Wilson disease protein

Wilson disease protein (WND), also known as ATP7B protein, is a copper-transporting P-type ATPase which is encoded by the "ATP7B" gene. The ATP7B protein is located in the trans-Golgi network of the liver and brain and balances the copper level in the body by excreting excess copper into bile and plasma. Genetic disorder of the ATP7B gene may cause Wilson's disease, a disease in which copper accumulates in tissues, leading to neurological or psychiatric issues and liver diseases.
Gene.
Wilson disease protein is associated with "ATP7B" gene, approximately 80 Kb, located on human chromosome 13 and consists of 21 exons. The mRNA transcribed by "ATP7B" gene has a size of 7.5 Kb, and which encodes a protein of 1465 amino acids.
The gene is a member of the P-type cation transport ATPase family and encodes a protein with several membrane-spanning domains, an ATPase consensus sequence, a hinge domain, a phosphorylation site, and at least two putative copper-binding sites. This protein functions as a monomer, exporting copper out of the cells, such as the efflux of hepatic copper into the bile. Alternate transcriptional splice variants, encoding different isoforms with distinct cellular localizations, have been characterized. Wilson's disease is caused by various mutations. One of the common mutations is single base pair mutation, H1069Q.
Structure.
ATP7B protein is a copper-transporting P-type ATPase, synthesized as a membrane protein of 165 KDa in human hepatoma cell line, and which is 57% homologous to Menkes disease-associated protein ATP7A.
ATP7B consists of several domains:
The CPC motif (Cys-Pro-Cys) in transmembrane segment 6 characterizes the protein as a heavy metal transporting ATPase.
The copper binding motif also shows a high affinity to other transition metal ions such as zinc Zn(II), cadmium Cd(II), gold Au(III), and mercury Hg(II). However, copper is able to decrease the zinc binding affinity at low concentration and increase copper binding affinity dramatically with increasing concentration to ensure a strong binding between the motif and copper.
As a P-type ATPases, ATP7B undergoes auto-phosphorylation of a key conserved aspartic acid (D) residue in the DKTGT motif. The ATP binding to the protein initiates the reaction and copper binds to the transmembrane region. Then phosphorylation occurs at the aspartic acid residue in the DKTGT motif with Cu release. Then dephosphorylation of the aspartic acid residue recovers the protein to ready for the next transport.
Function.
Most of ATP7B protein is located in the trans-Golgi network (TGN) of hepatocytes, which is different from its homologous protein ATP7A. Small amount of ATP7B is located in the brain.
As a copper-transporting protein, one major function is delivering copper to copper dependent enzymes in Golgi apparatus (e.g. holo-ceruloplasmin (CPN)).
In the human body, the liver plays an important role in copper regulation including removal of extra copper. ATP7B participates in the physiological pathway in the copper removal process in two ways: secreting copper into plasma and excreting copper into bile.
Interactions.
ATOX1.
ATP7B receives copper from cytosolic protein antioxidant 1 copper chaperone (ATOX1). This protein targets ATP7B directly in liver in order to transport copper. ATOX1 transfers copper from cytosol to the metal binding domain of ATP7B which control the catalytic activity of ATP7B.
Several mutations in ATOX1 can block the copper pathways and cause Wilson disease.
GLRX.
ATP7B interacts with glutaredoxin-1 (GLRX). Subsequent transport is promoted through the reduction of intramolecular disulfide bonds by GLRX catalysis.
Associations with Wilson's disease.
Wilson disease happens when accumulation of copper inside the liver causes mitochondrial damage and cell destruction and shows symptoms of hepatic disease. Then, the loss of excretion of copper in bile leads to an increasing concentration of copper level in urine and causes kidney problems. Therefore, symptoms of Wilson's disease could be various including kidney disease and neurological disease. The major cause is the malfunction of ATP7B by single base pair mutations, deletions, frame-shifts, splice errors in "ATP7B" gene.


Pixantrone

Pixantrone (rINN; trade name Pixuvri)
is an experimental antineoplastic (anti-cancer) drug, an analogue of mitoxantrone with fewer toxic effects on cardiac tissue. It acts as a topoisomerase II poison and intercalating agent. The code name BBR 2778 refers to pixantrone dimaleate, the actual substance commonly used in clinical trials.
History.
Anthracyclines are important chemotherapy agents. However, their use is associated with irreversible and cumulative heart damage. Investigators have attempted to design related drugs that maintain the biological activity, but do not possess the cardiotoxicity of the anthracyclines. Pixantrone was developed to reduce heart damage related to treatment while retaining efficacy.
Random screening at the US National Cancer Institute of a vast number of compounds provided by the Allied Chemical Company led to the discovery of ametantrone as having significant anti-tumor activity. Further investigation regarding the rational development of analogs of ametantrone led to the synthesis of mitoxantrone, which also exhibited marked anti-tumor activity Mitoxantrone was considered as an analog of doxorubicin with less structural complexity but with a similar mode of action. In clinical studies, mitoxantrone was shown to be effective against numerous types of tumors with less toxic side effects than those resulting from doxorubicin therapy. However, mitoxantrone was not totally free of cardiotoxicity. A number of structurally modified analogs of mitoxantrone were synthesized and structure-activity relationship studies made. BBR 2778 was originally synthesized by University of Vermont researchers Miles P. Hacker and Paul A. Krapcho and initially characterized in vitro for tumor cell cytotoxicity and mechanism of action by studies at the Boehringer Mannheim Italia Research Center, Monza, and University of Vermont, Burlington. Other studies have been completed at the University of Texas M. D. Anderson Cancer Center, Houston, the Istituto Nazionale Tumori, Milan, and the University of Padua. In the search for novel heteroanalogs of anthracenediones, it was selected as the most promising compound. Toxicological studies indicated that BBR 2778 was not cardiotoxic, and US patents are held by the University of Vermont. An additional US patent application was completed in June 1995 by Boehringer Mannheim, Italy.
Novuspharma, an Italian company, was established in 1998 following the merger of Boehringer Mannheim and Hoffmann-La Roche, and BBR 2778 was developed as Novuspharma's leading anti-cancer drug, pixantrone. A patent application for the injectable preparation was filed in May 2003.
In 2003, Cell Therapeutics, a Seattle biotechnology company, acquired pixantrone through a merger with Novuspharma.
Clinical trials.
Pixantrone is a substance that is being studied in the treatment of cancer. It belongs to the family of drugs called antitumor antibiotics. phase III clinical trials of pixantrone have been completed. Pixantrone is being studied as an antineoplastic for different kinds of cancer, including solid tumors and hematological malignancies such as non-Hodgkin lymphomas.
Animal studies demonstrated that pixantrone does not worsen pre-existing heart muscle damage, suggesting that pixantrone may be useful in patients pretreated with anthracyclines. While only minimal cardiac changes are observed in mice given repeated cycles of pixantrone, 2 cycles of traditional anthracyclines doxorubicin or mitoxantrone result in marked or severe heart muscle degeneration.
Clinical trials substituting pixantrone for doxorubicin in standard first-line treatment of patients with aggressive non-Hodgkin's lymphoma, had a reduction in severe side effects when compared to patients treated with standard doxorubicin-based therapy. Despite pixantrone patients receiving more treatment cycles, a three-fold reduction in the incidence of severe heart damage was seen as well as clinically significant reductions in infections and thrombocytopenia, and a significant reduction in febrile neutropenia. These findings could have major implications for treating patients with breast cancer, lymphoma, and leukemia, where debilitating cardiac damage from doxorubicin might be prevented. Previous treatment options for multiply relapsed aggressive non-Hodgkin lymphoma had disappointing response rates.
The completed phase II RAPID trial compared the CHOP-R regimen of Cyclophosphamide, Doxorubicin, Vincristine, Prednisone, and Rituximab to the same regimen, but substituting Doxorubicin with Pixantrone. The objective was to show that Pixantrone was not inferior to Doxorubicin and less toxic to the heart.
Pixantrone was shown to have potentially reduced cardiotoxicity and demonstrated promising clinical activity in these phase II studies in heavily pretreated non-Hodgkin lymphoma patients.
The pivotal phase III EXTEND (PIX301) randomized clinical trial studied pixantrone to see how well it works compared to other chemotherapy drugs in treating patients with relapsed non-Hodgkin's lymphoma. The complete response rate in patients treated with pixantrone has been significantly higher than in those receiving other chemotherapeutic agents for treatment of relapsed/refractory aggressive non-Hodgkin lymphoma.
Administration.
It can be administered through a peripheral vein rather than a central implanted catheter as required for other similar drugs.
Regulatory approval.
U.S. Food and Drug Administration.
The FDA granted fast track designation for pixantrone in patients who had previously been treated two or more times for relapsed or refractory aggressive NHL. Study sponsor Cell Therapeutics announced that Pixantrone achieved the primary efficacy endpoint. The minutes of the Oncologic Drugs Advisory Committee meeting of March 22, 2010 show that this had not in fact been achieved with statistical significance and this combined with major safety concerns lead to the conclusion that the trial was not sufficient to support approval. In April 2010 the FDA asked for an additional trial.
European Medicines Agency.
On May 5, 2009, Pixantrone became available in Europe on a Named-Patient Basis. A named-patient program is a compassionate use drug supply program under which physicians can legally supply investigational drugs to qualifying patients. Under a named-patient program, investigational drugs can be administered to patients who are suffering from serious illnesses prior to the drug being approved by the European Medicines Evaluation Agency. "Named-patient" distribution refers to the distribution or sale of a product to a specific healthcare professional for the treatment of an individual patient. In Europe, under the named-patient program the drug is most often purchased through the national health system.
In 2012 pixantrone received conditional marketing authorization in the European Union as Monotherapy to Treat Adult Patients with Multiply Relapsed or Refractory Aggressive Non-Hodgkin B-Cell Lymphomas.
Research.
Pixantrone is as potent as mitoxantrone in animal models of multiple sclerosis. Pixantrone has a similar mechanism of action as mitoxantrone on the effector function of lymphomonocyte B and T cells in experimental allergic encephalomyelitis but with lower cardiotoxicity. Pixantrone inhibits antigen specific and mitogen induced lymphomononuclear cell proliferation, as well as IFN-gamma production. Clinical trials are currently ongoing in Europe.
Pixantrone also reduces the severity of experimental autoimmune myasthenia gravis in Lewis rats, and in vitro cell viability experiments indicated that Pixantrone significantly reduces amyloid beta (A beta(1-42)) neurotoxicity, a mechanism implicated in Alzheimer's disease.


ADP-specific phosphofructokinase

In enzymology, an ADP-specific phosphofructokinase () is an enzyme that catalyzes the chemical reaction
Thus, the two substrates of this enzyme are ADP and D-fructose 6-phosphate, whereas its two products are AMP and D-fructose 1,6-bisphosphate.
This enzyme belongs to the family of transferases, specifically those transferring phosphorus-containing groups (phosphotransferases) with an alcohol group as acceptor. The systematic name of this enzyme class is ADP:D-fructose-6-phosphate 1-phosphotransferase. This enzyme is also called ADP-6-phosphofructokinase, ADP-dependent phosphofructokinase.
Structural studies.
As of late 2007, only one structure has been solved for this class of enzymes, with the PDB accession code .


