Prestin

Prestin is a protein that is critical to sensitive hearing in mammals. It is encoded by the "SLC26A5" (solute carrier anion transporter family 26, member 5) gene.
Prestin is the motor protein of the outer hair cells of the inner ear of the mammalian cochlea. It is highly expressed in the outer hair cells, and is not expressed in the nonmotile inner hair cells. Immunolocalization shows prestin is expressed in the lateral plasma membrane of the outer hair cells, the region where electromotility occurs. The expression pattern correlates with the appearance of outer hair cell electromotility.
Function.
Prestin is essential in auditory processing. It is specifically expressed in the lateral membrane of outer hair cells (OHCs) of the cochlea. There is no significant difference between prestin density in high-frequency and low-frequency regions of the cochlea in fully developed mammals. There is good evidence that prestin has undergone adaptive evolution in mammals associated with acquisition of high frequency hearing in mammals. The prestin protein shows several parallel amino acid replacements in bats, whales, and dolphins that have independently evolved ultrasonic hearing and echolocation, and these represent rare cases of convergent evolution at the sequence level.
Prestin (mol. wt. 80 kDa) is a member of a distinct family of anion transporters, SLC26. Members of this family are structurally well conserved and can mediate the electroneutral exchange of chloride and carbonate across the plasma membrane of mammalian cells, two anions found to be essential for outer hair cell motility. Unlike the classical, enzymatically driven motors, this new type of motor is based on direct voltage-to-displacement conversion and acts several orders of magnitude faster than other cellular motor proteins. A targeted gene disruption strategy of prestin showed a >100-fold (or 40 dB) loss of auditory sensitivity.
Prestin is a transmembrane protein that mechanically contracts and elongates leading to electromotility of outer hair cells (OHC). Electromotility is the driving force behind the somatic motor of the cochlear amplifier, which is a mammalian evolution that increases sensitivity to incoming sound wave frequencies and, thus, amplifies the signal. Previous research has suggested that this modulation takes place via an extrinsic voltage-sensor (partial anion transporter model), whereby chloride binds to the intracellular side of prestin and enters a defunct transporter, causing prestin elongation. However, there is new evidence that prestin acts through an intrinsic voltage-sensor (IVS) in which intracellular chloride binds allosterically to prestin to modify shape.
Intrinsic voltage sensing.
In this model of intrinsic voltage-sensing, the movement of ions generates a nonlinear capacitance (NLC). Based upon the generated voltage and the depolarized or hyperpolarized state of the cell, prestin will transition through two distinct steps, representing the three-state model of prestin modulation. Experiments show that with increasing depolarizing stimuli, prestin transitions from an elongated state to an intermediate state to a contracted state, increasing its NLC. Under hyperpolarizing conditions, NLC decreases and prestin transitions back to its elongated state. Of significance, increased membrane tension as characterized by prestin elongation decreases the chloride allosteric binding site affinity for chloride, perhaps playing a role in regulation of prestin modulation. The total estimated displacement of prestin upon modulation from elongated to contracted state is 3–4 nm2. A recent study supports the IVS model showing that mutations of 12 residues that span the intracellular side of prestin's core membrane resulted in significant decrease in NLC. Eight of the 12 residues were positively charged and are hypothesized to make up the allosteric chloride binding site of prestin.
Anion transport.
Although previously thought to be absent, anion transport has also been shown to be an important aspect of prestin's ability to drive electromotility of hair cells. This mechanism is independent of prestin's voltage-sensing capabilities based upon mutagenesis experiments showing that different mutations lead to effects in either anion-uptake or NLC, but not both. It is suggested that prestin contains an intrinsic anion-uptake mechanism based upon research showing concentration dependent [14C]formate uptake in Chinese hamster ovary (CHO) cells. These results could not be reproduced in oocytes. Therefore, prestin may require an associated cofactor for anion uptake in oocytes; however, this hypothesis is still under question. Experiments have shown that various anions can compete for prestin uptake including malate, chloride, and alkylsulfonic anions.
Discovery.
Prestin was discovered by Peter Dallos's group in 2000 and named from the musical notation presto because of the speed of the protein.
The prestin molecule was patented by its discoverers in 2003.
Clinical significance.
Mutations in the SLC26A5 gene have been associated with non-syndromic hearing loss.
Blockers.
Electromotile function of mammalian prestin is blocked by the amphiphilic anion salicylate at millimolar concentrations. Application of salicylate blocks prestin function in a dose-dependent and readily reversible manner.


Acetolactate decarboxylase

In enzymology, an acetolactate decarboxylase () is an enzyme that catalyzes the chemical reaction
Hence, this enzyme has one substrate, (S)-2-hydroxy-2-methyl-3-oxobutanoate, and two products, (R)-2-acetoin and CO2.
This enzyme belongs to the family of lyases, specifically the carboxy-lyases, which cleave carbon-carbon bonds. The systematic name of this enzyme class is (S)-2-hydroxy-2-methyl-3-oxobutanoate carboxy-lyase [(R)-2-acetoin-forming]. Other names in common use include alpha-acetolactate decarboxylase, and (S)-2-hydroxy-2-methyl-3-oxobutanoate carboxy-lyase. This enzyme participates in butanoate metabolism and c5-branched dibasic acid metabolism.
Structural studies.
As of late 2007, only one structure has been solved for this class of enzymes, with the PDB accession code .


3,4-dihydroxyphenylacetate 2,3-dioxygenase

In enzymology, a 3,4-dihydroxyphenylacetate 2,3-dioxygenase () is an enzyme that catalyzes the chemical reaction
Thus, the two substrates of this enzyme are 3,4-dihydroxyphenylacetate and O2, whereas its product is 2-hydroxy-5-carboxymethylmuconate semialdehyde.
This enzyme belongs to the family of oxidoreductases, specifically those acting on single donors with O2 as oxidant and incorporation of two atoms of oxygen into the substrate (oxygenases). The oxygen incorporated need not be derived from O2. The systematic name of this enzyme class is 3,4-dihydroxyphenylacetate:oxygen 2,3-oxidoreductase (decyclizing). Other names in common use include 3,4-dihydroxyphenylacetic acid 2,3-dioxygenase, HPC dioxygenase, and homoprotocatechuate 2,3-dioxygenase. This enzyme participates in tyrosine metabolism. It employs one cofactor, iron.
Structural studies.
As of late 2007, eight structures have been solved for this class of enzymes, with PDB accession codes , , , , , , , and .


Heterotetramer


Lactase-phlorizin hydrolase

Lactase-phlorizin hydrolase may refer to:


Potato carboxypeptidase inhibitor

Potato carboxypeptidase inhibitor (PCI) is a naturally occurring protease inhibitor peptide in potatoes that can form complexes with several metallo-carboxypeptidases, inhibiting them in a strong competitive way with a Ki in the nanomolar range. PCI consists of 39 amino acids (MW 4295 Da) forming a 27-residue globular core stabilized by three disulfide bridges and a C-terminal tail with residues 35–39. PCI contains a small cysteine-rich module, called a T-knot scaffold, that is shared by several different protein families, including the EGF family.
Medicinal properties.
Because of the structural similarities with EGF, PCI inhibits tumor cell growth. Mechanism of action is inhibition of receptor dimerization and receptor trans-autophosphorylation induced by epidermal growth factor (EGF). PCI blocks the formation and activation of ErbB1/ErbB-2 (EGFR and HER2) heterodimers that have a prominent role in carcinoma development.PCI also inhibits transforming growth factor alpha (TGF-alpha).
In addition for pancreatic enzymes carboxypeptidase A and B, PCI also inhibits carboxypeptidase R without affecting the activity of carboxypeptidase N in the circulation and have therefore use in thrombolytic therapy (blood clot lysis).
See also.
Scaffold (disambiguation)
Protein kinase
Chemotherapy
Thrombolysis
Cancer research


Amino-acid racemase

In enzymology, an amino-acid racemase () is an enzyme that catalyzes the chemical reaction
Hence, this enzyme has one substrate, L-amino acid, and one product, D-amino acid.
This enzyme belongs to the family of isomerases, specifically those racemases and epimerases acting on amino acids and derivatives. The systematic name of this enzyme class is amino-acid racemase. This enzyme is also called L-amino acid racemase. This enzyme participates in 4 metabolic pathways: glycine, serine and threonine metabolism, cysteine metabolism, D-glutamine and D-glutamate metabolism, and D-arginine and D-ornithine metabolism. It employs one cofactor, pyridoxal phosphate.
Structural studies.
As of late 2007, 5 structures have been solved for this class of enzymes, with PDB accession codes , , , , and .


SNF

SNF may refer to:


Calx-beta motif

In molecular biology, the calx-beta motif is a protein motif which is present as a tandem repeat in the cytoplasmic domains of Calx sodium-calcium exchangers, which are used to expel calcium from cells. This motif overlaps domains used for calcium binding and regulation. The calx-beta motif is also present in the cytoplasmic tail of mammalian integrin-beta4, which mediates the bi-directional transfer of signals across the plasma membrane, as well as in some cyanobacterial proteins. This motif contains a series of beta-strands and turns that form a self-contained beta-sheet.


