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Merops Boehmi
MEROPS is an online database for peptidases (also known as proteases, proteinases and proteolytic enzymes) and their inhibitors. The classification scheme for peptidases was published by Rawlings & Barrett in 1993, and that for protein inhibitors by Rawlings ''et al.'' in 2004.Rawlings, N.D., Tolle, D.P. & Barrett, A.J. (2004) "Evolutionary families of peptidase inhibitors." ''Biochem J'' 378, 705-716. The most recent version, MEROPS 12.3, was released in September 2020. Overview The classification is based on similarities at the tertiary and primary structural levels. Comparisons are restricted to that part of the sequence directly involved in the reaction, which in the case of a peptidase must include the active site, and for a protein inhibitor the reactive site. The classification is hierarchical: sequences are assembled into families, and families are assembled into clans. Each peptidase, family, and clan has a unique identifier. Classification Family The families of pept ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Proteolytic Enzymes
Proteolysis is the breakdown of proteins into smaller polypeptides or amino acids. Uncatalysed, the hydrolysis of peptide bonds is extremely slow, taking hundreds of years. Proteolysis is typically catalysed by cellular enzymes called proteases, but may also occur by intra-molecular digestion. Proteolysis in organisms serves many purposes; for example, digestive enzymes break down proteins in food to provide amino acids for the organism, while proteolytic processing of a polypeptide chain after its synthesis may be necessary for the production of an active protein. It is also important in the regulation of some physiological and cellular processes including apoptosis, as well as preventing the accumulation of unwanted or misfolded proteins in cells. Consequently, abnormality in the regulation of proteolysis can cause disease. Proteolysis can also be used as an analytical tool for studying proteins in the laboratory, and it may also be used in industry, for example in food process ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Standard Deviation
In statistics, the standard deviation is a measure of the amount of variation or dispersion of a set of values. A low standard deviation indicates that the values tend to be close to the mean (also called the expected value) of the set, while a high standard deviation indicates that the values are spread out over a wider range. Standard deviation may be abbreviated SD, and is most commonly represented in mathematical texts and equations by the lower case Greek letter σ (sigma), for the population standard deviation, or the Latin letter '' s'', for the sample standard deviation. The standard deviation of a random variable, sample, statistical population, data set, or probability distribution is the square root of its variance. It is algebraically simpler, though in practice less robust, than the average absolute deviation. A useful property of the standard deviation is that, unlike the variance, it is expressed in the same unit as the data. The standard deviation of a popu ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Science And Technology In Cambridgeshire
Science is a systematic endeavor that builds and organizes knowledge in the form of testable explanations and predictions about the universe. Science may be as old as the human species, and some of the earliest archeological evidence for scientific reasoning is tens of thousands of years old. The earliest written records in the history of science come from Ancient Egypt and Mesopotamia in around 3000 to 1200 BCE. Their contributions to mathematics, astronomy, and medicine entered and shaped Greek natural philosophy of classical antiquity, whereby formal attempts were made to provide explanations of events in the physical world based on natural causes. After the fall of the Western Roman Empire, knowledge of Greek conceptions of the world deteriorated in Western Europe during the early centuries (400 to 1000 CE) of the Middle Ages, but was preserved in the Muslim world during the Islamic Golden Age and later by the efforts of Byzantine Greek scholars who brought Greek ma ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Proteomics Organizations
Proteomics is the large-scale study of proteins. Proteins are vital parts of living organisms, with many functions such as the formation of structural fibers of muscle tissue, enzymatic digestion of food, or synthesis and replication of DNA. In addition, other kinds of proteins include antibodies that protect an organism from infection, and hormones that send important signals throughout the body. The proteome is the entire set of proteins produced or modified by an organism or system. Proteomics enables the identification of ever-increasing numbers of proteins. This varies with time and distinct requirements, or stresses, that a cell or organism undergoes. Proteomics is an interdisciplinary domain that has benefited greatly from the genetic information of various genome projects, including the Human Genome Project. It covers the exploration of proteomes from the overall level of protein composition, structure, and activity, and is an important component of functional genomics. ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Protein Classification
Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residue (biochemistry), residues. Proteins perform a vast array of functions within organisms, including Enzyme catalysis, catalysing metabolic reactions, DNA replication, Cell signaling, responding to stimuli, providing Cytoskeleton, structure to cells and Fibrous protein, organisms, and Intracellular transport, transporting molecules from one location to another. Proteins differ from one another primarily in their sequence of amino acids, which is dictated by the Nucleic acid sequence, nucleotide sequence of their genes, and which usually results in protein folding into a specific Protein structure, 3D structure that determines its activity. A linear chain of amino acid residues is called a polypeptide. A protein contains at least one long polypeptide. Short polypeptides, containing less than 20–30 residues, are rarely considered to be proteins and are commonly called pept ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Proteases
