This definitive work provides a comprehensive treatment of the mathematical background and working methods of three-dimensional reconstruction from tilt series. Special emphasis is placed on the problems presented by limitations of data collection in the transmission electron microscope.

The book, extensively revised and updated, takes the reader from biological specimen preparation to three-dimensional images of the cell and its components.

Volume One of this two-volume sequence focuses on the basic characterization of known protein structures, and structure prediction from protein sequence information. Eleven chapters survey of the field, covering key topics in modeling, force fields, classification, computational methods, and structure prediction. Each chapter is a self contained review covering definition of the problem and historical perspective; mathematical formulation; computational methods and algorithms; performance results; existing software; strengths, pitfalls, challenges, and future research.

The actin cytoskeleton plays a central role in many cellular processes including cell motility, cytokinesis, endocytosis and phagocytosis. The structure and dynamics of the actin cytoskeleton is regulated by a large number of proteins that interact with monomeric and/or filamentous actin. Actin Monomer Binding Proteins provides a comprehensive view on actin monomer-binding proteins and the mechanisms by which they contribute to actin dynamics and various actin-dependent cellular processes. This new title contains chapters that describe the basic mechanisms of actin dynamics as well as the structural principles by which various actin-binding proteins interact with actin.

Volume Two of this two-volume sequence presents a comprehensive overview of protein structure prediction methods and includes protein threading, De novo methods, applications to membrane proteins and protein complexes, structure-based drug design, as well as structure prediction as a systems problem. A series of appendices review the biological and chemical basics related to protein structure, computer science for structural informatics, and prerequisite mathematics and statistics.

A comprehensive guide to the revolutionary area of systems biology and its application in cell culture engineering, this volume presents an overall picture of the current topics central to structural and functional genomics, proteomics, metabolomics and bioinformatics, including such hot topics as RNAi, metabolic engineering and unfolded protein response. It includes reviews of the cellular response of environmental modulation such as low temperature and osmolarity, critical assessments of the applications of metablomics and fluxomics approaches, examination of the utility of modulation of key genes and a presentation of a theory of chemical organisation which provides new view on the system's structure. The clearly written chapters by experts in the field describe methods applicable to investigating the unique facets of cell culture.

X-ray crystallography has long been a vital method for studying the structure of proteins and other macromolecules. As the importance of proteins continues to grow, in fields from biochemistry and biophysics to pharmaceutical development and biotechnology, many researchers have found that a knowledge of X-ray diffraction is an indispensable tool. In this new edition of his essential work, Dr. Jan Drenth, recognized internationally for his numerous contributions to crystallographic research, has provided an up-to-date and technically rigorous introduction to the subject. Principles of Protein X-ray Crystallography provides the theoretical background necessary to understand how the structure of proteins is determined at atomic resolution. It is intended to serve as an introduction for graduate students, postdoctoral researchers, and established scientists who want to use protein crystallography in their own endeavors, or need to understand the subject in order to critically evaluate the literature. New additions to the book include a section on twinning, an additional chapter on crystal growth and a discussion of single-wavelength anomalous dispersion (SAD).

The contents of this book focus on the recent investigations in molecular bi- ogywhereapplicationsoftopologyseemtobeverystimulating. Thevolumeis based on the talks and lectures given by participants of the three-month p- gram"TopologyinCondensedMatter,"whichwasheldintheMaxPlanck- stitut fur Physik komplexer Systeme, Dresden, Germany, 8May-31July 2002, under the scienti?c direction of Professors M. Kl eman, S. Novikov and - self. The aim of this program was to discuss recent applications of topology to several areas in condensed matter physics and molecular biology. The ?rst volume "Topology in Condensed Matter" is concerned with m- ern applications of geometrical and topological techniques to such new and classic ?elds of physics like electron theory of metals, theory of nano-crystals, aperiodic and liquid crystals, quantum computation and so on. This volume is published simultaneously in "Springer Series in Solid-State Physics." The present volume gives an exposition of the role of topology in the theory of proteins and DNA. The last thirty years a?rmed very e?cient - plications of modern mathematics, especially topology, in physics. The union of mathematics and physics was very stimulating for both sides. On the other hand, the impact of mathematics in biology has been rather limited. H- ever here also some interesting results were obtained. In particular, there are applications of knot theory in the theory of circular closed DNA. The - cent discoveries in molecular biology indicate future successful applications of topology."

