Analysis of binding properties and specificity through identification of the interface forming residues (IFR) for serine proteases in silico docked to different inhibitors

Abstract

BackgroundEnzymes belonging to the same super family of proteins in general operate on variety of substrates and are inhibited by wide selection of inhibitors. In this work our main objective was to expand the scope of studies that consider only the catalytic and binding pocket amino acids while analyzing enzyme specificity and instead, include a wider category which we have named the Interface Forming Residues (IFR). We were motivated to identify those amino acids with decreased accessibility to solvent after docking of different types of inhibitors to sub classes of serine proteases and then create a table (matrix) of all amino acid positions at the interface as well as their respective occupancies. Our goal is to establish a platform for analysis of the relationship between IFR characteristics and binding properties/specificity for bi-molecular complexes.ResultsWe propose a novel method for describing binding properties and delineating serine proteases specificity by compiling an exhaustive table of interface forming residues (IFR) for serine proteases and their inhibitors. Currently, the Protein Data Bank (PDB) does not contain all the data that our analysis would require. Therefore, an in silico approach was designed for building corresponding complexesThe IFRs are obtained by "rigid body docking" among 70 structurally aligned, sequence wise non-redundant, serine protease structures with 3 inhibitors: bovine pancreatic trypsin inhibitor (BPTI), ecotine and ovomucoid third domain inhibitor. The table (matrix) of all amino acid positions at the interface and their respective occupancy is created. We also developed a new computational protocol for predicting IFRs for those complexes which were not deciphered experimentally so far, achieving accuracy of at least 0.97.ConclusionsThe serine proteases interfaces prefer polar (including glycine) residues (with some exceptions). Charged residues were found to be uniquely prevalent at the interfaces between the "miscellaneous-virus" subfamily and the three inhibitors. This prompts speculation about how important this difference in IFR characteristics is for maintaining virulence of those organisms.Our work here provides a unique tool for both structure/function relationship analysis as well as a compilation of indicators detailing how the specificity of various serine proteases may have been achieved and/or could be altered. It also indicates that the interface forming residues which also determine specificity of serine protease subfamily can not be presented in a canonical way but rather as a matrix of alternative populations of amino acids occupying variety of IFR positions.

The Natural Polypeptides as Significant Elastase Inhibitors

“…This assumption leads to the conclusion that polypeptides also inhibit elastase in a competitive way using Michaelis-Menten kinetics, since the residue between Thr and Ahp units presumably defines the specificity toward specific serine proteases (Matern et al, 2003b;Yamaki et al, 2005;Salvador et al, 2013). Through identification of the IFR (interface forming residues) for serine proteases in silico docked to different inhibitors, it was concluded that the serine proteases interfaces prefer polar residues (with some exceptions) (Ribeiro et al, 2010).…”

Identification of New Sphingomyelinases D in Pathogenic Fungi and Other Pathogenic Organisms

“…A construct “nanoenvironment” was previously defined in our earlier work regarding the characterization for the specificity of ligand binding, protein function preservation in mutants and the specificity of enzymes based on the type of interface residues (Fernandez et al, 2003 [29]; Marcellino et al, 1996 [30] and Ribeiro et al, 2010 [31], respectively). As defined by Murakami et al (2005)[2], His12 and His47 are the key catalytic residues, followed by the metal ion coordinating residues Glu32, Asp34 and Asp91.…”

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“…In this approach, both the ligand and the receptor have very stiff structures, thereby the name rigid body docking. Although simplistic, the method was successfully used for the analysis of the serine proteases specificity 7 .…”