Vault (organelle)

The vault or vault cytoplasmic ribonucleoprotein is a eukaryotic organelle whose function is not yet fully understood. Discovered and isolated by Nancy Kedersha and Leonard Rome in 1986, vaults are cytoplasmic organelles which, when negative-stained and viewed under an electron microscope, resemble the arches of a cathedral's vaulted ceiling, with 39-fold (Or D39d) symmetry. They are present in many types of eukaryotic cells, and appear to be highly conserved among eukaryotes.
Morphology.
Vaults are large ribonucleoprotein particles. About 3 times the size of a ribosome and weighing approximately 13 MDa, they are found in most eukaryotic cells and all higher eukaryotes. They measure 34 nm by 60 nm from a negative stain, 26 nm by 49 nm from cryo-electron microscopy, and 35 nm by 59 nm from STEM. The vaults consist primarily of proteins, making it difficult to stain with conventional techniques. The protein structure consists of an outer shell composed of 78 copies of the ~100 KDa major vault protein (MVP). Inside are two associated vault proteins, TEP1 and VPARP. TEP1, also known as the telomerase-associated protein 1, is 290 KDa and VPARP (also known as PARP4) is related to poly-(ADP-ribose) polymerase (PARP) and is 193 KDa. Vaults from higher eukaryotes also contain one or several small vault RNAs (vRNAs, also known as vtRNAs) of 86–141 bases within.
Function.
Despite not being fully elucidated, vaults have been associated with the nuclear pore complexes and their octagonal shape appears to support this. Vaults have been implicated in a broad range of cellular functions including nuclear-cytoplasmic transport, mRNA localization, drug resistance, cell signaling, nuclear pore assembly, and innate immunity. The three vault proteins (MVP, VPARP, and TEP1) have each been knocked out individually and in combination (VPARP and TEP1) in mice. All of the knockout mice are viable and no major phenotypic alterations have been observed. Dictyostelium encode three different MVPs, two of which have been knocked out singly and in combination. The only phenotype seen in the Dictyostelium double knockout was growth retardation under nutritional stress. If vaults are involved in an essential cellular functions, it seems likely that redundant systems exist that can ameliorate their loss.
Association with cancer.
In the late 1990s, researchers found that vaults (especially the MVP) were over-expressed in cancer patients who were diagnosed with multidrug resistance, that is the resistance against many chemotherapy treatments. Although this does not prove that increased number of vaults led to drug resistance, it does hint at some sort of involvement. This has potential in discovering the mechanisms behind drug-resistance in tumor cells and improving anticancer drugs.
Evolutionary conservation.
Vaults have been identified in mammals, amphibians, avians and "Dictyostelium discoideum". The Vault model used by the Pfam database identifies homologues in "Paramecium tetraurelia", Kinetoplastida, many vertebrates, a cnidarian (starlet sea anemone), molluscs, "Trichoplax adhaerens", flatworms, "Echinococcus granulosus" and Choanoflagellate.
Although vaults have been observed in many eukaryotic species, a few species do not appear to have the ribonucleoprotein. These include:
These four species are model organisms for plants, nematodes, animal genetics and fungi respectively. Despite these exceptions, the high degree of similarity of vaults in organisms that do have them implies some sort of evolutionary importance.
Vault engineering.
The Rome lab at UCLA has collaborated with a number of groups to use the baculovirus system to produce large quantities of vaults. When the major vault protein (MVP) is expressed in insect cells, vault particles are assembled on polyribosomes in the cytoplasm. By using molecular genetic techniques to modify the gene encoding the major vault protein, vault particles have been produced with chemically active peptides attached to their sequence. These modified proteins are incorporated into the inside of the vault particle without altering its basic structure. Proteins and peptides can also be packaged into vaults by attachment of a packaging domain derived from the VPARP protein. A number of modified vault particles have been produced in order to test the concept that vaults can be bio-engineered to allow their use in a wide variety of biological applications including drug delivery, biological sensors, enzyme delivery, controlled release, and environmental remediation.
A vault has been packaged with a chemokine for potential use to activate the immune system to attack lung cancer, and this approach has undergone phase I trials.


Electron transfer complex I

Electron transfer complex I may refer to:


Env (gene)

"Env" is a viral gene that encodes the protein forming the viral envelope. The expression of the "env" gene enables retroviruses to target and attach to specific cell types, and to infiltrate the target cell membrane.
Analysis of the structure and sequence of several different "env" genes suggests that Env proteins are type 1 fusion machines. Type 1 fusion machines initially bind a receptor on the target cell surface, which triggers a conformational change, allowing for binding of the fusion protein. The fusion peptide inserts itself in the host cell membrane and brings the host cell membrane very close to the viral membrane to facilitate membrane fusion.
While there are significant differences in sequence of the "env" gene between retroviruses, the gene is always located downstream of "gag", "pro", and "pol". The "env" mRNA must be spliced for expression.
The mature product of the "env" gene is the viral spike protein, which has two main parts: the surface protein (SU) and the transmembrane protein (TM). The tropism of the virus is determined by the SU protein domain because it is responsible for the receptor-binding function of the virus. The SU domain therefore determines the specificity of the virus for a single receptor molecule.
Physical structure.
Oligomerization.
The retroviral glycoproteins are oligomeric complexes that are composed of SU-TM heterodimers, which are made in the endoplasmic reticulum after the translation of the glycosylated Env precursor. The arrangement of these heterodimers determines the 3D structure of the knobbed spike on the viral surface. The Env proteins of the Avian Sarcoma and Leukosis virus (ASLV) and the Murine Leukemia Virus (MLV) are both trimers of SU-TM heterodimers. The Env protein of Human Immunodeficiency Virus (HIV) also has a trimeric structure of heterodimers. It is believed that the intracellular transport of the nascent protein depends, to some extent, on the oligomerization of Env precursors, which allows hydrophobic sequences to be buried inside the protein structure. This oligomerization has also been implicated in fusion initiation with the membrane of the target cell.
Post-translational modification.
Env can be modified by the addition of mannose-rich oligosaccharides, a process that takes place in the rough endoplasmic reticulum and is carried out by the enzymes of the host cell. Cotranslational glycosylation take place at the asparagine in the Asn-X-Ser or Asn-X-Thr motifs. Different retroviruses vary widely in N-linked glycosylation sites: HIV-1 can have as many as 30 sites glycosylated, 25 of which reside in gp120. At the other end of the spectrum, MMTV (Mouse Mammary Tumor Virus has only 4 sites for oligosaccharide addition (two on gp52 and two on gp37). The addition of oligosaccharides is believed to play a role in the proper folding of Env, presumably by stabilizing the protein structure. Without proper folding, protein transport and function can be severely compromised. The importance of glycosylation of Env in HIV-1 was ascertained by synthesizing the glycoprotein in the presence of a glycosylation inhibitor, tunicamycin. The synthesized protein was incorrectly folded and incapable of binding CD4. Receptor binding was only minimally affected, however, when the secreted "env" product was enzymatically deglycosylated.
In HIV.
The "env" gene codes for the gp160 protein which forms a homotrimer, and is cleaved into gp120 and gp41 by the host cell protease, furin. To form an active fusion protein, SU gp120 and TM gp41 polypeptides remain non-covalently bound together, but this interaction is often not stable, leading to shed, soluble gp120 and membrane-bound, gp41 'stumps'. Separately, cleavage by furin is inefficient, and virions often are released with inactive, uncleaved gp160. Because of the high prevalence of these inactive forms, the immune system often produces antibodies which target inactive Env, rather than active forms of the envelope protein. "See Replication cycle of HIV."
"Env" expression is regulated by the gene product of "rev". Experimental deletion of "rev" resulted in the inability to detect the Env protein and levels of "env" mRNA in the cell cytoplasm were significantly diminished. However, when total cellular RNA was analyzed, "env" RNA totals were not significantly difference in the presence and absence of "rev" coexpression. It was found that without "rev" expression, there was a marked increase in nuclear "env" RNA, which suggests that "rev" plays an important role in the nuclear export of "env" mRNA. The role of "rev" was further elucidated when it was found that Rev acts in trans to target a specific sequence present in the "env" gene of HIV-1 to initiate export of incompletely spliced HIV-1 RNA from the nucleus.
gp120.
Exposed on the surface of the viral envelope, the glycoprotein gp120 binds to the CD4 receptor on any target cell that has such a receptor, particularly the helper T-cell. Strains of HIV-1 have been isolated that are able to enter host cells that are CD4 negative. This CD4-independence is associated with spontaneous mutation in the "env" gene. The presence of a co-receptor, CXCR4, is sufficient for this mutant strain to infect human cells. The strain with this phenotype was found to have seven mutations in the sequence coding for gp120 and it is proposed that these mutations induce conformational changes in gp120 that allow the virus to directly interact with the co-receptor.
Since CD4 receptor binding is the most obvious step in HIV infection, gp120 was among the first targets of HIV vaccine research. These efforts have been hampered by the fusion mechanism used by HIV, which makes neutralization by antibodies extremely difficult. Prior to binding the host cell, gp120 remains effectively hidden from antibodies because it is buried in the protein and shielded by sugars. Gp120 is only exposed when in close proximity to a host cell and the space between the viral and host cell membranes is small enough to sterically hinder the binding of antibodies.
gp41.
The glycoprotein gp41 is non-covalently bound to gp120, and provides the second step by which HIV enters the cell. It is originally buried within the viral envelope, but when gp120 binds to a CD4 receptor, gp120 changes its conformation causing gp41 to become exposed, where it can assist in fusion with the host cell.
Fusion inhibitor drugs such as enfuvirtide block the fusion process by binding to gp41.
Env in MMTV.
The Mouse Mammary Tumor Virus (MMTV) "env" gene codes for a polyprotein gp70 () that is cleaved to yield the surface (SU) and transmembrane (TM) Env products. Gp52 is the SU subunit in MMTV and gp36 is the TM subunit. Gp52 is a 52,000-dalton glycoprotein and gp36 is a 36,000-dalton glycoprotein.
MMTV Env is of particular interest to researchers because of the discovery that it encodes an immunoreceptor tyrosine-based activation motif (ITAM) that has been shown to transform human and murine mammary cell in culture. This ITAM depolarizes epithelial acinar structures, thereby changing the phenotype of the cells and causing them to become cancerous.
Env in ASLV.
Subgroup A.
Avian Sarcoma and Leukosis Viruses (ASLV) have ten subgroups (A through J). The envelope glycoprotein of subgroup A is called EnvA and its "env" gene codes for precursor protein known as Pr95. This precursor is cleaved by host cell enzymes to yield the surface protein subunit, gp85, and the transmembrane protein subunit, gp37, which heterodimerize and then form a trimer. The virus cannot infect cells before the processing of the envelope precursor protein is completed. For the virus to penetrate the cytosol of a host cell, a low pH is necessary.
Env in MLV.
The "env" gene of Murine Leukemia Virus (MLV) codes for the 71,000-dalton glycoprotein, gp71. This membrane receptor was isolated from Rauscher murine leukemia virus (R-MuLV).
Env in mammalian evolution.
The retroviral protein env has been captured multiple times during mammalian evolution and is expressed in placental tissue, where it facilitates fusion of fetal and maternal cells. The protein is called syncytin in mammals.