RNA-binding protein

RNA-binding proteins (often abbreviated as RBPs) are proteins that bind to the double or single stranded RNA in cells and participate in forming ribonucleoprotein complexes.
RBPs contain various structural motifs, such as RNA recognition motif (RRM), dsRNA binding domain, zinc finger and others.
They are cytoplasmic and nuclear proteins. However, since most mature RNA is exported from the nucleus relatively quickly, most RBPs in the nucleus exist as complexes of protein and pre-mRNA called heterogeneous ribonucleoprotein particles (hnRNPs).
RBPs have crucial roles in various cellular processes such as: cellular function, transport and localization. They especially play a major role in post-transcriptional control of RNAs, such as: splicing, polyadenylation, mRNA stabilization, mRNA localization and translation. Eukaryotic cells encode diverse RBPs, approximately 500 genes, with unique RNA-binding activity and protein–protein interaction. During evolution, the diversity of RBPs greatly increased with the increase in the number of introns. Diversity enabled eukaryotic cells to utilize RNA exons in various arrangements, giving rise to a unique RNP (ribonucleoprotein) for each RNA. Although RBPs have a crucial role in post-transcriptional regulation in gene expression, relatively few RBPs have been studied systematically.
Structure.
Many RBPs have modular structures and are composed of multiple repeats of just a few specific basic domains that often have limited sequences. These sequences are then arranged in varying combinations to fulfill the need for diversity. A specific protein's recognition of a specific RNA has evolved through the rearrangement of these few basic domains. Each basic domain recognizes RNA, but many of these proteins require multiple copies of one of the many common domains to function.
Diversity.
As nuclear RNA emerges from RNA polymerase, RNA transcripts are immediately covered with RNA-binding proteins that regulate every aspect of RNA metabolism and function including RNA biogenesis, maturation, transport, cellular localization and stability. All RBPs bind RNA, however they do so with different RNA-sequence specificities and affinities, which allows the RBPs to be as diverse as their targets and functions. These targets include mRNA, which codes for proteins, as well as a number of functional non-coding RNAs. NcRNAs almost always function as ribonucleoprotein complexes and not as naked RNAs. These non-coding RNAs include microRNAs, small interfering RNAs (siRNA), as well as splicesomal small nuclear RNAs (snRNA).
Function.
RNA processing and modification.
Alternative splicing.
Alternative splicing is a mechanism by which different forms of mature mRNAs (messengers RNAs) are generated from the same gene. It is a regulatory mechanism by which variations in the incorporation of the exons into mRNA leads to the production of more than one related protein, thus expanding possible genomic outputs. RBPs function extensively in the regulation of this process. Some binding proteins such as neuronal specific RNA-binding proteins, namely NOVA1, control the alternative splicing of a subset of hnRNA by recognizing and binding to a specific sequence in the RNA (YCAY where Y indicates pyrimidine, U or C). These proteins then recruit splicesomal proteins to this target site. SR proteins are also well known for their role in alternative splicing through the recruitment of snRNPs that form the splicesome, namely U1 snRNP and U2AF snRNP. However, RBPs are also part of the splicesome itself. The splicesome is a complex of snRNA and protein subunits and acts as the mechanical agent that removes introns and ligates the flanking exons. Other than core splicesome complex, RBPs also bind to the sites of "Cis"-acting RNA elements that influence exons inclusion or exclusion during splicing. These sites are referred to as exonic splicing enhancers (ESEs), exonic splicing silencers (ESSs), intronic splicing enhancers (ISEs) and intronic splicing silencers (ISSs) and depending on their location of binding, RBPs work as splicing silencers or enhancers [].
RNA editing.
The most extensively studied form of RNA editing involves the ADAR protein. This protein functions through post-transcriptional modification of mRNA transcripts by changing the nucleotide content of the RNA. This is done through the conversion of adenosine to inosine in an enzymatic reaction catalyzed by ADAR. This process effectively changes the RNA sequence from that encoded by the genome and extends the diversity of the gene products. The majority of RNA editing occurs on non-coding regions of RNA; however, some protein-encoding RNA transcripts have been shown to be subject to editing resulting in a difference in their protein's amino acid sequence. An example of this is the glutamate receptor mRNA where glutamine is converted to arginine leading to a change in the functionality of the protein.
Polyadenylation.
Polyadenylation is the addition of a "tail" of adenylate residues to an RNA transcript about 20 bases downstream of the AAUAAA sequence within the three prime untranslated region. Polyadenylation of mRNA has a strong effect on its nuclear transport, translation efficiency, and stability. All of these as well as the process of polyadenylation depend on binding of specific RBPs. All eukaryotic mRNAs with few exceptions are processed to receive 3' poly (A) tails of about 200 nucleotides. One of the necessary protein complexes in this process is CPSF. CPSF binds to the 3' tail (AAUAAA) sequence and together with another protein called poly(A)-binding protein, recruits and stimulates the activity of poly(A) polymerase. Poly(A) polymerase is inactive on its own and requires the binding of these other proteins to function properly.
Export.
After processing is complete, mRNA needs to be transported from the cell nucleus to cytoplasm. This is a three-step process involving the generation of a cargo-carrier complex in the nucleus followed by translocation of the complex through the nuclear pore complex and finally release of the cargo into cytoplasm. The carrier is then subsequently recycled. TAP/NXF1:p15 heterodimer is thought to be the key player in mRNA export. Over-expression of TAP in "Xenopus laevis" frogs increases the export of transcripts that are otherwise inefficiently exported. However TAP needs adaptor proteins because it is unable interact directly with mRNA. Aly/REF protein interacts and binds to the mRNA recruiting TAP.
mRNA localization.
mRNA localization is critical for regulation of gene expression by allowing spatially regulated protein production. Through mRNA localization proteins are transcribed in their intended target site of the cell. This is especially important during early development when rapid cell cleavages give different cells various combinations of mRNA which can then lead to drastically different cell fates. RBPs are critical in the localization of this mRNA that insures proteins are only transcribed in their intended regions. One of these proteins is ZBP1. ZBP1 binds to beta-actin mRNA at the site of transcription and moves with mRNA into the cytoplasm. It then localizes this mRNA to the lamella region of several asymmetric cell types where it can then be translated. FMRP is another RBP involved in RNA localization. It was shown that in addition to other functions for FMRP in RNA metabolism, FMRP is involved in the stimulus-induced localization of several dendritic mRNAs in neuronal dendrites.
Translation.
Translational regulation provides a rapid mechanism to control gene expression. Rather than controlling gene expression at the transcriptional level, mRNA is already transcribed but the recruitment of ribosomes is controlled. This allows rapid generation of proteins when a signal activates translation. ZBP1 in addition to its role in the localization of B-actin mRNA is also involved in the translational repression of beta-actin mRNA by blocking translation initiation. ZBP1 must be removed from the mRNA to allow the ribosome to properly bind and translation to begin.
Protein–RNA interactions.
RNA-binding proteins exhibit highly specific recognition of their RNA targets by recognizing their sequences and structures. Specific binding of the RNA-binding proteins allow them to distinguish their targets and regulate a variety of cellular functions via control of the generation, maturation, and lifespan of the RNA transcript. This interaction begins during transcription as some RBPs remain bound to RNA until degradation whereas others only transiently bind to RNA to regulate RNA splicing, processing, transport, and localization. In this section, three classes of the most widely studied RNA-binding domains (RNA-recognition motif, double-stranded RNA-binding motif, zinc-finger motif) will be discussed.
RNA-recognition motif (RRM).
The RNA recognition motif, which is the most common RNA-binding motif, is a small protein domain of 75–85 amino acids that forms a four-stranded β-sheet against the two α-helices. This recognition motif exerts its role in numerous cellular functions, especially in mRNA/rRNA processing, splicing, translation regulation, RNA export, and RNA stability. Ten structures of an RRM have been identified through NMR spectroscopy and X-ray crystallography. These structures illustrate the intricacy of protein–RNA recognition of RRM as it entails RNA–RNA and protein–protein interactions in addition to protein–RNA interactions. Despite their complexity, all ten structures have some common features. All RRMs' main protein surfaces' four-stranded β-sheet was found to interact with the RNA, which usually contacts two or three nucleotides in a specific manner. In addition, strong RNA binding affinity and specificity towards variation are achieved through an interaction between the inter-domain linker and the RNA and between RRMs themselves. This plasticity of the RRM explains why RRM is the most abundant domain and why it plays an important role in various biological functions.
Double-stranded RNA-binding motif.
The double-stranded RNA-binding motif (dsRM, dsRBD), a 70–75 amino-acid domain, plays a critical role in RNA processing, RNA localization, RNA interference, RNA editing, and translational repression. All three structures of the domain solved as of 2005 possess uniting features that explain how dsRMs only bind to dsRNA instead of dsDNA. The dsRMs were found to interact along the RNA duplex via both α-helices and β1-β2 loop. Moreover, all three dsRBM structures make contact with the sugar-phosphate backbone of the major groove and of one minor groove, which is mediated by the β1-β2 loop along with the N-terminus region of the alpha helix 2. This interaction is a unique adaptation for the shape of an RNA double helix as it involves 2'-hydroxyls and phosphate oxygen. Despite the common structural features among dsRBMs, they exhibit distinct chemical frameworks, which permits specificity for a variety for RNA structures including stem-loops, internal loops, bulges or helices containing mismatches.
Zinc fingers.
CCHH-type zinc-finger domains are the most common DNA-binding domain within the eukaryotic genome. In order to attain high sequence-specific recognition of DNA, several zinc fingers are utilized in a modular fashion. Zinc fingers exhibit ββα protein fold in which a β-hairpin and a α-helix are joined together via a ion. Furthermore, the interaction between protein side-chains of the α-helix with the DNA bases in the major groove allows for the DNA-sequence-specific recognition. Despite its wide recognition of DNA, there has been recent discoveries that zinc fingers also have the ability to recognize RNA. In addition to CCHH zinc fingers, CCCH zinc fingers were recently discovered to employ sequence-specific recognition of single-stranded RNA through an interaction between intermolecular hydrogen bonds and Watson-Crick edges of the RNA bases. CCHH-type zinc fingers employ two methods of RNA binding. First, the zinc fingers exert non-specific interaction with the backbone of a double helix whereas the second mode allows zinc fingers to specifically recognize the individual bases that bulge out. Differing from the CCHH-type, the CCCH-type zinc finger displays another mode of RNA binding, in which single-stranded RNA is identified in a sequence-specific manner. Overall, zinc fingers can directly recognize DNA via binding to dsDNA sequence and RNA via binding to ssRNA sequence.
Role in embryonic development.
RNA-binding proteins' transcriptional and post-transcriptional regulation of RNA has a role in regulating the patterns of gene expression during development. Extensive research on the nematode "C. elegans" has identified RNA-binding proteins as essential factors during germline and early embryonic development. Their specific function involves the development of somatic tissues (neurons, hypodermis, muscles and excretory cells) as well as providing timing cues for the developmental events. Nevertheless, it is exceptionally challenging to discover the mechanism behind RBPs' function in development due to the difficulty in identifying their RNA targets. This is because most RBPs usually have multiple RNA targets. However, it is indisputable that RBPs exert a critical control in regulating developmental pathways in a concerted manner.
Germline development.
In "Drosophila melanogaster", Elav, Sxl and tra-2 are RNA-binding protein encoding genes that are critical in the early sex determination and the maintenance of the somatic sexual state. These genes impose effects on the post-transcriptional level by regulating sex-specific splicing in "Drosophila". Sxl exerts positive regulation of the feminizing gene "tra" to produce a functional tra mRNA in females. In "C. elegans", RNA-binding proteins including FOG-1, MOG-1/-4/-5 and RNP-4 regulate germline and somatic sex determination. Furthermore, several RBPs such as GLD-1, GLD-3, DAZ-1, PGL-1 and OMA-1/-2 exert their regulatory functions during meiotic prophase progression, gametogenesis, and oocyte maturation.
Somatic development.
In addition to RBPs' functions in germline development, post-transcriptional control also plays a significant role in somatic development. Differing from RBPs that are involved in germline and early embryo development, RBPs functioning in somatic development regulate tissue-specific alternative splicing of the mRNA targets. For instance, MEC-8 and UNC-75 containing RRM domains localize to regions of hypodermis and nervous system, respectively. Furthermore, another RRM-containing RBP, EXC-7, is revealed to localize in embryonic excretory canal cells and throughout the nervous system during somatic development.
Neuronal development.
ZBP1 was shown to regulate dendritogenesis (dendrite formation) in hippocampal neurons. Other RNA-binding proteins involved in dendrite formation are Pumilio and Nanos, FMRP, CPEB and Staufen 1
Role in cancer.
RBPs are emerging to play a crucial role in tumor development. Hundreds of RBPs are markedly dysregulated across human cancers and showed predominant downregulation in tumors related to normal tissues. Many RBPs are differentially expressed in different cancer types for example KHDRBS1(Sam68), ELAVL1(HuR), FXR1. For some RBPs, the change in expression are related with Copy Number Variations (CNV), for example CNV gains of BYSL in colorectal cancer cells. and ESRP1, CELF3 in breast cancer, RBM24 in liver cancer, IGF2BP2, IGF2BP3 in lung cancer or CNV losses of KHDRBS2 in lung cancer. Some expression changes are cause due to protein affecting mutations on these RBPs for example NSUN6, ZC3H13, ELAC1, RBMS3, and ZGPAT, SF3B1, SRSF2, RBM10, U2AF1, SF3B1, PPRC1, RBMXL1, HNRNPCL1 etc. Several studies have related this change in expression of RBPs to aberrant alternative splicing in cancer.
Current research.
As RNA-binding proteins exert significant control over numerous cellular functions, they have been a popular area of investigation for many researchers. Due to its importance in the biological field, numerous discoveries regarding RNA-binding proteins' potentials have been recently unveiled. Recent development in experimental identification of RNA-binding proteins has extended the number of RNA-binding proteins significantly
RNA-binding protein Sam68 controls the spatial and temporal compartmentalization of RNA metabolism to attain proper synaptic function in dendrites. Loss of Sam68 results in abnormal posttranscriptional regulation and ultimately leads to neurological disorders such as fragile X-associated tremor/ataxia syndrome. Sam68 was found to interact with the mRNA encoding β-actin, which regulates the synaptic formation of the dendritic spines with its cytoskeletal components. Therefore, Sam68 plays a critical role in regulating synapse number via control of postsynaptic β-actin mRNA metabolism.
Neuron-specific CELF family RNA-binding protein UNC-75 specifically binds to the UUGUUGUGUUGU mRNA stretch via its three RNA recognition motifs for the exon 7a selection in "C. elegans"' neuronal cells. As exon 7a is skipped due to its weak splice sites in non-neuronal cells, UNC-75 was found to specifically activate splicing between exon 7a and exon 8 only in the neuronal cells.
The cold inducible RNA binding protein CIRBP plays a role in controlling the cellular response upon confronting a variety of cellular stresses, including short wavelength ultraviolet light, hypoxia, and hypothermia. This research yielded potential implications for the association of disease states with inflammation.
Serine-arginine family of RNA-binding protein Slr1 was found exert control on the polarized growth in Candida albicans. Slr1 mutations in mice results in decreased filamentation and reduces damage to epithelial and endothelial cells that leads to extended survival rate compared to the Slr1 wild-type strains. Therefore, this research reveals that SR-like protein Slr1 plays a role in instigating the hyphal formation and virulence in "C. albicans".


