The effects of side chain hydrophobicity on the denaturation of simple β-hairpins

Literature Information

Publication Date 2010-06-23
DOI 10.1039/B924593F
Impact Factor 3.676
Authors

Haiyan Wei, Qiang Shao, Yi Qin Gao


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Abstract

To investigate the sequence dependence in the molecular mechanism of urea induced denaturation, molecular dynamics denaturing simulations of two β-hairpin peptides, a fast folding peptide 1 (SESYINPDGTWTVTE) and a slow folding TRPZIP4 (GEWTWDDATKTWTWTE), were performed in urea aqueous solutions. It was found that β-hairpin denaturation by urea is highly dependent on the hydrophobicity of the side chains. The two β-hairpin peptides studied here and the GB1 studied previously display three different denaturant processes in urea solution by which the breaking of backbone native hydrogen bonds takes different orders. The variation of their denaturing mechanism is well correlated to the variation in their structural properties. In peptide 1, which has only a loosely packed hydrophobic core formed by residues Trp11 and Ile5, all backbone native hydrogen bonds (1 to 5) are broken in a short period of time. Whereas for TRPZIP4 with a compact hydrophobic core of four tryptophan residues, the backbone native hydrogen bonds (1 to 6) are considerably more stable, with the middle hydrogen bonds protected well by the hydrophobic core being the most stable. The comparison of different β-hairpin peptides shows that the side-chain packing on each face of the strands plays a major role in the stability of the backbone native hydrogen bonds in urea solution, and indicates that protein denaturation by urea can be highly sequence dependent.

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Physical Chemistry Chemical Physics

Physical Chemistry Chemical Physics
CiteScore: 5.5
Self-citation Rate: 10.3%
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Physical Chemistry Chemical Physics (PCCP) is an international journal co-owned by 19 physical chemistry and physics societies from around the world. This journal publishes original, cutting-edge research in physical chemistry, chemical physics and biophysical chemistry. To be suitable for publication in PCCP, articles must include significant innovation and/or insight into physical chemistry; this is the most important criterion that reviewers and Editors will judge against when evaluating submissions. The journal has a broad scope and welcomes contributions spanning experiment, theory, computation and data science. Topical coverage includes spectroscopy, dynamics, kinetics, statistical mechanics, thermodynamics, electrochemistry, catalysis, surface science, quantum mechanics, quantum computing and machine learning. Interdisciplinary research areas such as polymers and soft matter, materials, nanoscience, energy, surfaces/interfaces, and biophysical chemistry are welcomed if they demonstrate significant innovation and/or insight into physical chemistry. Joined experimental/theoretical studies are particularly appreciated when complementary and based on up-to-date approaches.

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