Flumequine

Flumequine is a synthetic fluoroquinolone antibiotic used to treat bacterial infections. It is a first-generation fluoroquinolone antibacterial that has been removed from clinical use and is no longer being marketed. The marketing authorization of flumequine has been suspended throughout the EU. It kills bacteria by interfering with the enzymes that cause DNA to unwind and duplicate. Flumequine was used in veterinarian medicine for the treatment of enteric infections (all infections of the intestinal tract), as well as to treat cattle, swine, chickens, and fish, but only in a limited number of countries. It was occasionally used in France (and a few other European Countries) to treat urinary tract infections under the trade name Apurone. However this was a limited indication
because only minimal serum levels were achieved.
History.
The first quinolone used was nalidixic acid (was marketed in many countries as Negram) followed by the fluoroquinolone flumequine. The first-generation fluoroquinolone agents, such as flumequine, had poor distribution into the body tissues and limited activity. As such they were used mainly for treatment of urinary tract infections. Flumequine (benzo quinolizine) was first patented in 1973, (German Patent) by Rikker Labs. Flumequine is a known antimicrobial compound described and claimed in U.S. Pat. No. 3,896,131 (Example 3), July 22, 1975. Flumequine is the first quinolone compound with a fluorine atom at the C6-position of the related quinolone basic molecular structure. Even though this was the first fluoroquinolone, it is often overlooked when classifying the drugs within this class by generations and excluded from such a list.
Though used frequently to treat farm animals and on occasion household pets, flumequine was also used to treat urinary tract infections in humans. Flumequine, was used transiently treat urinary infections until ocular toxicity was reported. as well as liver damage and anaphylactic shock.
In 2008, the United States Food and Drug Administration (FDA) requested that all quinolone/fluoroquinolone drugs package inserts include a Black Boxed Warning concerning the risk of spontaneous tendon ruptures, which would have included flumequine. The FDA also requested that the manufacturers send out Dear Doctor Letters regarding this new warning. Such tendon problems have also been associated with flumequine.
Drug residue.
The use of flumequine in food animals had sparked considerable debate. Significant and harmful residues of quinolones have been found in animals treated with quinolones and later slaughtered and sold as food products. There has been significant concern regarding the amount of flumequine residue found within food animals such as fish, poultry and cattle. In 2003 the Joint FAO/WHO Committee on Food Additives (JECFA) withdrew the maximum residue limits (MRLs) for flumequine and carbadox based on evidence showing both are direct acting genotoxic carcinogens, therefore the Committee was unable to establish an Acceptable Daily Intake (ADI) for human exposure to such residues. Subsequently, in 2006, the JEFCA, re-established the ADI having received appropriate evidence and MRLs were re-specified. The role of JECFA is to evaluate toxicology, residue chemistry and related information and make recommendations for acceptable daily intake (ADI) levels and maximum residue limits (MRLs). At its 16th session, held May 2006, the Committee on Residues of Veterinary Drugs in Foods (CCRVDF) requested information on registered uses of flumequine. As the CCRVDF did not receive any information regarding the registered uses of flumequine that they had requested, the committee members agreed to discontinue work on the MRLs for flumequine in shrimp.
Licensed uses.
Urinary tract infections (veterinary and human)
Availability.
Veterinary use:
Human use:
Mode of action.
Ciprofloxacin is a broad-spectrum antibiotic that is active against both
Gram-positive and Gram-negative bacteria. It functions by inhibiting DNA gyrase, a type II topoisomerase, and topoisomerase IV, enzymes necessary to separate bacterial DNA, thereby inhibiting cell division.
This mechanism can also affect mammalian cell replication. In particular, some congeners of this drug family (for example those that contain the C-8 fluorine), display high activity not only against bacterial topoisomerases, but also against eukaryotic topoisomerases and are toxic to cultured mammalian cells and "in vivo" tumor models.
Although quinolones are highly toxic to mammalian cells in culture, its mechanism of cytotoxic action is not known. Quinolone induced DNA damage was first reported in 1986 (Hussy et al.).
Recent studies have demonstrated a correlation between mammalian cell cytotoxicity of the quinolones and the induction of micronuclei.
As such, some fluoroquinolones may cause injury to the chromosome of eukaryotic cells.
There continues to be considerable debate as to whether or not this DNA damage is to be considered one of the mechanisms of action concerning the severe adverse reactions experienced by some patients following fluoroquinolone therapy.
Adverse reactions.
Flumequine was associated with severe ocular toxicity, which precluded its use in human patients. Drug-induced calculi (kidney stones) has been associated with such therapy as well. Anaphylactic shock induced by flumequine therapy has also been associated with its use. Anaphylactoid reactions such as shock, urticaria, and Quincke’s oedema have been reported to generally appear within two hours after taking the first tablet. There were eighteen reports listed within the WHO file in 1996. As with all drugs within this class, flumequine therapy may result in severe central nervous system (CNS) reactions, phototoxicity resulting in skin reactions like erythema, pruritus, urticaria and severe rashes, gastrointestinal and neurological disorders.
Drug interactions.
Flumequine was found to have no effect on theophylline pharmacokinetics.
Chemistry.
Flumequine is a 9-fluoro-6,7-dihydro-5-methyl-1-oxo-1H,5H-benzo[ij]quinolizine-2-carboxylic acid. The molecular formula is C14H12FNO3. It is a white powder, odorless, flavorless, insoluble in water but soluble in organic solvent.
Pharmacokinetics.
Flumequine is considered to be well absorbed and is excreted in the urine and feces as the glucuronide conjugates of the parent drug and 7-hydroxyflumequine. It is eliminated within 168 hours post-dosing. However, studies concerning the calf liver showed additional unidentified residues, of which a new metabolite, ml, represented the major single metabolite 24 hours after the last dose and at all subsequent time points. The metabolite ml, which exhibited no antimicrobial activity, was present in both free and protein-bound fractions. The major residue found in the edible tissues of sheep, pigs, and chickens was parent drug together with minor amounts of the 7-hydroxy-metabolite. The only detected residue in trout was the parent drug.


NLRP2

NACHT, LRR and PYD domains-containing protein 2 is a protein that in humans is encoded by the "NLRP2" gene.
NALP proteins, such as NALP2, are characterized by an N-terminal pyrin domain (PYD) and are involved in the activation of caspase-1 (CASP1; MIM 147678) by Toll-like receptors(see TLR4). They may also be involved in protein complexes that activate proinflammatory caspases (Tschopp et al., 2003).[supplied by OMIM]
Function.
The NLRP2 gene is one of the family members of nucleotide-binding and leucine-rich repeat receptor (NLR). Information from many literature sources indicates that an N-terminal pyrin effector domain (PYD) is one of the components of the NLRP2 gene. Other components include a centrally-located nucleotide-binding and oligomerization domain (NACHT) and C-terminal leucine-rich repeats (LRR). The products of NLRP2 gene are known to interact with IkB kinase (IKK) complex components. It can also regulate the activities of both caspase-1 and nuclear factor kappa-light-chain-enhancer of activated B cells (NF-kB). The pyrin domain is essential and adequate to suppress the activities of NF-kB (Minkiewicz, de Rivero Vaccari and Keane 1113). An allelic variant (rs147585490) is known to block the NF-kB transcriptional activities. NLRP2 gene is one of the NLR family; it is believed to contribute to the regulation of immune responses (Minkiewicz, de Rivero Vaccari and Keane 1121). Although it is not well understood, the NLRP2 gene is responsible for maintaining fertility in females and contributes to the normal birth. The NPRP2 gene encodes for a human protein known as “NACHT, LRR and PYD domains-containing protein 2”. NALP2, which is one of the NALP proteins, has an N-terminal pyrin characterization also encoded as MIM 608107 and PYD domain. The NALP2 protein has a role in the activation process of caspase-1, which is encoded as CASP1; MIM 147678. The activation process occurs through the Toll-like receptors. The NALP2 may also take part in protein complexes, which initiates the activation of proinflammatory caspases. NLR family regulates the functioning of the immune system, which technically compromises the normal functions of the body including reproduction.
Discovery.
The NLR gene family where the NLRP2 gene belongs was first extracted from zebrafish, which is a common specimen for the study of immune systems. The NLRP2 gene is believed to have originated from the NLR gene family through mutation. The mutation was initiated by the need for organisms to fit a dynamic environment and diversification in the evolution stages. Also, the mutation of the NLR gene family proteins was also due to the ability of pathogens to subvert the defense mechanism of the host. Therefore, the organisms were forced to device new ways of detecting and counteracting the effects of the resistant pathogens. The evolution of the NLR proteins defines the origin of the NLRP2 gene. The NLRP2 gene is now an innate immune sensor for pathogens and sterile stress signal (SSS) in multi-cellular organisms.
Mutation and infertility.
The deficiency of NLRP2 gene results in the inhibition of the activation of oocytes. The NLRP2 gene is exclusively expressed in oocytes. Therefore, it regulates the quality of the oocytes, which explains its relation to infertility in females.


Histone-like nucleoid-structuring protein

In molecular biology, the histone-like nucleoid-structuring (H-NS) protein belongs to a family of bacterial proteins that play a role in the formation of nucleoid structure and affect gene expression under certain conditions. The protein has a homologue that is encoded by many large, conjugative plasmids.
Mechanism.
A major function of H-NS is to influence DNA topology. It is believed that H-NS achieves this by forming complexes with itself and binding to different sections of DNA, bringing them together. Another major role of H-NS is to turn off the expression of genes. H-NS regulates gene expression by binding to AT rich DNA, which is a common feature of promoters, and of horizontally acquired genes. Relief of suppression by H-NS can be achieved by the binding of another protein, or by changes in DNA topology which can occur due to changes in temperature and osmolarity, for example.
H-NS can also interact with other proteins and influence their function, for example it can interact with the flagellar motor protein FliG to increase its activity.


Phosphoramidon

Phosphoramidon is a chemical compound derived from cultures of "Streptomyces tanashiensis". It is an inhibitor of the enzyme thermolysin, a membrane metallo-endopeptidase inhibitor, and an endothelin converting enzyme inhibitor. Chemically, phosphoramidon differs from its closely related peptidase inhibitor talopeptin by a single stereocenter.
Because of its enzyme inhibitory properties, phosphoramidon is widely used as a biochemical tool.


