Protein Conformational Dynamics

In this book, we will probe the question how biological molecules exert their functionality and regulate biological processes. We suggest that the conformational dynamics of proteins is critical in regulating biological functions and/or catalyzing biochemical reactions. In last decade, the advancements in computational biology, nuclear magnetic resonance including paramagnetic relaxation enhancement, and fluorescence-based ensemble/single-molecule techniques have shown that biological molecules (proteins, DNAs and RNAs) fluctuate under equilibrium conditions. The conformational and energetic spaces that these fluctuations explore likely contain active conformations that are critical for their function. More interestingly, these fluctuations can respond actively to external cues, so that they can exert layers of tight regulations on the biological processes that they dictate. A growing number of studies have suggested that conformational dynamics of proteins governs their role in regulating biological functions, e.g. signaling transduction, molecular recognition, apoptosis, protein/ion/other molecules translocation, gene expression, et al. On the experimental side, advances in nuclear magnetic resonance including paramagnetic relaxation enhancement, and fluorescence-based ensemble/single-molecule techniques have offered deep insights in the conformational motions of a number of proteins. These studies greatly enrich our knowledge in the interplay between structure and function. On the theoretical side, novel theoretical approaches and detailed computational simulations have provided powerful tools in the study of enzyme catalysis, protein/drug design, protein/ion/other molecule translocation, protein folding/aggregation et al. These work contain detailed information not only in the conformational motions of a biological system, but also in the potential govern force of the conformational dynamics (transient interactions, chemical and physical origins, thermodynamic properties). Therefore, new development in computational simulations will greatly harness our understanding of how these molecules function in various biological events. In this book, we review recent progress in theoretical and computational studies of protein dynamics.