Overview of Protein Motions

In this volume we summarize first the elements of protein structure and provide a brief overview of the internal motions of proteins, their relation to the structural elements, and their functional role. We then outline the theoretical methods that are being used to study motional phenomena and thermodynamics. A description is given of the potential functions that determine the important interactions, and the various approaches that can be used to study the dynamics are outlined. Since the motions of interest involve times from femtoseconds to seconds or longer, a range of dynamical methods is required. 

This chapter presents a general theoretical formulation for PCET and summarizes the applications of this theory to a wide range of experimentally relevant systems. Section 16.2 reviews the fundamental physical concepts of PCET reactions and discusses approaches for inclusion of the proton donor-acceptor motion, explicit molecular solvent and protein, and the corresponding dynamical effects. Section 16.3 provides an overview of theoretical studies of PCET reactions in solution and in proteins. General conclusions are given in Section 16.4. 

Chapter 5 provides an overview of Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry and its applications in the structural characterization of peptides and proteins. The principles of FT-ICR, that is, ion motion, ion excitation/ detection, and instrumental considerations, are discussed and an explanation of the features of FT-ICR that make it so suitable for peptide/protein analysis is presented. New methods for the fragmentation of peptide and protein ions in FT-ICR mass spectrometry, such as sustained off-resonance irradiation collision-induced dissociation (SORI-CID), infrared multiphoton dissociation (IRMPD), blackbody infrared radiative dissociation (BIRD), surface-induced dissociation (SID), and electron capture dissociation (BCD), are described in detail. Innovative hybrid FT-ICR instruments, which have recently become available, are reviewed. In conclusion, the chapter discusses the applications of FT-ICR in bottom-up and top-down proteomics. 

The theory of solvent-effects and some of its applications are overviewed. The generalized selfcon-sistent reaction field (SCRF)theory has been used to give a unified approach to quantum chemical calculations of subsystems embedded in a given milieu. The statistical mechanical theory of projected equations of motion has been briefly described. This theory underlies applications of molecular dynamics simulations to the study of solvent and thermal bath effects on carefully defined subsystem of interest. The relationship between different approaches used so far to calculate solvent effects and the general SCRF has been established. Recent work using the continuum approach to model the surrounding media is overviewed. Monte Carlo and molecular dynamics studies of solvent effects on molecular properties and chemical reactions together with simulations of solvent effects on protein structure and dynamics are reviewed. 

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