Protein folding stands as one of the major interdisciplinary challenges of the last fifteen years, involving biology, chemistry, medicine and physics. In this book solvent effects, and the related hydrophobic effect, on proteins are investigated. Using a simple lattice model of proteins, in which the solvent is semi-explicitly taken into account, thermodynamical quantities can be investigated and the crucial role the solvent plays in protein folding can be demonstrated. Of particular relevance is our observation that a simple model, in which the potential energy is described in terms of the interactions between amino-acids only, does not correctly reproduce solvent effects. Approaches like this, in which solvent effects are treated implicitly, are commonly employed in many of more sophisticated models for protein folding dynamics. Our results are then of great importance as they suggest the treatment of the solvent in these models may need to be re-examined.

This volume explores experimental and computational approaches to measuring the most widely studied protein assemblies, including condensed liquid phases, aggregates, and crystals. The chapters in this book are organized into three parts: Part One looks at the techniques used to measure protein-protein interactions and equilibrium protein phases in dilute and concentrated protein solutions; Part Two describes methods to measure kinetics of aggregation and to characterize the assembled state; and Part Three details several different computational approaches that are currently used to help researchers understand protein self-assembly. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Thorough and cutting-edge, Protein Self-Assembly: Methods and Protocols is a valuable resource for researchers who are interested in learning more about this developing field.

This book covers the theory and applications of continuum solvation models. The main focus is on the quantum-mechanical version of these models, but classical approaches and combined or hybrid techniques are also discussed. Devoted to solvation models in which reviews of the theory, the computational implementation Solvation continuum models are treated using the different points of view from experts belonging to different research fields Can be read at two levels: one, more introductive, and the other, more detailed (and more technical), on specific physical and numerical aspects involved in each issue and/or application Possible limitations or incompleteness of models is pointed out with, if possible, indications of future developments Four-colour representation of the computational modeling throughout.

Protein Actions: Principles and Modeling is aimed at graduates, advanced undergraduates, and any professional who seeks an introduction to the biological, chemical, and physical properties of proteins. Broadly accessible to biophysicists and biochemists, it will be particularly useful to student and professional structural biologists and molecular biophysicists, bioinformaticians and computational biologists, biological chemists (particularly drug designers) and molecular bioengineers. The book begins by introducing the basic principles of protein structure and function. Some readers will be familiar with aspects of this, but the authors build up a more quantitative approach than their competitors. Emphasizing concepts and theory rather than experimental techniques, the book shows how proteins can be analyzed using the disciplines of elementary statistical mechanics, energetics, and kinetics. These chapters illuminate how proteins attain biologically active states and the properties of those states. The book ends with a synopsis the roles of computational biology and bioinformatics in protein science.

Solvent Effects on Chemical Phenomena, Volume I discusses the developments in the understanding of solvent effects on chemical phenomena in solution. This five-chapter volume begins with a discussion on the general concepts of various solvation types, including positive and negative, inner and outer sphere, and mixed component. The subsequent chapter deals with the determination of the actual solvation number for single ions. A short list of the total effective hydration numbers of electrolytes determined from temperature dependence of proton shifts is also provided in this chapter. Another chapter presents a number of examples of the unusual properties of certain mixed aqueous systems. The solvent effects on reaction rates and mechanisms are highlighted in the concluding chapter. This chapter also covers various types of solvents, such as protic and dipolar aprotic. The enthalpy and entropy of activation in salvation and the Finkelstein reactions are also discussed. Research chemists and scientists, teachers, and students with courses in solution chemistry will greatly benefit from this volume.

Protein Simulation focuses on predicting how protein will act in vivo. These studies use computer analysis, computer modeling, and statistical probability to predict protein function.* Force Fields* Ligand Binding* Protein Membrane Simulation* Enzyme Dynamics* Protein Folding and unfolding simulations