1.
Pfam
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Pfam is a database of protein families that includes their annotations and multiple sequence alignments generated using hidden Markov models. The most recent version, Pfam 31.0, was released in March 2017, the general purpose of the Pfam database is to provide a complete and accurate classification of protein families and domains. Originally, the rationale behind creating the database was to have a method of curating information on known protein families to improve the efficiency of annotating genomes. The Pfam classification of families has been widely adopted by biologists because of its wide coverage of proteins. Early genome projects, such as human and fly used Pfam extensively for functional annotation of genomic data, the Pfam website allows users to submit protein or DNA sequences to search for matches to families in the database. If DNA is submitted, a translation is performed, then each frame is searched. Family is the class, which simply indicates that members are related. Domains are defined as a structural unit or reusable sequence unit that can be found in multiple protein contexts. Repeats are not usually stable in isolation, but rather are required to form tandem repeats in order to form a domain or extended structure. Motifs are usually shorter sequence units found outside of globular domains, the descriptions of Pfam families are managed by the general public using Wikipedia. As of release 29.0,76. 1% of protein sequences in UniprotKB matched to at least one Pfam domain, new families come from a range of sources, primarily the PDB and analysis of complete proteomes to find genes with no Pfam hit. For each family, a subset of sequences are aligned into a high-quality seed alignment. Sequences for the alignment are taken primarily from pfamseq with some supplementation from UniprotKB. This seed alignment is used to build a profile hidden Markov model using HMMER. This HMM is then searched against sequence databases, and all hits that reach a curated gathering threshold are classified as members of the protein family, the resulting collection of members is then aligned to the profile HMM to generate a full alignment. For each family, a curated gathering threshold is assigned that maximises the number of true matches to the family while excluding any false positive matches. False positives are estimated by observing overlaps between Pfam family hits that are not from the same clan and this threshold is used to assess whether a match to a family HMM should be included in the protein family. Upon each update of Pfam, gathering thresholds are reassessed to prevent overlaps between new and existing families, domains of Unknown Function represent a growing fraction of the Pfam database
2.
InterPro
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The contents of InterPro consist of diagnostic signatures and the proteins that they significantly match. The signatures consist of models which describe protein families, domains or sites, models are built from the amino acid sequences of known families or domains and they are subsequently used to search unknown sequences in order to classify them. Each of the databases of InterPro contribute towards a different niche, from very high-level. InterPros intention is to provide a one-stop-shop for protein classification, where all the signatures produced by the different member databases are placed into entries within the InterPro database. Signatures which represent equivalent domains, sites or families are put into the same entry, additional information such as a description, consistent names and Gene Ontology terms are associated with each entry, where possible. InterPro contains three main entities, proteins, signatures and entries, the proteins in UniProtKB are also the central protein entities in InterPro. Information regarding which signatures significantly match these proteins are calculated as the sequences are released by UniProtKB, only signatures deemed to be of sufficient quality are integrated into InterPro. InterPro also includes data for splice variants and the contained in the UniParc. The signatures from InterPro come from 11 member databases, which are listed below, cATH-Gene3D describes protein families and domain architectures in complete genomes. Protein families are formed using a Markov clustering algorithm, followed by multi-linkage clustering according to sequence identity, mapping of predicted structure and sequence domains is undertaken using hidden Markov models libraries representing CATH and Pfam domains. Functional annotation is provided to proteins from multiple resources, functional prediction and analysis of domain architectures is available from the Gene3D website. HAMAP stands for High-quality Automated and Manual Annotation of microbial Proteomes, HAMAP profiles are manually created by expert curators they identify proteins that are part of well-conserved bacterial, archaeal and plastid-encoded proteins families or subfamilies. PANTHER is a collection of protein families that have been subdivided into functionally related subfamilies. Hidden Markov models are built for each family and subfamily for classifying additional protein sequences, Pfam is a large collection of multiple sequence alignments and hidden Markov models covering many common protein domains and families. The primary PIRSF classification unit is the family, whose members are both homologous and homeomorphic. PRINTS is a compendium of protein fingerprints, a fingerprint is a group of conserved motifs used to characterise a protein family, its diagnostic power is refined by iterative scanning of UniProt. Usually the motifs do not overlap, but are separated along a sequence, ProDom domain database consists of an automatic compilation of homologous domains. Current versions of ProDom are built using a procedure based on recursive PSI-BLAST searches
3.
Protein Data Bank
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The Protein Data Bank is a crystallographic database for the three-dimensional structural data of large biological molecules, such as proteins and nucleic acids. The PDB is overseen by a called the Worldwide Protein Data Bank. The PDB is a key resource in areas of structural biology, most major scientific journals, and some funding agencies, now require scientists to submit their structure data to the PDB. Many other databases use protein structures deposited in the PDB, for example, SCOP and CATH classify protein structures, while PDBsum provides a graphic overview of PDB entries using information from other sources, such as Gene ontology. By 1971, one of Meyers programs, SEARCH, enabled researchers to access information from the database to study protein structures offline. SEARCH was instrumental in enabling networking, thus marking the beginning of the PDB. Upon Hamiltons death in 1973, Tom Koeztle took over direction of the PDB for the subsequent 20 years, in January 1994, Joel Sussman of Israels Weizmann Institute of Science was appointed head of the PDB. In October 1998, the PDB was transferred to the Research Collaboratory for Structural Bioinformatics, the new director was Helen M. Berman of Rutgers University. In 2003, with the formation of the wwPDB, the PDB became an international organization, the founding members are PDBe, RCSB, and PDBj. Each of the four members of wwPDB can act as deposition, data processing, the data processing refers to the fact that wwPDB staff review and annotate each submitted entry. The data are automatically checked for plausibility. The PDB database is updated weekly, likewise, the PDB holdings list is also updated weekly. As of 14 March 2017, the breakdown of current holdings is as follows,103,514 structures in the PDB have a structure factor file,9,057 structures have an NMR restraint file. 2,826 structures in the PDB have a chemical shifts file, therefore, the final conformation of the protein is obtained, in the latter case, by solving a distance geometry problem. A few proteins are determined by cryo-electron microscopy, the significance of the structure factor files, mentioned above, is that, for PDB structures determined by X-ray diffraction that have a structure file, the electron density map may be viewed. The data of such structures is stored on the electron density server, however, since 2007, the rate of accumulation of new protein structures appears to have plateaued. The file format used by the PDB was called the PDB file format. This original format was restricted by the width of computer punch cards to 80 characters per line, around 1996, the macromolecular Crystallographic Information file format, mmCIF, which is an extension of the CIF format started to be phased in
4.
