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Biomolecule large-amplitude motion and solvation dynamics: modelling and probes from THz to X-rays 

Authors: David M. Leitner a;  Martina Havenith b; Martin Gruebele c
Affiliations:   a Department of Chemistry, University of Nevada, Reno, NV 89557, USA
b Lehrstuhl fuumlr Physikalische Chemie II, Ruhr-Universitaumlt Bochum, 44780 Bochum, Germany
c Departments of Chemistry and Physics, Center for Biophysics and Computational Biology, University of Illinois, Urbana, IL 61801, USA
DOI: 10.1080/01442350600862117
Publication Frequency: 4 issues per year
Published in: journal International Reviews in Physical Chemistry, Volume 25, Issue 4 October 2006 , pages 553 - 582
Formats available: HTML (English) : PDF (English)
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Abstract

Biomolecules are innately flexible, and undergo large-amplitude motions that affect the surrounding solvation shell. Dynamical X-ray scattering provides direct insight into global shape changes that the biomolecule undergoes during folding (1 nm and up length scale). THz spectroscopy directly probes solvation and collective motions on a somewhat smaller length scale (0.3-1 nm). Infrared spectroscopy looks at the influence of such motions on localized vibrational modes (up to 0.5 nm length scale). Molecular dynamics simulations and models of vibrational energy flow within biomolecules complement such experimental studies by providing a molecular-level explanation for the experimental observations. In this review, we consider the interplay between simulation and experiment across length scales for biomolecules such as carbohydrates and globular proteins.
Contents PAGE
1. Introduction 554
2. Experimental tools 556
2.1. Infrared spectroscopy 557
2.2. THz absorption spectroscopy 560
2.3. SAXS 561
3. Theoretical tools 564
3.1. Molecular dynamics simulations 565
3.2. Spectral density 565
3.3. Computational studies of energy flow 567
3.4. Hydrogen bond dynamics in solvation shells 568
3.5. The fractal nature of biomolecules 569
4. Two cases: carbohydrate solutions and protein folding/solvation \ dynamics 572
4.1. Carbohydrates 572
4.2. Proteins 575
5. Summary and outlook 579
Acknowledgments 580
References 580
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