Jelly roll fold

The jelly roll or Swiss roll fold is a protein fold or supersecondary structure composed of eight beta strands arranged in two four-stranded sheets. The name of the structure was introduced by Jane S. Richardson in 1981, reflecting its resemblance to the jelly or Swiss roll cake. The fold is an elaboration on the Greek key motif and is sometimes considered a form of beta barrel. It is very common in viral proteins, particularly viral capsid proteins. Taken together, the jelly roll and Greek key structures comprise around 30% of the all-beta proteins annotated in the Structural Classification of Proteins (SCOP) database.
Structure.
The basic jelly roll structure consists of eight beta strands arranged in two four-stranded antiparallel beta sheets which pack together across a hydrophobic interface. The strands are traditionally labeled B through I for the historical reason that the first solved structure, of a jelly roll capsid protein from the tomato bushy stunt virus, had an additional strand A outside the fold's common core. The sheets are composed of strands BIDG and CHEF, folded such that strand B packs opposite strand C, I opposite H, etc.
Viral proteins.
A large number of viruses build their exterior capsids from proteins containing either a single or a double jelly roll fold. This shared capsid architecture is thought to reflect ancient evolutionary relationships, possibly dating to before the last universal common ancestor (LUCA) of cellular life. Other viral lineages use evolutionarily unrelated proteins to build their enclosed capsids, which likely evolved independently at least twice and possibly many times, with links to proteins of cellular origin.
Single jelly roll capsid proteins.
Single jelly roll capsid (JRC) proteins are found in at least sixteen distinct viral families, mostly with icosahedral capsid structures and including both RNA viruses and DNA viruses. Many viruses with single jelly roll capsids are positive-sense single-stranded RNA viruses. Two groups of double-stranded DNA viruses with single-JRC capsids are the "Papillomaviridae" and "Polyomaviridae", both of which have fairly small capsids; in these viruses, the architecture of the assembled capsid orients the axis of the jelly roll parallel or "horizontally" relative to the capsid surface. A large-scale analysis of viral capsid components suggested that the single horizontal jelly roll is the most common fold among capsid proteins, accounting for about 28% of known examples.
Another group of viruses uses single jelly roll proteins in their capsids, but in the vertical rather than horizontal orientation. These viruses are evolutionarily related to the large group of double jelly-roll viruses known as the PRD1-adenovirus viral lineage, with similar capsid architecture realized through assembly of two distinct single jelly-roll major capsid proteins expressed from distinct genes. These single vertical jelly-roll viruses comprise the taxon Helvetiavirae. Known viruses with vertical single jelly roll capsids infect extremophilic prokaryotes.
Double jelly roll proteins.
Double jelly roll capsid proteins consist of two single jelly roll folds connected by a short linker region. They are found in both double-stranded DNA viruses and single-stranded DNA viruses of at least ten different viral families, including viruses that infect all domains of life, and spanning a large capsid size range. In the double jelly roll capsid architecture, the jelly roll axis is oriented perpendicular or "vertically" relative to the capsid surface.
Double jelly roll proteins are believed to have evolved from single jelly roll proteins by gene duplication. It is likely that vertical single jelly roll viruses represent a transitional form, and that the vertical and horizontal jelly roll capsid proteins have independent evolutionary origins from ancestral cellular proteins. The degree of structural similarity among double-jelly-roll virus capsids has led to the conclusion that these viruses likely have a common evolutionary origin despite their diversity in size and in host range; this has become known as the PRD1-adenovirus lineage (Bamfordvirae). Many members of this group have been identified through metagenomics and in some cases have few to no other viral genes in common. Although most members of this group have icosahedral capsid geometry, a few families such as the "Poxviridae" and "Ascoviridae" have oval or brick-shaped mature virions; poxviruses such as "Vaccinia" undergo dramatic conformational changes mediated by highly derived double jelly roll proteins during maturation and likely derive from an icosahedral ancestor. Shared double-jelly-roll capsid proteins, along with other homologous proteins, have also been cited in support of the proposed order "Megavirales" containing the nucleocytoplasmic large DNA viruses (NCLDV).
Double jelly roll proteins have not been observed in cellular proteins; they appear to be unique to viruses. For this reason, detecting clear homology to double jelly roll proteins in the sequences of polinton/Maverick transposable elements widespread in eukaryotic genomes is considered evidence of these genetic elements' close evolutionary relationship to viruses.
Non-capsid proteins.
Single jelly rolls also occur in non-capsid viral proteins, including minor components of the assembled virion as well as non-virion proteins such as polyhedrin.
Cellular proteins.
While double jelly rolls are not found in proteins of cellular origin, single jelly rolls do occur. One such class of cellular proteins is the nucleoplasmins, which serve as molecular chaperone proteins for histone assembly into nucleosomes. The N-terminal domain of nucleoplasmins possesses a single jelly roll fold and assembled into a pentamer. Similar structures have since been reported in additional groups of chromatin remodeling proteins. Jelly roll motifs with identical beta-sheet connectivity are also found in tumor necrosis factor ligands and proteins from the bacterium "Yersinia pseudotuberculosis" that belong to a class of viral and bacterial proteins known as superantigens.
More broadly, the members of the extremely diverse cupin superfamily are also often described as jelly rolls; though the common core of the cupin domain structure contains only six beta strands, many cupins have eight. Examples include the non-heme dioxygenase enzymes and JmjC-family histone demethylases.
Evolution.
Comparative studies of proteins classified as jelly roll and Greek key structures suggest that the Greek key proteins evolved significantly earlier than their more topologically complex jelly roll counterparts. Structural bioinformatics studies comparing virus capsid jelly-roll proteins to other proteins of known structure indicates that the capsid proteins form a well-separated cluster, suggesting that they are subject to a distinctive set of evolutionary constraints. One of the most notable features of viral capsid jelly roll proteins is their ability to form oligomers in a repeated tiling pattern to produce a closed protein shell; the cellular proteins that are most similar in fold and topology are mostly also oligomers. It has been proposed that viral jelly-roll capsid proteins have evolved from cellular jelly-roll proteins, potentially on several independent occasions, at the earliest stages of cellular evolution.
History and nomenclature.
The name "jelly roll" was first used for the structure composed of an elaboration on the Greek key motif by Jane S. Richardson in 1981 and was intended to reflect the structure's resemblance to a jelly or Swiss roll cake. The structure has been given a variety of descriptive names, including a wedge, beta barrel, and beta roll. The edges of the two sheets do not meet to form regular hydrogen bonding patterns, and so it is often not considered to be a true beta barrel, though the term is in common use in describing viral capsid architecture. Cellular proteins containing jelly roll-like structures may be described as a cupin fold, a JmjC fold, or a double-stranded beta helix.