Neuraminidase
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Neuraminidase enzymes are glycoside hydrolase enzymes that cleave the glycosidic linkages of neuraminic acids. Neuraminidase enzymes are a family, found in a range of organisms. The best-known neuraminidase is the viral neuraminidase, a target for the prevention of the spread of influenza infection. The viral neuraminidases are frequently used as antigenic determinants found on the surface of the influenza virus, some variants of the influenza neuraminidase confer more virulence to the virus than others. Other homologues are found in cells, which have a range of functions. At least four mammalian sialidase homologues have been described in the human genome, sialidase activities include assistance in the mobility of virus particles through the respiratory tract mucus and in the elution of virion progeny from the infected cell. Swiss-Prot lists 137 types of neuraminidase from various species as of October 18,2006, nine subtypes of influenza neuraminidase are known, many occur only in various species of duck and chicken. Subtypes N1 and N2 have been linked to epidemics in man. It has a head consisting of four co-planar and roughly spherical subunits, and it comprises a single polypeptide chain that is oriented in the opposite direction to the hemagglutinin antigen. The composition of the polypeptide is a chain of six conserved polar amino acids, followed by hydrophilic. β-Sheets predominate as the level of protein conformation. The enzymatic mechanism of influenza virus sialidase has been studied by Taylor et al. shown in Figure 1, the enzyme catalysis process has four steps. The first step involves the distortion of the α-sialoside from a 2C5 chair conformation to a pseudoboat conformation when the sialoside binds to the sialidase, the second step leads to an oxocarbocation intermediate, the sialosyl cation. The third step is the formation of Neu5Ac initially as the α-anomer, there are two major proteins on the surface of influenza virus particles. One is the lectin haemagglutinin protein with three relatively shallow sialic acid-binding sites and the other is enzyme sialidase with the site in a pocket. After the X-ray crystal structures of several influenza virus sialidases were available, the unsaturated sialic acid derivative 2-deoxy-2, 3-didehydro-D-N-acetylneuraminic acid, a sialosyl cation transition-state analogue, is believed the most potent inhibitor core template. Structurally modified Neu5Ac2en derivatives may give more effective inhibitors, many Neu5Ac2en-based compounds have been synthesized and tested for their influenza virus sialidase inhibitory potential. A series of amide-linked C9 modified Neu5Ac2en have been reported by Megesh, glycoside hydrolase Neuraminidase inhibitors Neuraminidase at the US National Library of Medicine Medical Subject Headings Orthomyxoviruses, Robert B
5.
Enzyme
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Enzymes /ˈɛnzaɪmz/ are macromolecular biological catalysts. Enzymes accelerate, or catalyze, chemical reactions, the molecules at the beginning of the process upon which enzymes may act are called substrates and the enzyme converts these into different molecules, called products. Almost all metabolic processes in the cell need enzymes in order to occur at rates fast enough to sustain life, the set of enzymes made in a cell determines which metabolic pathways occur in that cell. The study of enzymes is called enzymology, enzymes are known to catalyze more than 5,000 biochemical reaction types. Most enzymes are proteins, although a few are catalytic RNA molecules, enzymes specificity comes from their unique three-dimensional structures. Like all catalysts, enzymes increase the rate of a reaction by lowering its activation energy, some enzymes can make their conversion of substrate to product occur many millions of times faster. An extreme example is orotidine 5-phosphate decarboxylase, which allows a reaction that would take millions of years to occur in milliseconds. Chemically, enzymes are like any catalyst and are not consumed in chemical reactions, enzymes differ from most other catalysts by being much more specific. Enzyme activity can be affected by other molecules, inhibitors are molecules that decrease enzyme activity, many drugs and poisons are enzyme inhibitors. An enzymes activity decreases markedly outside its optimal temperature and pH, some enzymes are used commercially, for example, in the synthesis of antibiotics. French chemist Anselme Payen was the first to discover an enzyme, diastase and he wrote that alcoholic fermentation is an act correlated with the life and organization of the yeast cells, not with the death or putrefaction of the cells. In 1877, German physiologist Wilhelm Kühne first used the term enzyme, the word enzyme was used later to refer to nonliving substances such as pepsin, and the word ferment was used to refer to chemical activity produced by living organisms. Eduard Buchner submitted his first paper on the study of yeast extracts in 1897, in a series of experiments at the University of Berlin, he found that sugar was fermented by yeast extracts even when there were no living yeast cells in the mixture. He named the enzyme that brought about the fermentation of sucrose zymase, in 1907, he received the Nobel Prize in Chemistry for his discovery of cell-free fermentation. Following Buchners example, enzymes are usually named according to the reaction they carry out, the biochemical identity of enzymes was still unknown in the early 1900s. Sumner showed that the enzyme urease was a protein and crystallized it. These three scientists were awarded the 1946 Nobel Prize in Chemistry, the discovery that enzymes could be crystallized eventually allowed their structures to be solved by x-ray crystallography. This high-resolution structure of lysozyme marked the beginning of the field of structural biology, an enzymes name is often derived from its substrate or the chemical reaction it catalyzes, with the word ending in -ase
6.
Sialic acid
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Sialic acid is a generic term for the N- or O-substituted derivatives of neuraminic acid, a monosaccharide with a nine-carbon backbone. It is also the name for the most common member of this group, Sialic acids are found widely distributed in animal tissues and to a lesser extent in other organisms, ranging from plants and fungi to yeasts and bacteria, mostly in glycoproteins and gangliosides. That is because it seems to have appeared late in evolution, however, it has been observed in Drosophila embryos and other insects and in the capsular polysaccharides of certain strains of bacteria. In humans the brain has the highest sialic acid concentration, where these acids play an important role in neural transmission, in general, the amino group bears either an acetyl or a glycolyl group, but other modifications have been described. The hydroxyl substituents may vary considerably, acetyl, lactyl, methyl, sulfate, the term sialic acid was first introduced by Swedish biochemist Gunnar Blix in 1952. The sialic acid family includes 43 derivatives of the nine-carbon sugar neuraminic acid, the numbering of the sialic acid structure begins at the carboxylate carbon and continues around the chain. The configuration that places the carboxylate in the position is the alpha-anomer. The alpha-anomer is the form that is found when sialic acid is bound to glycans, however, in solution, it is mainly in the beta-anomeric form. Sialic acid is synthesized by glucosamine 6 phosphate and acetyl CoA through a transferase and this becomes N-acetylmannosamine-6-P through epimerization, which reacts with phosphoenolpyruvate producing N-acetylneuraminic-9-P. This compound is synthesized in the nucleus of the animal cell, in bacterial systems, sialic acids are biosynthesized by an aldolase enzyme. The enzyme uses a derivative as a substrate, inserting three carbons from pyruvate into the resulting sialic acid structure. These enzymes can be used for synthesis of sialic acid derivatives. Sialic acid-rich glycoproteins bind selectin in humans and other organisms, metastatic cancer cells often express a high density of sialic acid-rich glycoproteins. This overexpression of sialic acid on surfaces creates a charge on cell membranes. This creates repulsion between cells and helps these late-stage cancer cells enter the blood stream, many bacteria also use sialic acid in their biology, although this is usually limited to bacteria that live in association with higher animals. Many of these incorporate sialic acid into cell surface features like their lipopolysaccharide and capsule, other bacteria simply use sialic acid as a good nutrient source, as it contains both carbon and nitrogen and can be converted to fructose-6-phosphate, which can then enter central metabolism. Sialic acid-rich oligosaccharides on the glycoconjugates found on surface membranes help keep water at the surface of cells, the sialic acid-rich regions contribute to creating a negative charge on the cells surfaces. Since water is a molecule with partial positive charges on both hydrogen atoms, it is attracted to cell surfaces and membranes
7.