Difloxacin

Difloxacin (INN), marketed under the trade name Dicural, is a second-generation, synthetic fluoroquinolone antibiotic used in veterinary medicine. It has broad-spectrum, concentration dependent, bactericidal activity; however, its efficacy is not as good as enrofloxacin or pradofloxacin.
Indications and Usage.
In 1997, the United States Food and Drug Administration approved difloxacin hydrochloride tablets for use in canines. Unlike other fluoroquinolones difloxacin has not been approved by the FDA for use in cats. It is also contraindicated for use in food animals.
The recommended dosing is 5–10 mg/kg once daily. This is based on the linear pharmacokinetics exhibited by difloxacin over the 5–60 mg/kg range. So the maximum dose is well within the established safety range, but drug accumulation in tissues prompts a recommendation that the medication should not be used for periods longer than thirty days. If there is no noticeable improvement after five days, then the condition should be reevaluated and all therapy options reconsidered. Difloxacin is indicated for infections caused by susceptible microorganisms in the conditions listed below.
Microbiology.
Difloxacin is a bactericidal, broad-spectrum antibiotic that has activity against Gram-negative bacteria and Gram-positive bacteria. It exerts its antibacterial effect by interfering with the bacterial enzyme DNA gyrase, which is needed for the maintenance and synthesis of bacterial DNA. The minimum inhibitory concentrations (MICs) of pathogens isolated in clinical field trials conducted in the United States between 1991 and 1993 were determined using National Committee for Clinical Laboratory Standards (NCCLS).
Mechanism of action.
The primary mode of action of fluoroquinolones involves interaction with enzymes essential for major DNA functions such as replication, transcription and recombination. Difloxacin inhibits DNA gyrase (also known as "Topoisomerase II"), an enzyme required for negative super coiling during DNA replication Cell death can occur through the inability of bacteria to maintain the DNA super helical structure.
Pharmacokinetics.
Difloxacin is rapidly and almost completely absorbed after oral administration, and approximately 50% is bound to circulating plasma proteins. It is metabolized primarily by the liver through glucuronidation and secreted in the bile. It can also be reabsorbed with the bile. This allows reentry into the blood stream and recirculation, a mechanism that can extend the half-life. The longer half-life allows for once daily dosing. In contrast to other fluoroquinolones, renal clearance accounts for only 5% of the removal of difloxacin from the canine system, which makes it an attractive choice for dogs with compromised renal function.
aTotal body clearance/F = Dose/AUC
bSteady state volume of distribution/F = Dose•AUMC/AUC2
cVolume of distribution (area)/F = Vdβ = (T1/2)(CL/F)/0.693
As mentioned above, Difloxacin is not FDA-approved for use in cats. This is because the major route of metabolism is through glucuronidation, an enzymatic pathway that cats lack. Therefore, administration to cats would likely result in toxicity.
Difloxacin is stored at room temperature in a cool, dry place.
Chemical and Drug Interactions.
Difloxacin has been used concurrently with ectoparasiticides, antiepileptics, anesthetics, antihistamines, and topical anti-inflammatory drugs without adverse effects. It inhibits the metabolism of theophylline, caffeine, cyclosporine and warfarin. Azlocillin, cimetidine and probenecid increase blood levels of difloxacin. Compounds (i.e. sucralfate, antacids, multivitamins) containing di- and trivalent cations (i.e. iron, aluminum, calcium, magnesium and zinc) may substantially interfere with the absorption of quinolones from the intestinal tract resulting in decreased bioavailability. Therefore, the concurrent oral administration of quinolones with foods, supplements or other preparations containing any of these compounds should be avoided.
Adverse effects.
Like other fluoroquinolones, difloxacin causes arthropathy in immature growing animals, particularly dogs. Otherwise, it is very well tolerated. The most common adverse effects are gastrointestinal effects such as vomiting, diarrhea and anorexia, even in overdose. Only supportive measures, and not additional treatment, are recommended for management of overdose or toxicity as the reactions are self-limiting.
Contraindications include small and medium breeds of dogs that are less than 8 months old; large breeds less than 12 months old; giant breeds less than 18 months old; those with suspected CNS disorders; and hypersensitivity to difloxacin or any other fluoroquinolone.
Human Warnings.
Difloxacin has been approved for animal use only. Keep out of reach of children. Avoid contact with eyes. In case of contact, immediately flush eyes with copious amounts of water for fifteen minutes. In case of dermal contact, wash skin with soap and water. Consult a physician if symptoms persists following exposure. Individuals with a history of hypersensitivity to quinolones should avoid this product. In humans, there is a risk of user photosensitization within a few hours after excessive exposure to quinolones. If excessive accidental exposure occurs, avoid direct sunlight.
Research.
The minimum dose (5 mg/kg) was confirmed in a clinical trial performed by HTI Bio-services, Inc. It evaluated the effective dose for the treatment of an infected dermal wound. The study included forty-eight mixed breed dogs (both male and female) with weights ranging from 14.5-24.5 kilograms. These dogs were randomly placed into treatment groups. Once wounds were created, the dogs were inoculated with culture both containing both "Escherichia coli" and "Klebsiella pneumoniae". Pertinent observations and measurements were then taken and tabulated. Culture scores were significantly reduced, confirming 5 mg/kg to be an effective dose.
Clinical field trials were also performed to evaluate both the efficacy and safety of difloxacin tablets. Clinical signs of bacterial infections were defined in a protocol. Dogs who presented to investigators with these signs were admitted into the study. In total, eighteen veterinarians located in four different geographical areas of the U.S. (Southeast, Midwest, Northwest, and West) conducted these clinical efficacy and safety evaluations.
Society and Culture.
Cost.
Difloxacin tablets are not available to the public for over-the-counter purchase. It can only be obtained by prescription from a veterinarian. At least two company, Henan Sunny Industry Co. Ltd. Turtle Pharma Private Limited provides industrial-size amounts.
Marketing.
Dicural was sponsored by Fort Dodge Animal Health through New Animal Drug Application (NADA) 141-096. It offers veterinarians once-per-day dosing by providing excellent tissue penetration. Difloxacin can only be obtained either from a veterinarian or by a medical prescription from a veterinarian. It is available as the hydrochloride salt in scored tablets of different strengths for easier dosing adjustments. For differentiation, the milligram strengths, 11.4 mg, 45.4 mg and 136 mg, are colored blue, white and orange, respectively.
Fort Dodge Animal Health was acquired by Zoetis in 2009. In February 2012, the Municipality of Ulianopolis (State of Para, Brazil) filed a complaint against Fort Dodge Saúde Animal Ltda. (FDSAL) and five other large companies alleging that waste sent to a local waste incineration facility for destruction, but that was not ultimately destroyed as the facility lost its operating permit, caused environmental impacts requiring cleanup. The Municipality is seeking recovery of cleanup costs purportedly related to FDSAL's share of all waste accumulated at the incineration facility awaiting destruction, and compensatory damages to be allocated among the six defendants. The prosecutor granted a request for a face-to-face meeting on November 6, 2015.


Isopeptidase

An isopeptidase is a protease enzyme that hydrolyzes isopeptide bonds, or amide bonds that occur outside the main chain in a polypeptide chain.
In protein degradation.
Isopeptide bonds occur in the linkage of protein amino acid side chains to proteins such as ubiquitin and SUMO in the protein degradation pathway. In eukaryotes, enzymes with isopeptidase activity are often involved in this pathway; all five classes of deubiquitinating enzymes have isopeptidase activity. Examples include Ulp1 peptidase and USP5 (formerly known as isopeptidase T).
In lasso peptide processing.
Isopeptidases have also been identified in prokaryotes that express lasso peptides, or peptides with a knotted conformation established by the presence of a non-main-chain linkage between an acidic amino acid and the peptide's N-terminus to form the knot. (Some lasso peptides also have topological complexity conferred by disulfide bonds.) Isopeptidase enzymes linearize the peptides by cleaving the isopeptide bond.


Protein S

Protein S (also known as PROS) is a vitamin K-dependent plasma glycoprotein synthesized in the liver. In the circulation, Protein S exists in two forms: a free form and a complex form bound to complement protein C4b-binding protein (C4BP). In humans, protein S is encoded by the "PROS1" gene.
History.
Protein S is named for Seattle, Washington, where it was originally discovered and purified by Earl Davie's group in 1977.
Structure.
Protein S is partly homologous to other vitamin K-dependent plasma coagulation proteins, such as protein C and factors VII, IX, and X. Similar to them, it has a Gla domain and several EGF-like domains (four rather than two), but no serine protease domain. Instead, there is a large C-terminus domain that is homologous to plasma steroid hormone-binding proteins such as sex hormone-binding globulin and corticosteroid-binding globulin. It may play a role in the protein functions as either a cofactor for activated protein C (APC) or in binding C4BP.
Additionally, protein S has a peptide between the Gla domain and the EGF-like domain, that is cleaved by thrombin. The Gla and EGF-like domains stay connected after the cleavage by a disulfide bond. However, protein S loses its function as an APC cofactor following either this cleavage or binding C4BP.
Function.
The best characterized function of Protein S is its role in the anti coagulation pathway, where it functions as a cofactor to Protein C in the inactivation of Factors Va and VIIIa. Only the free form has cofactor activity.
Protein S binds to negatively charged phospholipids via the carboxylated Gla domain. This property allows Protein S to facilitate the removal of cells that are undergoing apoptosis, a form of structured cell death used by the body to remove unwanted or damaged cells. In healthy cells, an ATP (adenosine triphosphate)-dependent enzyme removes negatively charged phospholipids such as phosphatidyl serine from the outer leaflet of the cell membrane. An apoptotic cell (that is, one undergoing apoptosis) no longer actively manages the distribution of phospholipids in its outer membrane and hence begins to display negatively charged phospholipids on its exterior surface. These negatively charged phospholipids are recognized by phagocytes such as macrophages. Protein S binds to the negatively charged phospholipids and functions as a bridge between the apoptotic cell and the phagocyte. This bridging expedites phagocytosis and allows the cell to be removed without giving rise to inflammation or other signs of tissue damage.
Protein S also binds to the nascent complement complex C5,6,7 and prevents this complex from inserting into a membrane. This function prevents the inappropriate activation of the complement system, which would cause uncontrolled systemic inflammation. In fact, Protein S was first discovered in 1977 in this role and it is named after the membrane "site" that it occupies in the complex.
Pathology.
Mutations in the PROS1 gene can lead to Protein S deficiency which is a rare blood disorder which can lead to an increased risk of thrombosis.
Interactions.
Protein S has been shown to interact with Factor V.