Befloxatone

Befloxatone (MD-370,503) is a reversible inhibitor of monoamine oxidase A.


Apicidin

Apicidin is a fungal metabolite, as well as a histone deacetylase inhibitor.


Vermistatin

Vermistatin is an organic compound and a metabolite of mine-dwelling "Penicillium vermiculatum" found in Berkeley Pit Lake, Butte, Montana. Penisimplicissin is a vermistatin analog with anticancer activity.


GP (nerve agent)

GP is an organophosphate nerve agent of the G-series, with a relatively slow rate of hydrolysis, and thus high stability and persistence in the environment.


Potassium uptake permease

The potassium (K+) uptake permease (KUP) family (TC# 2.A.72) is a member of the APC superfamily of secondary carriers. Proteins of the KUP/HAK/KT family include the KUP (TrkD) protein of "E. coli" and homologues in both Gram-positive and Gram-negative bacteria. High affinity (20 μM) K+ uptake systems (Hak1, TC# 2.A.72.2.1) of the yeast "Debaryomyces occidentalis" as well as the fungus, "Neurospora crassa", and several homologues in plants have been characterized. "Arabidopsis thaliana" and other plants possess multiple KUP family paralogues. While many plant proteins cluster tightly together, the Hak1 proteins from yeast as well as the two Gram-positive and Gram-negative bacterial proteins are distantly related on the phylogenetic tree for the KUP family. All currently classified members of the KUP family can be found in the Transporter Classification Database.
Structure and function.
"Escherichia coli".
The "E. coli" protein is 622 amino acyl residues long and has 12 established transmembrane spanners (440 residues) with a requisite hydrophilic, C-terminal domain of 182 residues, localized to the cytoplasmic side of the membrane. Deletion of most of the hydrophilic domain reduces but does not abolish KUP transport activity. The function of the C-terminal domain is not known. The "E. coli" KUP protein is believed to be a secondary transporter. Uptake is blocked by protonophores such as CCCP (but not arsenate), and evidence for a proton symport mechanism has been presented. The "N. crassa" protein was earlier shown to be a K+:H+ symporter, establishing that the KUP family consists of secondary carriers.
Yeast.
The yeast high affinity (KM = 1 μM) K+ transporter Hak1 is 762 amino acyl residues long with 12 putative TMSs. Like the "E. coli" KUP protein, it possesses a C-terminal hydrophilic domain, probably localized to the cytoplasmic side of the membrane. Hak1 may be able to accumulate K+ 106-fold against a concentration gradient. The plant high and low affinity K+ transporters can complement K+ uptake defects in "E. coli."
TRK.
TRK transporters, responsible for the bulk of K+ accumulation in plants, fungi, and bacteria, mediate ion currents driven by the large membrane voltages (-150 to -250 mV) common to non-animal cells. Bacterial TRK proteins resemble K+ channels in their primary sequence, crystallize as membrane dimers having intramolecular K+-channel-like folding, and complex with a cytoplasmic collar formed of four RCK domains. Fungal TRK proteins possess a large built-in regulatory domain and a highly conserved pair of transmembrane helices (TMSs 7 and 8, ahead of the C-terminus), postulated to facilitate intramembranal oligomerization.These fungal HAK proteins are chloride channels mediating efflux, a process suppressed by osmoprotective agents. It involve hydrophobic gating and resembles conduction by Cys-loop ligand-gated anion channels. Possibly, the tendency of hydrophobic or amphipathic transmembrane helices to self-organize into oligomers creates novel ionic pathways through membranes: hydrophobic nanopores, pathways of low selectivity governed by the chaotropic behavior of individual ionic species under the influence of membrane voltage.
Transport reaction.
The generalized transport reaction for members of the KUP family is:


3alpha-hydroxyglycyrrhetinate dehydrogenase

In enzymology, a 3alpha-hydroxyglycyrrhetinate dehydrogenase () is an enzyme that catalyzes the chemical reaction
Thus, the two substrates of this enzyme are 3alpha-hydroxyglycyrrhetinate and NADP+, whereas its 3 products are 3-oxoglycyrrhetinate, NADPH, and H+.
This enzyme belongs to the family of oxidoreductases, specifically those acting on the CH-OH group of donor with NAD+ or NADP+ as acceptor. The systematic name of this enzyme class is 3alpha-hydroxyglycyrrhetinate:NADP+ 3-oxidoreductase.


Adibendan

Adibendan is an inhibitor of phosphodiesterase III.


Tivantinib

Tivantinib (ARQ197; by Arqule, Inc.) is an experimental small molecule anti-cancer drug. It is a bisindolylmaleimide that binds to the dephosphorylated MET kinase "in vitro". (MET is a growth factor receptor.) Tivantinib is being tested clinically as a highly selective MET inhibitor. However, the mechanism of action of tivantinib is still unclear.
Tivantinib displays cytotoxic activity via molecular mechanisms that are independent from its ability to bind MET, notably tubulin binding, which likely underlies tivantinib cytotoxicity.
Possible applications include non-small-cell lung carcinoma, hepatocellular carcinoma, and oesophageal cancer.
In 2017, it was announced that a phase III clinical trial for advanced hepatocellular carcinoma had failed to meet the primary endpoint.


Spilanthol

Spilanthol is a fatty acid amide isolated from "Acmella oleracea". It is believed to be responsible for the local anesthetic properties of the plant.
Spilanthol permeates the human skin and the inside lining of the cheeks in the mouth (buccal mucosa), resulting in local as well as systemic pharmacological concentrations.


Laminin, beta 2

Laminin subunit beta-2 is a protein that in humans is encoded by the "LAMB2" gene.
Function.
Laminins, a family of extracellular matrix glycoproteins, are the major noncollagenous constituent of basement membranes. They have been implicated in a wide variety of biological processes including cell adhesion, differentiation, migration, signaling, neurite outgrowth and metastasis. Laminins are composed of 3 non identical chains: laminin alpha, beta and gamma (formerly A, B1, and B2, respectively) and they form a cruciform structure consisting of 3 short arms, each formed by a different chain, and a long arm composed of all 3 chains. Each laminin chain is a multidomain protein encoded by a distinct gene. Several isoforms of each chain have been described. Different alpha, beta and gamma chain isomers combine to give rise to different heterotrimeric laminin isoforms, which were formerly designated by Arabic numerals in the order of their discovery, e.g. alpha1beta1gamma1 heterotrimer was known as laminin 1, but the nomenclature now calls for using the numbers of each individual laminin subunit isoform, e.g. what was formerly Laminin 1 is now Laminin 111, and what was formerly Laminin 5 is now Laminin 332. The biological functions of the different chains and trimer molecules are largely unknown, but some of the chains have been shown to differ with respect to their tissue distribution, presumably reflecting diverse functions in vivo. This gene encodes the beta chain isoform laminin, beta 2. The beta 2 chain contains the 7 structural domains typical of beta chains of laminin, including the short alpha region. However, unlike beta 1 chain, beta 2 has a more restricted tissue distribution. It is enriched in the basement membrane of muscles at the neuromuscular junctions, kidney glomerulus and vascular smooth muscle. Transgenic mice in which the beta 2 chain gene was inactivated by homologous recombination, showed defects in the maturation of neuromuscular junctions and impairment of glomerular filtration. Alternative splicing involving a non consensus 5' splice site (gc) in the 5' UTR of this gene has been reported. It was suggested that inefficient splicing of this first intron, which does not change the protein sequence, results in a greater abundance of the un


Leukotriene A4 synthase

Leukotriene A4 synthase may refer to:


Monocarboxylate transporter 3

Monocarboxylate transporter 3 (MCT3) also known as solute carrier family 16 member 8 is a protein that in humans is encoded by the "SLC16A8" gene. MCT is a proton-coupled monocarboxylate transporter. It catalyzes the rapid transport across the plasma membrane of many monocarboxylates such as lactate, pyruvate, branched-chain oxo acids derived from leucine, valine and isoleucine, and the ketone bodies acetoacetate, beta-hydroxybutyrate and acetate. It also functions as high-affinity pyruvate transporter.
Expression of SLC16A8 is confined to the retinal pigment epithelium and choroid plexus epithelia, where it is located on the basal membrane in contrast to MCT1 which is found on the apical membrane.


Aminocarboxymuconate-semialdehyde decarboxylase

In enzymology, an aminocarboxymuconate-semialdehyde decarboxylase () is an enzyme that catalyzes the chemical reaction
Hence, this enzyme has one substrate, 2-amino-3-(3-oxoprop-1-en-1-yl)but-2-enedioate, and two products, 2-aminomuconate semialdehyde and CO2.
This enzyme belongs to the family of lyases, specifically the carboxy-lyases, which cleave carbon-carbon bonds. This enzyme participates in tryptophan metabolism.
Nomenclature.
The systematic name of this enzyme class is 2-amino-3-(3-oxoprop-1-en-1-yl)but-2-enedioate carboxy-lyase (2-aminomuconate-semialdehyde-forming). Other names in common use include picolinic acid carboxylase, picolinic acid decarboxylase, alpha-amino-beta-carboxymuconate-epsilon-semialdehade decarboxylase, alpha-amino-beta-carboxymuconate-epsilon-semialdehyde, beta-decarboxylase, 2-amino-3-(3-oxoprop-2-enyl)but-2-enedioate carboxy-lyase, and 2-amino-3-(3-oxoprop-1-en-1-yl)but-2-enedioate carboxy-lyase.