Glycoprotein
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Glycoproteins are proteins that contain oligosaccharide chains covalently attached to polypeptide side-chains. The carbohydrate is attached to the protein in a cotranslational or posttranslational modification and this process is known as glycosylation. Secreted extracellular proteins are often glycosylated, in proteins that have segments extending extracellularly, the extracellular segments are also often glycosylated. Glycoproteins are also often important integral membrane proteins, where they play a role in cell–cell interactions and it is important to distinguish endoplasmic reticulum-based glycosylation of the secretory system without reversible cytosolic-nuclear glycosylation. In contrast, classical secretory glycosylation can be structurally essential, for example, inhibition of asparagine-linked, i. e. N-linked, glycosylation can prevent glycoprotein folding and full inhibition can be toxic to an individual cell. In contrast, perturbation of terminal processing, which occurs in the Golgi apparatus, is dispensable for isolated cells but can lead to human disease, a famous example of this latter effect is the ABO blood system. There are several types of glycosylation, although the first two are the most common, in N-glycosylation, sugars are attached to nitrogen, typically on the amide side-chain of asparagine. In O-glycosylation, sugars are attached to oxygen, typically on serine or threonine, in P-glycosylation, sugars are attached to phosphorus on a phosphoserine. In C-glycosylation, sugars are attached directly to carbon, such as in the addition of mannose to tryptophan, in glypiation, a GPI glycolipid is attached to the C-terminus of a polypeptide, serving as a membrane anchor. Monosaccharides commonly found in eukaryotic glycoproteins include, The sugar group can assist in protein folding or improve proteins stability, one example of glycoproteins found in the body is mucins, which are secreted in the mucus of the respiratory and digestive tracts. The sugars when attached to give them considerable water-holding capacity. Glycoproteins are important for blood cell recognition, especially in mammals. Examples of glycoproteins in the system are, molecules such as antibodies. Molecules of the major histocompatibility complex, which are expressed on the surface of cells, sialyl Lewis X antigen on the surface of leukocytes. H antigen of the ABO blood compatibility antigens, other examples of glycoproteins include, glycoprotein IIb/IIIa, an integrin found on platelets that is required for normal platelet aggregation and adherence to the endothelium. Components of the zona pellucida, which surrounds the oocyte, and is important for sperm-egg interaction, structural glycoproteins, which occur in connective tissue. These help bind together the fibers, cells, and ground substance of connective tissue and they may also help components of the tissue bind to inorganic substances, such as calcium in bone. Glycoprotein-41 and glycoprotein-120 are HIV viral coat proteins, soluble glycoproteins often show a high viscosity, for example, in egg white and blood plasma
8.
Hemagglutinin (influenza)
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Influenza hemagglutinin or haemagglutinin is a glycoprotein found on the surface of influenza viruses. It is responsible for binding the virus to cells with sialic acid on the membranes and it is also responsible for the fusion of the viral envelope with the endosome membrane, after the pH has been reduced. The name hemagglutinin comes from the ability to cause red blood cells to clump together in vitro. HA has at least 18 different antigens and these subtypes are named H1 through H18. H16 was discovered in 2004 on influenza A viruses isolated from black-headed gulls from Sweden, h17 was discovered in 2012 in fruit bats. Most recently, H18 was discovered in a Peruvian bat in 2013, the first three hemagglutinins, H1, H2, and H3, are found in human influenza viruses. Viral neuraminidase is another protein found on the surface of influenza, influenza viruses are characterized by the type of HA and NA that they carry, hence H1N1, H5N2 etc. A highly pathogenic avian flu virus of H5N1 type has been found to infect humans at a low rate and this finding seems to explain how an H5N1 virus that normally does not infect humans can mutate and become able to efficiently infect human cells. The hemagglutinin of the H5N1 virus has been associated with the high pathogenicity of this flu virus strain, firstly, it allows the recognition of target vertebrate cells, accomplished through the binding to these cells sialic acid-containing receptors. Secondly, once bound it facilitates the entry of the genome into the target cells by causing the fusion of host endosomal membrane with the viral membrane. HA binds to the sialic acid which is present on the surface of its target cells. The cell then attempts to begin digesting the contents of the endosome by acidifying its interior, however, as soon as the pH within the endosome drops to about 6. This so-called fusion peptide acts like a grappling hook by inserting itself into the endosomal membrane. Once this has happened, the contents of the virus, including its RNA genome, are free to pour out into the cells cytoplasm, HA is a homotrimeric integral membrane glycoprotein. It is shaped like a cylinder, and is approximately 13.5 nanometres long, the three identical monomers that constitute HA are constructed into a central α helix coil, three spherical heads contain the sialic acid binding sites. HA monomers are synthesized as precursors that are glycosylated and cleaved into two smaller polypeptides, the HA1 and HA2 subunits. Each HA monomer consists of a long, helical chain anchored in the membrane by HA2, since hemagglutinin is the major surface protein of the influenza A virus and is essential to the entry process, it is the primary target of neutralizing antibodies. This is because these antibodies bind near the top of the hemagglutinin head, in contrast, some antibodies have been found to have no effect on attachment
9.
Neuraminidase inhibitor
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Neuraminidase inhibitors are a class of drugs which block the neuraminidase enzyme. They are commonly used as antiviral drugs because they block the function of viral neuraminidases of the influenza virus, Oseltamivir a prodrug, Zanamivir, Laninamivir, and Peramivir belong to this class. Unlike the M2 inhibitors, which work only against the influenza A, the neuraminidase inhibitors oseltamivir and zanamivir were approved in the US and Europe for treatment and prevention of influenza A and B. Peramivir acts by binding to the neuraminidase of the influenza viruses. However, Laninamivir in the cells is slowly released into the respiratory tract, thus the mechanism of the long-lasting activity of laninamivir is basically different from that of Peramivir. The efficacy was highly debated in recent years, however, after the pandemic caused by H1N1 in 2009, the effectiveness of early treatment with neuraminidase inhibitors in reducing serious cases and deaths was reported in various countries. Common side effects include nausea and vomiting, the abnormal behaviours of children after taking oseltamivir that have been reported may be an extension of delirium or hallucinations caused by influenza. It occurs in the stages of the illness, such as within 48 hours after onset of the illness. Therefore, children with influenza are advised to be observed by their parents until 48 hours after the onset of the illness, regardless of whether the child is treated with NAIs. Laninamivir Oseltamivir Peramivir Zanamivir Cyanidin-3-sambubioside Coptisine Berberine Discovery and development of Neuraminidase Inhibitors
10.
Hemagglutinin-neuraminidase
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Hemagglutinin-neuraminidase refers to a single viral protein that has both hemagglutinin and neuraminidase activity. This is in contrast to the found in influenza, where both functions exist but in two separate proteins. However it does show a similarity to influenza viral neuraminidase and has a six-bladed beta-propeller structure. Hemagglutinin-neuraminidase allows the virus to stick to a potential host cell, hemagglutinin-neuraminidase can be found in a variety of paramyxoviruses including Mumps virus, Human parainfluenza virus 3, and the avian pathogen Newcastle disease virus
11.
Hemagglutinin
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Hemagglutinin or haemagglutinin refers to a substance that causes red blood cells to agglutinate. This process is called hemagglutination or haemagglutination, antibodies and lectins are commonly known hemagglutinins. The bedside card method of blood grouping relies on visual agglutination to determine an individuals blood group, the card has dried blood group antibody reagents fixed onto its surface and a drop of the individuals blood is placed on each area on the card. The presence or absence of visual agglutination enables a quick and convenient method of determining the ABO, agglutination of red blood cells is used in the Coombs test. Cold agglutinin disease Hemagglutination assay Phytohaemagglutinins, hemagglutinins produced by plants Hemagglutinin
12.
