specific tissue types or coupling it to down-regulation of cinnamyl alcohol dehydrogenase (CAD), the latter challenge at least can be somewhat mitigated.


Zoptarelin doxorubicin

Zoptarelin doxorubicin (developmental code names AEZS-108, AN-152) consists of doxorubicin linked to a small peptide agonist to the luteinizing hormone-releasing hormone (LHRH) receptor. It has been developed as a potential treatment for a number of human cancers. The LHRH receptor is aberrantly present on the cell surface of approximately 80% of endometrial and ovarian cancers, 86% of prostate cancers and about 50% of breast cancers. Whereas in normal tissues, expression of this receptor is mainly confined to the pituitary gland, reproductive organs and hematopoietic stem cells. To a lesser extent the LHRH receptor is also found on the surface of bladder, colorectal, and pancreatic cancers, sarcomas, lymphomas, melanomas, and renal cell carcinomas.
The proposed method of action is that upon administration zoptarelin doxorubicin binds to the LHRH receptor and is subsequently internalized, concentrating the toxic doxorubicin within cancer cells and the small subset of normal tissues, as opposed to the completely systemic distribution observed with untargeted chemotherapeutics. The specific targeting of the doxorubicin to LHRH receptor bearing cells is also proposed to reduce the cardiotoxicity observed in the administration of unconjugated doxorubicin.
Zoptarelin doxorubicin was invented by Andrew V. Schally while at the Tulane University School of Medicine, New Orleans and subsequently at the Sylvester Comprehensive Cancer Center, University of Miami. It has been subsequently developed by AEterna Zentaris Inc. In June 2016, Aeterna stated that it plans to submit an NDA to the FDA by mid 2017. Zoptarelin doxorubicin was discontinued for all indications under development in May 2017.
The U.S. Food and Drug Administration (FDA) has granted it orphan drug status for ovarian cancer and endometrial cancer.
Clinical trials.
Promising results have been reported from a phase II clinical trial for ovarian cancer and endometrial cancer. Phase II trials have also been undertaken for prostate, breast and bladder cancer, although no results for these trials have been reported in peer-reviewed literature. A phase I trial in prostate cancer indicated that nine out ten evaluable patients achieved disease stabilization through administration of zoptarelin doxorubicin.
A phase III trial for endometrial cancer was initiated in April 2013 and it the primary completion date is estimated to be December 2016. In May 2017 the results were disclosed, showing that the drug did not extend overall survival nor did it improve the safety profile compared to doxorubicin.


Lipoprotein lipase deficiency

Lipoprotein lipase deficiency is a genetic disorder in which a person has a defective gene for lipoprotein lipase, which leads to very high triglycerides, which in turn causes stomach pain and deposits of fat under the skin, and which can lead to problems with the pancreas and liver, which in turn can lead to diabetes. The disorder only occurs if a child acquires the defective gene from both parents (it is autosomal recessive). It is managed by restricting fat in diet to less than 20 g/day.
Signs and symptoms.
The disease often presents in infancy with colicky pain, failure to thrive, and other symptoms and signs of the chylomicronemia syndrome. In women the use of estrogens or first pregnancy are also well known trigger factors for initial manifestation of LPLD. At all ages, the most common clinical manifestation is recurrent abdominal pain and acute pancreatitis. The pain may be epigastric, with radiation to the back, or it may be diffuse, with the appearance of an emergent acute abdomen. Other typical symptoms are eruptive xanthomas (in about 50% of patients), lipemia retinalis and hepatosplenomegaly.
Complications.
Patients with LPLD are at high risk of acute pancreatitis, which can be life-threatening, and can lead to chronic pancreatic insufficiency and diabetes.
Diagnosis.
Lab tests show massive accumulation of chylomicrons in the plasma and corresponding severe hypertriglyceridemia. Typically, the plasma in a fasting blood sample appears creamy (plasma lactescence).
Familial LPL deficiency should be considered in anyone with severe hypertriglyceridemia and the chylomicronemia syndrome. The absence of secondary causes of severe hypertriglyceridemia (like e.g. diabetes, alcohol, estrogen-, glucocorticoid-, antidepressant- or isotretinoin-therapy, certain antihypertensive agents, and paraproteinemic disorders) increases the possibility of LPL deficiency. In this instance besides LPL also other loss-of-function mutations in genes that regulate catabolism of triglyceride-rich lipoproteins (like e.g. ApoC2, ApoA5, LMF-1, GPIHBP-1 and GPD1) should also be considered
The diagnosis of familial lipoprotein lipase deficiency is finally confirmed by detection of either homozygous or compound heterozygous pathogenic gene variants in "LPL" with either low or absent lipoprotein lipase enzyme activity.
Lipid measurements
· Milky, lipemic plasma revealing severe hyperchylomicronemia;
· Severely elevated fasting plasma triglycerides (>2000 mg/dL);
LPL enzyme
· Low or absent LPL activity in post-heparin plasma;
· LPL mass level reduced or absent in post-heparin plasma;
Molecular genetic testing
The LPL gene is located on the short (p) arm of chromosome 8 at position 22. More than 220 mutations in the LPL gene have been found to cause familial lipoprotein lipase deficiency so far.
Treatment.
Treatment of LPLD has two different objectives: immediate prevention of pancreatitis attacks and long term reduction of cardiovascular disease risk. Treatment is mainly based on medical nutrition therapy to maintain plasma triglyceride concentration below 11,3 mmol/L (1000 mg/dL). Maintenance of triglyceride levels below 22,6 mmol/L (2000 mg/dL) prevents in general from recurrent abdominal pain.
Strict low fat diet and avoidance of simple carbohydrates.
Restriction of dietary fat to not more than 20 g/day or 15% of the total energy intake is usually sufficient to reduce plasma triglyceride concentration, although many patients report that to be symptom free a limit of less than 10g/day is optimal. Simple carbohydrates should be avoided as well. Medium-chain triglycerides can be used for cooking, because they are absorbed into the portal vein without becoming incorporated into chylomicrons. Fat-soluble vitamins A, D, E, and K, and minerals should be supplemented in patients with recurrent pancreatitis since they often have deficiencies as a result of malabsorption of fat. However, the diet approach is difficult to sustain for many of the patients.
Lipid lowering drugs.
Lipid-lowering agents such as fibrates and omega-3-fatty acids can be used to lower TG levels in LPLD; however, those drugs are very often not effective enough to reach treatment goals in LPLD patients. Statins should be considered to lower elevated non-HDL-Cholesterol.
Additional measures are avoidance of agents known to increase endogenous triglyceride levels, such as alcohol, estrogens, diuretics, isotretinoin, antidepressants (e.g. sertraline) and b-adrenergic blocking agents.
Gene therapy.
In 2012, the European Commission approved alipogene tiparvovec (Glybera), a gene therapy for adults diagnosed with familial LPLD (confirmed by genetic testing) and suffering from severe or multiple pancreatitis attacks despite dietary fat restrictions. It was the first gene therapy to receive marketing authorization in Europe; it was priced at about $1 million per treatment, and as of 2016, only one person had been treated with it commercially. A total of 31 patients were treated with Glybera, most for free in clinical trials before the drug was taken off the market.
Incidence.
The disorder affects about 1 out of 1,000,000 people; however, epidemiological data are limited and there are regional differences due to cofounder effect (e.g. in Canada) or intermarriage.


Signalosome

Signalosomes are large supramolecular protein complexes that undergo clustering (oligomerisation or polymerisation) and/or colloidal phase separation to form biomolecular condensates that increase the local concentration and signalling activity of the individual components. They are an example of molecular self-assembly and self-organisation in cell biology.
Examples.
Wnt signalosome: Transduction of Wnt signals from the plasma membrane depends on clustering of LRP6 receptors with Dishevelled (Dvl) proteins to recruit the Axin complex for inactivation.
B-cell receptor (BCR) signalosome: The B-cell receptor (BCR) binds antigen and undergoes clustering to induce signal transduction.
T-cell receptor (TCR) signalosome: Antigen presentation to T-cells is recognised by the T-cell receptor (TCR), which initiates clustering and activation of downstream signalling to induce T-cell responses.
COP9 signalosome: Catalyses the hydrolysis of NEDD8 protein from the Cullin subunit of Cullin-RING ubiquitin ligases (CRL). Therefore, it is responsible for CRL deneddylation – at the same time, it is able to bind deneddylated cullin-RING complex and retain them in deactivated form. COP9 signalosome thus serves as a sole deactivator of CRLs.
RIP1/RIP3 Necrosome: A signalling complex involved in necrotic cell death.
Inflammasomes: The AIM2 and NLRP3 inflammasomes are filamentous assemblies that elicit host defense inside cells by activating caspase-1 for cytokine maturation and cell death.


