Simple model of pH-induced protein denaturation.
Identifieur interne : 001507 ( PubMed/Corpus ); précédent : 001506; suivant : 001508Simple model of pH-induced protein denaturation.
Auteurs : T. Hidaka ; A. Shimada ; Y. Nakata ; H. Kodama ; H. Kurihara ; T. Tokihiro ; S. IharaSource :
- Physical review. E, Statistical, nonlinear, and soft matter physics [ 1550-2376 ] ; 2015.
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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
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pubmed:26274205Le document en format XML
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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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<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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