Ricola

Ricola Ltd./Ricola AG is a Swiss manufacturer of cough drops and breath mints. The head office of Ricola is located in Laufen, Basel-Country.
Business.
Ricola listed sales of 307.2 million Swiss francs in (2016) and employs 400 workers. Around 200 independent production companies in the surrounding area service Ricola. In order to obtain enough herbs for the production of its herbal drops, the firm contracts over 100 self-managed farms in the Valais, Emmental, Val Poschiavo and at the southern foot of the Jura Mountains, in central Switzerland, and in Ticino. Ricola is known for its commercials featuring Heidi (Ramona Pringle) depicting mountaineers shouting "Ri-co-la!" and blowing through a large Alphorn.
In a 2019 survey of US pharmacists, Ricola was recommended by 14% of US pharmacists, in third place, among brand name sore throat products. The survey did not cover store brands.
A class action suit in February 2019 alleged non-natural ingredients (malic acid, aspartame, citric acid, sorbitol, ascorbic acid, sodium ascorbate) while labels say "Naturally Soothing" or "Naturally Helps Support Immune System". In November 2019 the judge dismissed two claims and let two claims proceed. An earlier class action suit in November 2015 alleged industrially synthesized ingredients were used (ascorbic acid, citric acid, and malic acid) while labels stated "Naturally Soothing".
The suit was withdrawn without explanation in January 2016.
History.
Ricola began in 1930 when Emil Wilhelm Richterich and Daniel Ruoss Sr. established Confiseriefabrik Richterich & Co. Laufen after the purchase of a small bakery in Laufen, just outside Basel. Under Richterich, the bakery specialized in confectionery such as “Fünfermocken," a sweet which was similar to caramel. In 1940 Richterich created Ricola's Swiss Herbal Sweet incorporating a blend of 13 herbs. In the 1950s the sweet became appreciated for its ability to be dissolved in boiling water, creating an aromatic herbal tea or tisane, which inspired Richterich to create a Ricola Herbal Tea a few years later.
In 1967, Emil Richterich and his sons Hans Peter and Alfred renamed the company Ricola, an abbreviation of Richterich & Compagnie Laufen. Export began in the 1970s, introducing Ricola's products to foreign markets. At the end of the decade, Ricola moved to a new purpose-built factory in the vicinity of Laufen, where its headquarters are still located.
In 1976, after extensive research on sugar-free confectionery, Ricola launched Switzerland’s first chewable, sugarless herbal sweet. Ricola first started to advertise its products on television in the 1980s, an era that saw increased awareness of the need for good dental hygiene, increasing the demand for sugar-free products such as the ones that Ricola offered. In 1988 the company started packaging their products in small boxes.
The company is now managed by Thomas P. Meier as CEO and Felix Richterich as President of the Board. Today, Ricola exports to over 50 countries in Asia, North America and Europe.
Herbs.
While the active ingredient in most Ricola products is menthol, an important part of Ricola products is the herb mixture. The following herbs are noted as being part of Ricola's classic blend of 13 herbs:
In the United States, ten herbs make up the herbal mixture, three of which are not in the above list. These are Linden Flowers ("Tilia platyphyllos"), Wild Thyme ("Thymus serpyllum") and Hyssop ("Hyssopus officinalis").
Ricola herb gardens.
Ricola has six show gardens in Switzerland. Visitors to the herb gardens can learn about the original herbal blend in their natural environment and learn all about the cultivation and power of herbs. The gardens can be visited as tourist attractions and are located at the following locations:
The herbs used to produce Ricola's cough drops are not cultivated in these gardens, but in natural plantations in the Swiss mountains in accordance with strict organic or BioSuisse guidelines. Ricola ensures that its cultivation areas are not situated near industrial sites or the road networks to avoid contact with harmful pollutants. Over 100 self-managed farms are under contract to Ricola in the Valais, Emmental, Puschlav and the Jura Mountains, in Central Switzerland and Ticino. No pesticides, insecticides or herbicides are used in herb cultivation.
Awards.
The company has won several awards:


HSPA7

Heat shock 70kDa protein 7 (HSP70B) also known as HSPA7 is a human gene. The protein encoded by this gene is a member of the Hsp70 family of heat shock proteins.


Cache domain

In molecular biology, the cache domain is an extracellular protein domain that is predicted to have a role in small-molecule recognition in a wide range of proteins, including the animal dihydropyridine-sensitive voltage-gated Ca2+ channel alpha-2delta subunit, and various bacterial chemotaxis receptors. The name Cache comes from CAlcium channels and CHEmotaxis receptors. This domain consists of an N-terminal part with three predicted strands and an alpha-helix, and a C-terminal part with a strand dyad followed by a relatively unstructured region. The N-terminal portion of the (unpermuted) Cache domain contains three predicted strands that could form a sheet analogous to that present in the core of the PAS domain structure. Cache domains are particularly widespread in bacteria such as "Vibrio cholerae". The animal calcium channel alpha-2delta subunits might have acquired a part of their extracellular domains from a bacterial source. The Cache domain appears to have arisen from the GAF-PAS fold despite their divergent functions.


Chlordecone reductase

In enzymology, a chlordecone reductase () is an enzyme that catalyzes the chemical reaction
Thus, the two substrates of this enzyme are chlordecone alcohol and NADP+, whereas its 3 products are chlordecone, NADPH, and H+.
This enzyme belongs to the family of oxidoreductases, specifically those acting on the CH-OH group of donor with NAD+ or NADP+ as acceptor. The systematic name of this enzyme class is chlordecone-alcohol:NADP+ 2-oxidoreductase. This enzyme is also called CDR.
Structural studies.
As of late 2007, only one structure has been solved for this class of enzymes, with the PDB accession code .


Membrane-associated guanylate kinase

The membrane-associated guanylate kinases (MAGUK) are a superfamily of proteins. The MAGUKs are defined by their inclusion of PDZ, SH3 and GUK domains, although many of them also contain regions homologous of CaMKII, WW and L27 domains. The GUK domain that they have is structurally very similar to that of the guanylate kinases, however it is known to be catalytically inactive as the P-Loop which binds ATP is absent. It is thought that the MAGUKs have subfunctionalized the GUK domain for their own purposes, primarily based on its ability to form protein–protein interactions with cytoskeleton proteins, microtubule/actin based machinery and molecules involved in signal transduction.
MAGUKs also contain multiple PDZ domains, or short peptide binding sequences commonly bind to the C-terminus of interacting proteins. The number of PDZ domain copies varies between different members of the MAGUK family. The PDZ domains found within each family member often have different binding partners, due to variations in their amino acid compositions. The SH3 domain is again a protein–protein interaction domain. Its family generally bind to PXXP sites, but in MAGUKs it is known to bind to other sites as well. One of the most well known features is that it can form an intramolecular bond with the GUK domain, creating what is known as a GUK-SH3 'closed' state.
Examples.
Humans genes encoding members of the MAGUK protein superfamily include:


MMTP2

Multiple myeloma tumor-associated protein 2 is a protein in humans that is encoded by the MMTP2 gene.


AMP nucleosidase

In enzymology, an AMP nucleosidase () is an enzyme that catalyzes the chemical reaction
Thus, the two substrates of this enzyme are AMP and H2O, whereas its two products are D-ribose 5-phosphate and adenine.
This enzyme belongs to the family of hydrolases, specifically those glycosylases that hydrolyse N-glycosyl compounds. The systematic name of this enzyme class is AMP phosphoribohydrolase. Other names in common use include adenylate nucleosidase, and adenosine monophosphate nucleosidase. This enzyme participates in purine metabolism.
Structural studies.
As of late 2007, 5 structures have been solved for this class of enzymes, with PDB accession codes , , , , and .


Sterol

Sterol is a chemical compound with formula , whose molecule is derived from that of gonane by replacement of a hydrogen atom in position 3 by a hydroxyl group. It is therefore an alcohol of gonane.
The name is also used generically for compounds that are derived from this one by substituting other chemical groups for some of the hydrogen atoms, or modifying the bonds in the ring.
These sterols or steroid alcohols are a subgroup of the steroids and an important class of organic molecules. They occur naturally in plants, animals, and fungi, and can be also produced by some bacteria (however likely with different functions). The most familiar type of animal sterol is cholesterol, which is vital to cell membrane structure, and functions as a precursor to fat-soluble vitamins and steroid hormones.
While technically alcohols, sterols are classified by biochemists as lipids (fats in the broader sense of the term).
Types.
Sterols of plants are called "phytosterols" and sterols of animals are called "zoosterols". The most important zoosterol is cholesterol; notable phytosterols include campesterol, sitosterol, and stigmasterol. Ergosterol is a sterol present in the cell membrane of fungi, where it serves a role similar to cholesterol in animal cells.
Role in biochemistry.
Sterols and related compounds play essential roles in the physiology of eukaryotic organisms. For example, cholesterol forms part of the cellular membrane in animals, where it affects the cell membrane's fluidity and serves as secondary messenger in developmental signaling. In humans and other animals, corticosteroids such as cortisol act as signaling compounds in cellular communication and general metabolism. Sterols are common components of human skin oils.
Phytosterols as a nutritional supplement.
Phytosterols, more commonly known as plant sterols, have been shown in clinical trials to block cholesterol absorption sites in the human intestine, thus helping to reduce cholesterol absorption in humans. They are currently approved by the U.S. Food and Drug Administration for use as a food supplement; however, there is some concern that they may block absorption not only of cholesterol, but of other important nutrients as well. At present, the American Heart Association has recommended that supplemental plant sterols be taken only by those diagnosed with elevated cholesterol, and has particularly recommended that they not be taken by pregnant women or nursing mothers.
Preliminary research has shown that phytosterols may have anticancer effects.
Chemical classification and structure.
Sterols are a subgroup of steroids with a hydroxyl group at the 3-position of the A-ring. They are amphipathic lipids synthesized from acetyl-coenzyme A via the HMG-CoA reductase pathway. The overall molecule is quite flat. The hydroxyl group on the A ring is polar. The rest of the aliphatic chain is non-polar.


Glyceryl hydroxystearate

Glyceryl hydroxystearate, also known as glyceryl monohydroxystearate (GMHS), is an organic chemical compound with the molecular formula C21H42O5. It is a whitish- or pale yellow-colored powder found in a variety of cosmetics and skin-care products.
Uses.
Glyceryl hydroxystearate is an ingredient found in some personal-care products. It is commonly used as an emollient, emulsifying agent, or bodying agent. It is often found in facial-care, foot-care, and lip-care products, sunblock, self-tanners, moisturizers, shampoos, creams, lotions, soaps, concealers, and roll-ons and sun-exposure treatments.


Fatty acid methyl ester

Fatty acid methyl esters (FAME) are a type of fatty acid ester that are derived by transesterification of fats with methanol. The molecules in biodiesel are primarily FAME, usually obtained from vegetable oils by transesterification. They are used to produce detergents and biodiesel. FAME are typically produced by an alkali-catalyzed reaction between fats and methanol in the presence of base such as sodium hydroxide, sodium methoxide or potassium hydroxide. One of the reasons for FAME use in biodiesel instead of free fatty acids is to nullify any corrosion that free fatty acids would cause to the metals of engines, production facilities and so forth. Free fatty acids are only mildly acidic, but in time can cause cumulative corrosion unlike their esters. As an improved quality, FAMEs also usually have about 12-15 units higher cetane number than their unesterified counterparts.
Other details.
Every microorganism has its specific FAME profile (microbial fingerprinting). After triglycerides, fatty acids and certain other lipids of some cultured microbes are esterified, they become volatile enough for analysis with gas chromatography which is used to create FAME profile. These profiles can be used as a tool for microbial source tracking (MST) to identify pathological bacteria strains and for characterizing new species of bacteria.
For example, a profile created from cultured bacteria from some water sample can be compared to a profile of known pathological bacteria to find out if the water is polluted by feces or not.