Pleurotolysin

Pleurotolysin (TC# 1.C.97.1.1), a sphingomyelin-specific cytolysin. Its A (17 kDa; Q8X1M9) and B (59 kDa; Q5W9E8) components are assembled into a transmembrane pore complex. The Pleurotolysin Pore-Forming (Pleurotolysin) Family (TC# 1.C.97) is a family of pore forming proteins belonging to the MACPF superfamily.
Function.
Proteins with membrane-attack complex/perforin (MACPF) domains have a variety of biological roles, including defense and attack, organismal development, and cell adhesion and signaling. The distribution of these proteins in fungi appears to be restricted to some Pezizomycotina and Basidiomycota species only, in correlation with the aegerolysins (PF06355). These two protein groups coincide in only a few species, and they operate as cytolytic bi-component pore-forming agents. Representative proteins include pleurotolysin B, which has a MACPF domain, the aegerolysin-like protein pleurotolysin A, and the very similar ostreolysin A (TC# 1.C.97.3.2) that has been purified from oyster mushroom ("Pleurotus ostreatus"). These act in concert to perforate natural and artificial lipid membranes with high cholesterol and sphingomyelin contents. The complex has a 13-meric rosette-like structure with a central lumen that is ~ 4-5 nm in diameter. The opened transmembrane pore is non-selectively permeable to ions and smaller neutral solutes, and is a cause of cytolysis of a colloid-osmotic type.
Research.
Sakurai et al. 2004 cloned complementary and genomic DNAs encoding pleurotolysin, and studied pore-forming properties of recombinant proteins. Recombinant pleurotolysin A lacking the first methionine was purified as a 17-kDa protein with sphingomyelin-binding activity. The cDNA for pleurotolysin B encoded a precursor consisting of 523 amino acyl residues, of which 48 N-terminal amino acyl residues were absent in natural pleurotolysin B. Mature and precursor forms of pleurotolysin B were expressed as insoluble 59- and 63-kDa proteins, respectively. Although neither recombinant pleurotolysin A nor B alone was hemolytically active at higher concentrations of up to 100 mg/ml, they cooperatively assembled into a membrane pore complex on human erythrocytes and lysed the cell.
Homologues.
In this TC family, both constituents of pleurotolysin and ostreolysin (A and B) are included under TC#s 1.C.97.1.1 and 1.C.97.1.2, respectively. However, homologues of Pleurotolysin B are found under TC#s 1.C.97.1.3 - 1.C.97.1.9 while homologues of Pleurotolysin A are found under TC#s 1.C.97.2.1 - 1.C.97.2.4 and TC#s 1.C.97.3.1 - 1.C.97.3.8. Pleurotolysins A are not homologous to Pleurotolysins B. While some homologues depend on the presence of both constituents for pore formation, as noted for both pleurotolysin and ostreolysin, some homologues of both A and B can form pores without the other. While Pleurotolysin B is in the MACPF superfamily (TC# 1.C.39) while Pleurotolysin A is in the Aegerolysin superfamily.
Erylysin.
Another two-component hemolysin, erylysin A and B (EryA and EryB; TC# 1.C.97.1.2), was isolated from an edible mushroom, "Pleurotus eryngii". Hemolytic activity was exhibited only by the EryA and EryB mixture.
Aegerolysin.
While Pleurotolysin B is in the MACPF superfamily (TC# 1.C.39), Pleurotolysin A is in the Aegerolysin superfamily. Several members of the Aegerolysin family have been used as tools to detect and visualize ceramide phosphoethanolamine, a major sphingolipid in invertebrates but not in animals. It may be distantly related to members of the Equinatoxin Family (TC# 1.C.38).
The aegerolysin family consists of several bacterial and eukaryotic aegerolysin-like proteins. It has been found that aegerolysin and ostreolysin are expressed during formation of primordia and fruiting bodies and possibly play a role in the initial phase of fungal fruiting. The bacterial members of this family are expressed during sporulation. Ostreolysin is cytolytic to various erythrocytes and tumor cells because of pore formation. Several members of the Aegerolysin family have been used as tools to detect and visualize ceramide phosphoethanolamine, a major sphingolipid in invertebrates but not in animals. It may be distantly related to members of the Equinatoxin Family (TC# 1.C.38).


Estradiol furoate

Estradiol furoate (EF), or estradiol 17β-furoate, sold under the brand name Di-Folliculine, is an estrogen medication and estrogen ester which is no longer marketed. It is the C17β furoate ester of estradiol. Estradiol benzoate has also been marketed under the brand name Di-Folliculine, and should not be confused with estradiol furoate.
The duration of action of the related estradiol ester estradiol 3-furoate by intramuscular injection was studied in women in 1952. Its duration in oil solution was found to be similar to that of estradiol benzoate in oil solution and shorter than that of estradiol dipropionate in oil solution.


Raffinose

Raffinose is a trisaccharide composed of galactose, glucose, and fructose. It can be found in beans, cabbage, brussels sprouts, broccoli, asparagus, other vegetables, and whole grains. Raffinose can be hydrolyzed to D-galactose and sucrose by the enzyme α-galactosidase (α-GAL), an enzyme not found in the human digestive tract. α-GAL also hydrolyzes other α-galactosides such as stachyose, verbascose, and galactinol, if present. The enzyme does not cleave β-linked galactose, as in lactose.
Chemical properties.
The raffinose family of oligosaccharides (RFOs) are alpha-galactosyl derivatives of sucrose, and the most common are the trisaccharide raffinose, the tetrasaccharide stachyose, and the pentasaccharide verbascose. RFOs are almost ubiquitous in the plant kingdom, being found in a large variety of seeds from many different families, and they rank second only to sucrose in abundance as soluble carbohydrates.
Raffinose may have a form of a white crystalline powder. It is odorless and has a sweet taste approximately 10% that of sucrose.
Biochemical properties.
Energy source.
It is non-digestible in humans and other monogastric animals (pigs and poultry) who do not possess the α-GAL enzyme to break down RFOs. These oligosaccharides pass undigested through the stomach and small intestine. In the large intestine, they are fermented by bacteria that do possess the α-GAL enzyme and make short-chain fatty acids (SCFA)(acetic, propionic, butyric acids), as well as the flatulence commonly associated with eating beans and other vegetables. These SCFAs have been recently found to impart a number of health benefits. α-GAL is present in digestive aids such as the product Beano.
Disease relevance.
Research has shown that the differential ability to utilize raffinose by strains of the bacteria "Streptococcus pneumoniae", impacts their ability to cause disease.
Uses.
Procedures concerning cryopreservation have used raffinose to provide hypertonicity for cell desiccation prior to freezing. Either raffinose or sucrose is used as a base substance for sucralose.
Raffinose is also used in:


NADH-coenzyme Q oxidoreductase

NADH-coenzyme Q oxidoreductase may stand for


SGTA

Small glutamine-rich tetratricopeptide repeat-containing protein alpha is a protein that in humans is encoded by the "SGTA" gene. "SGTA" orthologs have also been identified in several mammals for which complete genome data are available.
Function.
This gene encodes a protein which is capable of interacting with the major nonstructural protein of parvovirus H-1 and 70-kDa heat shock cognate protein; however, its function is not known. Since this transcript is expressed ubiquitously in various tissues, this protein may serve a housekeeping function.
Interactions.
SGTA has been shown to interact with Growth hormone receptor.


Benzil reductase

Benzil reductase may refer to:


GAK (protein)

Cyclin G-associated kinase (GAK) is a serine/threonine kinase that in humans is encoded by the "GAK" gene.
Function.
In all eukaryotes, the cell cycle is governed by cyclin-dependent protein kinases (CDKs), whose activities are regulated by cyclins and CDK inhibitors in a diverse array of mechanisms that involve the control of phosphorylation and dephosphorylation of Ser, Thr or Tyr residues. Cyclins are molecules that possess a consensus domain called the 'cyclin box.' In mammalian cells, 9 cyclin species have been identified, and they are referred to as cyclins A through I. Cyclin G is a direct transcriptional target of the p53 tumor suppressor gene product and thus functions downstream of p53. GAK is an association partner of cyclin G and CDK5.
Cyclin G-associated kinase received its name because it immunoprecipitated with cyclin G though it now appears to not be associated with it. Cyclin G-associated kinase is homologous in function to the protein auxilin which when in association with Hsc70 uncoats clathrin in neuronal cells. However, the location of Cyclin G-associated kinase is not in the brain but near the trans-Golgi network of non-neuronal cells such as those found in the liver and testes. GAK is also known to be associated with focal adhesions though the exact relationship between the two is unknown.
Structure.
A structure of GAK was determined using X-ray diffraction to a resolution of 2.10 Å.
Cyclin G-associated kinase is a two domain cystolic protein. The domain of interest is the C-terminal domain which consists of three subdomains such as a C-terminal J domain, a clathrin-binding domain, and a tension-like N-terminal domain. The other domain is the N terminal kinase domain which is a functional Ser/Thr protein kinase. The N-terminal kinase domain is able to phosphorylate histone H1. The subdomain tension-like N terminal function has not yet determined, though the domain shares high homology to the tumor suppressant PTEN. The key characteristic is the cysteine group which is required for phosphorylation; however the tension-like N terminal subdomain is absent of some important functional residues that PTEN has. The C-terminal J domain is responsible for the interaction with Hsc70, which is a molecular chaperone responsible for the uncoating of clathrin-coated vesicles during endocytosis. The clathrin-binding domain gathers clathrin into baskets. At pH 7 GAK allows Hsc70 to uncoat clathrin baskets and at pH 6 Hsc70 binds clathrin baskets without uncoating clathrin. Without taking into account GAK’s kinase domain, GAK is 43% identical to auxilin, a neuronal cell uncoating clathrin cofactor, in its amino acid composition. GAK is 57% homologous to auxilin if conserved residues are included in the comparison. Though similar domains of these two molecules suggest and have similar functions, the proteins carry these functions out in different manners. GAK initiates the assembly of clathrin baskets stoichiometrically, but at the different pHs it will either bind the Hsc70 to the baskets or induce the Hsc70 to uncoat the clathrin baskets catalytically which is one difference between auxilin and GAK. This catalytic route explains why less GAK than auxilin is needed to carry out a similar function.


