7. Molecular Dynamics of Proteins and Their Functional Activity

This chapter presents a brief overview of physical and computer methods for studying the mechanisms and frequencies of the molecular dynamics of proteins and enzymes, illustrated with typical examples. The list of methods used includes the following: spin and Mössbauer labels and probes, fluorescence quenching, fluorescence dynamic Stokes shift, Förster resonance energy transfer (FRET), nuclear magnetic resonance, differential scanning calorimetry, small-wide-angle X-ray scattering, femtosecond time-resolved X-ray solution scattering, and neutron scattering. Protein dynamics occur at time scales from millisecond to subfemtosecond. The range of time-scales involved in substrate turnover step of enzyme catalyzed reactions and internal protein dynamics are similar. The protein motions necessary for catalysis are an intrinsic property of the enzyme and may limit the overall turnover rate. Recent works on selected protein systems have addressed the role of dynamics in enzyme evolution. In some cases, connections among hydration layer dynamics, solvation shell structure, protein surface structure and their function has been revealed. Particular attention was paid to works in which a relationship is established between specific stages of the enzymatic process and specific molecular dynamic modes.