Zanamivir
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Zanamivir is a medication used to treat and prevent influenza caused by influenza A and B viruses. It is an inhibitor and was developed by the Australian biotech firm Biota Holdings. It was licensed to Glaxo in 1990 and approved in the US in 1999, in 2006, it was approved for prevention of influenza A and B. Zanamivir was the first neuraminidase inhibitor commercially developed and it is currently marketed by GlaxoSmithKline under the trade name Relenza as a powder for oral inhalation. Zanamivir is used for the treatment of infections caused by influenza A and influenza B viruses and it decreases the risk of ones getting symptomatic, but not asymptomatic influenza. As of 2009, no influenza has shown any signs of resistance in the US, since then, genes expressing resistance to zanamivir were found in Chinese people infected with avian influenza A H7N9 during treatment with zanamivir. In otherwise-healthy individuals, benefits overall appear to be small, zanamivir shortens the duration of symptoms of influenza-like illness by less than a day. In children with asthma there was no effect on the time to first alleviation of symptoms. Whether it affects the risk of ones need to be hospitalized or the risk of death is not clear, there is no proof that zanamivir reduced hospitalizations or pneumonia and other complications of influenza, such as bronchitis, middle ear infection, and sinusitis. Zanamivir did not reduce the risk of self reported investigator mediated pneumonia or radiologically confirmed pneumonia in adults, the effect on pneumonia in children was also not significant. Low to moderate evidence indicates it decreases the risk of ones getting influenza by 1% to 12% in those exposed, also there was no evidence of reduction of risk of person-to-person spread of the influenza virus. The evidence for a benefit in preventing influenza is weak in children, as of 2009, no influenza had shown any signs of resistance in the US. A meta-analysis from 2011 found that zanamivir resistance had been rarely reported, antiviral resistance can emerge during or after treatment with antivirals in certain people. In 2013 genes expressing resistance to zanamivir were found in Chinese patients infected with avian influenza A H7N9, dosing is limited to the inhalation route. This restricts its usage, as treating asthmatics could induce bronchospasms, in 2006 the Food and Drug Administration found that breathing problems, including deaths, were reported in some patients after the initial approval of Relenza. Most of these patients had asthma or chronic obstructive pulmonary disease, Relenza therefore was not recommended for treatment or prophylaxis of seasonal influenza in individuals with asthma or chronic obstructive pulmonary disease. In 2009 the zanamivir package insert contains precautionary information regarding risk of bronchospasm in patients with respiratory disease, in adults there was no increased risk of reported adverse events in trials. There was little evidence of the harms associated with the treatment of children with zanamivir
13.
Peramivir
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Peramivir is an antiviral drug developed by BioCryst Pharmaceuticals for the treatment of influenza. Peramivir is an inhibitor, acting as a transition-state analogue inhibitor of influenza neuraminidase. It is approved for intravenous administration, in October 2009, the U. S. Food and Drug Administration issued an emergency use authorization for the use of peramivir based on safety data from phase I, phase II, and limited phase III trial data. The emergency use authorization for peramivir expired in June 2010, on 19 December 2014, the FDA approved peramivir to treat influenza infection in adults. Peramivir has also approved in Japan and South Korea and is available in Japan as Rapiacta. As of 2015, it is the only option for treating swine flu. In October 2009, it was reported that the antiviral drug peramivir had been life-saving effective in intravenous treating 8 serious cases of swine flu. The U. S. government gave BioCryst Pharmaceuticals more than $77 million to finish the Phase III clinical development of peramivir, in 2009 the department of Health and Human Services had already given about $180 million to the program. Biocryst also donated 1200 courses of treatment to the US department of Health, the Emergency Use Authorization expired on June 23,2010. The difference between peramivir and control group for the endpoint, clinical or virologic, was small. But a H274Y virus mutation showed resistance to oseltamivir and peramivir, but not to zanamivir, ultimately 3. 2% of Apdm09 viruses collected between 2009 and 2012 had highly reduced peramivir inhibition due to the H275Y NA mutation. BioCryst Pharmaceuticals submitted a new application to the U. S. Food. Peramivir was approved for administration in Dec 2014. FDA Approval for Peramivir Peramivir, Requirements for Administration under EUA BioCryst Pharmaceuticals, Inc
14.
Influenza A virus subtype H5N1
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Influenza A virus subtype H5N1, also known as A or simply H5N1, is a subtype of the influenza A virus which can cause illness in humans and many other animal species. It is enzootic in many populations, especially in Southeast Asia. One strain of HPAI A is spreading globally after first appearing in Asia and it is epizootic and panzootic, killing tens of millions of birds and spurring the culling of hundreds of millions of others to stem its spread. Many references to bird flu and H5N1 in the popular media refer to this strain, eleven outbreaks of H5N1 were reported worldwide in June 2008 in five countries compared to 65 outbreaks in June 2006 and 55 in June 2007. In July 2013 the WHO announced a total of 630 confirmed human cases which resulted in the deaths of 375 people since 2003. Several H5N1 vaccines have been developed and approved, and stockpiled by a number of countries, including the United States, Britain, France, Canada, HPAI A is considered an avian disease, although there is some evidence of limited human-to-human transmission of the virus. A risk factor for contracting the virus is handling of infected poultry and he called for adequate resources to fight what he sees as a major world threat to possibly billions of lives. Experts have identified key events marking the progression of a flu virus towards becoming pandemic. H5N1 may cause more than one influenza pandemic, as it is expected to continue mutating in birds regardless of whether humans develop herd immunity to a pandemic strain. Influenza pandemics from its genetic offspring may include influenza A virus subtypes other than H5N1, the severity of the infection depends in large part on the state of the infected persons immune systems and whether they had been exposed to the strain before. No one knows if these or other symptoms will be the symptoms of a humanized H5N1 flu, the avian influenza hemagglutinin binds alpha 2-3 sialic acid receptors, while human influenza hemagglutinins bind alpha 2-6 sialic acid receptors. This means when the H5N1 strain infects humans, it will replicate in the respiratory tract. There is as yet no human form of H5N1, so all humans who have caught it so far have caught avian H5N1. The reported mortality rate of highly pathogenic H5N1 avian influenza in a human is high, WHO data indicate 60% of cases classified as H5N1 resulted in death. However, there is evidence the actual mortality rate of avian flu could be much lower. In one case, a boy with H5N1 experienced diarrhea followed rapidly by a coma without developing respiratory or flu-like symptoms, there have been studies of the levels of cytokines in humans infected by the H5N1 flu virus. Of particular concern is elevated levels of tumor necrosis factor-alpha, an associated with tissue destruction at sites of infection. Flu virus-induced increases in the level of cytokines is also associated with flu symptoms, including fever, chills, vomiting, tissue damage associated with pathogenic flu virus infection can ultimately result in death
15.
