A look at the methods and algorithms used to predict protein structure

A thorough knowledge of the function and structure of proteins is critical for the advancement of biology and the life sciences as well as the development of better drugs, higher-yield crops, and even synthetic bio-fuels. To that end, this reference sheds light on the methods used for protein structure prediction and reveals the key applications of modeled structures. This indispensable book covers the applications of modeled protein structures and unravels the relationship between pure sequence information and three-dimensional structure, which continues to be one of the greatest challenges in molecular biology.

With this resource, readers will find an all-encompassing examination of the problems, methods, tools, servers, databases, and applications of protein structure prediction and they will acquire unique insight into the future applications of the modeled protein structures. The book begins with a thorough introduction to the protein structure prediction problem and is divided into four themes: a background on structure prediction, the prediction of structural elements, tertiary structure prediction, and functional insights. Within those four sections, the following topics are covered: Databases and resources that are commonly used for protein structure predictionThe structure prediction flagship assessment (CASP) and the protein structure initiative (PSI)Definitions of recurring substructures and the computational approaches used for solving sequence problemsDifficulties with contact map prediction and how sophisticated machine learning methods can solve those problemsStructure prediction methods that rely on homology modeling, threading, and fragment assemblyHybrid methods that achieve high-resolution protein structuresParts of the protein structure that may be conserved and used to interact with other biomoleculesHow the loop prediction problem can be used for refinement of the modeled structuresThe computational model that detects the differences between protein structure and its modeled mutant

Whether working in the field of bioinformatics or molecular biology research or taking courses in protein modeling, readers will find the content in this book invaluable.

This book offers a comprehensive overview of the microbiological fundamentals and biotechnological applications of methanotrophs: aerobic proteobacteria that can utilize methane as their sole carbon and energy source. It highlights methanotrophs' pivotal role in the global carbon cycle, in which they remove methane generated geothermally and by methanogens. Readers will learn how methanotrophs have been employed as biocatalysts for mitigating methane gas and remediating halogenated hydrocarbons in soil and underground water. Recently, methane has also attracted considerable attention as a potential next-generation carbon feedstock for industrial biotechnology, because of its abundance and low price. Methanotrophs can be used as biocatalysts for the production of fuels, chemicals and biomaterials including methanobactin from methane under environmentally benign production conditions. Sharing these and other cutting-edge insights, the book offers a fascinating read for all scientists and students of microbiology and biotechnology.

This book introduces characteristic features of the protein structure prediction (PSP) problem. It focuses on systematic selection and improvement of the most appropriate metaheuristic algorithm to solve the problem based on a fitness landscape analysis, rather than on the nature of the problem, which was the focus of methodologies in the past. Protein structure prediction is concerned with the question of how to determine the three-dimensional structure of a protein from its primary sequence. Recently a number of successful metaheuristic algorithms have been developed to determine the native structure, which plays an important role in medicine, drug design, and disease prediction. This interdisciplinary book consolidates the concepts most relevant to protein structure prediction (PSP) through global non-convex optimization. It is intended for graduate students from fields such as computer science, engineering, bioinformatics and as a reference for researchers and practitioners.

This book presents various examples of how advanced fluorescence and spectroscopic analytical methods can be used in combination with computer data processing to address different biochemical questions. The main focus is on evolutionary biochemistry and the description of biochemical and metabolic issues; specifically, the use of pulse amplitude modulated fluorescence (PAM) for the functional analysis of the cellular state, as well as results obtained by means of the derivative spectroscopy method characterizing structural reorganization of a cell under the influence of external factors, are discussed. The topics presented here will be of interest to biologists, geneticists, biophysicists and biochemists, as well as experts in analytical chemistry, pharmaceutical chemistry and radio chemistry and radio activation studies with protonen and alpha-particles. It also offers a valuable resource for advanced undergraduate and graduate students in biological, physical and chemical disciplines whose work involves derivative spectrophotometry and PAM-fluorescence.

