MersV1, PubMed, Corpus, bibRecord, 001507

Simple model of pH-induced protein denaturation.

Identifieur interne : 001507 ( PubMed/Corpus ); précédent : 001506; suivant : 001508

Simple model of pH-induced protein denaturation.

Auteurs : T. Hidaka ; A. Shimada ; Y. Nakata ; H. Kodama ; H. Kurihara ; T. Tokihiro ; S. Ihara

Source :

Physical review. E, Statistical, nonlinear, and soft matter physics [ 1550-2376 ] ; 2015.

RBID : pubmed:26274205

English descriptors

KwdEn :
- Hydrogen-Ion Concentration, Hydrophobic and Hydrophilic Interactions, Models, Molecular, Protein Conformation, Proteolysis, Static Electricity.
MESH :
- Hydrogen-Ion Concentration, Hydrophobic and Hydrophilic Interactions, Models, Molecular, Protein Conformation, Proteolysis, Static Electricity.

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.

DOI: 10.1103/PhysRevE.92.012709
PubMed: 26274205

Links to Exploration step

pubmed:26274205

Le document en format XML

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<affiliation><nlm:affiliation>Graduate School of Medicine and Faculty of Medicine, The University of Tokyo, Hongo, Tokyo 113-0033, Japan.</nlm:affiliation>
</affiliation>
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<author><name sortKey="Shimada, A" sort="Shimada, A" uniqKey="Shimada A" first="A" last="Shimada">A. Shimada</name>
<affiliation><nlm:affiliation>Graduate School of Medicine and Faculty of Medicine, The University of Tokyo, Hongo, Tokyo 113-0033, Japan.</nlm:affiliation>
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<author><name sortKey="Nakata, Y" sort="Nakata, Y" uniqKey="Nakata Y" first="Y" last="Nakata">Y. Nakata</name>
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<author><name sortKey="Kodama, H" sort="Kodama, H" uniqKey="Kodama H" first="H" last="Kodama">H. Kodama</name>
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<author><name sortKey="Tokihiro, T" sort="Tokihiro, T" uniqKey="Tokihiro T" first="T" last="Tokihiro">T. Tokihiro</name>
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<author><name sortKey="Ihara, S" sort="Ihara, S" uniqKey="Ihara S" first="S" last="Ihara">S. Ihara</name>
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<term>Static Electricity</term>
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<front><div type="abstract" xml:lang="en">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. </div>
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<ArticleTitle>Simple model of pH-induced protein denaturation.</ArticleTitle>
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<Abstract><AbstractText>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. </AbstractText>
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Simple model of pH-induced protein denaturation.

Simple model of pH-induced protein denaturation.

Source :

English descriptors

Abstract

Links to Exploration step

Le document en format XML

Pour manipuler ce document sous Unix (Dilib)

Pour mettre un lien sur cette page dans le réseau Wicri

Pour générer des pages wiki