Amino acid
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Amino acids are organic compounds containing amine and carboxyl functional groups, along with a side chain specific to each amino acid. The key elements of an acid are carbon, hydrogen, oxygen. About 500 amino acids are known and can be classified in many ways, in the form of proteins, amino acids comprise the second-largest component of human muscles, cells and other tissues. Outside proteins, amino acids perform critical roles in such as neurotransmitter transport. In biochemistry, amino acids having both the amine and the acid groups attached to the first carbon atom have particular importance. They are known as 2-, alpha-, or α-amino acids and they include the 22 proteinogenic amino acids, which combine into peptide chains to form the building-blocks of a vast array of proteins. These are all L-stereoisomers, although a few D-amino acids occur in bacterial envelopes, as a neuromodulator, twenty of the proteinogenic amino acids are encoded directly by triplet codons in the genetic code and are known as standard amino acids. The other two are selenocysteine, and pyrrolysine, pyrrolysine and selenocysteine are encoded via variant codons, for example, selenocysteine is encoded by stop codon and SECIS element. N-formylmethionine is generally considered as a form of methionine rather than as a separate proteinogenic amino acid, codon–tRNA combinations not found in nature can also be used to expand the genetic code and create novel proteins known as alloproteins incorporating non-proteinogenic amino acids. Many important proteinogenic and non-proteinogenic amino acids also play critical roles within the body. Nine proteinogenic amino acids are called essential for humans because they cannot be created from other compounds by the human body, others may be conditionally essential for certain ages or medical conditions. Essential amino acids may also differ between species, because of their biological significance, amino acids are important in nutrition and are commonly used in nutritional supplements, fertilizers, and food technology. Industrial uses include the production of drugs, biodegradable plastics, the first few amino acids were discovered in the early 19th century. In 1806, French chemists Louis-Nicolas Vauquelin and Pierre Jean Robiquet isolated a compound in asparagus that was subsequently named asparagine, cystine was discovered in 1810, although its monomer, cysteine, remained undiscovered until 1884. Glycine and leucine were discovered in 1820, usage of the term amino acid in the English language is from 1898. Proteins were found to yield amino acids after enzymatic digestion or acid hydrolysis, in the structure shown at the top of the page, R represents a side chain specific to each amino acid. The carbon atom next to the group is called the α–carbon. Amino acids containing an amino group bonded directly to the alpha carbon are referred to as amino acids
16.
Glycoside hydrolase
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Glycoside hydrolases assist in the hydrolysis of glycosidic bonds in complex sugars. Together with glycosyltransferases, glycosidases form the catalytic machinery for the synthesis. Glycoside hydrolases are found in all domains of life. In prokaryotes, they are both as intracellular and extracellular enzymes that are largely involved in nutrient acquisition. One of the important occurrences of glycoside hydrolases in bacteria is the enzyme beta-galactosidase, deficiency in specific lysosomal glycoside hydrolases can lead to a range of lysosomal storage disorders that result in developmental problems or death. Glycoside hydrolases are found in the tract and in saliva where they degrade complex carbohydrates such as lactose, starch. In the gut they are found as glycosylphosphatidyl anchored enzymes on endothelial cells, the enzyme O-GlcNAcase is involved in removal of N-acetylglucosamine groups from serine and threonine residues in the cytoplasm and nucleus of the cell. The glycoside hydrolases are involved in the biosynthesis and degradation of glycogen in the body, glycoside hydrolases are classified into EC3.2.1 as enzymes catalyzing the hydrolysis of O- or S-glycosides. Glycoside hydrolases can also be classified according to the outcome of the hydrolysis reaction. Glycoside hydrolases can also be classified as exo or endo acting, dependent upon whether they act at the end or in the middle, respectively, glycoside hydrolases may also be classified by sequence or structure based methods. Sequence-based classifications are among the most powerful method for suggesting function for newly sequenced enzymes for which function has not been biochemically demonstrated. A classification system for glycosyl hydrolases, based on similarity, has led to the definition of more than 100 different families. This classification is available on the CAZy web site, the database provides a series of regularly updated sequence based classification that allow reliable prediction of mechanism, active site residues and possible substrates. The online database is supported by CAZypedia, an encyclopedia of carbohydrate active enzymes. Based on three-dimensional structural similarities, the families have been classified into clans of related structure. Recent progress in glycosidase sequence analysis and 3D structure comparison has allowed the proposal of a hierarchical classification of the glycoside hydrolases. Again, two residues are involved, which are usually enzyme-borne carboxylates, one acts as a nucleophile and the other as an acid/base. In the first step the nucleophile attacks the centre, resulting in the formation of a glycosyl enzyme intermediate
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H5N1 genetic structure
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H5N1 genetic structure is the molecular structure of the H5N1 viruss RNA. H5N1 is an Influenza A virus subtype, experts believe it might mutate into a form that transmits easily from person to person. If such a mutation occurs, it remain an H5N1 subtype or could shift subtypes as did H2N2 when it evolved into the Hong Kong Flu strain of H3N2. H5N1 has mutated through antigenic drift into dozens of highly pathogenic varieties, genotype Z emerged through reassortment in 2002 from earlier highly pathogenic genotypes of H5N1 that first appeared in China in 1996 in birds and in Hong Kong in 1997 in humans. The H5N1 viruses from human infections and the closely related avian viruses isolated in 2004 and 2005 belong to a single genotype and this infection of humans coincided with an epizootic of H5N1 influenza in Hong Kong’s poultry population. This panzootic outbreak was stopped by the killing of the entire domestic poultry population within the territory, the name H5N1 refers to the subtypes of surface antigens present on the virus, hemagglutinin type 5 and neuraminidase type 1. Genotype Z of H5N1 is now the dominant genotype of H5N1, genotype Z is endemic in birds in southeast Asia and represents a long term pandemic threat. Influenza A viruses have 11 genes on eight separate RNA molecules, PB2 PB1 PB1-F2 PA HA NP NA M1 and M2 NS1 NEP/NS2 Two of the most important RNA molecules are HA, HA creates a surface antigen that is especially important in transmissibility. PB1 creates a viral polymerase molecule that is important in virulence. Hemagglutinin forms spikes at the surface of flu viruses that function to attach viruses to cells and this attachment is required for efficient transfer of flu virus genes into cells, a process that can be blocked by antibodies that bind to the hemagglutinin proteins. Swine influenza viruses have the ability to both types of sialic acid receptors. Humans have avian-type receptors at low densities and chickens have human-type receptors at very low densities. These are the types of mutations that can change a bird flu virus into a flu pandemic virus, one in five were lethal to mice at low doses. Both the viruses from the 1957 pandemic and 1968 pandemic carried an avian flu virus PB1 gene, the authors suggest that picking up an avian flu virus PB1 gene may be a critical step in a potential flu pandemic virus arising through reassortment. PB1 codes for the PB1 protein and the PB1-F2 protein, the PB1 protein is a critical component of the viral polymerase. PB1-F2 likely contributes to viral pathogenicity and might have an important role in determining the severity of pandemic influenza and this was discovered by Chen et al. and reported in Nature. After comparing viruses from the Hong Kong 1997 H5N1 outbreak, one amino acid change was found in the PB1-F2 sequence at position 66 that correlated with pathogenicity and this same amino acid change was also found in the PB1-F2 protein of the 1918 pandemic A/Brevig Mission/18 virus. The Orthomyxovirus family consists of 5 genera, Influenzavirus A, Influenzavirus B, Influenzavirus C, Isavirus, the RNA viruses include the negative-sense ssRNA viruses which include the Family Orthomyxoviridae which contains five genera, classified by variations in nucleoprotein antigens
18.
