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Low-Frequency, Functional, Modes of Proteins: All-Atom and Coarse-Grained Normal Mode Analysis

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Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes

Part of the book series: Springer Series in Bio-/Neuroinformatics ((SSBN,volume 1))

Abstract

The directions of the largest thermal fluctuations of the structure of a protein in its native state are the directions of its low-frequency modes (below 1 THZ), named acoustical modes by analogy with the acoustical phonons of a material. The acoustical modes of a protein assist its conformational changes and are related to its biological functions. Low-frequency modes are difficult to detect experimentally. A survey of experimental data of low-frequency modes of proteins is presented. Theoretical approaches, based on normal mode analysis, are of first interest to understand the role of the low-frequency modes in proteins. In this chapter, the fundamentals of normal mode analysis using all-atom models and coarse-grained elastic models are reviewed. They are applied to proteins intimately related to human diseases: ubiquitin and the 70kDa Heat-Shock Protein (Hsp70). The ubiquitin protein is a single domain protein which is a benchmark for biomolecular Nuclear Magnetic Resonance spectroscopy. Present all-atom calculations predict a “boson peak” near 20 cm− 1 in the inelastic neutron scattering spectra of this protein. The molecular chaperone Hsp70 is an exemplary model to illustrate the different properties of the low-frequency modes of a multi-domain protein, which occurs in two well distinct structural states (open and closed states). The role of the low-frequency modes in the transition between the two states of Hsp70 is analyzed in detail. It is shown that the low-frequency modes provide an easy means of communication between protein domains separated by a large distance.

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  1. Laboratoire Interdisciplinaire Carnot de Bourgogne, Unité Mixte de Recherche 6303, Centre National de la Recherche Scientifique-Université de Bourgogne, 9 Avenue Alain Savary, BP 47870, F-21078, Dijon Cedex, France

    Adrien Nicolaï, Patrice Delarue & Patrick Senet

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  1. Adrien Nicolaï
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  2. Patrice Delarue
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  3. Patrick Senet
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Correspondence to Adrien Nicolaï .

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  1. , Faculty of Chemistry, University of Gdansk, Sobieskiego 18, Gdansk, 80-952, Poland

    Adam Liwo

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Nicolaï, A., Delarue, P., Senet, P. (2014). Low-Frequency, Functional, Modes of Proteins: All-Atom and Coarse-Grained Normal Mode Analysis. In: Liwo, A. (eds) Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes. Springer Series in Bio-/Neuroinformatics, vol 1. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-28554-7_15

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  • DOI: https://doi.org/10.1007/978-3-642-28554-7_15

  • Publisher Name: Springer, Berlin, Heidelberg

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