Thermodynamics of Conformational Transitions in a Disordered Protein Backbone Model

Justin A. Drake, Bernard Pettitt

Research output: Contribution to journalArticle

3 Citations (Scopus)

Abstract

Conformational entropy is expected to contribute significantly to the thermodynamics of structural transitions in intrinsically disordered proteins or regions in response to protein/ligand binding, posttranslational modifications, and environmental changes. We calculated the backbone (dihedral) conformational entropy of oligoglycine (GlyN), a protein backbone mimic and model intrinsically disordered region, as a function of chain length (N=3, 4, 5, 10, and 15) from simulations using three different approaches. The backbone conformational entropy scales linearly with chain length with a slope consistent with the entropy of folding of well-structured proteins. The entropic contributions of second-order dihedral correlations are predominantly through intraresidue ϕ-ψ pairs, suggesting that oligoglycine may be thermodynamically modeled as a system of independent glycine residues. We find the backbone conformational entropy to be largely independent of global structural parameters, like the end-to-end distance and radius of gyration. We introduce a framework referred to herein as “ensemble confinement” to estimate the loss (gain) of conformational free energy and its entropic component when individual residues are constrained to (released from) particular regions of the ϕ-ψ map. Quantitatively, we show that our protein backbone model resists ordering/folding with a significant, unfavorable ensemble confinement free energy because of the loss of a substantial portion of the absolute backbone entropy. Proteins can couple this free-energy reservoir to distal binding events as a regulatory mechanism to promote or suppress binding.

Original languageEnglish (US)
Pages (from-to)2799-2810
Number of pages12
JournalBiophysical Journal
Volume114
Issue number12
DOIs
StatePublished - Jun 19 2018

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Entropy
Thermodynamics
Proteins
Intrinsically Disordered Proteins
Post Translational Protein Processing
Protein Binding
Glycine
Ligands

ASJC Scopus subject areas

  • Biophysics

Cite this

Thermodynamics of Conformational Transitions in a Disordered Protein Backbone Model. / Drake, Justin A.; Pettitt, Bernard.

In: Biophysical Journal, Vol. 114, No. 12, 19.06.2018, p. 2799-2810.

Research output: Contribution to journalArticle

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