PBxplore: a tool to analyze local protein structure and deformability with Protein Blocks.

Jonathan Barnoud,Vincent Jallu,Pierre Poulain,Pierrick Craveur,Agnel Praveen Joseph,Alexandre G De Brevern,Hubert Santuz

doi:10.7717/peerj.4013

Abstract

This paper describes the development and application of a suite of tools, called PBxplore, to analyze the dynamics and deformability of protein structures using Protein Blocks (PBs). Proteins are highly dynamic macromolecules, and a classical way to analyze their inherent flexibility is to perform molecular dynamics simulations. The advantage of using small structural prototypes such as PBs is to give a good approximation of the local structure of the protein backbone. More importantly, by reducing the conformational complexity of protein structures, PBs allow analysis of local protein deformability which cannot be done with other methods and had been used efficiently in different applications. PBxplore is able to process large amounts of data such as those produced by molecular dynamics simulations. It produces frequencies, entropy and information logo outputs as text and graphics. PBxplore is available at https://github.com/pierrepo/PBxplore and is released under the open-source MIT license.

Highlights

Proteins are highly dynamic macromolecules (Frauenfelder, Sligar & Wolynes, 1991; Bu & Callaway, 2011)
In the context of structures issued from molecular dynamics (MD) simulations, the concept of deformability / rigidity is independent to the one of mobility
The β3 subunit has been reported in cases of alloimmune thrombocytopenia (Kaplan, 2006; Kaplan & Freedman, 2007). We studied this protein by MD simulations (for more details, see references (Jallu et al, 2012; Jallu et al, 2013; Jallu et al, 2014))

Summary

Introduction

Proteins are highly dynamic macromolecules (Frauenfelder, Sligar & Wolynes, 1991; Bu & Callaway, 2011) To analyze their inherent flexibility, computational biologists often use molecular dynamics (MD) simulations. Alternative in silico approaches assess protein motions through the protein residue network (Atilgan, Turgut & Atilgan, 2007) or dynamical correlations from MD simulations (Ghosh & Vishveshwara, 2007; Dixit & Verkhivker, 2011). Another noticeable development is the MOdular NETwork Analysis (MONETA), which localizes the perturbations propagation throughout a protein structure (Laine, Auclair & Tchertanov, 2012)

Methods

Results

Conclusion