Simple model of pH -induced protein denaturation

T. Hidaka, A. Shimada, Y. Nakata, H. Kodama, H. Kurihara, T. Tokihiro, S. Ihara

Research output: Contribution to journalArticlepeer-review

2 Citations (Scopus)

Abstract

The pH-induced conformational changes of proteins are systematically studied in the framework of a hydrophobic-polar (HP) model, in which proteins are dramatically simplified as chains of hydrophobic (H) and polar (P) beads on a lattice. We express the electrostatic interaction, the principal driving force of pH-induced unfolding that is not included in the conventional HP model, as the repulsive energy term between P monomers. As a result of the exact enumeration of all of the 14- to 18-mers, it is found that lowest-energy states in many sequences change from single "native" conformations to multiple sets of "denatured" conformations with an increase in the electrostatic repulsion. The switching of the lowest-energy states occurs in quite a similar way to real proteins: it is almost always between two states, while in a small fraction of ≥16-mers it is between three states. We also calculate the structural fluctuations for all of the denatured states and find that the denatured states contain a broad range of incompletely unfolded conformations, similar to "molten globule" states referred to in acid or alkaline denatured real proteins. These results show that the proposed model provides a simple physical picture of pH-induced protein denaturation.

Original languageEnglish
Article number012709
JournalPhysical Review E - Statistical, Nonlinear, and Soft Matter Physics
Volume92
Issue number1
DOIs
Publication statusPublished - 2015 Jul 7
Externally publishedYes

ASJC Scopus subject areas

  • Statistical and Nonlinear Physics
  • Statistics and Probability
  • Condensed Matter Physics

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