This volume provides protocol references covering recent developments in the aptamer field. Within the last decade, aptamers have become more and more popular, and their sophisticated biophysical properties together with their ability to be easily modified and, thus, adapted to various regimens makes them a very promising class of compounds. Divided into three sections, the book covers selection, a series of analytical methods to assess biophysical properties of aptamer-target interactions, as well as various applications of aptamers. Written for the highly successful Methods in Molecular Biology series, 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. Practical and easy to follow, Nucleic Acid Aptamers: Selection, Characterization, and Application provides a state-of-the-art summary of recent developments in the aptamer field and will be a helpful resource for scientists in the life sciences working with aptamers as tools to elucidate biological systems.

Rapid progress has been made in our understanding of the molecular mechanisms of cell growth and oncogenesis during the past decade. Special attention has been given to the presentation of the frequently neglected close correlation between changes in signal transduction and metabolic pathways during oncogenesis. This book advances the knowledge of mechanisms regulating metabolism and functioning of vitamin A and offers the most recent results of research on the clinical efficiency of retinoids in skin disorders and cancer. The book presents recent findings on the regulation of cell growth in normal and neoplastic tissues by growth factors including hormones, and by the activation and inactivation of oncogenes and tumor suppressor genes, respectively. It also offers a survey of the molecular and cell biochemistry of retinoids. Basic researchers in biochemistry, pharmacology and cell biology as well as clinicians will find this book very informative and up-to-date. This book advances the knowledge of mechanisms regulating metabolism and functioning of vitamin A and offers the most recent results of research on clinical efficiency of retinoids in skin disorders and cancer. Basic researchers in biochemistry, pharmacology, cell biology, and clinicians will find this book very informative and up-to-date. The chapters, organized in six sections, are contributed by leading scientists who have been working in the retinoid field for decades. Their experience and competence is aknowledged worldwide.

This book discusses the latest developments in plant-mediated fabrication of metal and metal-oxide nanoparticles, and their characterization by using a variety of modern techniques. It explores in detail the application of nanoparticles in drug delivery, cancer treatment, catalysis, and as antimicrobial agent, antioxidant and the promoter of plant production and protection. Application of these nanoparticles in plant systems has started only recently and information is still scanty about their possible effects on plant growth and development. Accumulation and translocation of nanoparticles in plants, and the consequent growth response and stress modulation are not well understood. Plants exposed to these particles exhibit both positive and negative effects, depending on the concentration, size, and shape of the nanoparticles. The impact on plant growth and yield is often positive at lower concentrations and negative at higher ones. Exposure to some nanoparticles may improve the free-radical scavenging potential and antioxidant enzymatic activities in plants and alter the micro-RNAs expression that regulate the different morphological, physiological and metabolic processes in plant system, leading to improved plant growth and yields. The nanoparticles also carry out genetic reforms by efficient transfer of DNA or complete plastid genome into the respective plant genome due to their miniscule size and improved site-specific penetration. Moreover, controlled application of nanomaterials in the form of nanofertilizer offers a more synchronized nutrient fluidity with the uptake by the plant exposed, ensuring an increased nutrient availability. This book addresses these issues and many more. It covers fabrication of different/specific nanomaterials and their wide-range application in agriculture sector, encompassing the controlled release of nutrients, nutrient-use efficiency, genetic exchange, production of secondary metabolites, defense mechanisms, and the growth and productivity of plants exposed to different manufactured nanomaterials. The role of nanofertilizers and nano-biosensors for improving plant production and protection and the possible toxicities caused by certain nanomaterials, the aspects that are little explored by now, have also been generously elucidated.