Cyclic nucleotide phosphodiesterase

3'5'-cyclic nucleotide phosphodiesterases are a family of phosphodiesterases. Generally, these enzymes hydrolyze some nucleoside 3',5'-cyclic phosphate to some nucleoside 5'-phosphate thus controlling the cellular levels of the cyclic second messengers and the rates of their degradation.
Some examples of nucleoside 3',5'-cyclic phosphate include:
There are 11 distinct phosphodiesterase families (PDE1–PDE11) with a variety in isoforms and splicing having unique three-dimensional structure, kinetic properties, modes of regulation, intracellular localization, cellular expression, and inhibitor sensitivities.
Nomenclature.
The systematic for this enzyme is 3',5'-cyclic-nucleotide 5'-nucleotidohydrolase. Other names in use include cyclic 3',5'-mononucleotide phosphodiesterase, PDE, cyclic 3',5'-nucleotide phosphodiesterase, cyclic 3',5'-phosphodiesterase, 3',5'-nucleotide phosphodiesterase, 3':5'-cyclic nucleotide 5'-nucleotidohydrolase, 3',5'-cyclonucleotide phosphodiesterase, 3', 5'-cyclic nucleoside monophosphate phosphodiesterase, 3': 5'-monophosphate phosphodiesterase (cyclic CMP), cytidine 3':5'-monophosphate phosphodiesterase (cyclic CMP), cyclic 3',5-nucleotide monophosphate phosphodiesterase, nucleoside 3',5'-cyclic phosphate diesterase, nucleoside-3',5-monophosphate phosphodiesterase)
Function.
Phototransduction.
Retinal 3',5'-cGMP phosphodiesterase (PDE) is located in photoreceptor outer segments and is an important enzyme in phototransduction.
PDE in rod cells are oligomeric, made up of two heavy catalytic subunits, α (90 kDa) and β (85 kDa,) and two lighter inhibitory γ subunits (11 kDa each).
PDE in rod cells are activated by transducin. Transducin is a G protein which upon GDP/GTP exchange in the transducin α subunit catalyzed by photolyzed rhodopsin. The transducin α subunit (Tα) is released from the β and γ complex and diffuses into the cytoplasmic solution to interact and activate PDE.
Activation by Tα.
There are two proposed mechanisms for the activation of PDE. The first proposes that the two inhibitory subunits are differentially bound, sequentially removable and exchangeable between the native complex PDEαβγ2 and PDEαβ. GTP-bound-Tα removes the inhibitory γ subunits one at a time from the αβ catalytic subunits. The second and more likely mechanism states that the GTP-Tα complex binds to the γ subunits but rather than dissociating from the catalytic subunits, it stays with the PDEαβ complex. Binding of the GTP-Tα complex to the PDE γ subunits likely causes a conformational shift in the PDE, allowing better access to the site of cGMP hydrolysis on PDEαβ.
Structure.
The binding site for PDE α and β subunits are likely to be in the central region of the PDE γ subunits. The C-terminal of the PDE γ subunit is likely to be involved in inhibition of PDE α and β subunits, the binding site for Tα and GTPase accelerating activity for the GTP-bound Tα.
In cones, PDE is a homodimer of alpha chains, associated with several smaller subunits. Both rod and cone PDEs catalyze the hydrolysis of cAMP or cGMP to their 5' monophosphate form. Both enzymes also bind cGMP with high affinity. The cGMP-binding sites are located in the N-terminal half of the protein sequence, while the catalytic core resides in the C-terminal portion.
Examples.
Human genes encoding proteins containing this domain include:


NLRC3

NLRC3, short for NOD-like receptor family CARD domain containing 3, is an intracellular protein that plays a role in the immune system. It was previously known as "nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 3" (NOD3) and CLR16.2. NLRC3 inhibits the activity of T cells. NLRC3 also inhibits the mTOR signalling pathway to block cellular proliferation.


Ganoderenic acid

Ganoderenic acids are bio-active sterols isolated from "Ganoderma lucidum".


Calcineurin-like phosphoesterase

The calcineurin-like phosphoesterases are a family of enzymes related to calcineurin. It includes a diverse range of phosphoesterases, including protein phosphoserine phosphatases, nucleotidases, sphingomyelin phosphodiesterases and 2'-3' cAMP phosphodiesterases as well as some bacterial nucleases. The most conserved region is a centre on the metal chelating residues.


PDIA2

Protein disulfide isomerase family A member 2 is a protein that in humans is encoded by the PDIA2 gene.
Function.
This gene encodes a member of the disulfide isomerase (PDI) family of endoplasmic reticulum (ER) proteins that catalyze protein folding and thiol-disulfide interchange reactions. The encoded protein has an N-terminal ER-signal sequence, two catalytically active thioredoxin (TRX) domains, two TRX-like domains and a C-terminal ER-retention sequence. The protein plays a role in the folding of nascent proteins in the endoplasmic reticulum by forming disulfide bonds through its thiol isomerase, oxidase, and reductase activity. The encoded protein also possesses estradiol-binding activity and can modulate intracellular estradiol levels. [provided by RefSeq, Sep 2017].


Lymphocyte homing receptor

Lymphocyte homing receptors are cell adhesion molecules expressed on lymphocyte cell membranes that recognize addressins on target tissues. "Lymphocyte homing" refers to adhesion of the circulating lymphocytes in blood to specialized endothelial cells within lymphoid organs. These diverse tissue-specific adhesion molecules on lymphocytes ("homing receptors") and on endothelial cells ("vascular addressins") contribute to the development of specialized immune responses.
Free lymphocytes constantly recirculate in blood after their re-entry from lymphoid tissue, via lymphatic and thoracic ducts. This happens so that the full repertoire of antigenic specificities of lymphocytes is continuously represented throughout the body. Homing happens in tissue-specific manner—e.g. B lymphocytes migrate better to mucosa-associated lymphoid tissue (Peyer's patches), and T lymphocytes preferentially to the peripheral lymph nodes.
The process of lymphocyte homing is deliberate, mediated by lymphocyte-endothelial recognition mechanisms that enable antigen-specific immune responses. Lymphocyte homing receptor control of organ-specific lymphocyte trafficking is thought to prevent autoreactivity in immune responses during B and T cell differentiation. Recently, lymphocyte homing has become a topic of interest for investigation of treatments for multiple sclerosis, type 1 diabetes mellitus, leukemia, and psoriasis.
Homing mechanisms.
Naive lymphocyte homing.
Naive lymphocytes are able to circulate into secondary lymphoid tissues, Peyer’s patches, lymph nodes, and the spleen. Because they have not yet been exposed to antigen, these lymphocytes are undifferentiated and express few homing receptors.
High endothelial venules (HEVs) are cells found in secondary lymphoid organs that express large quantities of cell adhesion molecules, enabling undifferentiated lymphocytes to bind. After entering lymph nodes and Peyer’s patches via HEVs, naive T and B cells are exposed to antigen circulating in lymph and differentiate to contribute to the adaptive immune response. HEVs develop from cytokine production after exposure to antigen and express adhesion molecules from the selectin family, mucin-like family, and the Ig superfamily. Naive lymphocyte extravasation into Peyer’s patches is often mediated by L-selectin and limited expression of α4 integrins and other homing receptors prevents these lymphocytes from accessing mucosal effector tissue.
Mature lymphocyte homing.
Mature lymphocytes are constantly recirculating in the blood and can traffic to secondary lymphoid tissue as well as target tissue including mucosal tissues of the lamina propria, inflammation, and other extralymphoid immune effector sites. Lymphocyte homing receptor expression is altered by antigen exposure. This function enables the adaptive immune system to specialize an immune response in different parts of the body.
Upon exposure to antigens, lymphocytes lack homing ability during a period of sessile differentiation and cell division, and antigen specific lymphocytes are stored in the spleen for 1–3 days. Subsequently, antigen-stimulated B and T cells express homing receptors particularly for the HEV in initial site of immunization tissue. Furthermore, lymphocytes can alter cell adhesion molecule “activatability” to increase binding ability. Organ-specific lymphocyte homing is important for antigen-specificity and in avoiding autoimmune cross-reactions.
Extravasation of lymphocytes.
Lymphocyte homing occurs in four steps leading to extravasation into target tissue; Rolling, activation, activation-dependent “arrest”, and diapedesis. Mediated by lymphocyte receptors and vascular ligand interactions, “tethering” is a reversible linkage that leads to either rolling along the vessel wall or transient immediate arrest. L-selectin is able to mediate vessel adhesion whereas α4 integrins, α4β1 or α4β7, can perform primary or secondary adhesion through a stronger tethering and even contribute to transendothelial migration of lymphocytes. L-selectin, for example, is also able to be cleaved by an enzyme, ensuring proper binding of lymphocytes and allowing release of non-target cells. While attached to the vessel, lymphocytes test target tissue for chemokines and pro-adhesive factors that then prompt “arrest.” In addition to α4 integrins, LFA-1 and Mac-1 mediate the prevention of lymphocyte transendothelial migration into target tissues. While initial adhesion indicates the start of lymphocyte homing, there is regulation of each step of extravasation.
Examples of lymphocyte homing receptors.
α4β7 is an α4 integrin class homing receptor that targets lymphocytes in the gut expressing mucosal adhesion molecule-1(MAdCAM-1), mostly expressed in Peyer’s patches. Additionally, α4β1 with the ligand vascular adhesion molecule-1(VCAM-1) function in lymphocyte trafficking and inflammation.
Two other well known examples are CD34 and GLYCAM-1.


ADF-H domain

In molecular biology, ADF-H domain (actin-depolymerising factor homology domain) is an approximately 150 amino acid motif that is present in three phylogenetically distinct classes of eukaryotic actin-binding proteins.
The ADF-H domain consists of a six-stranded mixed beta-sheet in which the four central strands (beta2-beta5) are anti-parallel and the two edge strands (beta1 and beta6) run parallel with the neighbouring strands. The sheet is surrounded by two alpha-helices on each side .


2-coumarate O-beta-glucosyltransferase

In enzymology, a 2-coumarate O-beta-glucosyltransferase () is an enzyme that catalyzes the chemical reaction
Thus, the two substrates of this enzyme are UDP-glucose and trans-2-hydroxycinnamate, whereas its two products are UDP and trans-beta-D-glucosyl-2-hydroxycinnamate.
This enzyme belongs to the family of glycosyltransferases, specifically the hexosyltransferases. The systematic name of this enzyme class is UDP-glucose:trans-2-hydroxycinnamate O-beta-D-glucosyltransferase. Other names in common use include uridine diphosphoglucose-o-coumarate glucosyltransferase, and UDPG:o-coumaric acid O-glucosyltransferase. This enzyme participates in phenylpropanoid biosynthesis.