When I received an invitation from Ron Landes (Landes Bioscience) to edit a book on CtBP family proteins, I was gratified to realize that the importance of these proteins has reached the level of deserving a 'separate' book. As the reader can see, there has been significant advancement in our understanding of the fijnctions of these proteins in the past ten years since CtBPl was cloned in our laboratory. Genetic and biochemical studies with Drosophila provided the critical evidence to show that dCtBP is a transcriptional CO repressor. Genetic studies with mutant mice have established that these proteins are essential for animal development. The CtBP family proteins are unique in several aspects. They were the first among proteins containing a metabolic enzyme fold to be implicated in transcriptional regulation. The vertebrate CtBPs exhibit distinct nuclear and cytosolic activities. The crystal struaures of CtBPl and molecular modeling studies have illuminated the mo- lecular basis of its dual activity and the interaction with target peptides. The organization of the vertebrate CtBP2 gene has provided a novel example of genomic consolidation indicating how a single gene could code for two di- verse proteins. I believe that this book will be a valuable reference source for new researchers to understand more about the CtBP family proteins and their role in growth, development and oncogenesis.

Protein Phosphatase Protocols presents a broad range of protocols for the study of protein phosphatases, all written by experts and innovators from phosphatase laboratories around the world. This volume is a compendium of resources for the study of protein phosphatases and their potential as drug targets. Experimental methodologies are taken from proteomics, bioinformatics, genomics, biochemistry, RNAi, and genetics.

This book brings together three decades worth of collaborative research to address the question "What sustains life?" In part a scientific response to Schroedinger's work "What is Life?" Urry's text contains elements of memoir, history, and a solid, informative scientific core that will interest both the general reader, student, and professional researcher.

Protein engineering is a fascinating mixture of molecular biology, protein structure analysis, computation, and biochemistry, with the goal of developing useful or valuable proteins. Protein Engineering Protocols will consider the two general, but not mutually exclusive, strategies for protein engineering. The first is known as rational design, in which the scientist uses detailed knowledge of the structure and function of the protein to make desired changes. The s- ond strategy is known as directed evolution. In this case, random mutagenesis is applied to a protein, and selection or screening is used to pick out variants that have the desired qualities. By several rounds of mutation and selection, this method mimics natural evolution. An additional technique known as DNA shuffling mixes and matches pieces of successful variants to produce better results. This process mimics recombination that occurs naturally during sexual reproduction. The first section of Protein Engineering Protocols describes rational p- tein design strategies, including computational methods, the use of non-natural amino acids to expand the biological alphabet, as well as impressive examples for the generation of proteins with novel characteristics. Although procedures for the introduction of mutations have become routine, predicting and und- standing the effects of these mutations can be very challenging and requires profound knowledge of the system as well as protein structures in general.

The adsorption of proteins at interfaces plays a role in many ?elds, such as health, food, environment and analysis. Fundamental aspects are useful when considering applications. We focus here especially on solid-liquid interfaces and present a few fundamental studies regarding adsorption - netics and conformational changes, and examples of applications to sensors and membranes. The ?rst part is dedicated to fundamental studies performed using - tical waveguide lightmode spectroscopy, as an example of a technique that has the advantage of not requiring labelled proteins, but is limited to s- ci?c supports. Conversely, the radiolabelling of proteins, which has the disadvantage of any labelling process, allows application to any kind of s- faces. As proteins bear both positive and negative charges, we can expect thein?uenceofanelectric?eldnormaltothe interfaceonthe pack- ing order at interfaces. The re?ning of data treatment may also lead to the determination of useful structural parameters. The balance between protein-surface and protein-protein interactions is a key point for the - scription of the structure at high coverage of the surface. Electrokinetic methods, like measurement of the streaming potential, may be helpful in the electrical characterisation of the interfacial layer facing the solution. The second part includes different bench techniques that were dev- oped to improve the sensitivity of the characterisation of the orientation and structure of the proteins at interfaces: dual polarisation interferometry and total internal re?ection ellipsometry are such recent examples.

Protein Folding Protocols presents protocols for studying and characterizing protein folding from the unfolded to the folded state. Covering experiment and theory, bioinformatics approaches, and state-of-the-art simulation protocols for better sampling of the conformational space, this volume describes a broad range of techniques to study, predict, and analyze the protein folding process.
Protein Folding Protocols also provides sample approaches toward the prediction of protein structure starting from the amino acid sequence, in the absence of overall homologous sequences. These approaches have tremendous implications, ranging from drug design, functional assignment, comprehension of the nature of regulation, understanding molecular machines, viral entry into cells, and putting together cellular pathways and their dynamics.

