CleavPredict: A Platform for Reasoning about Matrix Metalloproteinases Proteolytic Events

Abstract

CleavPredict (http://cleavpredict.sanfordburnham.org) is a Web server for substrate cleavage prediction for matrix metalloproteinases (MMPs). It is intended as a computational platform aiding the scientific community in reasoning about proteolytic events. CleavPredict offers in silico prediction of cleavage sites specific for 11 human MMPs. The prediction method employs the MMP specific position weight matrices (PWMs) derived from statistical analysis of high-throughput phage display experimental results. To augment the substrate cleavage prediction process, CleavPredict provides information about the structural features of potential cleavage sites that influence proteolysis. These include: secondary structure, disordered regions, transmembrane domains, and solvent accessibility. The server also provides information about subcellular location, co-localization, and co-expression of proteinase and potential substrates, along with experimentally determined positions of single nucleotide polymorphism (SNP), and posttranslational modification (PTM) sites in substrates. All this information will provide the user with perspectives in reasoning about proteolytic events. CleavPredict is freely accessible, and there is no login required.

Matrix Metalloproteinase (MMP) Proteolysis of the Extracellular Loop of Voltage-gated Sodium Channels and Potential Alterations in Pain Signaling

“…CleavPredict allows us and others to locate in silico, with a nearly 100% accuracy, the MMP cleavage sites in the peptide sequences. The cross-validation tests involving the hundreds of the MMP cleavage sequences identified by others (17,(21)(22)(23)(24)(25) validated the accuracy of our cleavage prediction software. Specifically, false prediction rate, accuracy, and specificity were 2-3, 94 -96, and 97-98%, respectively, for MMP-9, suggesting that, in addition to the previously known cleavage targets, we can now identify novel, previously unrecognized substrates of this proteinase (17,20).…”

“…MMP-9 activity is stimulated by a limited set of conditions that are prevalent in inflammation, including peripheral nerve injury, and also in neurogenesis (27,28). Because our software correctly predicts a vast majority of MMP-9 substrates (17,20) and because the R907Q missense mutation reduced the presentation of the mutant protein at the plasma membrane, we hypothesized that the mutation enhanced the susceptibility of the membrane Nav1.7 to MMP-9 proteolysis, leading to the fragmented channel incapable of assembling a functional pore at the plasma membrane.…”

“…Recently, using substrate phage display (17,18), we identified some of the cleavage preferences of the matrix metalloproteinase (MMP) family members (19). Here, we employed a high throughput multiplexed peptide-centric profiling technology involving the cleavage of 18,583 peptides by the 18 individual proteinases from the main subgroups of the MMP family (20).…”

“…Volumes of the experimental data we acquired, merged with advanced bioinformatics, enabled comparison of the MMP cleavage preferences on a global scale and led to the previously unprecedented level of knowledge in MMP biology. Based on this newly acquired knowledge, we then developed cleavage prediction algorithms and the substrate specificity profiling software (17). This now freely available software (CleavPredict) readily identifies the cleavage site sequences within either individual proteins/peptides or the whole proteome and then ranks the probability of these site cleavages by the individual MMPs.…”

“…The algorithm is based on the position weight matrices (PWMs) approach. The original cleavage data were derived from the analysis of specific substrates selected from phage display libraries (17,18).…”