Cyanase

In molecular biology, cyanase (, also known as cyanate hydratase or cyanate lyase) is an enzyme which catalyses the bicarbonate dependent metabolism of cyanate to produce ammonia and carbon dioxide. The systematic name of this enzyme is carbamate hydrolyase. In "E. coli", cyanase is an inducible enzyme and is encoded for by the "cynS" gene. Cyanate is a toxic anion, and cyanase catalyzes the metabolism into the benign products of carbon dioxide and ammonia.
Enzyme Reaction.
Cyanase catalyzes the metabolic conversion of toxic cyanate to carbamate (H2NCOO−). The enzyme does this by first catalyzing the conversion of cyanate to carbamate, which then spontaneously decomposes to carbon dioxide and ammonia:
The resulting net reaction is:
The kinetic mechanism is a rapid equilibrium where bicarbonate and cyanate both act as substrates. Bicarbonate acts a recycling substrate to cyanase in the production carbamate which then decomposes to complete the metabolism, rather than metabolism via a hydrolysis reaction as formerly believed.
A positively charged active site forms a pocket with two anion binding sites, bonded via ionic interaction. Positively charged amino acids that make up the protein help form this site between subunits. This adjacent anion binding site structure accommodates a complex of cyanate and bicarbonate, allowing the carbamate producing reaction to proceed.
Enzyme Structure.
Some bacteria can overcome the toxicity of environmental cyanate by degrading it via this enzyme. Cyanate hydratase is found in bacteria and plants. Cyanase is functionally active as a homodecamer, composed of 5 complexes of dimers. Each of these monomer subunits is 17 kDa and supports half-site binding of substrates. The cyanase monomer is composed of two domains. The N-terminal domain shows structural similarity to the DNA-binding alpha-helix bundle motif. The C-terminal domain has an 'open fold' with no structural homology to other proteins. The dimer structure reveals the C-terminal domains to be intertwined, and a decamer is formed by a pentamer of these dimers. The active site of the enzyme is located between dimers and is composed of residues from four adjacent subunits of the homodecamer.
Connecting these two domains in the monomer is the single cysteine residue. The disulfide bond links 156 amino acid units. Forming the larger complexes of the pentamer and decamer requires the presence of cyanate, or a substrate analog like azide. The final native enzyme complex is a complex of 5 dimers.
The crystallization of cyanase shows that cyanase crystals are triclinic with one homodecamer in the asymmetric unit.
The active site of cyanase accommodates two anions, bicarbonate and cyanate. Three catalytic residues, Arg96, Glu99, and Ser122, form this pocket that stabilizes the anions with ionic interactions. The positively charged and polar amino acid residues allow the active site to bind anions. The active site sits between dimers, noted by the Arg96 in each monomer to be in close proximity.
The structure of cyanase has been shown to be similar in its prokaryotic and eukaryotic forms.
Enzyme Activity.
Cyanase is regulated both transcriptionally and in its enzymatic activity. Transcription of cyanase is elevated with the presence of extracellular cyanate, a toxic ion, but also down regulated by the presence of excess arginine, the catalytic amino acid. Cyanase requires the product of the reaction catalyzed by cyanate permease. Activity of cyanase is also dependent on the concentration of its substrates, cyanate and bicarbonate.
Because bicarbonate is itself a recycling substrate and the kinetics of cyanase include a rapid and random equilibrium, bicarbonate can also act as an enzyme inhibitor. At low concentrations, bicarbonate shows uncompetitive inhibition, where it binds to the one of enzyme's anionic binding sites, and inhibit cyanate binding, or bicarbonate can bind once more so that the enzyme complex is bound to two bicarbonates in its double anion active site. At higher concentrations, the trend moves toward non-competitive inhibition, where the incorrect, dead-end complex must decompose to the initial separated units before the binding action can begin again.
This random equilibrium of cyanate and bicarbonate complexing with the enzyme causing substrate inhibition is referred to as ping pong inhibition.
Functional Relevance.
Cyanase is an important enzyme for plants and microbacteria as cyanate is a toxic enzyme that is prevalent in many environments. Further cyanase activity has been found to be encoded in "cynH", a gene only found in marine cyanobacteria. There is a dodecapeptide, a partial region near the N-terminus of cyanate, that as a novel cationic α-helical antimicrobial peptide, known by CL 14-25.
Cyanase is also important as an energy metabolizer to fix Nitrogen in nitrifiers. Cyanate is an important source of reduced nitrogen in aquatic and terrestrial ecosystems, and although it is a toxic ion, it can be converted to ammonium and carbon dioxide by a cyanase enzyme, supplying energetic Nitrogen compounds to the organism. The activity of cyanase is heavily dependent on the present of bicarbonate, and to overcome this bottleneck, a combined application of cyanase and carbonic anhydrase has been used in a study.


LRRC8D

Leucine-rich repeat-containing protein 8D is a protein that in humans is encoded by the "LRRC8D" gene. Researchers have found out that this protein, along with the other LRRC8 proteins LRRC8A, LRRC8B, LRRC8C, and LRRC8E, is a subunit of the heteromer protein Volume-Regulated Anion Channel. Volume-Regulated Anion Channels (VRACs) are crucial to the regulation of cell size by transporting chloride ions and various organic osmolytes, such as taurine or glutamate, across the plasma membrane, and that is not the only function these channels have been linked to.
While LRRC8D is one of many proteins that can be part of VRAC, it is in fact one of the most important subunits for the channel’s ability to function; the other protein of importance is LRRC8A. However, while we know it is necessary for specific VRAC function, other studies have found that it is not sufficient for the full range of usual VRAC activity. This is where the other LRRC8 proteins come in, as the different composition of these subunits affects the range of specificity for VRACs.
In addition to its role in VRACs, the LRRC8 protein family is also associated with agammaglobulinemia-5.


Type XVIII collagen

Type XVIII collagen is a type of collagen which can be cleaved to form endostatin. The endostatin is from the c terminus end of the collagen XVIII, and is known to have an inhibitory effect on the growth of blood vessels. This is seen with tumors, where endostatin inhibits the growth of the blood vessels of the tumor as well as the overall growth of the tumor.
The collagen XVIII is located within the basement membrane, and plays a major role in the integrity of the structure of the basement membrane for both endothelial and epithelial cells. The collagen XVIII has three different isoforms. While each of the isoforms has the same C-terminus end, they have a varying structure on the N-terminus end, which results in the formation of short, medium or long form Collagen XVIII.
Type XVIII Collagen and Knobloch Syndrome.
Knobloch Syndrome is a type of inherited autosomal recessive disorder in which a mutation occurs in the endostatin COL18A1 protein encoding gene, which codes for production of type XVIII collagen. It is speculated that the mutation of type XVIII collagen that occurs in Knobloch syndrome can be located in several variants of endostatin, a gene that interacts with type XVIII collagen to not only develop the ocular system, but to also maintain its visual functionality. Evidence has been found for Knobloch syndrome development in genomes containing no mutations in the COL18A1 gene, and thus different variants of endostatin genes can also be responsible for the disease. One such variant of endostatin genes is the D1437N gene, which occurs after two mutations in the COL18A1 gene: the first is a one-base pair mutation insertion, and the other is an amino acid substitution of a conserved amino acid of endostatin. This amino acid substitution is deleterious because it blocks the endostatin variant from interacting with laminin. This discovery was significant in that it provided a new genetic locus for Knobloch syndrome, which helped to explain the development of the disease from genomes free of mutation in the COL18A1 gene.
The mutations in type XVIII collagen result in a multitude of abnormalities in vision and eye structure, some of which include high myopia, vitreoretinal degeneration, retinal detachment, macular abnormalities, and occipital encephalocele. Additionally, fragile iris, overgrowth of blood vessels in the retina, and an excess of electron-dense deposits, which leads to a disease called dense deposit disease, may also occur in Knobloch syndrome. Type XVIII collagen functions to provide strength, structural integrity, and cohesiveness to the basement membrane region in endothelial and epithelial cells of many different types of tissues. When type XVIII collagen is mutated at the COL18A1 gene, exon 2 in the sequence is skipped, which results in production of an early termination codon in exon 4 of this gene's transcript. This type of mutation particularly affects only one isoform of type XVIII collagen - the short isoform type, while the medium and long isoforms are unaffected.


Henry Tate

Sir Henry Tate, 1st Baronet (11 March 18195 December 1899) was an English sugar merchant and philanthropist, noted for establishing the Tate Gallery in London.
Life and career.
Born in White Coppice, a hamlet near Chorley, Lancashire, Tate was the son of a Unitarian clergyman, the Reverend William Tate, and his wife Agnes Booth. When he was 13, he became a grocer's apprentice in Liverpool. After a seven-year apprenticeship, he was able to set up his own shop. His business was successful, and grew to a chain of six stores by the time he was 35. In 1859 Tate became a partner in John Wright & Co. sugar refinery, selling his grocery business in 1861. By 1869, he had gained complete control of the company, and renamed it as Henry Tate & Sons. In 1872, he purchased the patent from German Eugen Langen for making sugar cubes, and in the same year built a new refinery in Liverpool. In 1877 he opened a refinery at Silvertown, London, which remains in production. At the time, much of Silvertown was still marshland. Tate was a modest, rather retiring man, well known for his concern with workers’ conditions. He built the Tate Institute opposite his Thames Refinery, with a bar and dance hall for the workers' recreation.
Tate rapidly became a millionaire and donated generously to charity. In 1889 he donated his collection of 65 contemporary paintings to the government, on the condition that they be displayed in a suitable gallery, toward the construction of which he also donated £80,000. The National Gallery of British Art, nowadays known as Tate Britain, was opened on 21 July 1897, on the site of the old Millbank Prison.
Tate made many donations, often anonymously and always discreetly. He supported "alternative" and non-establishment causes. There was £10,000 for the library of Manchester College, founded in Manchester in 1786 as a dissenting academy to provide religious nonconformists with higher education. He also gave the College (which had retained its name during moves to York, London and finally Oxford), £5,000 to promote the ‘theory and art of preaching’. In addition he gave £20,000 to the (homoeopathic) Hahnemann Hospital in Liverpool in 1885. He particularly supported health and education with his money, giving £42,500 for Liverpool University, £3,500 for Bedford College for Women, and £5,000 for building a free library in Streatham. Additional provisions were made for libraries in Balham, South Lambeth, and Brixton. He also gave £8,000 to the Liverpool Royal Infirmary, and £5,000 to the Queen Victoria Jubilee Institute, which became the Queen's Institute for District Nurses.
Tate was made a baronet on 27 June 1898. He had refused this title more than once until – after he had spent £150,000 to build the Millbank Gallery, endowed it with his personal collection, and presented it to the nation – he was told the Royal Family would be offended if he refused again.
In 1921, after Tate's death, Henry Tate & Sons merged with Abram Lyle & Sons to form Tate & Lyle.
In 2001, a blue plaque commemorating Sir Henry was unveiled on the site of his first shop at 42 Hamilton Street, Birkenhead. In 2006 a Wetherspoons pub in his home town of Chorley was named after the sugar magnate.
Personal life.
Tate married Jane Wignall on 1 March 1841 in Liverpool. They had three sons. Tate lived at Park Hill by Streatham Common, South London, and is buried in nearby West Norwood Cemetery, the gates of which are opposite a public library that he endowed. Park Hill became a nunnery after his death until refurbishment as housing around 2004.