Recent major advances in our understanding of modulating protein functions has led to the development of new methods and algorithms to predict and decipher how amino acid sequences shape three-dimensional structures. Protein Design: Methods and Applications presents the most up-to-date protein design and engineering strategies so that readers can undertake their own projects with a maximum chance of success.
The authors present integrated computational approaches that require various degrees of computational complexity, and the major accomplishments that have been achieved in the design and structural characterization of helical peptides and proteins. Other topics of discussion include: design of structural elementary motifs, entire proteins, and interfaces of protein complexes, and of amyloidogenic polypeptides and amyloid inhibitors.
Authoritative and cutting-edge, Protein Design: Methods and Applications will be of major interest to protein scientists, biochemists, and all experimentalists selecting the strategy most adaptable for their design problem.

This text provides an up-to-date collection of theoretical and experimental studies into protein folding, misfolding, aggregation, and stability. Additionally, issues faced during the development of protein products are illustrated. It contains an introductory chapter for readers new to the protein folding field. The book provides a thorough and clear discussion of computational approaches to understanding and modeling protein aggregation.

Leading researchers and innovators describe in step-by-step detail the latest techniques that promise to significantly impact the practice of proteomics, as well as its success in developing novel clinical agents. The methods span the entire spectrum of top-down and bottom-up approaches, including microarrays, gels, chromatography, and affinity separations, and address every aspect of the human proteome, both quantitatively and qualitatively. The techniques of protein detection utilized are diverse and range from fluorescence and resonance light scattering to surface plasmon resonance and mass spectrometry. The protocols follow the successful Methods in Molecular Biology (TM) series format, each offering step-by-step laboratory instructions, an introduction outlining the principles behind the technique, lists of the necessary equipment and reagents, and tips on troubleshooting and avoiding known pitfalls.

Biological membranes have long been identified as key elements in a wide variety of cellular processes including cell defense communication, photosynthesis, signal transduction, and motility; thus they emerge as primary targets in both basic and applied research. This book brings together in a single volume the most recent views of experts in the area of proteina "lipid interactions, providing an overview of the advances that have been achieved in the field in recent years, from very basic aspects to specialized technological applications. Topics include the application of X-ray and neutron diffraction, infrared and fluorescence spectroscopy, and high-resolution NMR to the understanding of the specific interactions between lipids and proteins within biological membranes, their structural relationships, and the implications for the biological functions that they mediate. Also covered in this volume are the insertion of proteins and peptides into the membrane and the concomitant formation of definite lipid domains within the membrane.

This book addresses the most recent advances in the transport of proteins across a variety of biological membranes. In addressing this topic, this volume includes several new twists not previously addressed in the literature. In the last few years, the study of protein translocation has been revolutionized by the availability of structural information on many of the components and complexes involved in the process. Unlike earlier books written on protein translocation, this volume considers these advances. In addition, several chapters discuss facets of protein translocation from a systems biology perspective, considered by many to be the next paradigm for biological study. Readers of this book will come away with a deeper understanding of the problems facing researchers of protein translocation and see how the most modern biological techniques and approaches are being recruited to answer those questions. The chapters are also written such that problems awaiting future investigation are clearly presented.

Molecular chaperones are involved in a wide variety of essential cellular processes in living cells. A subset of molecular chaperones have been initially described as heat shock proteins protecting cells from stress damage by keeping cellular proteins in a folding competent state and preventing them from irreversible aggregation. Later it became obvious that molecular chaperones are also expressed constitutively in the cell and are involved in complex processes such as protein synthesis, intracellular protein transport, post-translational modification and secretion of proteins as well as receptor signalling. Hence, it is not surprising that molecular chaperones are implicated in the pathogenesis of many relevant diseases and could be regarded as potential pharmacological targets. Starting with the analysis of the mode of action of chaperones at the molecular, cellular and organismic level, this book will then describe specific aspects where modulation of chaperone action could be of pharmacological and therapeutic interest.

Protein Folding Kinetics - Biophysical Methods (2nd Edition) gives a deep insight into the principles and concepts of the kinetic and structural resolution of fast chemical and biophysical reactions of proteins with emphasis on protein-folding reactions. The study of fast protein-folding reactions and the understanding of the folding paradox have significantly advanced due to the recent development of new biophysical methods which allow not only kinetic resolution in the sub-millisecond time scale but also structural resolution with unprecedented precision. Pathways and structures of early and late folding events and the transition state structures of fast- and ultrafast-folding proteins can now be studied in far more detail. Important techniques include biophysical, chemical, molecular biological and mathematical methods, in particular protein engineering, Phi-value analysis, time-resolved circular dichroism, optical triggers and pulsed infrared LASER methods, pressure and temperature jump, ultrafast mixing, stopped flow and quenched flow, dielectric relaxation and electric-field-jump, acoustic relaxation, fluorescence- and isotope-labeling, H/D exchange methods, NMR line broadening and stopped-flow NMR, transition state theory, solutions of rate equations, and evolutionary computer programming. Protein Folding Kinetics - Biophysical Methods is written for students and researchers in biochemistry, biophysics, and related fields.