Transmembrane protein 222

Transmembrane protein 222 is a protein that in humans is encoded by the "TMEM222" gene. One notable feature of the protein encoded by this gene is the presence of three predicted transmembrane domains. The TMEM222 protein is predicted to most likely localize to the secretory vesicles.
Gene Features.
TMEM222 has a domain of unknown function (DUF778). Aliases of this gene include DKFZP564D0478, RP11-4K3__A.4, C1orf160, and MGC111002. Accession NM_032125.2, the longest coding sequence (1629 bp), encodes a protein of 208 amino acid residues (23230 Daltons), which is considered the consensus coding sequence (CCDS297.2). There are two isoforms of the protein encoded by this gene. They are similar except the second (Q9H0R3-2) is lacking the first 96 amino acid residues that are present in the first (Q9H0R3-1).
Gene Expression.
ACEVIEW has labeled TMEM222 as highly expressed with 3.8 times more expression than the average gene in the database. There is expression evidence from 166 tissues including brain, lung, colon, kidney, and placenta.
Homology.
Orthologs and distant homologs of the human TMEM222 have been identified throughout Eukaryota especially in plants and animals. No paralogs of this gene have been found in the human genome.
Distant Homolog.
A distant homolog of TMEM222, RTH (RTE1-Homolog), is a homolog of RTE1 (Reversion-to-Ethylene Perception 1), which is known to induce conformational changes in ETR1 (Ethylene receptor 1) that result in negative regulation corresponding with loss of ethylene perception.
Protein Interactions.
Evidence from yeast two-hybrid screening exists for two protein interactions with this gene. One is a serine protease (PRSS23) that has been identified to be involved in mouse ovulation and is excreted into the extracellular matrix. The other protein is an ab-hydrolase (HLA-B associated transcript 5) that is integral to the membrane, and its corresponding gene is located in the genome near Tumor Necrosis Factor (TNF)-alpha and TNF-beta.


DHSA

3,4-DHSA is an organic compound which is the intermediate product of the metabolism of cholesterol, by the bacteria most commonly responsible for tuberculosis ("Mycobacterium tuberculosis"). 3,4-DHSA is an acronym for 3,4-dihydroxy-9,10-seco-androst-1,3,5(10)-triene-9,17-dione, the official name of this substance. It is classified as a secosteroid, since one of the four rings of cholesterol from which it is derived is broken.
3,4-DHSA is a catecholic intermediate (a compound containing an aromatic ring with two adjacent hydroxyl groups) produced by "M. tuberculosis" during the breakdown of cholesterol. 3,4-DHSA is also produced by other bacteria such as "Comamonas testosteroni".
A particular type of enzyme known as extradiol dioxygenase is responsible for the oxidation and ring opening of 3,4-DHSA to 4,9-DSHA (see metabolic scheme below). "M. tuberculosis" bacteria that are deficient in this enzyme are less lethal than wild-type bacteria. 3,4-DHSA itself appears to be toxic to the bacteria while the breakdown products of 3,4-DHSA can be used as energy source by the bacteria. Hence blocking the oxidation of 3,4-DHSA by the extradiol dioxygenase enzyme may be useful in the treatment of tuberculosis.
A crystal structure of DHSA in complex with "M. tuberculosis" iron-dependent extradiol dioxygenase has been determined.


Cytotoxic necrotising factor family

In molecular biology, the cytotoxic necrotising factor family of proteins includes bacterial cytotoxic necrotising factor proteins and the related dermonecrotic toxin (DNT) from "Bordetella" species. Cytotoxic necrotizing factor 1 (CNF1) is a toxin whose structure from "Escherichia coli" revealed a 4-layer alpha/beta/beta/alpha structure containing mixed beta-sheets. CNF1 is expressed in strains of "E. coli" causing uropathogenic and neonatal meningitis. CNF1 alters host cell actin cytoskeleton and promotes bacterial invasion of the blood–brain barrier endothelial cells. CNF1 belongs to a unique group of large cytotoxins that cause constitutive activation of Rho guanosine triphosphatases (GTPases), which are key regulators of the actin cytoskeleton .
"Bordetella" dermonecrotic toxin (DNT) stimulates the assembly of actin stress fibres and focal adhesions by deamidating or polyaminating Gln63 of the small GTPase Rho. DNT is an A-B toxin composed of an N-terminal receptor-binding (B) domain and a C-terminal enzymatically active (A) domain.


Ent-kaurene oxidase

Ent-kaurene oxidase (, Formerly ) is an enzyme with systematic name "ent-kaur-16-ene,NADPH:oxygen oxidoreductase (hydroxylating)". This enzyme catalyses the following chemical reaction
Ent-kaurene oxidase requires cytochrome P450.


D-lactate dehydratase

D-lactate dehydratase (, "glyoxylase III") is an enzyme with systematic name "(R)-lactate hydro-lyase". This enzyme catalyses the following chemical reaction
The enzyme converts methylglyoxal to D-lactate.


Apolipoprotein C-II

Apolipoprotein C-II or apolipoprotein C2 is a protein that in humans is encoded by the "APOC2" gene.
The protein encoded by this gene is secreted in plasma where it is a component of very low density lipoproteins and chylomicrons. This protein activates the enzyme lipoprotein lipase in capillaries, which hydrolyzes triglycerides and thus provides free fatty acids for cells. Mutations in this gene cause hyperlipoproteinemia type IB, characterized by xanthomas, pancreatitis, and hepatosplenomegaly, but no increased risk for atherosclerosis. Lab tests will show elevated blood levels of triglycerides, cholesterol, and chylomicrons


Glycoside hydrolase family 36

In molecular biology, glycoside hydrolase family 36 is a family of glycoside hydrolases.
Glycoside hydrolases are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycoside hydrolases, based on sequence similarity, has led to the definition of >100 different families. This classification is available on the CAZy web site, and also discussed at CAZypedia, an online encyclopedia of carbohydrate active enzymes.
Glycoside hydrolase family 36 together with family 31 and family 27 alpha-galactosidases form the glycosyl hydrolase clan GH-D, a superfamily of alpha-galactosidases, alpha-N-acetylgalactosaminidases, and isomaltodextranases which are likely to share a common catalytic mechanism and structural topology.
Alpha-galactosidase () (melibiase) catalyzes the hydrolysis of melibiose into galactose and glucose. In man, the deficiency of this enzyme is the cause of Fabry's disease (X-linked sphingolipidosis). Alpha-galactosidase is present in a variety of organisms. There is a considerable degree of similarity in the sequence of alpha-galactosidase from various eukaryotic species. "Escherichia coli" alpha-galactosidase (gene melA), which requires NAD and magnesium as cofactors, is not structurally related to the eukaryotic enzymes; by contrast, an "Escherichia coli" plasmid encoded alpha-galactosidase (gene rafA ) contains a region of about 50 amino acids which is similar to a domain of the eukaryotic alpha-galactosidases. Alpha-N-acetylgalactosaminidase () catalyzes the hydrolysis of terminal non-reducing N-acetyl-D-galactosamine residues in N-acetyl-alpha-D- galactosaminides. In man, the deficiency of this enzyme is the cause of Schindler and Kanzaki diseases. The sequence of this enzyme is highly related to that of the eukaryotic alpha-galactosidases.
This family also includes raffinose synthase proteins, also known as seed inhibition (Sip1) proteins. Raffinose (O-alpha- D-galactopyranosyl- (1-->6)- O-alpha- D-glucopyranosyl-(1<-->2)- O-beta- D-fructofuranoside) is a widespread oligosaccharide in plant seeds and other tissues. Raffinose synthase is the key enzyme that channels sucrose into the raffinose oligosaccharide pathway.
Glycoside hydrolase family 36 also includes enzymes with α-N-acetylgalactosaminidase and stachyose synthase activities.
Glycoside hydrolase family 36 can be subdivided into 11 families, GH36A to GH36K.