Antigenic shift
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The term is often applied specifically to influenza, as that is the best-known example, but the process is also known to occur with other viruses, such as visna virus in sheep. Antigenic shift is a case of reassortment or viral shift that confers a phenotypic change. Antigenic shift is contrasted with antigenic drift, which is the natural mutation over time of strains of influenza which may lead to a loss of immunity. Antigenic drift occurs in all types of influenza including influenzavirus A, influenza B, antigenic shift, however, occurs only in influenzavirus A because it infects more than just humans. Affected species include mammals and birds, giving influenza A the opportunity for a major reorganization of surface antigens. Influenza B and C principally infect humans, minimizing the chance that a reassortment will change its phenotype drastically, antigenic shift is important for the emergence of new viral pathogens as it is a pathway that viruses may follow to enter a new niche. It could occur with primate viruses and may be a factor for the appearance of new viruses in the species such as HIV. Influenza A viruses are found in different animals, including ducks, chickens, pigs, humans, whales, horses. Influenza B viruses circulate widely principally among humans, though it has recently found in seals. Flu strains are named after their types of hemagglutinin and neuraminidase surface proteins, so they will be called, for example, H3N2 for type-3 hemagglutinin, some strains of avian influenza can infect pigs or other mammalian hosts. When two different strains of influenza infect the same cell simultaneously, their protein capsids and lipid envelopes are removed, exposing their RNA, the host cell then forms new viruses that combine their antigens, for example, H3N2 and H5N1 can form H5N2 this way. Because the human immune system has difficulty recognizing the new strain, it may be highly dangerous. Influenza viruses which have undergone antigenic shift have caused the Asian Flu pandemic of 1957, the Hong Kong Flu pandemic of 1968, the most recent 2009 H1N1 outbreak was a result of antigenic shift and reassortment between human, avian, and swine viruses. One increasingly worrying situation is the possible antigenic shift between avian influenza and human influenza and this antigenic shift could cause the formation of a highly virulent virus. Antigenic shift occurs because the genome of the virus is segmented, a mnemonic to remember segmented viruses is BOAR, Bunyaviridae, Orthomyxoviridae, Arenavirus and Reoviridae. This is most striking when one considers that the coevolution of prokaryotes and viruses in the environment has been going on since before eukaryotes appeared on earth. 1918 flu pandemic Coinfection Superinfection Viral Shift Bouvier, Nicole M. Palese, Peter
19.
Influenza research
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Influenza research involves investigating molecular virology, pathogenesis, host immune responses, genomics, and epidemiology regarding influenza. The main goal of research is to develop influenza countermeasures such as vaccines, therapies, improved influenza countermeasures require basic research on how viruses enter cells, replicate, mutate, evolve into new strains and induce an immune response. Solutions to limitations in current vaccine methods are being researched, before 2004, all previous highly pathogenic avian flu virus strains circulated only among domesticated poultry and by culling all of them in the area, the strains were made extinct. Previous HPAI strains only existed in domesticated birds and this current HPAI H5N1 strain has turned out to be different. In October 2004 researchers discovered H5N1 is far more dangerous than previously believed because waterfowl, from this point on, avian flu experts increasingly referred to containment as a strategy that can delay but not prevent a future avian flu pandemic. Nonetheless, there is still hope it will mutate into some low pathogenic strain over time, but as time has gone on, the hope has come to look less and less likely. The result is that billions of dollars every year are going to be needed in expenditures that would not be required if it did go away, poultry farming is especially hard hit. How to best spend pandemic mitigation funds and poultry farming protection funds is a question that to be answered requires billions in flu research and new flu vaccine manufacturing factories. Since avian flu is not going away as was hoped, more data is needed to figure out how best to cope.8 billion pandemic preparedness bill passed in 2005. The federal government says its goal is to be able to distribute a vaccine to every American within six months of a pandemic, currently, flu vaccines are produced in specialized chicken eggs, but that technique does not allow for speedy mass vaccinations. ABC News reported on April 1,2006 that Beginning in late 1997, to address the H9N2 threat, NIAID contracted with Chiron Corporation to produce investigational batches of an inactivated vaccine, which will be evaluated clinically by NIAID early next year. Development and evaluation of a combination antiviral regimen against these potential pandemic influenza strains are now under way. A vaccine probably would not be available in the stages of population infection. Once a potential virus is identified, it takes at least several months before a vaccine becomes widely available. The capability to produce vaccines varies widely from country to country, in fact, distribution to and inside countries would probably be problematic. Several countries, however, have well-developed plans for producing large quantities of vaccine, for example, Canadian health authorities say that they are developing the capacity to produce 32 million doses within four months, enough vaccine to inoculate every person in the country. There are two technical problems associated with the development of a vaccine against H5N1. Trials using adjuvants such as alum or MF59 to try and lower the dose of vaccine are urgently needed
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PubMed Identifier
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PubMed is a free search engine accessing primarily the MEDLINE database of references and abstracts on life sciences and biomedical topics. The United States National Library of Medicine at the National Institutes of Health maintains the database as part of the Entrez system of information retrieval, from 1971 to 1997, MEDLINE online access to the MEDLARS Online computerized database primarily had been through institutional facilities, such as university libraries. PubMed, first released in January 1996, ushered in the era of private, free, home-, the PubMed system was offered free to the public in June 1997, when MEDLINE searches via the Web were demonstrated, in a ceremony, by Vice President Al Gore. Information about the journals indexed in MEDLINE, and available through PubMed, is found in the NLM Catalog. As of 5 January 2017, PubMed has more than 26.8 million records going back to 1966, selectively to the year 1865, and very selectively to 1809, about 500,000 new records are added each year. As of the date,13.1 million of PubMeds records are listed with their abstracts. In 2016, NLM changed the system so that publishers will be able to directly correct typos. Simple searches on PubMed can be carried out by entering key aspects of a subject into PubMeds search window, when a journal article is indexed, numerous article parameters are extracted and stored as structured information. Such parameters are, Article Type, Secondary identifiers, Language, publication type parameter enables many special features. As these clinical girish can generate small sets of robust studies with considerable precision, since July 2005, the MEDLINE article indexing process extracts important identifiers from the article abstract and puts those in a field called Secondary Identifier. The secondary identifier field is to store numbers to various databases of molecular sequence data, gene expression or chemical compounds. For clinical trials, PubMed extracts trial IDs for the two largest trial registries, ClinicalTrials. gov and the International Standard Randomized Controlled Trial Number Register, a reference which is judged particularly relevant can be marked and related articles can be identified. If relevant, several studies can be selected and related articles to all of them can be generated using the Find related data option, the related articles are then listed in order of relatedness. To create these lists of related articles, PubMed compares words from the title and abstract of each citation, as well as the MeSH headings assigned, using a powerful word-weighted algorithm. The related articles function has been judged to be so precise that some researchers suggest it can be used instead of a full search, a strong feature of PubMed is its ability to automatically link to MeSH terms and subheadings. Examples would be, bad breath links to halitosis, heart attack to myocardial infarction, where appropriate, these MeSH terms are automatically expanded, that is, include more specific terms. Terms like nursing are automatically linked to Nursing or Nursing and this important feature makes PubMed searches automatically more sensitive and avoids false-negative hits by compensating for the diversity of medical terminology. The My NCBI area can be accessed from any computer with web-access, an earlier version of My NCBI was called PubMed Cubby