Special features in the second edition:

-Includes detailed information and 12 color figures on the high resolution of folding transition states.

-Discusses structural determinants of the rate of protein folding on a timescale from microseconds to seconds.

-Provides information on self-evolving computer programs for protein-folding simulations and protein-structure predictions.

In Viral Membrane Proteins Structure, Function, and Drug Design, Wolfgang Fischer summarizes the current structural and functional knowledge of membrane proteins encoded by viruses. In addition, contributors to the book address questions about proteins as potential drug targets. The range of information covered includes signal proteins, ion channels, and fusion proteins.

This book has a place in the libraries of researchers and scientists in a wide array of fields, including protein chemistry, molecular biophysics, pharmaceutical science and research, bioanotechnology, molecular biology, and biochemistry.

A readily reproducible collection of established and emerging techniques for studying the interaction between proteins and ligands, including biochemical/bulk techniques, structure analysis, spectroscopy, single-molecule studies, and theoretical/computational tools. Among the highlights are surface plasmon resonance (SPR) and reflectometric biosensor approaches, high-throughput screening with confocal optics microscopy, single molecule fluorescence and fluorescence correlation spectroscopy (FCS), atomic force microscopy (AFM), crystallography of reaction intermediates, and time-resolved x-ray crystallography. The protocols follow the successful Methods in Molecular Biologya"[ series format, each offering step-by-step laboratory instructions, an introduction outlining the principle behind the technique, lists of the necessary equipment and reagents, and tips on troubleshooting and avoiding known pitfalls.

Hands-on researchers describe in step-by-step detail 73 proven laboratory methods and bioinformatics tools essential for analysis of the proteome. These cutting-edge techniques address such important tasks as sample preparation, 2D-PAGE, gel staining, mass spectrometry, and post-translational modification. There are also readily reproducible methods for protein expression profiling, identifying protein-protein interactions, and protein chip technology, as well as a range of newly developed methodologies for determining the structure and function of a protein. The bioinformatics tools include those for analyzing 2D-GEL patterns, protein modeling, and protein identification. All laboratory-based protocols follow the successful Methods in Molecular Biology (TM) series format, each offering step-by-step laboratory instructions, an introduction outlining the principle behind the technique, lists of the necessary equipment and reagents, and tips on troubleshooting and avoiding known pitfalls.

Leading experts in nanobiotechnology comprehensively review the most recent advances in instrumentation and methodology, as well as their applications in genomics and proteomics. The authors provide a wide variety of techniques and methods for dealing with protein functions and structures at the nanoscale level, including nanostructured systems, nanomaterials, carbon nanotubes and nanowires, optical nanosensors, and nanoelectrodes. Among the highlights are techniques for the in vivo tracking of biochemical processes using fluorescent molecular probes and nanosensors, and the exploration of biochemical processes and submicroscopic structures of living cells at unprecedented resolutions using near-field optics. Also discussed is the development of nanocarrier methodology for the targeted delivery of drugs whose shells are conjugated with antibodies for targeting specific antigens.

How one goes about analyzing proteins is a constantly evolving ?eld that is no longer solely the domain of the protein biochemist. Inves- gators from diverse disciplines ?nd themselves with the unanticipated task of identifying and analyzing a protein and studying its physical properties and biochemical interactions. In most cases, the ultimate goal remains understanding the role(s) that the target protein is playing in cellular physiology. It was my intention that this manual would make the initial steps in the discovery process less time consuming and less intimidating. This book is not meant to be read from cover to cover. The expanded Table of Contents and the index should help locate what you are seeking. My aim was to provide practically oriented information that will assist the experimentalist in benchtop problem solving. The appendices are ?lled with diverse information gleaned from catalogs, handbooks, and manuals that are presented in a distilled fashion designed to save trips to the library and calls to technical service representatives. The user is encouraged to expand on the tables and charts to 't individual experimental situations. This second edition pays homage to the computer explosion and the various genome projects that have revolutionized how benchtop scienti?c research is performed. Bioinformatics and In silico science are here to stay. However, the second edition still includes recipes for preparing buffers and methods for lysing cells.