Paramethasone

Paramethasone is a fluorinated glucocorticoid with anti-inflammatory and immunosuppressant properties.


Netherlands Proteomics Centre

The Netherlands Proteomics Centre (NPC) is a Dutch research center in the field of proteomics. The research is focused on the proteome, the entire set of proteins expressed by a genome, cell, tissue or organism.
The NPC was established by Prof. Dr. Albert Heck in 2003 and is located in the city of Utrecht. NPC is part of the Netherlands Genomics Initiative (NGI).
Cooperating institutions.
Within NPC there is a cooperation between seven universities, four academic medical centers and a number of biotechnology companies:


Bufalin

Bufalin, is a cardiotonic steroid originally isolated from the Chinese toad venom. It is a component found in many Chinese traditional medicine.
Usage.
Bufalin has an "in vitro" antitumor effects against various malignancies, including hepatocellular and lung carcinoma.
However, as with other bufadienolides, its use is hampered by its cardiotoxicity.


Endothiapepsin

Endothiapepsin (, "Endothia aspartic proteinase", "Endothia acid proteinase", "Endothia parasitica acid proteinase", "Endothia parasitica aspartic proteinase") is an enzyme. This enzyme catalyses the following chemical reaction
This enzyme is isolated from the ascomycete "Endothia parasitica".


5-formyltetrahydrofolate cyclo-ligase

In enzymology, a 5-formyltetrahydrofolate cyclo-ligase () is an enzyme that catalyzes the chemical reaction
Thus, the two substrates of this enzyme are ATP and 5-formyltetrahydrofolate, whereas its 3 products are ADP, phosphate, and 5,10-methenyltetrahydrofolate.
This enzyme belongs to the family of ligases, specifically the cyclo-ligases, which form carbon-nitrogen bonds. The systematic name of this enzyme class is 5-formyltetrahydrofolate cyclo-ligase (ADP-forming). Other names in common use include 5,10-methenyltetrahydrofolate synthetase (MTHFS), formyltetrahydrofolic cyclodehydrase, and 5-formyltetrahydrofolate cyclodehydrase. This enzyme participates in one carbon pool by folate.
Structural studies.
As of late 2007, 5 structures have been solved for this class of enzymes, with PDB accession codes , , , , and .
Role in pathology.
Mutations of the MTHFS gene cause the disease 5,10-methenyltetrahydrofolate synthetase deficiency.


D-proline dehydrogenase

D-proline dehydrogenase (, "D-Pro DH", "D-Pro dehydrogenase", "dye-linked D-proline dehydrogenase") is an enzyme with systematic name "D-proline:acceptor oxidoreductase". This enzyme catalyses the following chemical reaction
This enzyme is a flavoprotein (FAD).


GDP-mannose 4,6-dehydratase

In enzymology, a GDP-mannose 4,6-dehydratase () is an enzyme that catalyzes the chemical reaction
Hence, this enzyme has one substrate, GDP-mannose, and two products, GDP-4-dehydro-6-deoxy-D-mannose and H2O.
This enzyme belongs to the family of lyases, specifically the hydro-lyases, which cleave carbon-oxygen bonds. The systematic name of this enzyme class is GDP-mannose 4,6-hydro-lyase (GDP-4-dehydro-6-deoxy-D-mannose-forming). Other names in common use include guanosine 5'-diphosphate-D-mannose oxidoreductase, guanosine diphosphomannose oxidoreductase, guanosine diphosphomannose 4,6-dehydratase, GDP-D-mannose dehydratase, GDP-D-mannose 4,6-dehydratase, Gmd, and GDP-mannose 4,6-hydro-lyase. This enzyme participates in fructose and mannose metabolism. It employs one cofactor, NAD+.
GDP-Mannose 4, 6-Dehydratase Reaction.
The enzyme GDP-Mannose 4, 6-Dehydratase is in the lyase family of enzymes, specifically the hydro-lyases. Other names in use include guanosine 5'-diphosphate-D-mannose oxidoreductase, guanosine diphosphomannose oxidoreductase, guanosine diphosphomannose 4,6-dehydratase, GDP-D-mannose dehydratase, GDP-D-mannose 4,6-dehydratase, GMD, and GDP-mannose 4,6-hydro-lyase. The enzyme is a part of the GDP-Fucose de novo synthesis pathway and catalyzes the first step in the process that gives us GDP-Fucose which is essential for the transfer of Fucose sugars. Its primary structure contains 372 amino acids. This is an essential enzyme in that fucose plays a major role in cell immunity and signaling. Currently GDP-Mannose 4, 6-Dehydratase is not the target of any available drugs, however it is being experimentally targeted with the drug Guanosine-5'-Diphosphate. The chemical reaction of GDP-Mannose 4, 6-Dehydratase is as shown:
GDP-mannose ↔ GDP-4-dehydro-6-deoxy-D-mannose + H2O
Factors In The Reaction.
The enzymes substrate, what the enzyme is acting on, is the GDP-Mannose substance. No other substrates are use this enzyme for reactions.
When the enzyme undergoes its catalyzing process the main product is gets is when it converts GDP-mannose to GDP-4-dehydro-6-deoxy-D-mannose which is then subsequently converted to GDP-Fucose which is crucial for the body to process correctly. It acts as an intermediate step between GDP-Mannose and GDP-Fucose.
In the reaction that the enzyme uses it requires only one cofactor, a compound required for activation, which is NADP(+) however it is uncertain if this compound truly activates the enzyme.
GDP-Fucose is an allosteric inhibitor of the enzyme.
GDP-Fucose Biosynthesis Pathway.
The enzyme GDP-Mannose 4, 6-Dehydratase is only present in one pathway that we know of. This pathway is the GDP-mannose-dependent de novo pathway which provides most of the bodies GDP-Fucose whereas minor amounts come from fucose salvaging in the body.
In the pathway the enzyme is in an intermediate step that converts GDP-Mannose to GDP-4-dehydro-6-deoxy-D-mannose which is then converted into GDP-Fucose which is absolutely crucial to the body. The product of this pathway is fucosyltransferases which is then used in a different pathway that creates fucosylated glycans which is used for cell signaling and immunity in the body. Fucose is a deoxyhexose that is present in a wide variety of organisms. In most mammals, fucose-containing glycans have important roles in blood transfusion reactions, selectin-mediated leukocyte-endothelial adhesion, host-microbe interactions, and numerous ontogenic events. Along with those the body uses fucose as signaling branches of a cell and also as identification systems in immunity. However the enzyme only works at its top levels under normal body conditions. Increased pH or heat could severely denature the protein causing the enzyme to malfunction.
GDP-Mannose 4, 6-dehydratase Structure.
The enzyme contains four different subunits. Here is a link for a 3-D view of the enzyme http://www.rcsb.org/pdb/explore/jmol.do?structureId=1RPN&bionumber=1
Structural studies.
As of late 2007, 5 structures have been solved for this class of enzymes, with PDB accession codes , , , , and .


