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DATABASES |
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| OVERVIEW OF SERPIN SUPER FAMILY |
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Serpins (serine protease inhibitors or classified inhibitor family I4) are the largest and most broadly distributed superfamily of protease inhibitors. Serpin-like genes have been identified in animals, poxviruses, plants, bacteria and archaea, and over 1,500 members of this family have been identified to date. Analysis of the available genomic data reveals that all multicellular eukaryotes have serpins: humans, Drosophila, Arabidopsis thaliana and Caenorhabditis elegans have 36, 13, 29, and about 9 serpin-like genes, respectively.
Rarely, serpins perform a noninhibitory function. certain serpins function as molecular chaperones [9] or tumor suppressors.
A phylogenetic study of the superfamily divided the eukaryotic serpins into 16 ‘clades’. The proteins are named SERPINXy, where X is the clade and y is the number within that clade; many serpins also have alternative names from before this classification was proposed.
Serpins are relatively large molecules (about 330-500 amino acids) in comparison with protease inhibitors such as basic pancreatic trypsin inhibitor.
Over 70 serpin structures have been determined.
biophysical information, reveal that inhibitory serpins are ‘suicide’ or ‘single use’ inhibitors that use a unique and extensive conformational change to inhibit proteases.
Serpins appear to be ubiquitous in multicellular higher eukaryotes and in the poxviridae pathogens of mammals.
In humans, the two largest clades of the 36 serpins that have been identified are the extracellular ‘clade A’ molecules.
Recent bioinformatics and structural studies have also identified inhibitory serpins in the genomes of certain primitive unicellular eukaryotes as well as prokaryotes.
plant serpins may be involved in inhibiting proteases in plant pathogens.
One study convincingly demonstrated a close inverse correlation between the upregulation of Cucurbita maxima (squash) phloem serpin-1 (CmPS) and aphid survival.
the role of serpins in prokaryotes remains to be understood; again, these molecules are capable of inhibitory activity in vitro [20], but their targets in vivo and their function remain to be characterized.
Serpins are made up of three _ sheets (A, B and C) and 8-9 helices (termed hA-hI).
The region responsible for interaction with target proteases, the reactive center loop (RCL), forms an extended, exposed conformation above the body of the serpin scaffold.
Serpins use the S-to-R transition to inhibit target proteases.
In the final serpin-protease complex, the protease remains covalently linked to the serpin, the enzyme being trapped at the acyl-intermediate stage of the catalytic cycle.
Structural comparisons show that the protease in the final complex is severely distorted in comparison with the native conformation, and that much of the enzyme is disordered.
conformational changes lead to distortion at the active site, which prevents efficient hydrolysis of the acyl intermediate and the subsequent release of the protease.
It is possible that cleavage of such cryptic sites within the protease occurs in vivo and thus results in permanent enzyme inactivation.
These studies also showed that thermopin contains a4 amino-acid insertion at the carboxyl terminus that forms extensive interactions with conserved residues at the top of sheet A (called the ‘breach’; see later); biophysical data suggest that this region is important for proper and efficient folding of this unusual serpin.
A major advantage of the serpin fold over small protease inhibitors such as BPTI is that the inhibitory activity of serpins can be exquisitely controlled by specific cofactors. For example, human SERPINC1 (antithrombin) is a relatively poor inhibitor of the proteases thrombin and factor Xa until it is activated by the cofactor heparin.
The RCL is partially inserted into the top of the sheet; the residue (P1-Arg) responsible for docking into the primary specificity pocket (S1) of the protease is relatively inaccessible to docking with thrombin, as it is pointing towards and forming interactions with the body of the serpin.
In addition to loop expulsion and P1 exposure, long-chain heparin can bind both enzyme and inhibitor and thus provides an additional acceleration of the inhibitory interaction.
Structural studies on prokaryote and viral serpins have revealed several interesting variations of the serpin scaffold. Viral proteins are often ‘stripped down’ to a minimal scaffold in order to minimize the size of the viral genome. The structure of the viral serpin crmA, one of the smallest members of the serpin super family shows that it lacks helix hD.
Both the protease and the serpin as a result of serpin-enzyme complex formation provide an elegant mechanism for cells to specifically detect and clear inactivated serpin-protease complexes. In contrast, native or cleaved serpin alone are not internalized.
Serpins thus join a growing number of structurally distinct molecules that can misfold and cause important degenerative diseases, such as prions, polyglutamine regions of various proteins and the amyloid proteins that form inclusions in Alzheimer’s disease.
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| SLIDE SHOW |
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