ABSTRACT:Journal ArticleSCOPUS: ar.jinfo:eu-repo/semantics/publishe

A Facchiano

A Szilágyi

AH Elcock

ATR Laurie

B Shen

BH Dessailly

BK Shoichet

BM Beadle

C Deutsch

CT Porter

D Gilis

DF Yang

Dimitri Gilis

DM Jordan

E Capriotti

G Cheng

GN Somero

H Zhou

HM Berman

HY Fan

I Luque

IE Sanchez

J Cheng

J Damborsky

J Skolnick

J Thusberg

JA Capra

JD Bloom

Jean Marc Kwasigroch

JM Kwasigroch

KA Bava

L Ronga

LCS Tam

LD Cabrita

LT Huang

M Camps

M DePristo

M Masso

M Wilmanns

M Wolf-Watz

MA Johnston

Marianne Rooman

N Tokuriki

O Conchillo-Solé

O Lichtarge

P Yue

PC Ng

R Guerois

RW Zwanzig

S Jones

S Khan

S Sankararaman

S Vallet

S Yin

SB Zhang

SE Ozbabacan

SJ Hubbard

SM Lippow

TP Straatsma

V Mathys

V Parthiban

V Potapov

WL DeLano

Y Bromberg

Y Dehouck

Y Markert

Yves Dehouck

English

PubMed

Crossref

BMC Bioinformatics

PoPMuSiC 2.1: a web server for the estimation of protein stability changes upon mutation and sequence optimality

Jean Kwasigroch

Springer - Publisher Connector

Dehouck, Yves

Kwasigroch, Jean-Marc

Gilis, Dimitri

Rooman, Marianne

DI-fusion

PoPMuSiC 2.1: a web server for the estimation of protein stability changes upon mutation and sequence optimality.

Abstract Background The rational design of modified proteins with controlled stability is of extreme importance in a whole range of applications, notably in the biotechnological and environmental areas, where proteins are used for their catalytic or other functional activities. Future breakthroughs in medical research may also be expected from an improved understanding of the effect of naturally occurring disease-causing mutations on the molecular level. Results PoPMuSiC-2.1 is a web server that predicts the thermodynamic stability changes caused by single site mutations in proteins, using a linear combination of statistical potentials whose coefficients depend on the solvent accessibility of the mutated residue. PoPMuSiC presents good prediction performances (correlation coefficient of 0.8 between predicted and measured stability changes, in cross validation, after exclusion of 10% outliers). It is moreover very fast, allowing the prediction of the stability changes resulting from all possible mutations in a medium size protein in less than a minute. This unique functionality is user-friendly implemented in PoPMuSiC and is particularly easy to exploit. Another new functionality of our server concerns the estimation of the optimality of each amino acid in the sequence, with respect to the stability of the structure. It may be used to detect structural weaknesses, i.e. clusters of non-optimal residues, which represent particularly interesting sites for introducing targeted mutations. This sequence optimality data is also expected to have significant implications in the prediction and the analysis of particular structural or functional protein regions. To illustrate the interest of this new functionality, we apply it to a dataset of known catalytic sites, and show that a much larger than average concentration of structural weaknesses is detected, quantifying how these sites have been optimized for function rather than stability. Conclusion The freely available PoPMuSiC-2.1 web server is highly useful for identifying very rapidly a list of possibly relevant mutations with the desired stability properties, on which subsequent experimental studies can be focused. It can also be used to detect sequence regions corresponding to structural weaknesses, which could be functionally important or structurally delicate regions, with obvious applications in rational protein design.</p

Rooman Marianne

Gilis Dimitri

Kwasigroch Jean

Dehouck Yves

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https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-12-151?site=bmcbioinformatics.biomedcentral.com

PoPMuSiC 2.1: a web server for the estimation of protein stability changes upon mutation and sequence optimality

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