Automated molecular library generation of proteic fragments by virtual proteolysis for molecular modelling studies.

Edited by H. Michael; received 11 November 2005; revised and accepted 28 March 2006; published 29 August 2006ABSTRACT: This paper presents a computer aided design method useful for simulation of a set of proteolytic cleavagesupon target proteins obtained from the Brookhaven Data Bank. The method was developed by using algorithms that are ableto interface themselves with other software environments, in order to assist computer analyses in the molecular modellingfield, and allowing the generation of molecular libraries containing protein fragments produced by simulated proteolysis.These libraries include structures that differ for several amino acid deletions upon specified regions of the primary sequence.Target residues chosen for the simulation are compatible with enzymatic proteolysis methods used in conventional laboratoryprocedures. Furthermore, algorithms were able to identify a set of chemical-physical properties of the starting proteins, leadingthe simulation to find out the most suitable residues for proteolysis. The goal of these strategies is to generate fragments that areleaded to maintain the native-like condition of starting molecules, avoiding loss of conformational characteristics of the originaltertiary structure. Proteins chosen for generating proteolytic libraries were represented by naphthalene 1,2 dioxygenase andRigidoporus lignosus laccase.KEYWORDS: Molecular library generation, molecular modelling, closed loops, virtual proteolysis, screening and fragmenta-tion,leading proteins,targetaminoacids,hydrophobic profile,secondary structure,sequence comparison, foldingpathway, PDBfiles, NDO, RI laccase, 3D structures detection, enzymatic cleavage, protein design, laboratory procedures, soil bioremedation