Raman and Infrared Spectra of Acoustical, Functional Modes of Proteins from All-Atom and Coarse-Grained Normal Mode Analysis

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 acoustical modes in proteins. In this chapter, the fundamentals of normal mode analysis using all-atom models and coarse-grained elastic models are reviewed. Then, they are applied to: first, a protein studied in recent single molecule experiments, conalbumin and second, to a protein intimately related to human diseases: the 70 kDa Heat-Shock Protein (Hsp70). The conalbumin protein consists of two homologous N- and C-lobes and was recently used as a benchmark protein for Extraordinary Acoustic Raman (EAR) spectroscopy. Present all-atom calculations demonstrate that acoustical modes of conalbumin recently measured experimentally are both infrared and Raman active. 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), which might be also detectable in the sub-THz frequency range by single molecule spectroscopy. The role of the low-frequency modes in the transition between the two states of Hsp70 is analyzed in details. It is shown that the low-frequency modes provide an easy means of communication between protein domains separated by a large distance.