NADH-Q6 oxidoreductase

NADH-Q6 oxidoreductase may stand for


OGDH

Alpha-ketoglutarate dehydrogenase also known as 2-oxoglutarate dehydrogenase E1 component, mitochondrial is an enzyme that in humans is encoded by the "OGDH" gene.
Structure.
Gene.
The OGDH gene is located on the 7th chromosome, with the specific location being 7p14-p13. There are 26 exons located within the gene.
Protein.
This gene encodes a subunit that catalyzes the oxidative decarboxylation of alpha-ketoglutarate to Succinyl-CoA at its active site in the fourth step of the metabolic citric acid cycle by acting as a base to facilitate the decarboxylation. The main residues responsible for the catalysis are thought to be His 260, Phe 227, Gln685, His 729, Ser302, and His 298.
Function.
This gene encodes one subunit of the 2-oxoglutarate dehydrogenase complex. This complex catalyzes the overall conversion of 2-oxoglutarate (alpha-ketoglutarate) to succinyl-CoA and CO2 during the citric acid cycle. The protein is located in the mitochondrial matrix and uses thiamine pyrophosphate as a cofactor. The overall complex furthers catalysis by keeping the necessary substrates for the reaction close within the enzyme, thus creating a situation in which it is more likely that the substrate will be in the favorable conformation and orientation. This enzyme is also part of a larger multienzyme complex that channels the intermediates in the catalysis between subunits of the complex thus minimizing unwanted side reactions. Not only do the subunits ferry products back and forth, but each of the subunits in the E1o homodimer are connected via a cavity lined with acidic residues, thus increasing the dimer's ability to act as a base. The orientation of the cavity allows for direct transfer of the intermediate to the E2o subunit.
Mechanism.
The protein encoded by OGDH is thought to have a single active site. The enzyme also requires two cofactors in order for it to function properly, Thiamine diphosphate and a divalent magnesium ion. The specific mechanism of the subunit is currently unknown; however, there are several theories as to how it functions, among them is the Hexa Uni Ping Pong theory. Even though the mechanism isn't fully known the kinetic data have been calculated and are as follows: the Km is 0.14 ± 0.04 mM, and the Vmax is 9 ± 3 μmol/(min*mg).
Regulation.
This subunit, known as E1o, catalyzes a rate-limiting step in the citric acid cycle and lies far from equilibrium; the total change in Gibbs free energy is ΔG = −33 kJ/mol. The significant energy change makes it a crucial point of regulation not only for the citric acid cycle, but also for the entire cellular respiration pathway. As such, E1o is inhibited by both NADH and Succinyl-CoA via non competitive feedback inhibition.
Clinical significance.
A congenital deficiency in 2-oxoglutarate dehydrogenase activity is believed to lead to hypotonia, metabolic acidosis, and hyperlactatemia. It is characterized by the buildup of a chemical called lactic acid in the body and a variety of neurological problems. Signs and symptoms of this condition usually first appear shortly after birth, and they can vary widely among affected individuals. The most common feature is a potentially life-threatening buildup of lactic acid (lactic acidosis), which can cause nausea, vomiting, severe breathing problems, and an abnormal heartbeat. People with pyruvate dehydrogenase deficiency usually have neurological problems as well. Most have delayed development of mental abilities and motor skills such as sitting and walking. Other neurological problems can include intellectual disability, seizures, weak muscle tone (hypotonia), poor coordination, and difficulty walking. Some affected individuals have abnormal brain structures, such as underdevelopment of the tissue connecting the left and right halves of the brain (corpus callosum), wasting away (atrophy) of the exterior part of the brain known as the cerebral cortex, or patches of damaged tissue (lesions) on some parts of the brain. Because of the severe health effects, many individuals with pyruvate dehydrogenase deficiency do not survive past childhood, although some may live into adolescence or adulthood.


Endoglycosidase

An Endoglycosidase is an enzyme that releases oligosaccharides from glycoproteins or glycolipids. It may also cleave polysaccharide chains between residues that are not the terminal residue, although releasing oligosaccharides from conjugated protein and lipid molecules is more common.
It breaks the glycosidic bonds between two sugar monomer in the polymer. It is different from exoglycosidase that it does not do so at the terminal residue. Hence, it is used to release long carbohydrates from conjugated molecules. If an exoglycosidase were used, every monomer in the polymer would have to be removed, one by one from the chain, taking a long time. An endoglycosidase cleaves, giving a polymeric product.
PROTEIN-x1-x2-x3-x4-x5-x6-x7-x8-x9-x10-x11-...-xn
Mechanism Overview.
The mechanism is an enzymatic hydrolysis that requires two critical molecules; a proton donor (most likely an acid) and a nucleophile(most likely a base). The Endoglycosidases mechanism has two forms; an acid catalyzed protonation of the glycosidic oxygen yielding stereochemical retention at the anomeric carbon or an acid catalyzed protonation of the glycosidic oxygen with a concomitant attack of a water molecule activated by the base residue yielding a stereochemical inversion.
Both mechanisms exhibit the same distance between the proton donor and the glycosidic oxygen, situating the proton donor close enough to the glycosidic oxygen for hydrogen bonding. It is the distance between the nucleophile and the anomeric carbon where the two mechanisms begin to diverge. Because the inversion mechanism must accommodate enough space for the water molecule, the nucleophile is situated further away from the anomeric carbon. In the retention mechanism, this distance is only 5.5 -7 angstroms but increases to 9-10 angstroms in the inversion mechanism. Furthermore, the inversion mechanism was found to proceed through a single displacement mechanism involving an oxocarbenium ion-like transition state. Due to the retention mechanism's proximity between the two carboxyl groups, it goes through a double displacement mechanism that produces a covalent glycosyl-enzyme intermediate.
An exoglycosidase would remove each carbohydrate monomer (x) one by one from the end, starting at xn, whereas and endoglycosidase can cut at any glycosidic bond (-) and may cleave after a signature 'link oligosaccharide' that links certain carbohydrates to certain proteins.
Applications and potential uses.
There has been great potential shown in the use of endoglycosidase enzymes undergoing mutagenesis. This new mutated enzyme when exposed to the proper compounds will undergo oligosaccharide synthesis and will not hydrolyze the newly formed polymer chains. This is an extremely useful tool, as oligosaccharides have a great potential for use as therapeutics. For example, globo H hexasaccharide will indicate cancer related malignant cell transformation in the breast, prostate and ovaries.
Endoglycosidases also have potential application in fighting autoimmune diseases such as arthritis and systemic lupus erythematosus. In 2008, a team of researchers demonstrated that injection of endgoglycosidase S “efficiently removes the IgG-associated sugar domain in vivo and interferes with autoantibody-mediated proinflammatory processes in a variety of autoimmune models.” Clearly the manipulation and mutation of this enzyme holds great promise for being able to fight a variety of diseases in the body.


Fatty-acyl-CoA synthase

Fatty-acyl-CoA Synthase, or more commonly known as yeast fatty acid synthase (and not to be confused with Long Chain fatty acyl-CoA synthetase), is an enzyme complex responsible for fatty acid biosynthesis, and is of Type I Fatty Acid Synthesis (FAS). Yeast fatty acid synthase plays a pivotal role in fatty acid synthesis. It is a 2.6 MDa barrel shaped complex and is composed of two, unique multi-functional subunits: alpha and beta. Together, the alpha and beta units are arranged in an α6β6 structure. The catalytic activities of this enzyme complex involves a coordination system of enzymatic reactions between the alpha and beta subunits. The enzyme complex therefore consists of six functional centers for fatty acid synthesis.
Reaction.
The enzyme catalyzes the reaction:
Acetyl-CoA + n malonyl-CoA + 4n NADPH + 4n H+ formula_1 long-chain-acyl-CoA + n CoA + n CO2 + 4n NADP+
The 4 substrates of this enzyme are acetyl-CoA, malonyl-CoA, NADPH, and H+, whereas its 4 products are Acyl-CoA, CoA, CO2, and NADP+.
More specifically, the FAS catalysis mechanism consumes an acetyl-coenzyme A (acetyl-CoA) and seven malonyl-CoA molecules to produce a Palmitoyl-CoA.
Background.
Synthesis of fatty acids is generally performed by fatty acid synthase (FAS). Though the syntheses of fatty acids are very similar across all organisms, the enzymes and subsequent enzymatic mechanisms involved in fatty acid synthesis vary between eukaryotes and prokaryotes. There are two types of fatty acid synthesis (FAS) mechanisms: type I FAS and type II FAS. Type I FAS exists in eukaryotes, including mammalian cells and fungi. Type II FAS are found in prokaryotes. The type I FAS system utilizes a multi-enzyme complex, which are highly integrated, while the type II FAS system utilizes individual, separate enzymes to catalyze the reactions involved in fatty acid synthesis. Yeast fatty acyl synthase belongs to the Type I FAS and was the first of Type I FAS to be studied.
Structure.
Yeast fatty acyl synthase, of Type I FAS, is composed of a α6β6 complex in which an αβ unit forms one functional center for fatty acid synthesis. Yeast fatty acyl synthase therefore has six reaction units for its fatty acid synthesis, in which each of these units function independently from one another. Each α and β subunit, in turn, has four functional domains, and together, the eight functional domains catalyze all the reactions of fatty acid synthesis in yeast, which includes: activation, priming, elongation, and termination. Consequently, yeast FAS is incredibly unique due to its structural complexity, which contains 48 functional centers for one α6β6 complex and can efficiently performs 6 fatty acid syntheses separately at one time.
There are seven, total enzymatic reactions in fatty acid synthesis. These reactions include: activation, priming, four reactions in elongation, and termination. Five these reactions are performed in the beta subunit and two reactions are performed in the alpha subunit.
The 3D protein structure of the enzyme can be found here:PDB. The crystal structure of yeast fatty acid synthase has also been derived, showing both alpha and beta subunits.
Mechanism.
Activation.
The activation of yeast FAS occurs in the alpha subunit. The reaction is performed by the holo-(acyl-carrier-protein) synthase (ACPS) domain. ACPS attaches the 4′-phosphopantetheine prosthetic group of CoA to the acyl carrier protein (ACP) domain, which is found in the N terminus of the α subunit. ACP is the only “mobile” domain of the enzyme complex, in which it moves intermediate substrates along all of the catalytic centers the enzyme, most notably the alpha and beta subunits.
Priming.
The next step is priming, or the initiation of fatty acid synthesis. Priming is performed in the β subunit, and is catalyzed by the acetyltransferase (AT, equivalent to bacterial (acyl-carrier-protein) S-acetyltransferase) domain, which initiates the process of fatty acid synthesis. Here, acetyltransferase transfers the acetate group from acetyl-CoA onto the SH group of the 4′-phosphopantetheine prosthetic group of ACP, which had been attached during activation.
Elongation.
Elongation involves four main reactions:
Elongation itself occurs in mainly in the α subunit, though the entire process required for elongation is a coordinated system which involves the α and β subunits. ACP first delivers the acetate group, which had been attached during priming, to the ketoacyl synthase (KS) domain in the α subunit. ACP then moves back to the β subunit to the malonyl/palmitoyl-transacylase (MPT, equivalent to bacterial malonyl transacylase) domain and binds to a malonyl of malonyl-CoA, which will be used for elongation. The newly bound malonyl-ACP then swings back to the KS domain and transfers the malonate group for chain elongation. Now in the KS domain, the bound acyl group is condensed with the malonate to form 3-ketoacyl intermediate: β-ketobutyryl-ACP, releasing carbon dioxide in the process.
In the α subunit is also the ketoacyl reductase (KR) domain. The KR domain is NADPH dependent, and catalyzes substrate reduction, in which ketobutyryl-ACP is reduced to β-hydroxyacyl-ACP by NADPH.
The β-hydroxyacyl-ACP is then transferred back to the β subunit, where it is dehydrated in 3-Hydroxyacyl ACP dehydrase (DH) domain. Another reduction reaction then performed in the enoyl reductase (ER) domain of the β subunit to form a saturated acyl-ACP chain. Finally, ACP brings the substrate back to the KS domain of the α subunit for another cycle of elongation. The elongation cycle is often repeated 3 more times before termination.
Notice the unique characteristic of ACP, which is vital to fatty acid synthesis in its role of shuttling the reaction intermediates between the α and β subunits’ catalytic domains.
Termination.
Once the fatty acid chain reaches 16 or 18 carbons long after cycles of elongation, termination occurs. In the final round of elongation, rather than being taken back to the KS domain, the fatty acid product, which is still bound to ACP, is taken from the ER domain to the MPT domain. Here, CoA is attached to the fatty acid, and the resulting long chain fatty acyl-CoA is released into the cytosol.
Applications.
Fatty acids are key components of a cell, therefore, the regulation or inhibition of fatty acid synthesis hold severe consequences for cellular function. The malfunction of the fatty acid synthesis pathway can result in cancer and obesity. However, the significance of fatty acid synthesis also make the fatty acid synthesis pathway a potential target for the search and study of anticancer and antibiotic drugs. It has been found that in humans, fatty acid synthase, is overly expressed in cancer cells. Therefore, FAS, which has been associated only with energy production prior, is now associated with aggressive tumor growth and survival. Studies have also found that human fatty acid synthase is overly expressed in prostate cancer cells.


