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Interplay between partner and ligand facilitates the folding and binding of an intrinsically disordered protein.


Type

Article

Change log

Authors

Rogers, Joseph M 
Oleinikovas, Vladimiras 
Shammas, Sarah L 
Wong, Chi T 
De Sancho, David 

Abstract

Protein-protein interactions are at the heart of regulatory and signaling processes in the cell. In many interactions, one or both proteins are disordered before association. However, this disorder in the unbound state does not prevent many of these proteins folding to a well-defined, ordered structure in the bound state. Here we examine a typical system, where a small disordered protein (PUMA, p53 upregulated modulator of apoptosis) folds to an α-helix when bound to a groove on the surface of a folded protein (MCL-1, induced myeloid leukemia cell differentiation protein). We follow the association of these proteins using rapid-mixing stopped flow, and examine how the kinetic behavior is perturbed by denaturant and carefully chosen mutations. We demonstrate the utility of methods developed for the study of monomeric protein folding, including β-Tanford values, Leffler α, Φ-value analysis, and coarse-grained simulations, and propose a self-consistent mechanism for binding. Folding of the disordered protein before binding does not appear to be required and few, if any, specific interactions are required to commit to association. The majority of PUMA folding occurs after the transition state, in the presence of MCL-1. We also examine the role of the side chains of folded MCL-1 that make up the binding groove and find that many favor equilibrium binding but, surprisingly, inhibit the association process.

Description

Keywords

BCL-2, Protein folding, coarse-grained simulation, protein–protein interactions, stopped flow, Intrinsically Disordered Proteins, Kinetics, Ligands, Molecular Dynamics Simulation, Mutant Proteins, Mutation, Myeloid Cell Leukemia Sequence 1 Protein, Protein Binding, Protein Folding, Protein Structure, Secondary, Proto-Oncogene Proteins

Journal Title

Proc Natl Acad Sci U S A

Conference Name

Journal ISSN

0027-8424
1091-6490

Volume Title

111

Publisher

Proceedings of the National Academy of Sciences
Sponsorship
Wellcome Trust (095195/Z/10/Z)
Engineering and Physical Sciences Research Council (EP/J016764/1)