Folding dynamics of a small protein at room temperature via simulated coherent two-dimensional infrared spectroscopy

Literature Information

Publication Date 2010-08-02
DOI 10.1039/C0CP00375A
Impact Factor 3.676
Authors

Yun Xiang, Lili Duan


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Abstract

Understanding protein folding is of fundamental and practical importance in chemistry and biology. Despite the great success that has been made in tackling this problem, a detailed knowledge of how the elementary processes such as hydrogen-bond formation occur during protein folding has remained largely elusive. Using the combined power of molecular dynamics simulation with electrostatic polarization and coherent two-dimensional infrared spectroscopy, we are able to delineate the order of the hydrogen-bond formation event of a 17-residue peptide during its folding from an extended state to the native α-helix state. The folding is carried out by a single trajectory room-temperature molecular dynamics simulation that includes the polarization effect of hydrogen bonding, which is critical to the successful folding of the peptide. The onset and evolution of the isotope-labeled amide I vibration diagonal and cross peaks on the simulated 2DIR spectra allow us to build a structure-spectrum connection, and thus provide a microscopic picture of the helix folding process.

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Back cover

2022-01-24 Cover

DOI: 10.1039/D2CS90009B

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Physical Chemistry Chemical Physics

Physical Chemistry Chemical Physics
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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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