Fatty acid transport proteins

Fatty acid transport proteins (FATPs, SLC27, SLC27A) are a family of trans-membrane transport proteins, which allow and enhance the uptake of long chain fatty acids into cells. This subfamily is part of the solute carrier protein family. Within humans this family contains six very homologous proteins, which are expressed in all tissues of the body which use fatty acids:


Homotetramer


Mi-2/NuRD complex

In the field of molecular biology, the Mi-2/NuRD (Nucleosome Remodeling Deacetylase) complex, is a group of associated proteins with both ATP-dependent chromatin remodeling and histone deacetylase activities. , Mi-2/NuRD was the only known protein complex that couples chromatin remodeling ATPase and chromatin deacetylation enzymatic functions.
The NuRD complex contains seven subunits: the histone deacetylase core proteins HDAC1 and HDAC2, the histone-binding proteins RbAp46 and RbAp48, the metastasis-associated proteins MTA1 (or MTA2 / MTA3), the methyl-CpG-binding domain protein MBD3 (or MBD2) and the chromodomain-helicase-DNA-binding protein CHD3 (aka Mi-2alpha) or CHD4 (aka Mi-2beta).
The histone deacetylases HDAC1 and HDAC2 and the histone binding proteins RbAp48 and RbAp46 form a core complex shared between NuRD and Sin3-histone deacetylase complexes.
Overexpression of Mbd3, a subunit of NuRD, inhibits induction of iPSCs. Depletion of Mbd3, on the other hand, improves reprogramming efficiency only in fibroblast, that results in deterministic and synchronized iPS cell reprogramming (near 100% efficiency within seven days from mouse and human cells).


EP-B2

Endoprotease B, isoform 2 (EP-B2) is a cysteine protease found in barley. In studies, it has shown promise as a possible therapeutic for coeliac disease. Aspergillopepsin from "Aspergillus niger" has been shown to enhance the effects of EP-B2.


Bilobol

Bilobol is an alkylresorcinol, a type of phenolic lipids composed of long aliphatic chains and phenolic rings. Chemically, it is similar in structure to urushiol, the irritant found in poison ivy; it is a strong skin irritant itself.
Natural occurrences.
Bilobol can be found in "Ginkgo biloba" fruits.


2,3-dihydroxybenzoate 2,3-dioxygenase

In enzymology, a 2,3-dihydroxybenzoate 2,3-dioxygenase () is an enzyme that catalyzes the chemical reaction
Thus, the two substrates of this enzyme are 2,3-dihydroxybenzoate and O2, whereas its product is 2-carboxy-cis,cis-muconate.
This enzyme belongs to the family of oxidoreductases, specifically those acting on single donors with O2 as oxidant and incorporation of two atoms of oxygen into the substrate (oxygenases). The oxygen incorporated need not be derived from O2. The systematic name of this enzyme class is 2,3-dihydroxybenzoate:oxygen 2,3-oxidoreductase (decyclizing). This enzyme is also called 2,3-dihydroxybenzoate 2,3-oxygenase.


Albumin I

Albumin I (PA1b) is a hormone-like peptide found in the seeds of legumes such as the pea plant ("Pisum sativum") or soya bean ("Glycine max") which have been shown to have insecticidal properties.
It stimulates kinase activity upon binding a membrane bound 43 kDa receptor within the plant which affects cell proliferation.
The structure reveals an inhibitor cystine knot (knottin)-like fold, comprising three beta strands.


Delta-guaiene synthase

Delta-guaiene synthase () is an enzyme with systematic name "(2E,6E)-farnesyl-diphosphate diphosphate-lyase (cyclizing, delta-guaiene-forming)". This enzyme catalyses the following chemical reaction
This enzyme requires Mg2+.


SIN3B

Paired amphipathic helix protein Sin3b is a protein that in humans is encoded by the "SIN3B" gene.
Interactions.
SIN3B has been shown to interact with HDAC1, Zinc finger and BTB domain-containing protein 16, SUDS3 and IKZF1.


Cytidine monophosphoacetylneuraminate-lactosylceramide sialyltransferase

Cytidine monophosphoacetylneuraminate-lactosylceramide sialyltransferase may refer to:


2-hydroxypyridine 5-monooxygenase

In enzymology, a 2-hydroxypyridine 5-monooxygenase () is an enzyme that catalyzes the chemical reaction
The 3 substrates of this enzyme are 2-hydroxypyridine, an electron acceptor AH2, and O2, whereas its 3 products are 2,5-dihydroxypyridine, the reduction product A, 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 derive from O miscellaneous. The systematic name of this enzyme class is 2-hydroxypyridine,hydrogen-donor:oxygen oxidoreductase (5-hydroxylating). This enzyme is also called 2-hydroxypyridine oxygenase.


Queuosine

Queuosine is a modified nucleoside that is present in certain tRNAs in bacteria and eukaryotes. It contains the nucleobase queuine. Originally identified in "E. coli", queuosine was found to occupy the first anticodon position of tRNAs for histidine, aspartic acid, asparagine and tyrosine. The first anticodon position pairs with the third "wobble" position in codons, and queuosine improves accuracy of translation compared to guanosine. Synthesis of queuosine begins with GTP. In bacteria, three structurally unrelated classes of riboswitch are known to regulate genes that are involved in the synthesis or transport of pre-queuosine1, a precursor to queuosine: PreQ1-I riboswitches, PreQ1-II riboswitches and PreQ1-III riboswitches.


