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Exploring Protein-Peptide Binding Specificity through Computational Peptide Screening.

Författare

  • Arnab Bhattacherjee
  • Stefan Wallin

Summary, in English

The binding of short disordered peptide stretches to globular protein domains is important for a wide range of cellular processes, including signal transduction, protein transport, and immune response. The often promiscuous nature of these interactions and the conformational flexibility of the peptide chain, sometimes even when bound, make the binding specificity of this type of protein interaction a challenge to understand. Here we develop and test a Monte Carlo-based procedure for calculating protein-peptide binding thermodynamics for many sequences in a single run. The method explores both peptide sequence and conformational space simultaneously by simulating a joint probability distribution which, in particular, makes searching through peptide sequence space computationally efficient. To test our method, we apply it to 3 different peptide-binding protein domains and test its ability to capture the experimentally determined specificity profiles. Insight into the molecular underpinnings of the observed specificities is obtained by analyzing the peptide conformational ensembles of a large number of binding-competent sequences. We also explore the possibility of using our method to discover new peptide-binding pockets on protein structures.

Publiceringsår

2013

Språk

Engelska

Publikation/Tidskrift/Serie

PLoS Computational Biology

Volym

9

Issue

10

Dokumenttyp

Artikel i tidskrift

Förlag

Public Library of Science (PLoS)

Ämne

  • Bioinformatics and Systems Biology

Status

Published

ISBN/ISSN/Övrigt

  • ISSN: 1553-7358