Program

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Thursday June 25

Th3: Molecular films and 2D materials

Chair: D. Farías, Madrid, Spain

Contributed talk

Protein dynamics and function from a physicist point of view

A. Nicolaï^1,2, P. Delarue¹, and P. Senet¹

¹Laboratoire ICB, UMR 6303 CNRS-UB, Université de Bourgogne, France

²Ecole Polytechnique Fédérale de Lausanne, Suisse

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 [1,2]. In this talk, we present applications of these methods 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. [1]. Proteins can also subtend nonlinear excitations as we proven for the first time very recently by using molecular dynamics simulations and models from statistical physics [3]. How localized nonlinear excitations are related to the protein structure and sequence will be briefly described [3].

Figure 1: Typical low-frequency mode of the Human HSP70 Chaperone.

[1] A. Nicolaï, P. Delarue, P. Senet Chapter: Low-frequency, functional, modes of proteins: all-atom and coarse-grained normal mode analysis, in Comput. Methods on Study the Struct. & Dyn. of Biomolecules, Publisher: Springer-Verlag, Editors: A. Liwo, pp.483-524 (2014)

[2] F. Barakat, P. Delarue, P. Senet, unpublished

[3] A. Nicolaï, P. Delarue, P. Senet, submitted (2015)