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Science (journal)
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Science, also widely referred to as Science Magazine, is the peer-reviewed academic journal of the American Association for the Advancement of Science and one of the worlds top academic journals. It was first published in 1880, is circulated weekly and has a print subscriber base of around 130,000. Because institutional subscriptions and online access serve an audience, its estimated readership is 570,400 people. Unlike most scientific journals, which focus on a field, Science. According to the Journal Citation Reports, Sciences 2015 impact factor was 34.661, although it is the journal of the AAAS, membership in the AAAS is not required to publish in Science. Papers are accepted from authors around the world, competition to publish in Science is very intense, as an article published in such a highly cited journal can lead to attention and career advancement for the authors. Fewer than 7% of articles submitted are accepted for publication, Science is based in Washington, D. C. United States, with an office in Cambridge, England. Science was founded by New York journalist John Michels in 1880 with financial support from Thomas Edison, however, the journal never gained enough subscribers to succeed and ended publication in March 1882. Entomologist Samuel H. Scudder resurrected the journal one year later and had some success while covering the meetings of prominent American scientific societies, however, by 1894, Science was again in financial difficulty and was sold to psychologist James McKeen Cattell for $500. In an agreement worked out by Cattell and AAAS secretary Leland O. Howard, after Cattell died in 1944, the ownership of the journal was transferred to the AAAS. After Cattells death in 1944, the journal lacked a consistent editorial presence until Graham DuShane became editor in 1956. In 1958, under DuShanes leadership, Science absorbed The Scientific Monthly, physicist Philip Abelson, a co-discoverer of neptunium, served as editor from 1962 to 1984. Under Abelson the efficiency of the process was improved and the publication practices were brought up to date. During this time, papers on the Apollo program missions and some of the earliest reports on AIDS were published, biochemist Daniel E. Koshland, Jr. served as editor from 1985 until 1995. From 1995 until 2000, neuroscientist Floyd E. Bloom held that position, biologist Donald Kennedy became the editor of Science in 2000. Biochemist Bruce Alberts took his place in March 2008, geophysicist Marcia McNutt became editor-in-chief in June 2013. During her tenure the family of journals expanded to include Science Robotics and Science Immunology, jeremy M. Berg became editor-in-chief on July 1,2016
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Sucrase-isomaltase
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Sucrase-isomaltase (EC3.2.1.10, is a glucosidase enzyme located in on the brush border of the small intestine. Sucrase-isomaltase is a type II transmembrane glycoprotein located in the border of the small intestine. It has preferential expression in the membranes of enterocytes. The enzyme’s purpose is to digest dietary carbohydrates such as starch, glucose, by further processing the broken-down products, energy in the form of ATP can be generated. The systematic name of systematic name of sucrase-isomaltase is oligosaccharide 6-alpha-glucohydrolase and this enzyme catalyses the following chemical reaction Hydrolysis of -alpha-D-glucosidic linkages in some oligosaccharides produced from starch and glycogen by enzyme EC3.2.1.1. Hydrolysis uses water to cleave chemical bonds, sucrase-isomaltase’s mechanism results in a net retention of configuration at the anomeric center. Sucrase-isomaltase consists of two subunits, sucrase and isomaltase. The subunits originate from a precursor, pro-SI. By heterodimerizing the two subunits, the complex is formed. The enzyme is anchored in the brush border membrane by a hydrophobic segment located near the N-terminal of the isomaltase subunit. Before the enzyme is anchored to the membrane, pro-SI is mannose-rich and glycosylated, it moves from the ER to the Golgi, the O-linked glycosylation is necessary to target the protein to the apical membrane. In addition, there is a segment that is both O-linked glycosylated and Ser/Thr-rich, sucrase-isomaltase is composed of duplicated catalytic domains, N- and C-terminal. Scientists have discovered the structure for N-terminal human sucrase-isomaltase in apo form to 3.2 Å. The crystal structure shows that exists as a monomer. The researchers claim that the observance of SI dimers is dependent on experimental conditions, ntSI’s four monomers, A, B, C, and D are included in the crystal asymmetric unit and have identical active sites. The active site is composed of a binding pocket including -1. The non-reducing end of substrates binds to the pocket, while the non-reducing sugar ring has interactions with the buried -1 subsite, the reducing ring has interactions with the surface exposed +1 subsite. Furthermore, hydrophobic interactions with Leu233, Trp327, Trp435, Phe479, Val605, kotalonal, the inhibitor, It interacts with the catalytic nucleophile Asp472 and acid base catalyst Asp571
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Maltase
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Maltase is an enzyme located in on the brush border of the small intestine that breaks down the disaccharide maltose. Maltase catalyzes the hydrolysis of maltose to the sugar glucose. This enzyme is found in plants, bacteria, and yeast, acid maltase deficiency is categorized into three separate types based on the age of onset of symptoms in the affected individual. In humans, maltase will break down the form of the maltose. Vampire bats are the only known to not exhibit intestinal maltase activity. Maltase-glucoamylase Sucrase-isomaltase Maltases at the US National Library of Medicine Medical Subject Headings Structure and evolution of the mammalian maltase-glucoamylase and sucrase-isomaltase
24.
Trehalase
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Trehalase is a glycoside hydrolase enzyme located in on the brush border of the small intestine that catalyzes the conversion of trehalose to glucose. It is found in most animals, the non-reducing disaccharide trehalose is one of the most important storage carbohydrates, which is present in almost all forms of life except mammals. The disaccharide is hydrolyzed into two molecules of glucose by the enzyme trehalase, there are two types of trehalases found in Saccharomyces cerevisiae, viz. neutral trehalase and acid trehalase classified according to their pH optima. NT has an optimum pH of 7.0, while that of AT is 4.5, recently it has been reported that more than 90% of total AT activity in S. cerevisiae is extracellular and cleaves extracellular trehalose into glucose in the periplasmic space. One molecule of trehalose is hydrolyzed to two molecules of glucose by the enzyme trehalase, enzymatic hydrolysis of trehalose was first observed in Aspergillus niger by Bourquelot in 1893. Fischer reported this reaction in S. cerevisiae in 1895, since then the trehalose hydrolyzing enzyme, trehalase has been reported from many other organisms including plants and animals. Though trehalose is not known to be present in mammals, trehalase enzyme is found to be present in the brush border membrane. In the intestine the function of enzyme is to hydrolyze ingested trehalose. Individuals with a defect in their intestinal trehalase have diarrhea when they eat foods with high trehalose content, trehalose hydrolysis by trehalase enzyme is an important physiological process for various organisms, such as fungal spore germination, insect flight, and the resumption of growth in resting cells. Trehalose has been reported to be present as a carbohydrate in Pseudomonas, Bacillus, Rhizobium and in several actinomycetes. Most of the trehalase enzymes isolated from bacteria have as optimum pH of 6. 5-7.5, the trehalase enzyme of Mycobacterium smegmatis is a membrane bound protein. Periplasmic trehalase of Escherichia coli K12 is induced by growth at high osmolarity, the hydrolysis of trehalose into glucose takes place in the periplasm, and the glucose is then transported into the bacterial cell. Another cytoplasmic trehalase has also reported from E. coli. The gene, which encodes this cytoplasmic trehalase, exhibits high homology to the periplasmic trehalase, but, the enzyme trehalase is ubiquitous in plants. This is puzzling that trehalase is present in plants, though its substrate is absent. No clear role has been demonstrated for trehalase activity in plants and it has been suggested that trehalases could play a role in defense mechanisms or the enzyme could play a role in the degradation of trehalose derived from plant-associated microorganisms. In S. cerevisiae at least two distinct trehalases have been reported, one was reported to be regulated by cAMP-dependent phosphorylation. This enzyme activity was found in the cytosol, a second trehalase activity was found in the vacuoles of the same oraganism12
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Lactase