A protease (also called a peptidase, proteinase, or proteolytic enzyme) is an enzyme that catalyzes (increases reaction rate or "speeds up") proteolysis, breaking down proteins into smaller polypeptides or single amino acids, and spurring the formation of new protein products. They do this by cleaving the peptide bonds within proteins by hydrolysis, a reaction where water breaks bonds. Proteases are involved in many biological functions, including digestion of ingested proteins, protein catabolism (breakdown of old proteins), and cell signaling. In the absence of functional accelerants, proteolysis would be very slow, taking hundreds of years. Proteases can be found in all forms of life and viruses. They have independently evolved multiple times, and different classes of protease can perform the same reaction by completely different catalytic mechanisms. Hierarchy of proteases Based on catalytic residue Proteases can be classified into seven broad groups: * Serine proteases - ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Biological Databases
Biological databases are libraries of biological sciences, collected from scientific experiments, published literature, high-throughput experiment technology, and computational analysis. They contain information from research areas including genomics, proteomics, metabolomics, microarray gene expression, and phylogenetics. Information contained in biological databases includes gene function, structure, localization (both cellular and chromosomal), clinical effects of mutations as well as similarities of biological sequences and structures. Biological databases can be classified by the kind of data they collect (see below). Broadly, there are molecular databases (for sequences, molecules, etc.), functional databases (for physiology, enzyme activities, phenotypes, ecology etc), taxonomic databases (for species and other taxonomic ranks), images and other media, or specimens (for museum collections etc.) Databases are important tools in assisting scientists to analyze and explain ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Catalytic Triad
A catalytic triad is a set of three coordinated amino acids that can be found in the active site of some enzymes. Catalytic triads are most commonly found in hydrolase and transferase enzymes (e.g. proteases, amidases, esterases, acylases, lipases and β-lactamases). An acid- base-nucleophile triad is a common motif for generating a nucleophilic residue for covalent catalysis. The residues form a charge-relay network to polarise and activate the nucleophile, which attacks the substrate, forming a covalent intermediate which is then hydrolysed to release the product and regenerate free enzyme. The nucleophile is most commonly a serine or cysteine amino acid, but occasionally threonine or even selenocysteine. The 3D structure of the enzyme brings together the triad residues in a precise orientation, even though they may be far apart in the sequence (primary structure). As well as divergent evolution of function (and even the triad's nucleophile), catalytic triads show some ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
PA Clan
The PA clan ( Proteases of mixed nucleophile, superfamily A) is the largest group of proteases with common ancestry as identified by structural homology. Members have a chymotrypsin-like fold and similar proteolysis mechanisms but can have identity of <10%. The clan contains both and (different ). PA clan proteases can be found in , |
Protein Superfamily
A protein superfamily is the largest grouping (clade) of proteins for which common ancestry can be inferred (see homology (biology), homology). Usually this common ancestry is inferred from structural alignment and mechanistic similarity, even if no sequence similarity is evident. Sequence homology can then be deduced even if not apparent (due to low sequence similarity). Superfamilies typically contain several protein families which show sequence similarity within each family. The term ''protein clan'' is commonly used for protease and glycosyl hydrolases superfamilies based on the MEROPS and CAZy classification systems. Identification Superfamilies of proteins are identified using a number of methods. Closely related members can be identified by different methods to those needed to group the most evolutionarily divergent members. Sequence similarity Historically, the similarity of different amino acid sequences has been the most common method of inferring Sequence homology, h ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
TopFIND
TopFIND is the Termini oriented protein Function Inferred Database (TopFIND) is an integrated knowledgebase focused on protein termini, their formation by proteases and functional implications. It contains information about the processing and the processing state of proteins and functional implications thereof derived from research literature, contributions by the scientific community and biological databases. Background Among the most fundamental characteristics of a protein are the N- and C-termini defining the start and end of the polypeptide chain. While genetically encoded, protein termini isoforms are also often generated during translation, following which, termini are highly dynamic, being frequently trimmed at their ends by a large array of exopeptidases. Neo-termini can also be generated by endopeptidases after precise and limited proteolysis, termed processing. Necessary for the maturation of many proteins, processing can also occur afterwards, often resulting in dramat ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
The Proteolysis Map
The Proteolysis MAP (PMAP) is an integrated web resource focused on proteases. Rationale PMAP is to aid the protease researchers in reasoning about proteolytic networks and metabolic pathways. History and funding PMAP was originally created at the Burnham Institute for Medical Research, La Jolla, California. In 2004 the National Institutes of Health (NIH) selected a team led by Jeffrey W. Smith, to establish the Center on Proteolytic Pathways (CPP). As part of the NIH Roadmap for Biomedical research, the center develops technology to study the behavior of proteins and to disburse that knowledge to the scientific community at large. Focal point Proteases are a class of enzymes that regulate much of what happens in the human body, both inside the cell and out, by cleaving peptide bonds in proteins. Through this activity, they govern the four essential cell functions: differentiation, motility, division and cell death — and activate important extracellular episodes, such as ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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