Phosphoglycerate mutase

Phosphoglycerate mutase (PGM) is any enzyme that catalyzes step 8 of glycolysis. They catalyze the internal transfer of a phosphate group from C-3 to C-2 which results in the conversion of 3-phosphoglycerate (3PG) to 2-phosphoglycerate (2PG) through a 2,3-bisphosphoglycerate intermediate. These enzymes are categorized into the two distinct classes of either cofactor-dependent (dPGM) or cofactor-independent (iPGM). The dPGM enzyme () is composed of approximately 250 amino acids and is found in all vertebrates as well as in some invertebrates, fungi, and bacteria. The iPGM () class is found in all plants and algae as well as in some invertebrate, fungi, and Gram-positive bacteria. This class of PGM enzyme shares the same superfamily as alkaline phosphatase.
Mechanism.
PGM is an isomerase enzyme, effectively transferring a phosphate group (PO43−) from the C-3 carbon of 3-phosphoglycerate to the C-2 carbon forming 2-phosphoglycerate. There are a total of three reactions dPGM can catalyze: a mutase reaction resulting in the conversion of 3PG to 2PG and vice versa, a phosphatase reaction creating phosphoglycerate from 2,3-bisphosphoglycerate, and a synthase reaction producing 2,3-bisphosphoglycerate from 1,3-bisphosphoglycerate similar to the enzyme bisphosphoglycerate mutase. Kinetic and structural studies have provided evidence that indicate dPGM and bisphosphoglycerate mutase are paralogous structures. Both enzymes are contained in the superfamily that also contains the phosphatase portion of phosphofructokinase 2 and prostatic acid phosphatase.
The catalyzed mutase reaction involves two separate phosphoryl groups and the ending phosphate on the 2-carbon is not the same phosphate removed from the 3-carbon.
In the cofactor-dependent enzyme's initial state, the active site contains a phosphohistidine complex formed by phosphorylation of a specific histidine residue. When 3-phosphoglycerate enters the active site, the phosphohistidine complex is positioned as to facilitate transfer of phosphate from enzyme to substrate C-2 creating a 2,3-bisphosphoglycerate intermediate.
Dephosphorylation of the enzyme histidine actuates a local allosteric change in enzyme configuration which now aligns the substrates 3-C phosphate group with enzyme active site histidine and facilitates phosphate transfer returning the enzyme to its initial phosphorylated state and releasing product 2-phosphoglycerate. 2,3-bisphosphoglycerate is required a cofactor for dPGM. In contrast, the iPGM class is independent of 2,3-bisphosphoglycerate and catalyzes the intramolecular transfer of the phosphate group on monophosphoglycerates using a phosphoserineintermediate.
Reaction Summary.
3PG + P-Enzyme → 2,3BPG + Enzyme → 2PG + P-Enzyme
ΔG°′=+1.1kcal/mol
Isozymes.
Phosphoglycerate mutase exists primarily as a dimer of two either identical or closely related subunits of about 32kDa. The enzyme is found in organisms as simple as yeast through "Homo sapiens" and its structure is highly conserved throughout. (Yeast PGM≈74% conserved vs mammal form).
In mammals, the enzyme subunits appear to be either a muscle-derived form (m-type) or other tissue (b-type for brain where the b-isozyme was originally isolated). Existing as a dimer, the enzyme then has 3 isozymes depending on which subunit forms makeup the whole molecule (mm, bb or mb). The mm-type is found mainly in smooth muscle almost exclusively. The mb-isozyme is found in cardiac and skeletal muscle and the bb-type is found in the rest of tissues. While all three isozymes may be found in any tissue, the above distributions are based on prevalence in each.
Regulation.
Phosphoglycerate mutase has a small positive Gibbs free energy and this reaction proceeds easily in both directions. Since it is a reversible reaction, it is not the site of major regulation mechanisms or regulation schemes for the glycolytic pathway.
Anionic molecules such as vanadate, acetate, chloride ion, phosphate, 2-phosphoglycolate, and N-[tris(hydroxymethyl)methyl-2-amino]ethanesulfonate are known inhibitors of the mutase activity of dPGM. Studies have shown dPGM to be sensitive to changes in ionic concentration, where increasing concentrations of salts result in the activation of the enzyme’s phosphatase activity while inhibiting its mutase activity. Certain salts, such as KCl, are known to be competitive inhibitors in respect to 2-phosphoglycerate and mutase activity. Both phosphate and 2-phosphoglycolate are competitive inhibitors of mutase activity in respect to the substrates 2-phosphoglycerate and 2,3-bisphosphoglycerate.
Clinical significance.
In humans the PGAM2 gene which encodes this enzyme is located on the short arm of chromosome 7.
Deficiency of phosphoglycerate mutase causes glycogen storage disease type X, a rare autosomal recessive genetic disorder with symptoms ranging from mild to moderate; is not thought life-threatening and can be managed with changes in lifestyle. This presents as a metabolic myopathy and is one of the many forms of syndromes formerly referred to as muscular dystrophy. PGAM1 deficiency affects the liver, while PGAM2 deficiency affects the muscle.
Onset is generally noted as childhood to early adult though some who may be mildly affected by the disorder may not know they have it. Patients with PGAM deficiency are usually asymptomatic, except when they engage in brief, strenuous efforts which may trigger myalgias, cramps, muscle necrosis and myoglobinuria. An unusual pathologic feature of PGAM deficiency is the association with tubular aggregates. The symptoms are an intolerance to physical exertion or activity, cramps and muscle pain. Permanent weakness is rare. The disease is not progressive and has an excellent prognosis.
Human proteins containing this domain.
BPGM; PFKFB1; PFKFB2; PFKFB3; PFKFB4; PGAM1; PGAM2;
PGAM4; PGAM5; STS1; UBASH3A;


Exocyst

The exocyst is an octameric protein complex involved in vesicle trafficking, specifically the tethering and spatial targeting of post-Golgi vesicles to the plasma membrane prior to vesicle fusion. It is implicated in a number of cell processes, including exocytosis, cell migration, and growth.
Subunits.
The exocyst is composed of eight subunits, whose nomenclature differs between mammalian cells and "Saccharomyces cerevisiae".
Function.
The exocyst complex serves to direct vesicles after the Golgi complex to specific locations on the plasma membrane and to mediate their tethering and localization to the membrane immediately before fusion. Because of this function, the exocyst complex is heavily involved in exocytosis. Sec3 (EXOC1) and Exo70 (EXOC7) are localized to the plasma membrane, and are physically attached to the membrane by Rho GTPases such as CDC42. Other complementary exocyst components such as Sec15 (EXOC6) and Sec4 are localized to the vesicle membrane. Exocyst proteins on the plasma membrane bind vesicular exocyst proteins, bringing the vesicle very close to the plasma membrane in a fashion similar to the SNARE interactions to facilitate fusion.
The exocyst also interacts with Rho GTPases responsible for controlling cell polarity and the activity of the cytoskeleton.


FASTKD2

FAST kinase domain-containing protein 2 (FASTKD2) is a protein that in humans is encoded by the "FASTKD2" gene on chromosome 2. This protein is part of the FASTKD family, which is known for regulating the energy balance of mitochondria under stress. FASTKD2 has been implicated in mitochondrial encephalomyopathy, breast cancer, and prostate cancer.
Structure.
FASTKD2 shares structural characteristics of the FASTKD family, including a ~50-amino acid N-terminal mitochondrial targeting domain and three C-terminal domains: two FAST kinase-like domains (FAST_1 and FAST_2) and a RNA-binding domain (RAP). The mitochondrial targeting domain directs FASTKD2 to be imported into the mitochondria. Though the functions of the C-terminal domains are unknown, RAP possibly binds RNA during trans-splicing.
Function.
As a member of the FASTKD family, FASTKD2 localizes to the inner mitochondrial membrane to modulate their energy balance, especially under conditions of stress. Though ubiquitously expressed in all tissues, FASTKD2 appears more abundantly in skeletal muscle, heart muscle, and other tissues enriched in mitochondria. Nonetheless, FASTKD2 has been observed to mediate apoptosis independent of import into the mitochondria, suggesting that it interacts with proteins on the outer mitochondrial membrane. This protein possibly contributes its proapoptotic function through a caspase-dependent pathway, by activating proapoptotic factors or inhibiting antiapoptotic factors, but the exact mechanism remain unclear. FASTKD2 has also been validated as an RNA-binding protein.
Clinical significance.
FASTKD2 is an important apoptotic constituent. During a normal embryologic processes, or during cell injury (such as ischemia-reperfusion injury during heart attacks and strokes) or during developments and processes in cancer, an apoptotic cell undergoes structural changes including cell shrinkage, plasma membrane blebbing, nuclear condensation, and fragmentation of the DNA and nucleus. This is followed by fragmentation into apoptotic bodies that are quickly removed by phagocytes, thereby preventing an inflammatory response. It is a mode of cell death defined by characteristic morphological, biochemical and molecular changes. It was first described as a "shrinkage necrosis", and then this term was replaced by apoptosis to emphasize its role opposite mitosis in tissue kinetics. In later stages of apoptosis the entire cell becomes fragmented, forming a number of plasma membrane-bounded apoptotic bodies which contain nuclear and or cytoplasmic elements. The ultrastructural appearance of necrosis is quite different, the main features being mitochondrial swelling, plasma membrane breakdown and cellular disintegration. Apoptosis occurs in many physiological and pathological processes. It plays an important role during embryonal development as programmed cell death and accompanies a variety of normal involutional processes in which it serves as a mechanism to remove "unwanted" cells.
FASTKD2 has been linked to mitochondrial encephalomyopathy associated with cytochrome c oxidase deficiency (mitochondrial complex IV deficiency). Nonsense mutations in FASTKD2 produce a truncated protein that cuts off the RAP domain and part of the FAST domains, leading to dampened sensitivity to apoptotic stimuli. Moreover, breast cancer cells are protected against apoptosis by stimulating NRIF3/DD1 expression or DIF-1 knockdown, which thus suppresses the proapoptotic function of FASTKD2. The proapoptotic function is similarly observed in prostate cancer cells, but not in other cells; it is suggested that susceptibility to FASTKD2-mediated apoptosis requires certain factors to associate with the DIF-1 complex to bind. Thus far, activating and enhancing expression of FASTKD2 may prove effective in killing breast and prostate cancer cells.
Interactions.
FASTKD2 has been shown to interact with FASTKD3. The "FASTKD2" gene has been observed to bind the DIF-1 complex.


Holin superfamily VII

The Holin superfamily VII is a superfamily of integral membrane transport proteins. It is one of the seven different holin superfamilies in total. In general, these proteins are thought to play a role in regulated cell death, although functionality varies between families and individual members.
The Holin superfamily VII includes one TC family:
Superfamily VII consists of family TC# 1.E.36, which has six subfamilies, all distantly related to each other. Reddy and Saier (2013) found that there was also some indication that this family could possibly be related to the SPP1 Holin family (TC# 1.E.31) and the 2/3 Holin family (TC# 1.E.33). These three families share the characteristics that they consist of members that are of about the same sizes and have 2 transmembrane segments (TMSs). There is however an exception; subfamily 6 (TC# 1.E.36.6) includes proteins displaying 4 putative TMSs.


