Structural classification of the amide I sites of a β-hairpin with isotope label 2DIRspectroscopy

Literature Information

Publication Date 2010-07-01
DOI 10.1039/B925645H
Impact Factor 3.676
Authors

Santanu Roy, Thomas L. C. Jansen, Jasper Knoester


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Abstract

We present a theoretical study of the possibility to use isotope label two-dimensional infrared (2DIR) spectroscopy to obtain site specific structural information in trpzip2. This small β-hairpin peptide was designed as a model system for studying protein folding in β-sheet structures. In order to unravel the folding mechanism, the surroundings of local sites should be characterized, which in principle is possible by using 2DIR in combination with isotope labeling. This requires a classification that correlates local structures to two-dimensional spectra. To this end, we provide the first spectral simulation of the isotope label spectra of all the amide I sites in trpzip2. We find that the anti-diagonal width of the 2DIR peak associated with a labelled site is a good measure of solvent exposure and the key parameter to distinguish between solvent exposed and internal sites. The diagonal widths are not particularly sensitive to this, but they do reveal the presence of slowly interconverting turn structures.

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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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