Sequence-based prediction of protein binding mode landscapes

PLoS Comput Biol. 2020 May 26;16(5):e1007864. doi: 10.1371/journal.pcbi.1007864. eCollection 2020 May.

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

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

Substances

  • Eukaryotic Initiation Factor-2
  • Intrinsically Disordered Proteins
  • Proteins
  • SUI2 protein, S cerevisiae
  • Saccharomyces cerevisiae Proteins
  • TP53 protein, human
  • Tumor Suppressor Protein p53
  • EIF2AK2 protein, human
  • eIF-2 Kinase

Grants and funding

Monika Fuxreiter was supported by Hungarian Academy of Sciences HAS-11015 and National Research, Development and Innovation Office, Hungary GINOP-2.3.2-15-2016-00044. In all cases, the funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.