KPNA6

Importin subunit alpha-7 is a protein that in humans is encoded by the "KPNA6" gene.
Nucleocytoplasmic transport, a signal- and energy-dependent process, takes place through nuclear pore complexes embedded in the nuclear envelope. The import of proteins containing a nuclear localization signal (NLS) requires the NLS import receptor, a heterodimer of importin alpha and beta subunits also known as karyopherins. Importin alpha binds the NLS-containing cargo in the cytoplasm and importin beta docks the complex at the cytoplasmic side of the nuclear pore complex. In the presence of nucleoside triphosphates and the small GTP binding protein Ran, the complex moves into the nuclear pore complex and the importin subunits dissociate. Importin alpha enters the nucleoplasm with its passenger protein and importin beta remains at the pore. The protein encoded by this gene is a member of the importin alpha family.


2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase

2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (MEcPP synthase, IspF, ) is a zinc-dependent enzyme which participates in the MEP pathway (non-mevalonate pathway) of isoprenoid precursor biosynthesis. It catalyzes the chemical reaction:
Hence, this enzyme has one substrate, 4-diphosphocytidyl-2-C-methyl-D-erythritol 2-phosphate (CDP-MEP), and two products, 2-C-methyl-D-erythritol 2,4-cyclodiphosphate (MEcPP) and CMP.
The enzyme is considered a phosphorus-oxygen lyase. The systematic name of this enzyme class is 2-phospho-4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol CMP-lyase (cyclizing; 2-C-methyl-D-erythritol 2,4-cyclodiphosphate-forming). Other names in common use include IspF, YgbB and MEcPP synthase.
Structural studies.
As of late 2007, 20 structures have been solved for this class of enzymes, with PDB accession codes , , , , , , , , , , , , , , , , , , , and .


Glucuronidase

Glucuronidase may refer to several enzymes:


Glycoside hydrolase family 76

In molecular biology, glycoside hydrolase family 76 is a family of glycoside hydrolases.
Glycoside hydrolases are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycoside hydrolases, based on sequence similarity, has led to the definition of >100 different families. This classification is available on the CAZy web site, and also discussed at CAZypedia, an online encyclopedia of carbohydrate active enzymes.
Glycoside hydrolase family 76 is a family of alpha-1,6-mannanases () (CAZY GH_76).


(S)-scoulerine 9-O-methyltransferase

In enzymology, a (S)-scoulerine 9-O-methyltransferase () is an enzyme that catalyzes the chemical reaction
Thus, the two substrates of this enzyme are S-adenosyl methionine and (S)-scoulerine, whereas its two products are S-adenosylhomocysteine and (S)-tetrahydrocolumbamine.
This enzyme belongs to the family of transferases, specifically those transferring one-carbon group methyltransferases. The systematic name of this enzyme class is S-adenosyl-L-methionine:(S)-scoulerine 9-O-methyltransferase. This enzyme participates in alkaloid biosynthesis i.


TCF/LEF family

The TCF/LEF family is a group of transcription factors which bind to DNA through a SOX-like high mobility group domain. They are involved in the Wnt signaling pathway, where they recruit the coactivator beta-catenin to enhancer elements of genes they target. They can also recruit members of the Groucho family of corepressors.