GDP-4-dehydro-D-rhamnose reductase

In enzymology, a GDP-4-dehydro-D-rhamnose reductase () is an enzyme that catalyzes the chemical reaction
The 3 substrates of this enzyme are GDP-6-deoxy-D-mannose, NAD+, and NADP+, whereas its 4 products are GDP-4-dehydro-6-deoxy-D-mannose, NADH, NADPH, and H+.
This enzyme belongs to the family of oxidoreductases, specifically those acting on the CH-OH group of donor with NAD+ or NADP+ as acceptor. The systematic name of this enzyme class is GDP-6-deoxy-D-mannose:NAD(P)+ 4-oxidoreductase. Other names in common use include GDP-4-keto-6-deoxy-D-mannose reductase, GDP-4-keto-D-rhamnose reductase, and guanosine diphosphate-4-keto-D-rhamnose reductase. This enzyme participates in fructose and mannose metabolism.


Fatty acid ester

 Fatty acid esters (FAEs) are a type of ester that result from the combination of a fatty acid with an alcohol. When the alcohol component is glycerol, the fatty acid esters produced can be monoglycerides, diglycerides, or triglycerides. Dietary fats are chemically triglycerides.
Glycerol esters of fatty acids occur as colorless to brown powders, flakes, coarse powders, or granular or waxy lumps, or are a colorless to brown semi-fluids or liquids. They are odorless or have a characteristic odor.
Biodiesels are typically fatty acid esters made by the transesterification of vegetable fats and oils. In this process the glycerol component is replaced with a different alcohol. The most commonly used alcohol is methanol, producing fatty acid methyl esters (FAME). When ethanol is used fatty acid ethyl esters (FAEE) are created. Other alcohols used for the production of biodiesel include butanol and isopropanol.
Fatty acid ethyl esters are biomarkers for the consumption of ethanol (alcoholic beverages).


GTP-binding protein regulators

GTP-binding protein regulators regulate G proteins in several different ways. Small GTPases act as molecular switches in signaling pathways, which act to regulate functions of other proteins. They are "active" or 'ON' when it is bound to GTP and "inactive" or 'OFF' when bound to GDP. Activation and deactivation of small GTPases can be regarded as occurring in a cycle, between the GTP-bound and GDP-bound form, regulated by other regulatory proteins.
Exchangers.
The inactive form of GTPases (GDP-form) are activated by a class of proteins called Guanosine nucleotide exchange factors (GEFs). GEFs catalyse nucleotide exchange by encouraging the release of GDP from the small GTPase (by displacement of the small GTPase-associated Mg2+ ion) and GDP's replacement by GTP (which is in at least a 10-fold excess within the cell) . Inactivation of the active small GTPase is achieved through hydrolysis of the GTP by the small GTPase's intrinsic GTP hydrolytic activity.
Stimulators.
The rate of GTP hydrolysis for small GTPases is generally too slow to create physiologically relevant transient signals, and thus requires another class of regulatory proteins to accelerate this activity, the GTPase activating proteins (GAPs).
Inhibitors.
Another class of regulatory proteins, the Guanosine nucleotide dissociation inhibitors (GDIs), bind to the GDP-bound form of Rho and Rab small GTPases and not only prevent exchange (maintaining the small GTPase in an off-state), but also prevent the small GTPase from localizing at the membrane, which is their place of action.


Aldose reductase inhibitor

Aldose reductase inhibitors are a class of drugs being studied as a way to prevent eye and nerve damage in people with diabetes.
Mechanism.
Their target, aldose reductase, is an enzyme that is normally present in many other parts of the body, and catalyzes one of the steps in the sorbitol(polyol) pathway that is responsible for fructose formation from glucose. Aldose reductase activity increases as the glucose concentration rises in diabetes in those tissues that are not insulin sensitive, which include the lenses, peripheral nerves and glomerulus. Sorbitol does not diffuse through cell membranes easily and therefore accumulates, causing osmotic damage which leads to retinopathy and neuropathy.
Examples.
Natural sources reported to inhibit aldose reductase include indian gooseberry, spinach, cumin seeds, fennel seeds, basil leaves, lemon, black pepper, orange, curry leaves, cannabis, cinnamon and lichen. Luteolin, a type of flavonoid found mostly in leaves, and their synthetic derivatives are potential inhibitors of aldose reductase.
Diabetic cataract.
Diabetic cataract formation follows an increase in sugars in the lens. The excess sugar within the lens is reduced by aldose reductase to its alcohol, but the lens capsule is relatively impermeable to sugar alcohols. Because of the excess sugar alcohol (polyol), the lens imbibes water, causing osmotic imbalance. Eventually, increased sodium and decreased potassium levels and decreased glutathione levels lead to cataract formation. Topical administration of aldose reductase inhibitors have been shown to prevent the cataract in rats.
Asthma and COPD.
This class of drugs is also under investigation as a possible root pathology modulating treatment for asthma and COPD since it has been shown that they inhibit goblet cell metaplasia in the respiratory epithelium, thereby reducing the copious mucous secretion associated with these.


