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In the second part of my thesis I will focus on the influence of aqueous solvent on protein structures. Water is present in all biological systems, where it is not only a static medium of the reaction, but also an active part of the process called life, and it requires careful treatment. I compare models of implicit and explicit solvation for beta-turns, alpha-helices, and beta-sheets. I find that solvation by small water clusters can alter the molecular properties of gas phase molecules and continuous methods are not able to model all effects.
There has been improvement in robust prediction of secondary structure of real proteins. New models of aqueous solvation have been used to predict energy surface descriptions for protein structure.
Volume 72, Peptide Solvation and H-bonds, addresses the role of peptide backbone solvation in the energetics of protein folding. Particular attention is focused on modeling and computation. This volume will be of particular interest to biophysicists and structural biologists. Challenges the longstanding and basic assumptions of structural biology Discusses how to solve the problem of protein structure prediction Addresses the quantitation of the energetics of folding
Advances in Protein Chemistry
This book discusses how biological molecules exert their function and regulate biological processes, with a clear focus on how conformational dynamics of proteins are critical in this respect. In the 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, which introduces layers of tight regulation on the biological processes that they dictate. A growing number of studies have suggested that conformational dynamics of proteins govern their role in regulating biological functions, examples of this regulation can be found in signal transduction, molecular recognition, apoptosis, protein / ion / other molecules translocation and gene expression. On the experimental side, the technical advances have offered deep insights into the conformational motions of a number of proteins. These studies greatly enrich our knowledge of the interplay between structure and function. On the theoretical side, novel approaches and detailed computational simulations have provided powerful tools in the study of enzyme catalysis, protein / drug design, protein / ion / other molecule translocation and protein folding/aggregation, to name but a few. This work contains detailed information, not only on the conformational motions of biological systems, but also on the potential governing forces of conformational dynamics (transient interactions, chemical and physical origins, thermodynamic properties). New developments in computational simulations will greatly enhance our understanding of how these molecules function in various biological events.
The interfacial behaviour of surfactants and proteins, and their mixtures, is of importance in a wide range of areas such as food technology, detergency, cosmetics, coating processes, biomedicine, pharmacy and biotechnology. Methods such as surface and interfacial tension measurements and interfacial dilation and shear rheology characterise the relationships between these interfacial properties and the complex behaviour of foams and emulsions is established. Recently-developed experimental techniques, such as FRAP which enable the measurement of molecular mobility in adsorption layers, are covered in this volume. The development of theories to describe the thermodynamic surface state or the exchange of matter for proteins and protein/surfactant mixtures is also described. Features of this book: • Reflects the state-of-the-art research and application of protein interfacial layers rather than a snapshot of only some recent developments. • Emphasis is placed on experimental details as well as recent theoretical developments. • New experimental techniques applied to protein interfacial layers are described, such as FRAP or ADSA, or rheological methods to determine the mechanical behaviour of protein-modified interfaces. • A large number of practical applications, ranging from emulsions relevant in food technology for medical problems such as lung surfactants, to the characterisation of foams intrinsic to beer and champagne production. The book will be of interest to research and university institutes dedicated to interfacial studies in chemistry, biology, pharmacy, medicine and food engineering. Industrial departments for research and technology in food industry, pharmacy, medicine and brewery research will also find this volume of value.
The volume presents a survey of the research by Kurt Wüthrich and his associates during the period 1965 to 1994. A selection of reprints of original papers on the use of NMR spectroscopy in structural biology is supplemented with an introduction, which outlines the foundations and the historical development of the use of NMR spectroscopy for the determination of three-dimensional structures of biological macromolecules in solution. The original papers are presented in groups highlighting protein structure determination by NMR, studies of dynamic properties and hydration of biological macromolecules, and practical applications of the NMR methodology in fields such as enzymology, transcriptional regulation, immunosuppression and protein folding.