V-ATPase

Vacuolar-type ATPase (V-ATPase) is a highly conserved evolutionarily ancient enzyme with remarkably diverse functions in eukaryotic organisms. V-ATPases acidify a wide array of intracellular organelles and pump protons across the plasma membranes of numerous cell types. V-ATPases couple the energy of ATP hydrolysis to proton transport across intracellular and plasma membranes of eukaryotic cells. It is generally seen as the polar opposite of ATP synthase because ATP synthase is a proton channel that uses the energy from a proton gradient to produce ATP. V-ATPase however, is a proton pump that uses the energy from ATP hydrolysis to produce a proton gradient.
The Archaea-type ATPase (A-ATPase) is a related group of ATPases found in Archaea that often work as an ATP synthase. It forms a clade V/A-ATPase with V-ATPase. Most members of either group shuttle protons (), but a few members have evolved to use sodium ions () instead.
Roles played by V-ATPases.
V-ATPases are found within the membranes of many organelles, such as endosomes, lysosomes, and secretory vesicles, where they play a variety of roles crucial for the function of these organelles. For example, the proton gradient across the yeast vacuolar membrane generated by V-ATPases drives calcium uptake into the vacuole through an antiporter system. In synaptic transmission in neuronal cells, V-ATPase acidifies synaptic vesicles. Norepinephrine enters vesicles by V-ATPase.
V-ATPases are also found in the plasma membranes of a wide variety of cells such as intercalated cells of the kidney, osteoclasts (bone resorbing cells), macrophages, neutrophils, sperm, midgut cells of insects, and certain tumor cells. Plasma membrane V-ATPases are involved in processes such as pH homeostasis, coupled transport, and tumor metastasis. V-ATPases in the acrosomal membrane of sperm acidify the acrosome. This acidification activates proteases required to drill through the plasma membrane of the egg. V-ATPases in the osteoclast plasma membrane pump protons onto the bone surface, which is necessary for bone resorption. In the intercalated cells of the kidney, V-ATPases pump protons into the urine, allowing for bicarbonate reabsorption into the blood. In addition, other variety of biological processes, such as toxin delivery, viral entry, membrane targeting, apoptosis, regulation of cytoplasmic pH, proteolytic process, and acidification of intracellular systems, are important roles of V-ATPases.
V-ATPases also play a significant role in cell morphogenesis development. Disruption of the gene vma-1 gene which encodes for the catalytic subunit (A) of the enzyme severely impairs the rate of growth, differentiation, and the capacity to produce viable spores in fungus Neurospora crassa.
Structure.
The yeast V-ATPase is the best characterized. There are at least thirteen subunits identified to form a functional V-ATPase complex, which consists of two domains. The subunits belong to either the Vo domain (membrane associated subunits, lowercase letters on the figure) or the V1 domain (peripherally associated subunits, uppercase letters on the figure).
The V1 includes eight subunits, A-H, with three copies of the catalytic A and B subunits, three copies of the stator subunits E and G, and one copy of the regulatory C and H subunits. In addition, the V1 domain also contains the subunits D and F, which form a central rotor axle. The V1 domain contains tissue-specific subunit isoforms including B, C, E, and G. Mutations to the B1 isoform result in the human disease distal renal tubular acidosis and sensorineural deafness.
The Vo domain contains six different subunits, a, d, c, c', c", and e, with the stoichiometry of the c ring still a matter of debate with a decamer being postulated for the tobacco hornworm ("Manduca sexta") V-ATPase. The mammalian Vo domain contains tissue-specific isoforms for subunits a and d, while yeast V-ATPase contains two organelle-specific subunit isoforms of a, Vph1p, and Stv1p. Mutations to the a3 isoform result in the human disease infantile malignant osteopetrosis, and mutations to the a4 isoform result in distal renal tubular acidosis, in some cases with sensorineural deafness.
The V1 domain is responsible for ATP hydrolysis, whereas the Vo domain is responsible for proton translocation. ATP hydrolysis at the catalytic nucleotide binding sites on subunit A drives rotation of a central stalk composed of subunits D and F, which in turn drives rotation of a barrel of c subunits relative to the a subunit. The complex structure of the V-ATPase has been revealed through the structure of the "M. Sexta" and Yeast complexes that were solved by single-particle cryo-EM and negative staining, respectively. These structures have revealed that the V-ATPase has a 3-stator network, linked by a collar of density formed by the C, H, and a subunits, which, while dividing the V1 and Vo domains, make no interactions with the central rotor axle formed by the F, D, and d subunits. Rotation of this central rotor axle caused by the hydrolysis of ATP within the catalytic AB domains results in the movement of the barrel of c subunits past the a subunit, which drives proton transport across the membrane. A stoichiometry of two protons translocated for each ATP hydrolyzed has been proposed by Johnson.
In addition to the structural subunits of yeast V-ATPase, associated proteins that are necessary for assembly have been identified. These associated proteins are essential for Vo domain assembly and are termed Vma12p, Vma21p, and Vma22p. Two of the three proteins, Vma12p and Vma22p, form a complex that binds transiently to Vph1p (subunit a) to aid its assembly and maturation. Vma21p coordinates assembly of the Vo subunits as well as escorting the Vo domain into vesicles for transport to the Golgi.
V1.
The V1 domain of the V-ATPase is the site of ATP hydrolysis. Unlike Vo, the V1 domain is hydrophobic. This soluble domain consists of a hexamer of alternating A and B subunits, a central rotor D, peripheral stators G and E, and regulatory subunits C and H. Hydrolysis of ATP drives a conformational change in the six A|B interfaces and with it rotation of the central rotor D. Unlike with the ATP synthase, the V1 domain is not an active ATPase when dissociated.
Subunit C.
V-ATPase (Vacuolar-ATPase) C represents the C terminal subunit that is part of the V1 complex, and is localised to the interface between the V1 and Vo complexes.
Subunit C function.
The C subunit plays an essential role in controlling the assembly of V-ATPase, acting as a flexible stator that holds together the catalytic (V1) and membrane (VO) sectors of the enzyme . The release of subunit C from the ATPase complex results in the dissociation of the V1 and Vo subcomplexes, which is an important mechanism in controlling V-ATPase activity in cells. Essentially, by creating a high electrochemical gradient and low pH, this powers the enzyme to create more ATP.
Subunits E, G.
These related subunits make up the stalk(s) of A/V-ATPase. They are important in assembly, and may function as pushrods in activity. E has a cap to connect to A/B, while G does not. They likely evolved from a single protein by gene duplication.
Subunit H.
This subunit is only involved in activity and not in assembly. This subunit also acts as an inhibitor of free V1 subunits; it stops ATP hydrolysis when V1 and Vo are dissociated.
Vo.
The Vo domain is responsible for proton translocation. Unlike the F-type ATP synthase, the Vo domain generally transports protons against their own concentration gradient. Rotation of the Vo domain transports the protons in movement coordinated with the V1 domain, which is responsible for ATP hydrolysis. The Vo domain is hydrophilic and composed of several dissociable subunits. These subunits are present in the Vo domain to make this a functional proton translocase; they are described below.
Subunit a/I.
The 116kDa subunit (or subunit a) and subunit I are found in the Vo or Ao complex of V- or A-ATPases, respectively. The 116kDa subunit is a transmembrane glycoprotein required for the assembly and proton transport activity of the ATPase complex. Several isoforms of the 116kDa subunit exist, providing a potential role in the differential targeting and regulation of the V-ATPase for specific organelles.
The function of the 116-kDa subunit is not defined, but its predicted structure consists of 6–8 transmembranous sectors, suggesting that it may function similar to subunit a of FO.
Subunit d/C.
Subunit d in V-ATPases, called subunit C in A-ATpases, is a part of the Vo complex. They fit onto the middle of the c ring, so are thought to function as a rotor. There are two versions of this subunit in eukaryotes, d/d1 and d2.
In mammals, d1 (ATP6V0D1) is the ubiquitously expressed version and d2 (ATP6V0D2) is expressed in specific cell types only.
Subunit c.
Similar to the F-type ATP synthase, the transmembrane region of the V-ATPase includes a ring of membrane-spanning subunits that are primarily responsible for proton translocation. Dissimilar from the F-type ATP synthase, however, the V-ATPase has multiple related subunits in the c-ring; in fungi such as yeast there are three related subunits (of varied stoichiometry) and in most other eukaryotes there are two.
V-ATPase assembly.
Yeast V-ATPases fail to assemble when any of the genes that encode subunits are deleted except for subunits H and c". Without subunit H, the assembled V-ATPase is not active, and the loss of the c" subunit results in uncoupling of enzymatic activity.
The precise mechanisms by which V-ATPases assembly are still controversial, with evidence suggesting two different possibilities. Mutational analysis and "in vitro" assays have shown that preassembled Vo and V1 domains can combine to form one complex in a process called independent assembly. Support for independent assembly includes the findings that the assembled Vo domain can be found at the vacuole in the absence of the V1 domain, whereas free V1 domains can be found in the cytoplasm and not at the vacuole. In contrast, "in vivo" pulse-chase experiments have revealed early interactions between Vo and V1 subunits, to be specific, the a and B subunits, suggesting that subunits are added in a step-wise fashion to form a single complex in a concerted assembly process.
V-ATPase evolution.
A relatively new technique called ancestral gene resurrection has shed new light on the evolutionary history of the V-ATPase. It has been shown how the V-ATPase structure of the ancestral form consisting of two different proteins evolves into the fungi version with three different proteins. The V-Type ATPase is similar to the archaeal (so called) A-Type ATP synthase, a fact that supports an archaeal origin of eukaryotes (like Eocyte Hypothesis, see also Lokiarchaeota). The exceptional occurrence of some lineages of archaea with F-type and of some lineages of bacteria with A-type ATPase respectively is regarded as a result of horizontal gene transfer.
Regulation of V-ATPase activity.
V-ATPases are known to be specifically inhibited by macrolide antibiotics, such as concanamycin (CCA) and balifomycin A. "In vivo" regulation of V-ATPase activity is accomplished by reversible dissociation of the V1 domain from the Vo domain. After initial assembly, both the insect "Manduca sexta" and yeast V-ATPases can reversibly disassemble into free Vo and V1 domains after a 2- to 5-minute deprivation of glucose. Reversible disassembly may be a general mechanism of regulating V-ATPase activity, since it exists in yeast and insects. Reassembly is proposed to be aided by a complex termed RAVE (regulator of -ATPase of vacuolar and endosomal membranes). Disassembly and reassembly of V-ATPases does not require new protein synthesis but does need an intact microtubular network.
Human diseases.
Osteopetrosis.
Osteopetrosis is generic name that represents a group of heritable conditions in which there is a defect in osteoclastic bone resorption. Both dominant and recessive osteopetrosis occur in humans. Autosomal dominant osteopetrosis shows mild symptoms in adults experiencing frequent bone fractures due to brittle bones. A more severe form of osteopetrosis is termed autosomal recessive infantile malignant osteopetrosis. Three genes that are responsible for recessive osteopetrosis in humans have been identified. They are all directly involved in the proton generation and secretion pathways that are essential for bone resorption. One gene is carbonic anhydrase II (CAII), which, when mutated, causes osteopetrosis with renal tubular acidosis(type 3). Mutations to the chloride channel ClC7 gene also lead to both dominant and recessive osteopetrosis. Approximately 50% of patients with recessive infantile malignant osteopetrosis have mutations to the a3 subunit isoform of V-ATPase. In humans, 26 mutations have been identified in V-ATPase subunit isoform a3, found in osteoclasts, that result in the bone disease autosomal recessive osteopetrosis.
Distal renal tubular acidosis (dRTA).
The importance of V-ATPase activity in renal proton secretion is highlighted by the inherited disease distal renal tubular acidosis. In all cases, renal tubular acidosis results from a failure of the normal renal mechanisms that regulate systemic pH. There are four types of renal tubular acidosis. Type 1 is distal renal tubular acidosis and results from a failure of the cortical collecting duct to acidify the urine below pH 5. Some patients with autosomal recessive dRTA also have sensorineural hearing loss. Inheritance of this type of RTA results from either mutations to V-ATPase subunit isoform B1 or isoform a4 or mutations of band 3 (also called AE1), a Cl-/HCO3- exchanger. Twelve different mutations to V-ATPase isoform B1 and twenty-four different mutations in a4 lead to dRTA. Reverse transcription polymerase chain reaction studies have shown expression of the a4 subunit in the intercalated cell of the kidney and in the cochlea. dRTA caused by mutations in the a4 subunit gene in some cases can be associated with deafness due to a failure to normally acidify the endolymph of the inner ear.
X-linked myopathy with excessive autophagy (XMEA).
X-linked myopathy with excessive autophagy is a rare genetic disease resulting from mutations in the VMA21 gene. The disease has a childhood onset and results in a slowly progressive muscle weakness, typically beginning in the legs, and some patients can eventually require wheelchair assistance with advanced age. The Vma21 protein assists in assembly of the V-ATPase, and XMEA associated mutations result in decreased activity of the V-ATPase and increased lysosomal pH.
Nomenclature.
The term Vo has a lowercase letter "o" (not the number "zero") in subscript. The "o" stands for oligomycin, which binds to the homologous region in F-ATPase. It is worth noting that the human gene notations at NCBI designate it as "zero" rather than the letter "o". For example, the gene for the human c subunit of Vo is listed in NCBI gene database as "ATP6V0C" (with a zero), rather than "ATP6VOC" (with an "o"). Many pieces of literature make this mistake as well.


Glycoside hydrolase family 27

In molecular biology, glycoside hydrolase family 27 is a family of glycoside hydrolases.
Glycoside hydrolases are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycoside hydrolases, based on sequence similarity, has led to the definition of >100 different families. This classification is available on the CAZy web site, and also discussed at CAZypedia, an online encyclopedia of carbohydrate active enzymes.
Glycoside hydrolase family 27 together with family 31 and the family 36 alpha-galactosidases form the glycosyl hydrolase clan GH-D, a superfamily of alpha-galactosidases, alpha-N-acetylgalactosaminidases, and isomaltodextranases which are likely to share a common catalytic mechanism and structural topology.
Alpha-galactosidase () (melibiase) catalyzes the hydrolysis of melibiose into galactose and glucose. In man, the deficiency of this enzyme is the cause of Fabry's disease (X-linked sphingolipidosis). Alpha-galactosidase is present in a variety of organisms. There is a considerable degree of similarity in the sequence of alpha-galactosidase from various eukaryotic species. "Escherichia coli" alpha-galactosidase (gene melA), which requires NAD and magnesium as cofactors, is not structurally related to the eukaryotic enzymes; by contrast, an "Escherichia coli" plasmid encoded alpha-galactosidase (gene rafA ) contains a region of about 50 amino acids which is similar to a domain of the eukaryotic alpha-galactosidases. Alpha-N-acetylgalactosaminidase () catalyzes the hydrolysis of terminal non-reducing N-acetyl-D-galactosamine residues in N-acetyl-alpha-D- galactosaminides. In man, the deficiency of this enzyme is the cause of Schindler and Kanzaki diseases. The sequence of this enzyme is highly related to that of the eukaryotic alpha-galactosidases.