Degradosome

The degradosome is a multiprotein complex present in most bacteria that is involved in the processing of ribosomal RNA and the degradation of messenger RNA and is regulated by Non-coding RNA. It contains the proteins RNA helicase B, RNase E and Polynucleotide phosphorylase.
The store of cellular RNA in the cells is constantly fluctuating. For example, in "Escherichia coli", Messenger RNA's life expectancy is between 2 and 25 minutes, in other bacteria it might last longer. Even in resting cells, RNA is degraded in a steady state, and the nucleotide products of this process are later reused for fresh rounds of nucleic acid synthesis. RNA turnover is very important for gene regulation and quality control.
All organisms have various tools for RNA degradation, for instance ribonucleases, helicases, 3'-end nucleotidyltransferases (which add tails to transcripts), 5'-end capping and decapping enzymes and assorted RNA-binding proteins that help to model RNA for presentation as substrate or for recognition. Frequently, these proteins associate into stable complexes in which their activities are coordinate or cooperative. Many of these RNA metabolism proteins are represented in the components of the multi-enzyme RNA degradosome of "Escherichia coli", which is constituted by four basic components: the hydrolytic endo-ribonuclease RNase E, the phosphorolytic exo-ribonuclease PNPase, the ATP-dependent RNA helicase (RhIB) and a glycolytic enzyme enolase.
The RNA degradosome was discovered in two different laboratories while they were working on the purification and characterization of "E. coli", RNase E and the factors that could have an influence on the activity of the RNA-degrading enzymes, concretely, PNPase. It was found while two of its major compounds were being studied.
Structure.
The composition of this multienzyme may vary depending on the organism. The multiprotein complex RNA degradosome in "E. coli" consists of 4 canonical components:
There are some alternate forms of the RNA degradosome with different proteins that have been reported. Supplementary alternate degradosome components are PcnB (poly A polymerase) and the RNA helicases RhlE and SrmB. Other alternate components during cold shock include RNA helicase CsdA. Additional alternate degradosome components during stationary phase include Rnr (RNase R) and the putative RNA helicase HrpA. Ppk (polyphosphate kinase) is another constituent that has been reported to be part of the complex, the same as RNA chaperone Hfq, PAP (prostatic acid phosphatase), other kinds of chaperones and ribosomal proteins. These have been found in cell-extracted degradosome preparations from "E. coli".
The structure of RNA degradosome is not as rigid as it seems to be in the picture because this one is only a model to understand how it works. The RNA degradosome's structure is dynamic and each component interacts with the components that are close to it. So the structure is like a molecular domain where RNA can interact as a substrate with each of the components and when this happens, it is really difficult for RNA to scape from the complex.
Functions.
The RNA degradosome is a huge multi-enzyme association that is involved in RNA metabolism and post-transcriptional control of gene expression in numerous bacteria such as "Escherichia coli" and "Pseudoalteromonas haloplanktis". The multi-protein complex also serves as a machine for processing structured RNA precursors in the course of their maturation.
RNA helicase is considered to help in the process of degradation to develop the double helix structure in RNA stem-loops. Occasionally, copurification of rRNA with degradosome is appreciated, which suggests that the complex may take part in rRNA and mRNA degradation. There is very little clear information about the role of degradosome. Looking into the steps of the degradation of a transcript in "E. coli", what is known is that in the first place the endoribonucleases can cleave the substrates so that later the exoribonucleases can work on the products. RhIB has very little activity by itself but the interaction with RNAse E can stimulate it. The role of enolase in the degradation process of RNA is still not properly described, apparently it helps the complex to be more specific during the process of degradation.
One particularly intriguing aspect of the bacterial RNA degradosome is the presence of metabolic enzymes in many of the studied complexes. In addition to the enolase enzyme present in the "E. coli" degradosome, the metabolic enzymes aconitase and phosphofructokinase have been identified in the "C. crescentus" and "B. subtilis" degradosomes respectively. The reason for the presence of these enzymes is currently unclear.
Degradosome activation.
This multi-protein complex is stimulated by a non-coding RNA, called miRNA in Eukaryotic cells and sRNA in bacteria. Small sequences of aminoacid are usually used to target mRNA for its destruction. From here, there are two ways to do it: targeting "translation-initiation region" (TIR) or "coding DNA sequence" (CDS). Firstly, to attach sRNA to targeted mRNA a Hfq (chaperone protein) is needed. Once the attachment is done, if the complex Hfq-sRna ends on TIR, it blocks "ribosome binding site" (RBS) so ribosomes can not translate, and activates nucleases (RNase E) to eliminate mRNA. Another possibility is ending on another region, that makes the complex work as a finisher point of the translation. This way, the ribosomes can do their job of decoding, process that stops when they arrive to the complex, where all the destruction procedure is switched on.
RNA degradation.
The RNA's destruction process is very complicated. To make it easier to understand, we use as an example the mRNA degradation procedure in Escherichia coli because it is the best known process. It is mediated mainly by endo- and ribo- nucleases. The enzymes RNase II and PNPase (polynucleotide phosphorylase) degrade mRNA in a 3'→5' way. The degradosome has 4 compartments that have several ribonucleases. Initially, the synthesized RNA is a polyphosphate structure. This is why the dephosphorylation is needed, in order to obtain monophosphate by the action of a RNA pyrophosphohydrolase PppH. The transcripts have two parts: the phosphate terminal (P-terminal) and a stem-loop structure as an end. The P-terminal is endoribonucleolytically cleavaged by RNase E, while the stem-loop is digested by RNA helicases. If there are any secondary structures, the performance of polymerase PAP is needed to simplify the reduction by exoribonucleases such as PNPase. Finally, the scraps are processed by oligoribonucleases.
The process is analogous in other species and only changes in the enzymatic machinery. For example, bacillus subtilis instead of using RNase E as the endo-ribonuclease, it uses RNase Y or RNase J or in the archaea is used an exosome (vesicle) to this job.
Evolution.
The degradosome, which is dynamic in conformation, variable in composition and non-essential under determined laboratory conditions, has nevertheless been maintained throughout the evolution of many bacterial species (Archaea, Eukaryote, Escherichia coli, Mitochondria, etc.), due most likely to its diverse contributions in global cellular regulation. It has been experimentally demonstrated that the presence of degradosome is a selective benefit for "E. coli".
Degradosome-like structures have been thought to be part of many γ-proteobactria and have actually been found in other remote bacterial lineages. They are built upon RNase E. However, the composition of these degradosome-like assemblies is not always the same, it may be different on some proteic components.
The RNA degradosome of "E. coli".
Humans and other animals have "E. coli" as a commensal in their intestinal tract. It is one of the most studied organisms at laboratories and it has been a useful model for understanding genetic regulation in bacteria and other domains of life. The RNA degradosome of "E. coli" is a structure that plays diverse roles in RNA metabolism. It shares homologous components and functional analogy with similar assemblies found in all domains of life. One of its components is an ATP-dependent motor that is activated through protein-protein interactions and cooperates with the ribonucleases in an energy-dependent mode of RNA degradation.
"E. coli" does not have a 5'→3' degradation pathway. Its mRNA does not have 5' capped ends and there are not any 5'→3' exonucleases known. The same thing happens to other eubacteria, hence the 5'→3' degradation pathway could be an exclusive treat of eukaryotic cells.


Elastic fiber

Elastic fibers (or yellow fibers) are an essential component of the extracellular matrix composed of bundles of proteins (elastin) which are produced by a number of different cell types including fibroblasts, endothelial, smooth muscle, and airway epithelial cells. These fibers are able to stretch many times their length, and snap back to their original length when relaxed without loss of energy. Elastic fibers include elastin, elaunin and oxytalan.
Elastic tissue is classified as "connective tissue proper".
Elastic fibers are formed via elastogenesis, a highly complex process involving several key proteins including fibulin-4, fibulin-5, latent transforming growth factor β binding protein 4, and microfibril associated protein 4 In this process tropoelastin, the soluble monomeric precursor to elastic fibers is produced by elastogenic cells and chaperoned to the cell surface. Following excretion from the cell, tropoelastin self associates into ~200 nm particles by coacervation, an entropically driven process involving interactions between tropoelastin's hydrophobic domains, which is mediated by glycosaminoglycans, heparan, and other molecules. These particles then fuse to give rise to 1-2 micron spherules which continue to grow as they move down from the cells surface before being deposited onto fibrillin microfibrillar scaffolds.
Following deposition onto microfibrils tropoelastin is insolubilized via extensive crosslinking by members of the lysyl oxidase and lysyl oxidase like family of copper-dependent amine oxidases into amorphous elastin, a highly resilient, insoluble polymer that is metabolically stable over a human lifespan. These two families of enzymes react with the many lysine residues present in tropoelastin to form reactive aldehydes and allysine via oxidative deamination.
These reactive aldehydes and allysines can react with other lysine and allysine residues to form desmosine, isodesmosine, and a number of other polyfunctional crosslinks that join surrounding molecules of tropoelastin into an extensively crosslinked elastin matrix. This process creates a diverse array of intramolecular and intermolecular crosslinks These unique crosslinks are responsible for elastin's durability and persistence. Maintenance of crosslinked elastin is carried out by a number of proteins including lysyl oxidase-like 1 protein.
Mature elastic fibers consist of an amorphous elastin core surrounded by a glycosaminoglycans, heparan sulphate, and number of other proteins such as microfibrillar-associated glycoproteins, fibrillin, fibullin, and the elastin receptor.
Distribution.
Elastic fibers are found in the skin, lungs, arteries, veins, connective tissue proper, elastic cartilage, periodontal ligament, fetal tissue and other tissues which must undergo mechanical stretching. Elastic fibers are absent from scarring, keloids and dermatofibromas and they are decreased greatly, or are absent in anetodermas.
Histology.
Elastic fibers stain well with aldehyde fuchsin, orcein, and Weigert's elastic stain in histological sections.
The permanganate-bisulfite-toluidine blue reaction is a highly selective and sensitive method for demonstrating elastic fibers under polarizing optics. The induced birefringence demonstrates the highly ordered molecular structure of the elastin molecules in the elastic fiber. This is not readily apparent under normal optics.
Defects and disease.
There is evidence to believe that certain defects of any components of the elastic matrix may impair and alter the structural appearance of elastic and collagen fibers.
Cutis laxa and Williams syndrome have elastic matrix defects that have been directly associated with alterations in the elastin gene.
Alpha-1 antitrypsin deficiency is a genetic disorder where elastin is excessively degraded by elastase, a degrading protein released by neutrophils during the inflammatory response. This leads most often to emphysema and liver disease in affected individuals.
Buschke-Ollendorff syndrome, Menkes disease, pseudoxanthoma elasticum, and Marfan's syndrome have been associated with defects in copper metabolism and lysyl oxidase or defects in the microfibril (defects in fibrillin, or fibullin for example).
Hurler disease, a lysosomal storage disease, is associated with an altered elastic matrix.
Hypertension and some congenital heart defects are associated with alterations in the great arteries, arteries, and arterioles with alterations in the elastic matrix.
Elastosis.
"Elastosis" is the buildup of elastic fibers in tissues, and is a form of degenerative disease. There are a multitude of causes, but the most commons cause is actinic elastosis of the skin, also known as "solar elastosis", which is caused by prolonged and excessive sun exposure, a process known as photoaging. Uncommon causes of skin elastosis include elastosis perforans serpiginosa, perforating calcific elastosis and linear focal elastosis.


Procaspases


Cholesteryl ester transfer protein

Cholesteryl ester transfer protein (CETP), also called plasma lipid transfer protein, is a plasma protein that facilitates the transport of cholesteryl esters and triglycerides between the lipoproteins. It collects triglycerides from very-low-density (VLDL) or Chylomicrons and exchanges them for cholesteryl esters from high-density lipoproteins (HDL), and vice versa. Most of the time, however, CETP does a heteroexchange, trading a triglyceride for a cholesteryl ester or a cholesteryl ester for a triglyceride.
Genetics.
The "CETP" gene is located on the sixteenth chromosome (16q21).
Protein Fold.
The crystal structure of CETP is that of dimer of two TUbular LIPid (TULIP) binding domains. Each domain consists of a core of 6 elements: 4 beta-sheets forming an extended superhelix; 2 flanking elements that tend to include some alpha helix. The sheets wrap around the helices to produce a cylinder 6 x 2.5 x 2.5 nm. CETP contains two of these domains that interact head-to-head via an interface made of 6 beta-sheets, 3 from each protomer. The same fold is shared by Bacterial Permeability Inducing proteins (examples: BPIFP1 BPIFP2 BPIFA3 and BPIFB4), phospholipid transfer protein (PLTP), and long-Palate Lung, and Nasal Epithelium protein (L-PLUNC). The fold is similar to intracellular SMP domains, and originated in bacteria. The crystal structure of CETP has been obtained with bound CETP inhibitors. However, this has not resolved the doubt over whether CETP function as a lipid tube or shuttle.
Role in disease.
Rare mutations leading to reduced function of CETP have been linked to accelerated atherosclerosis. In contrast, a polymorphism (I405V) of the "CETP" gene leading to lower serum levels has also been linked to exceptional longevity and to metabolic response to nutritional intervention. However, this mutation also increases the prevalence of coronary heart disease in patients with hypertriglyceridemia. The D442G mutation, which lowers CETP levels and increases HDL levels also increases coronary heart disease.
Elaidic acid, a major component of trans fat, increases CETP activity.
Pharmacology.
As HDL can alleviate atherosclerosis and other cardiovascular diseases, and certain disease states such as the metabolic syndrome feature low HDL, pharmacological inhibition of CETP is being studied as a method of improving HDL levels. To be specific, in a 2004 study, the small molecular agent torcetrapib was shown to increase HDL levels, alone and with a statin, and lower LDL when co-administered with a statin. Studies into cardiovascular endpoints, however, were largely disappointing. While they confirmed the change in lipid levels, most reported an increase in blood pressure, no change in atherosclerosis, and, in a trial of a combination of torcetrapib and atorvastatin, an increase in cardiovascular events and mortality.
A compound related to torcetrapib, Dalcetrapib (investigative name JTT-705/R1658), was also studied, but trials have ceased. It increases HDL levels by 30%, as compared to 60% by torcetrapib. Two CETP inhibitors were previously under development. One was Merck's MK-0859 anacetrapib, which in initial studies did not increase blood pressure. In 2017, its development was abandoned by Merck. The other was Eli Lilly's evacetrapib, which failed in Phase 3 trials.