Retinoids have received considerable attention in recent years and due cognizance has been given to their versatility as biological response modifiers, as evidenced by the virtually explosive growth of literature in this field in the past few years. This volume has been designed to give a current state-of-the-art picture of retinoids. The perceived potential of retinoids in the treatment of certain disease stated has initiated attempts at identifying and synthesizing new retinoid derivatives with definable and selective effects on aberrant biological phenomena. Appropriately, therefore, we begin with the chemistry of retinoids and their derivatives together with discussions of their biological activity. Major advances have been made in understanding the mechanisms by which retinoids modulate physiological and phenotypic traits of cells. The transduction of retinoid signaling by the mediation of nuclear receptors of the steroid/thyroid receptor superfamily has now been studied extensively and the cloning and defining the characteristics of these receptors has been a focus of discussion in this volume. Retinoids also markedly modulate the transduction of extracellular signals such as those imparted by growth factors and hormones, and thus actively influence and control cellular proliferative patterns. Retinoids can alter epidermal growth factor receptor expression (Kawaguchi et al., 1994), responsiveness to thyroid hormone (Esfandiari et al., 1994; Pallet et al., 1994), inhibit the proliferative responses of hematopoietic progenitor cells to granulocyte colony stimulating factor (Smeland et al., 1994), and modulate secretion on interleukins by leukaemic cells (Balitrand et al., 1994), among other things. This has obvious implications for pharmacological manipulation of deregulated growth (Dickens and Colletta, 1993; Mulshine et al., 1993). Apoptosis is another component in the regulation of growth control. Apoptotic cell death is influenced by several agents and retinoids may function by interfering with apoptotic pathways of regulation of growth control and quite legitimately, therefore, the importance of this aspect of retinoid function has been duly recognized here.

The aim of this book is to show how supramolecular complexity of cell organization can dramatically alter the functions of individual macromolecules within a cell. The emergence of new functions which appear as a consequence of supramolecular complexity, is explained in terms of physical chemistry.
The book is interdisciplinary, at the border between cell biochemistry, physics and physical chemistry. This interdisciplinarity does not result in the use of physical techniques but from the use of physical concepts to study biological problems.
In the domain of complexity studies, most works are purely theoretical or based on computer simulation. The present book is partly theoretical, partly experimental and theory is always based on experimental results. Moreover, the book encompasses in a unified manner the dynamic aspects of many different biological fields ranging from dynamics to pattern emergence in a young embryo.
The volume puts emphasis on dynamic physical studies of biological events. It also develops, in a unified perspective, this new interdisciplinary approach of various important problems of cell biology and chemistry, ranging from enzyme dynamics to pattern formation during embryo development, thus paving the way to what may become a central issue of future biology.

This book sheds new light on the current state of knowledge concerning chromatin organization. Particular emphasis is given to the new imaging potential offered by super-resolution microscopy, which allows DNA imaging with a very high labeling density. From the early work on chromosomes by Walther Flemming in the nineteenth century to recent advances in genomics, the history of chromatin research now spans more than a century. The various milestones, such as the discovery of the double helix structure, the sequencing of the human genome, and the recent description of the genome in 3D space, show that understanding chromatin and chromosome function requires a clear understanding of its structure. Presenting cutting-edge data from super-resolution single molecule microscopy, the book demonstrates that chromatin manifests several levels of folding, from nucleosomes to chromosomes. Chromatin domains emerge as a new fundamental building block of chromatin architecture, with functions possibly related to gene regulation. A detailed description of chromatin folding in the pachytene stage of meiosis serves as a model for exploring this functionality, showing the apparent interplay between structure, function, and epigenetic regulation. Lastly, the book discusses possible new avenues of innovation to describe chromatin's organization and functions. Gathering essential insights on chromatin architecture, the book offers students an introduction to microscopy and its application to chromatin organization, while also providing advanced readers with new ideas for future research.

Hsp90 in Cancer: Beyond the Usual Suspects, the latest volume in the Advances in Cancer Research series, focuses on the multifunctional molecular chaperone Hsp90 which regulates the post-translational stability and function of a broad repertoire of client proteins and discusses some of the lesser-known aspects of how Hsp90 and its related family members enable oncogenic transformation and malignant progression.

Leading researchers are specially invited to provide a complete understanding of the key topics in these archetypal multidisciplinary fields. In a form immediately useful to scientists, this periodical aims to filter, highlight and review the latest developments in these rapidly advancing fields.