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Lactase is an enzyme produced by many organisms. It is located in the border of the small intestine of humans. Lactase is essential to the digestion of whole milk, it breaks down lactose. Lacking lactase, a person consuming dairy products may experience the symptoms of lactose intolerance, Lactase can be purchased as a food supplement, and is added to milk to produce lactose-free milk products. Lactase, a part of the family of enzymes, is a glycoside hydrolase involved in the hydrolysis of the disaccharide lactose into constituent galactose and glucose monomers. Lactase is present predominantly along the brush border membrane of the differentiated enterocytes lining the villi of the small intestine, in humans, lactase is encoded by the LCT gene. Lactase supplements are used to treat lactose intolerance. Lactase produced commercially can be extracted both from yeasts such as Kluyveromyces fragilis and Kluyveromyces lactis and from molds, such as Aspergillus niger, Lactase is also used to screen for blue white colonies in the multiple cloning sites of various plasmid vectors in Escherichia coli or other bacteria. Mechanism The optimum temperature for human lactase is about 37 °C for its activity and has an optimum pH of 6, in metabolism, the β-glycosidic bond in D-lactose is hydrolyzed to form D-galactose and D-glucose, which can be absorbed through the intestinal walls and into the bloodstream. The overall reaction that lactase catalyzes is C12H22O11 + H2O → C6H12O6 + C6H12O6 + heat, the catalytic mechanism of D-lactose hydrolysis retains the substrate anomeric configuration in the products. While the details of the mechanism are uncertain, the retention is achieved through a double displacement reaction. Studies of E. coli lactase have proposed that hydrolysis is initiated when a nucleophile on the enzyme attacks from the axial side of the galactosyl carbon in the β-glycosidic bond. The removal of the D-glucose leaving group may be facilitated by Mg-dependent acid catalysis, the enzyme is liberated from the α-galactosyl moiety upon equatorial nucleophilic attack by water, which produces D-galactose. Substrate modification studies have demonstrated that the 3′-OH and 2′-OH moieties on the ring are essential for enzymatic recognition. The 3′-hydroxy group is involved in binding to the substrate while the 2′- group is not necessary for recognition. This is demonstrated by the fact that a 2-deoxy analog is a competitive inhibitor. Elimination of specific hydroxyl groups on the glucopyranose moiety does not completely eliminate catalysis, Lactase also catalyzes the conversion of phlorizin to phloretin and glucose. Preprolactase, the primary product, has a single polypeptide primary structure consisting of 1927 amino acids
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Cellulase
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Cellulase is any of several enzymes produced chiefly by fungi, bacteria, and protozoans that catalyze cellulolysis, the decomposition of cellulose and of some related polysaccharides. The name is used for any naturally occurring mixture or complex of various such enzymes. Cellulases break down the molecule into monosaccharides such as beta-glucose. Cellulose breakdown is of economic importance, because it makes a major constituent of plants available for consumption. The specific reaction involved is the hydrolysis of the 1, 4-beta-D-glycosidic linkages in cellulose, hemicellulose, lichenin, because cellulose molecules bind strongly to each other, cellulolysis is relatively difficult compared to the breakdown of other polysaccharides such as starch. Most mammals have very limited ability to digest dietary fibres such as cellulose by themselves. In many herbivorous animals such as ruminants like cattle and sheep, cellulases are produced by a few types of animals, such as some termites. Several different kinds of cellulases are known, which differ structurally and mechanistically.5 cellulase, enzymes that cleave lignin are occasionally called cellulases, but this is usually considered erroneous. Five general types of cellulases based on the type of reaction catalyzed, exocellulases or cellobiohydrolases cleave two to four units from the ends of the exposed chains produced by endocellulase, resulting in tetrasaccharides or disaccharides, such as cellobiose. Exocellulases are further classified into type I, that work processively from the end of the cellulose chain, and type II. Cellobiases or beta-glucosidases hydrolyse the product into individual monosaccharides. Oxidative cellulases depolymerize cellulose by radical reactions, as for instance cellobiose dehydrogenase, cellulose phosphorylases depolymerize cellulose using phosphates instead of water. Avicelase has almost exclusively exo-cellulase activity, since avicel is a highly micro-crystalline substrate, within the above types there are also progressive and nonprogressive types. Progressive cellulase will continue to interact with a single polysaccharide strand, cellulase action is considered to be synergistic as all three classes of cellulase can yield much more sugar than the addition of all three separately. Most fungal cellulases have a structure, with one catalytic domain and one cellulose binding domain. This structure is adapted for working on a substrate. However, there are also cellulases that lack cellulose binding domains and these enzymes might have a swelling function. In many bacteria, cellulases in-vivo are complex enzyme structures organized in supramolecular complexes, numerous signature sequences known as dockerins and cohesins have been identified in the genomes of bacteria that produce cellulosomes
27.
Alpha-glucosidase
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Alpha-glucosidase is a glucosidase located in the brush border of the small intestine that acts upon α bonds. This is in contrast to beta-glucosidase, Alpha-glucosidase breaks down starch and disaccharides to glucose. Maltase, an enzyme that cleaves maltose, is nearly functionally equivalent. Other glucosidases include, Cellulase Beta-glucosidase Debranching enzyme Alpha-glucosidase hydrolyzes terminal non-reducing -linked alpha-glucose residues to release a single alpha-glucose molecule, Alpha-glucosidase is a carbohydrate-hydrolase that releases alpha-glucose as opposed to beta-glucose. Beta-glucose residues can be released by glucoamylase, a similar enzyme. The substrate selectivity of alpha-glucosidase is due to subsite affinities of the active site. Two proposed mechanisms include a displacement and an oxocarbenium ion intermediate. Rhodnius prolixus, an insect, forms hemozoin during digestion of host hemoglobin. Hemozoin synthesis is dependent on the binding site of alpha-glucosidase. Trout liver alpha-glucosidases were extracted and characterized and it was shown that for one of the trout liver alpha-glucosidases maximum activity of the enzyme was increased by 80% during exercise in comparison to a resting trout. This change was shown to correlate to an activity increase for liver glycogen phosphorylase and it is proposed that alpha-glucosidase in the glucosidic path plays an important part in complementing the phosphorolytic pathway in the liver’s metabolic response to energy demands of exercise. Yeast and rat small intestinal alpha-glucosidases have been shown to be inhibited by several groups of flavonoids, alpha-glucosidases can potentially be split, according to primary structure, into two families. The gene coding for human lysosomal alpha-glucosidase is about 20 kb long, human lysosomal alpha-glucosidase has been studied for the significance of the Asp-518 and other residues in proximity of the enzyme’s active site. It was found that substituting Asp-513 with Glu-513 interferes with posttranslational modification, additionally, the Trp-516 and Asp-518 residues have been deemed critical for the enzyme’s catalytic functionality. Kinetic changes in alpha-glucosidase have been shown to be induced by such as guanidinium chloride. These denaturants cause loss of activity and conformational change, a loss of enzyme activity occurs at much lower concentrations of denaturant than required for conformational changes. This leads to a conclusion that the active site conformation is less stable than the whole enzyme conformation in response to the two denaturants. Pompe disease, a disorder in which alpha-glucosidase is deficient, in 2006, the drug alglucosidase alfa became the first released treatment for Pompe disease and acts as an analog to alpha-glucosidase
28.
Acid alpha-glucosidase
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Lysosomal alpha-glucosidase, also called α-1, 4-glucosidase and acid maltase, is an enzyme that in humans is encoded by the GAA gene. Errors in this gene cause glycogen storage disease type II and this gene encodes acid alpha-glucosidase, which is essential for the degradation of glycogen to glucose in lysosomes. Different forms of acid alpha-glucosidase are obtained by proteolytic processing, defects in this gene are the cause of glycogen storage disease II, also known as Pompe disease, which is an autosomal recessive disorder with a broad clinical spectrum. Three transcript variants encoding the protein have been found for this gene. GeneReview/NIH/UW entry on Glycogen Storage Disease Type II Human GAA genome location and GAA gene details page in the UCSC Genome Browser
. PMID 18321971.