Cytokeratin

Cytokeratins are keratin proteins found in the intracytoplasmic cytoskeleton of epithelial tissue. They are an important component of intermediate filaments, which help cells resist mechanical stress. Expression of these cytokeratins within epithelial cells is largely specific to particular organs or tissues. Thus they are used clinically to identify the cell of origin of various human tumors.
Naming.
The term "cytokeratin" began to be used in the late 1970s, when the protein subunits of keratin intermediate filaments inside cells were first being identified and characterized. In 2006 a new systematic nomenclature for mammalian keratins was created, and the proteins previously called "cytokeratins" are simply called keratins (human epithelial category). For example, cytokeratin-4 (CK-4) has been renamed keratin-4 (K4). However, they are still commonly referred to as cytokeratins in clinical practice.
Types.
There are two categories of cytokeratins: the acidic type I cytokeratins and the basic or neutral type II cytokeratins. Within each category, cytokeratins are numbered in order of decreasing size, from low molecular weight (LMWCKs) to high molecular weight (HMWCKs). Cytokeratins are usually found in heterodimeric pairs of acidic and basic subunits of similar size.
Expression of these cytokeratins is largely organ or tissue specific. The subsets of cytokeratins which an epithelial cell expresses depends mainly on the type of epithelium, the moment in the course of terminal differentiation and the stage of development. Thus a specific cytokeratin expression profile allows the identification of epithelial cells. Furthermore, this applies also to the malignant counterparts of the epithelia, (carcinomas), as the cytokeratin profile is generally retained. Thus the study of cytokeratin expression by immunohistochemistry techniques is a tool of immense value widely used for tumor diagnosis and characterization in surgical pathology.
Molecular biology.
The cytokeratins are encoded by a family encompassing 30 genes. Among them, 20 are epithelial genes and the remaining 10 are specific for trichocytes.
All cytokeratin chains are composed of a central α-helix-rich domain (with a 50-90% sequence identity among cytokeratins of the same type and around 30% between cytokeratins of different type) with non-α-helical N- and C-terminal domains. The α-helical domain has 310-150 amino acids and comprises four segments in which a seven-residue pattern repeats. Into this repeated pattern, the first and fourth residues are hydrophobic and the charged residues show alternate positive and negative polarity, resulting in the polar residues being located on one side of the helix. This central domain of the chain provides the molecular alignment in the keratin structure and makes the chains form coiled dimers in solution.
The end-domain sequences of type I and II cytokeratin chains contain in both sides of the rod domain the subdomains V1 and V2, which have variable size and sequence. The type II also presents the conserved subdomains H1 and H2, encompassing 36 and 20 residues respectively. The subdomains V1 and V2 contain residues enriched by glycines and/or serines, the former providing the cytokeratin chain a strong insoluble character and facilitating the interaction with other molecules. These terminal domains are also important in defining the function of the cytokeratin chain characteristic of a particular epithelial cell type.
Two dimers of cytokeratin group into a keratin tetramer by anti-parallel binding. This cytokeratin tetramer is considered to be the main building block of the cytokeratin chain. By head-to-tail linking of the cytokeratin tetramers, the protofilaments are originated, which in turn intertwine in pairs to form protofibrils. Four protofibrils give place to one cytokeratin filament.
Cell biology.
In the cytoplasm, Keratin filaments associate laterally with each other to create bundles of ~50nm radius. The radius of these bundles is set by the interplay between long range electrostatic repulsion and short range hydrophobic attraction. These Keratin bundles span a complex network which extends from the surface of the nucleus to the cell membrane. Numerous accessory proteins are involved in the genesis and maintenance of such structure.
This association between the plasma membrane and the nuclear surface provides important implications for the organization of the cytoplasm and cellular communication mechanisms. Apart from the relatively static functions provided in terms of supporting the nucleus and providing tensile strength to the cell, the cytokeratin networks undergo rapid phosphate exchanges mediated depolymerization, with important implications in the more dynamic cellular processes such as mitosis and post-mitotic period, cell movement and differentiation.
Cytokeratins interact with desmosomes and hemidesmosomes, thus collaborating to cell-cell adhesion and basal cell-underlying connective tissue connection.
The intermediate filaments of the eukaryotic cytoskeleton, which the cytokeratins are one of its three components, have been probed to associate also with the ankyrin and spectrin complex protein network that underlies the cell membrane.


Steroid ester

A steroid ester is an ester of a steroid. They include androgen esters, estrogen esters, progestogen esters, and corticosteroid esters. Steroid esters may be naturally occurring/endogenous like DHEA sulfate or synthetic like estradiol valerate. Esterification is useful because it is often able to render the parent steroid into a prodrug of itself with altered chemical properties such as improved metabolic stability, water solubility, and/or lipophilicity. This, in turn, can enhance pharmacokinetics, for instance by improving the steroid's bioavailability and/or conferring depot activity and hence an extended duration with intramuscular or subcutaneous injection.
Esterification of steroids with fatty acids was developed to prolong the duration of effect of steroid hormones. By 1957, more than 500 steroid esters had been synthesized, most frequently of androgens. The longer the fatty acid chain, up to a certain optimal length, the longer the duration when prepared as an oil solution and injected. Across a chain length range of 6 to 12 carbon atoms, a length of 9 or 10 carbon atoms (nonanoate or decanoate ester) was found to be optimal in rodents in the case of testosterone esters. Fatty acid esters increase the lipophilicity of steroids, with longer fatty acids resulting in greater lipophilicity. The greater solubility in oil allows the steroid esters to be dissolved in a smaller oil volume, thereby allowing for larger doses with intramuscular injection. In addition, the greater the lipophilicity of the steroid, as measured by the octanol/water partition coefficient (logP), the slower its release from the oily depot at the injection site and the longer its duration.
Steroid esters can also be prepared as crystalline aqueous suspensions. Aqueous suspensions of steroid crystals result in prolongation of duration with intramuscular injection similarly to oil solutions. The duration is longer than that of oil solutions, intermediate between oil solutions and subcutaneous pellet implants. The sizes of crystals in suspensions varies and can range from 0.1 μm to some hundreds of μm. The duration of crystalline steroid suspensions increases directly with the size of the crystals. However, crystalline suspensions have an irritating effect in the body, and intramuscular injections of crystalline steroid suspensions result in painful local reactions. These reactions worsen with larger crystals, and for this reason, crystal sizes must be limited to minimize local reactions. Particle sizes of more than 300 μg in the case of estradiol benzoate by intramuscular injection have been found to be too painful for use.
In some cases, crystalline steroid suspensions are used not for prolongation of effect, but because the solubility of the steroid result in this preparation being the only practical way to deliver the steroid in a reasonable injection volume. Examples include cortisone acetate and hydrocortisone and its esters. A requirement of long-lasting crystalline steroid administration is that the steroid be sufficiently water-insoluble, so that it dissolves slowly and thereby attains a prolonged therapeutic effect. The crystals in suspensions can sometimes clump together or aggregate and grow in size. This can be avoided by careful formulation. Crystalline suspensions of steroids are prepared either by precipitation or by dispersing finely divided material in an aqueous suspension medium. Desired particle size can be achieved by grinding, for instance through the use of an atomizer.
Adolf Butenandt reported in 1932 that estrone benzoate in oil solution had a prolonged duration with injection in animals. No such prolongation of action occurred if it was given by intravenous injection. Estradiol benzoate was synthesized in 1933 and was marketed for use the same year.
Sulfur-based esters.
Certain sulfur-based steroid esters have a sulfamate or sulfonamide moiety as the ester, typically at the C3 and/or C17β positions. Like many other steroid esters, they are prodrugs. Unlike other steroid esters however, they bypass first-pass metabolism with oral administration and have high oral bioavailability and potency, abolished first-pass hepatic impact, and long elimination half-lives and durations of action. They are under development for potential clinical use. Examples include the estradiol esters estradiol sulfamate (E2MATE; also a potent steroid sulfatase inhibitor) and EC508 (estradiol 17β-(1-(4-(aminosulfonyl)benzoyl)--proline)), the testosterone ester EC586 (testosterone 17β-(1-((5-(aminosulfonyl)-2-pyridinyl)carbonyl)--proline)), and sulfonamide esters of levonorgestrel and etonogestrel.