This detailed volume explores numerous histochemical techniques through a series of lab-tested protocols for the detection of specific molecules or metabolic processes, both at light and electron microscopy. More in detail, the book is divided into six sections covering a variety of chemical targets. It begins with a section on vital histochemistry and continues with chapters on histochemistry as it relates to lectins, proteins, lipids, DNA and RNA, as well as plants. The volume also contains four overview chapters on vital histochemistry, lectin histochemistry, and DNA fluorochromes. Written for the highly successful Methods in Molecular Biology series, 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. Authoritative and practical, Histochemistry of Single Molecules: Methods and Protocols aims to effectively help scientists in very different research fields to elucidate biological issues though a unique approach to molecular biology in situ.

This volume details a comprehensive and extensive set of protocols for the study of autophagy in vitro and in vivo. Chapters focus on mammals, various model organisms, and provide protocols for the study of autophagy-related processes outside of the canonical autophagy pathways. 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. Authoritative and cutting-edge, Autophagy: Methods and Protocols aims to ensure successful results in the further study of this vital field.

The papers assembled in this volume were originally presented at the joint meeting of the Phytochemical Society of North America and the Mid-Atlantic Plant Molecular Biology Society, in August 2000. The symposium from which these chapters were prepared was entitled ""Regulation of Phytochemicals by Molecular Techniques"" and was organised by James Saunders and Ben Matthews. This joint meeting was timely because of recent landmark advances in molecular biology and genomics as well as the renewed interest in phytochemistry as a rich source of nutraceuticals, drugs, and alternatives to synthetic agriculture pesticides. Progress in genome sequencing in plants such as Arabidopsis and rice has been remarkable, as have expressed sequence tag (EST) projects in other plants, including maize and soybean. Recently, private and public sector participants of the Human Genome Project announced that a rough draft of the human genome has been constructed. These advances directly influence phytochemical investigations by providing both insight and tools for exploring and manipulating genomes.
The chapters cover a wide range of applications from molecular biology to phytochemistry, and from basic studies on promoters and gene expression to pathway regulation and engineering with transformed plants. A number of noteworthy aspects emerge from this volume: applications of molecular biology to phytochemical practical problems are succeeding; newly emerging molecular tools promise to open new doors to discovery; and remarkable progress has already occurred in phytochemical pathway engineering.

Recent advances in protein structural biology, coupled with new developments in human genetics, have opened the door to understanding the molecular basis of many metabolic, physiological, and developmental processes in human biology. Medical pathologies, and their chemical therapies, are increasingly being described at the molecular level. For single-gene diseases, and some multi-gene conditions, identification of highly correlated genes immediately leads to identification of covalent structures of the actual chemical agents of the disease, namely the protein gene products. Once the primary sequence of a protein is ascertained, structural biologists work to determine its three-dimensional, biologically active structure, or to predict its probable fold and/or function by comparison to the data base of known protein structures. Similarly, three-dimensional structures of proteins produced by microbiological pathogens are the subject of intense study, for example, the proteins necessary for maturation of the human HIV virus. Once the three-dimensional structure of a protein is known or predicted, its function, as well as potential binding sites for drugs that inhibit its function, become tractable questions. The medical ramifications of the burgeoning results of protein structural biology, from gene replacement therapy to "rational" drug design, are well recognized by researchers in biomedical areas, and by a significant proportion of the general population. The purpose of this book is to introduce biomedical scientists to important areas of protein structural biology, and to provide an insightful orientation to the primary literature that shapes the field in each subject.
The chapters in this volume cover aspects of protein structural biology which have led to the recognition of fundamental relationships between protein structure and function.

This volume covers some of the most widely used protocols on nanocanonical amino acids, providing details and advice for users to get each method up and running for their chosen application. Chapters have been divided into three parts describing methods for protein production in the test tube, in prokaryotes, and in eukaryotes. 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. Authoritative and practical, Noncanonical Amino Acids: Methods and Protocols aims to provide readers with techniques that enable them to design new experiments and create new areas of research.

This book is a passionate account of the scientific breakthroughs that led to the solution of the first protein structures and to the understanding of their function at atomic resolution. The book is divided into self-standing chapters that each deal with a protein or protein family. The subject is presented in a fluid, non-technical style that will engage student and scientists in biochemistry, biophysics, molecular and structure biology and physiology.