Apolipoprotein B

Apolipoprotein B (ApoB) is a protein that in humans is encoded by the "APOB" gene.
Function.
Apolipoprotein B is the primary apolipoprotein of chylomicrons, VLDL, Lp(a), IDL, and LDL particles (LDL - known commonly by the misnomer "bad cholesterol" when in reference to both heart disease and vascular disease in general), which is responsible for carrying fat molecules (lipids), including cholesterol, around the body to all cells within all tissues. While all the functional roles of ApoB within the LDL (and all larger) particles remain somewhat unclear, it is the primary organizing protein (of the entire complex shell enclosing/carrying fat molecules within) component of the particles and is absolutely required for the formation of these particles. What is also clear is that the ApoB on the LDL particle acts as a ligand for LDL receptors in various cells throughout the body (i.e., less formally, ApoB indicates fat carrying particles are ready to enter any cells with ApoB receptors and deliver fats carried within into the cells).
Through mechanisms only partially understood, high levels of ApoB, especially associated with the higher LDL particle concentrations, are the primary driver of plaques that cause vascular disease (atherosclerosis), commonly first becoming obviously symptomatic as heart disease, stroke & many other body wide complications after decades of progression. There is considerable evidence that concentrations of ApoB and especially the NMR assay (specific for LDL-particle concentrations) are superior indicators of vascular/heart disease driving physiology than either total cholesterol or LDL-cholesterol (as long promoted by the NIH starting in the early 1970s). However, primarily for historic cost/complexity reasons, cholesterol, and estimated LDL-cholesterol by calculation, remains the most commonly promoted lipid test for the risk factor of atherosclerosis. ApoB is routinely measured using immunoassays such as ELISA or nephelometry. Refined and automated NMR methods allow measurement distinctions between the many different ApoB particles.
Genetic disorders.
High levels of ApoB are related to heart disease.
Hypobetalipoproteinemia is a genetic disorder that can be caused by a mutation in the ApoB gene, "APOB". Abetalipoproteinaemia is usually caused by a mutation in the MTP gene, "MTP".
Mutations in gene "APOB100" can also cause familial hypercholesterolemia, a hereditary (autosomal dominant) form of metabolic disorder Hypercholesterolemia.
Mouse studies.
Most relevant information regarding mouse ApoB homologue, mApoB, has come from mouse studies. Mice overexpressing mApoB have increased levels of LDL "bad cholesterol" and decreased levels of HDL "good cholesterol". Mice containing only one functional copy of the mApoB gene show the opposite effect, being resistant to hypercholesterolemia. Mice containing no functional copies of the gene are not viable.
Molecular biology.
The protein occurs in the plasma in 2 main isoforms, ApoB48 and ApoB100. The first is synthesized exclusively by the small intestine, the second by the liver. ApoB-100 is the largest of the apoB group of proteins, consisting of 4563 amino acids. Both isoforms are coded by "APOB" and by a single mRNA transcript larger than 16 kb. ApoB48 is generated when a stop codon (UAA) at residue 2153 is created by RNA editing. There appears to be a "trans"-acting tissue-specific splicing gene that determines which isoform is ultimately produced. Alternatively, there is some evidence that a "cis"-acting element several thousand bp upstream determines which isoform is produced.
As a result of the RNA editing, ApoB48 and ApoB100 share a common N-terminal sequence, but ApoB48 lacks ApoB100's C-terminal LDL receptor binding region. In fact, ApoB48 is so-called because it constitutes 48% of the sequence for ApoB100.
ApoB 48 is a unique protein to chylomicrons from the small intestine. After most of the lipids in the chylomicron have been absorbed, ApoB48 returns to the liver as part of the chylomicron remnant, where it is endocytosed and degraded.
Clinical significance.
Benefits.
Role in innate immune system.
Very low-density lipoproteins and low-density lipoproteins interfere with the quorum sensing system that upregulates genes required for invasive "Staphylococcus aureus" infection. The mechanism of antagonism entails binding ApoB, to a "S. aureus" autoinducer pheromone, preventing signaling through its receptor. Mice deficient in ApoB are more susceptible to invasive bacterial infection.
Adverse effects.
Role in insulin resistance.
Overproduction of apolipoprotein B can result in lipid-induced endoplasmic reticulum stress and insulin resistance in the liver.
Role in lipoproteins and atherosclerosis.
ApoB100 is found in lipoproteins originating from the liver (VLDL, IDL, LDL). Importantly, there is one ApoB100 molecule per hepatic-derived lipoprotein. Hence, using that fact, one can quantify the "number" of lipoprotein particles by noting the total ApoB100 concentration in the circulation. Since there is one and only one ApoB100 per particle, the number of particles is reflected by the ApoB100 concentration. The same technique can be applied to individual lipoprotein classes (e.g. LDL) and thereby enable one to "count" them as well.
It is well established that ApoB100 levels are associated with coronary heart disease, they are a far better predictor of it than are LDL-C concentrations. Reason: LDL-C does not reflect actual particle concentrations & cholesterol cannot dissolve or move (in water) without particles to carry it. A simple way to understand this observation is the fact that ApoB100, one per particle, reflects actual lipoprotein particle concentration (independent of their cholesterol, or other lipid content). In this way, one can understand that the number of ApoB100-containing lipoprotein particles which can carry lipids into the artery walls is a key determinant, driver of atherosclerosis and heart disease.
One way to explain the above is to consider that large numbers of lipoprotein particles, and, in particular, large numbers of LDL particles, lead to competition at the ApoB100 receptor (i.e. LDL receptor) of peripheral cells. Since such competition will prolong the residence time of LDL particles in the circulation, it may lead to greater opportunity for them to undergo oxidation and/or other chemical modifications. Such modifications may lessen the particles' ability to be cleared by the classic LDL receptor and/or increase their ability to interact with so-called "scavenger" receptors. The net result is the shunting of LDL particles to these scavenger receptors. Scavenger receptors typically are found on macrophages, with cholesterol-laden macrophages being better known as "foam cells". Foam cells characterize atherosclerotic lesions. In addition to this possible mechanism of foam cell generation, an increase in the levels of chemically modified LDL particles may also lead to an increase in endothelial damage. This occurs as a result of modified-LDL's toxic effect on vascular endothelium as well as its ability both to recruit immune effector cells and to promote platelet activation.
The INTERHEART study found that the ApoB100 / ApoA1 ratio is more effective at predicting heart attack risk, in patients who had had an acute myocardial infarction, than either the ApoB100 or ApoA1 measure alone. (ApoA1 is the major HDL protein.) In the general population this remains unclear although in a recent study ApoB was the strongest risk marker for cardiovascular events. A small study suggests that added to fluvastatin treatment, omega 3 fatty acids daily, containing 460 mg of E-EPA and 380 mg of E-DHA (ethyl esters), may lower ApoB48 in hyperlipemic type 2 diabetics.
Interactions.
ApoB has been shown to interact with apo(a), PPIB, Calcitonin receptor and HSP90B1. Interaction of ApoB with proteoglycans, collagen, and fibronectin is believed to cause atherosclerosis.
Regulation.
The expression of "APOB" is regulated by cis-regulatory elements in the APOB 5′ UTR and 3′ UTR.
RNA editing.
The mRNA of this protein is subject to Cytidine to Uridine (C to U) site-specific RNA editing. ApoB100 and ApoB48 are encoded by the same gene, however, the differences in the translated proteins are not due to alternative splicing but are due to the tissue-specific RNA editing event.
ApoB mRNA editing was the first example of editing observed in vertebrates. Editing of ApoB mRNA occurs in all placental mammals. Editing occurs post transcriptionally as the nascent polynucleotides do not contain edited nucleosides.
Type.
C to U editing of ApoB mRNA requires an editing complex or holoenzyme (editosome) consisting of the C to U-editing enzyme Apolipoprotein B mRNA editing enzyme, catalytic polypeptide 1 (ApoBEC-1) as well as other auxiliary factors. ApoBEC-1 is a protein that in humans is encoded by the "APOBEC1" gene.[1]It is a member of the cytidine deaminase family. ApoBEC-1 alone is not sufficient for the editing of ApoB mRNA and requires at least one of these auxiliary factors, APOBEC1 complementation factor (A1CF) for editing to occur. A1CF contains 3 non identical repeats. It acts as the RNA binding subunit and directs ApoBEC-1 to the ApoB mRNA downstream of the edited cytidine. Other auxiliary factors are known to be part of the holoenzyme. Some of these proteins have been identified. these are CUG binding protein 2 (CUGBP2), SYNCRIP (glycine-arginine-tyrosine-rich RNA binding protein, GRY-RBP), heterogenous nuclear ribonucleoprotein (hnRNP)-C1, ApoBEC-1 binding protein (ABBP)1, ABBP2, KH-type splicing regulatory binding protein (KSRP), Bcl-2-associated anthogene 4 (BAG4), and auxiliary factor (AUX)240. All these proteins have been identified using detection assays and have all been demonstrated to interact with either ApoBEC-1, A1CF, or ApoB RNA. The function of these auxiliary proteins in the editing complex are unknown. As well as editing ApoB mRNA, the ApoBEC-1 editsome also edits the mRNA of NF1. mRNA editing of ApoB mRNA is the best defined example of this type of C to U RNA editing in humans.
Location.
Despite being a 14,000 residue long transcript, a single cytidine is targeted for editing. Within the ApoB mRNA a sequence consisting of 26 nucleotides necessary for editing is found. This is known as the editing motif. These nucleotides (6662–6687) were determined to be essential by site specific mutagenesis experiments. An 11 nucleotide portion of this sequence 4–5 nucleotides downstream from the editing site is an important region known as the mooring sequence. A region called the spacer element is found 2–8 nucleotides between the edited nucleoside and this mooring sequence. There is also a regulatory sequence 3′ to the editing site. The active site of ApoBEC-1, the catalytic component of the editing holoenzyme is thought to bind to an AU rich region of the mooring sequence with the aid of ACF in binding the complex to the mRNA.
The edited cytidine residue is located at nucleotide 6666 located in exon 26 of the gene. Editing at this site results in a codon change from a Glutamine codon (CAA) to an inframe stop codon (UAA). Computer modelling has detected for editing to occur, the edited Cytidine is located in a loop. The selection of the edited cytidine is also highly dependent on this secondary structure of the surrounding RNA. There are also some indications that this loop region is formed between the mooring sequence and the 3′ regulatory region of the ApoB mRNA. The predicted secondary structure formed by ApoB mRNA is thought to allow for contact between the residue to be edited and the active site of APOBEC1 as well as for binding of ACF and other auxiliary factors associated with the editosome.
Regulation.
Editing of ApoB mRNA in humans is tissue regulated, with ApoB48 being the main ApoB protein of the small intestine in humans. It occurs in lesser amounts in the colon, kidney and stomach along with the non edited version.
Editing is also developmentally regulated with the non edited version only being translated early in development but the edited form increases during development in the tissues where editing can occur.
Editing levels of ApoB mRNA have been shown to vary in response to changes in diet. exposure to alcohol and hormone levels.
Conservation.
ApoB mRNA editing also occurs in mice, and rats. In contrast to humans editing occurs in liver in mice and rats up to a frequency of 65%. It has not been observed in birds or lesser species.
Consequences.
Structure.
Editing results in a codon change creating an in-frame stop codon leading to translation of a truncated protein, ApoB48. This stop codon results in the translation of a protein that lacks the carboxyl terminus which contains the protein's LDLR binding domain. The full protein ApoB100 which has nearly 4500 amino acids is present in VLDL and LDL. Since many parts of ApoB100 are in an amphipathic condition, the structure of some of its domains is dependent on underlying lipid conditions. However, it is known to have the same overall folding in LDL having five main domains. Recently the first structure of LDL at human body temperature in native condition has been found using cryo-electron microscopy at a resolution of 16 Angstrom. The overall folding of ApoB-100 has been confirmed and some heterogeneity in the local structure of its domains have been mapped.
Function.
Editing is restricted to those transcripts expressed in the small intestine. This shorter version of the protein has a function specific to the small intestine. The main function of the full length liver expressed ApoB100 is as a ligand for activation of the LDL-R. However, editing results in a protein lacking this LDL-R binding region of the protein. This alters the function of the protein and the shorter ApoB48 protein as specific functions relative to the small intestine.
ApoB48 is identical to the amino-terminal 48% of ApoB100. The function of this isoform is in fat absorption of the small intestine and is involved in the synthesis, assembly and secretion of chylomicrons. These chylomicrons transport dietary lipids to tissues while the remaining chylomicrons along with associated residual lipids are in 2–3 hours taken up by the liver via the interaction of apolipoprotein E (ApoE) with lipoprotein receptors. It is the dominant ApoB protein in the small intestine of most mammals. It is a key protein in the exogenous pathway of lipoprotein metabolism. Intestinal proteins containing ApoB48 are metabolized to chylomicron remnant particles which are taken up by remnant receptors.


2-aminohexano-6-lactam racemase

In enzymology, a 2-aminohexano-6-lactam racemase () is an enzyme that catalyzes the chemical reaction
Hence, this enzyme has one substrate, L-2-aminohexano-6-lactam, and one product, D-2-aminohexano-6-lactam.
This enzyme belongs to the family of isomerases, specifically those racemases and epimerases acting on amino acids and derivatives. The systematic name of this enzyme class is 2-aminohexano-6-lactam racemase. This enzyme is also called alpha-amino-epsilon-caprolactam racemase.


Mitochondrial uncoupling protein 4

Mitochondrial uncoupling protein 4 is a protein that in humans is encoded by the "SLC25A27" gene.
Mitochondrial uncoupling proteins (UCP) are members of the larger family of mitochondrial anion carrier proteins (MACP). UCPs separate oxidative phosphorylation from ATP synthesis with energy dissipated as heat, also referred to as the mitochondrial proton leak. UCPs facilitate the transfer of anions from the inner to the outer mitochondrial membrane and the return transfer of protons from the outer to the inner mitochondrial membrane. They also reduce the mitochondrial membrane potential in mammalian cells. Tissue specificity occurs for the different UCPs and the exact methods of how UCPs transfer H+/OH- are not known. UCPs contain the three homologous protein domains of MACPs. Transcripts of this gene are detected only in brain tissue and are specifically modulated by various environmental conditions. Recently, the proton transport activity of UCP4 has also been shown to be activated by fatty acids and inhibited by purine nucleotides. In addition, reconstituted UCP4 exhibited a distinct conformation, compared to other UCPs in the family.


Casein kinase

Casein kinase, a type of kinase enzyme, may refer to:


CHAP domain

In molecular biology, the CHAP domain is a region between 110 and 140 amino acids that is found in proteins from bacteria, bacteriophages, archaea and eukaryotes of the family Trypanosomidae. The domain is named after the acronym cysteine, histidine-dependent amidohydrolases/peptidases. Many of these proteins are uncharacterised, but it has been proposed that they may function mainly in peptidoglycan hydrolysis. The CHAP domain is found in a wide range of protein architectures; it is commonly associated with bacterial type SH3 domains and with several families of amidase domains. It has been suggested that CHAP domain containing proteins utilise a catalytic cysteine residue in a nucleophilic-attack mechanism.
The CHAP domain contains two invariant residues, a cysteine and a histidine. These residues form part of the putative active site of CHAP domain containing proteins. Secondary structure predictions show that the CHAP domain belongs to the alpha + beta structural class, with the N-terminal half largely containing predicted alpha helices and the C-terminal half principally composed of predicted beta strands.
Some proteins known to contain a CHAP domain are listed below: