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How proteins' negative cooperativity emerges from entropic optimisation of versatile collective fluctuations

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JournalThe Journal of Chemical Physics
DateAccepted/In press - 31 Oct 2019
DateE-pub ahead of print (current) - 3 Dec 2019
Issue number21
Volume151
Number of pages11
Early online date3/12/19
Original languageEnglish

Abstract

The fact that allostery, a nonlocal signaling between distant binding sites, can arise mainly from the entropy balance of collective thermal modes, without conformational changes, is by now well known. However, the propensity to generate negative cooperativity is still unclear. Starting from an elastic-network picture of small protein complexes, in which effector binding is modeled by locally altering interaction strengths in lieu of adding a node-spring pair, we elucidate mechanisms particularly for such negative cooperativity. The approach via a few coupled harmonic oscillators with internal elastic strengths allows us to trace individual eigenmodes, their frequencies, and their statistical weights through successive bindings. We find that the alteration of the oscillators' couplings is paramount to covering both signs of allostery. Binding-modified couplings create a rich set of eigenmodes individually for each binding state, modes inaccessible to an ensemble of noninteracting units. The associated shifts of collective-mode frequencies, nonuniform with respect to modes and binding states, result in an enhanced optimizability, reflected by a subtle phase map of allosteric behaviors.

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© 2019 Author(s). This is an author-produced version of the published paper. Uploaded in accordance with the publisher’s self-archiving policy. Further copying may not be permitted; contact the publisher for details.

    Research areas

  • Allosteric Regulation, Entropy, Molecular Dynamics Simulation, Protein Conformation, Proteins/chemistry

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