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Sequence-based prediction of protein binding mode landscapes.

Published version
Peer-reviewed

Change log

Authors

Miskei, Marton 
Ambrus, Viktor 
Vendruscolo, Michele  ORCID logo  https://orcid.org/0000-0002-3616-1610

Abstract

Interactions between disordered proteins involve a wide range of changes in the structure and dynamics of the partners involved. These changes can be classified in terms of binding modes, which include disorder-to-order (DO) transitions, when proteins fold upon binding, as well as disorder-to-disorder (DD) transitions, when the conformational heterogeneity is maintained in the bound states. Furthermore, systematic studies of these interactions are revealing that proteins may exhibit different binding modes with different partners. Proteins that exhibit this context-dependent binding can be referred to as fuzzy proteins. Here we investigate amino acid code for fuzzy binding in terms of the entropy of the probability distribution of transitions towards decreasing order. We implement these entropy calculations into the FuzPred (http://protdyn-fuzpred.org) algorithm to predict the range of context-dependent binding modes of proteins from their amino acid sequences. As we illustrate through a variety of examples, this method identifies those binding sites that are sensitive to the cellular context or post-translational modifications, and may serve as regulatory points of cellular pathways.

Description

Keywords

Algorithms, Binding Sites, Computational Biology, Databases, Protein, Eukaryotic Initiation Factor-2, Fuzzy Logic, Humans, Intrinsically Disordered Proteins, Probability, Protein Binding, Protein Domains, Protein Folding, Protein Processing, Post-Translational, Proteins, ROC Curve, Saccharomyces cerevisiae, Saccharomyces cerevisiae Proteins, Tumor Suppressor Protein p53, eIF-2 Kinase

Journal Title

PLoS Comput Biol

Conference Name

Journal ISSN

1553-734X
1553-7358

Volume Title

16

Publisher

Public Library of Science (PLoS)
Sponsorship
Magyar Tudományos Akadémia (HAS-11015)
Nemzeti Kutatási Fejlesztési és Innovációs Hivatal (GINOP-2.3.2-15-2016-00044)
Magyar Tudományos Akadémia (Bolyai Janos Fellowship)