Download or read book Analysis of Protein protein Molecular Recognition written by Simon Jeremy Hubbard and published by . This book was released on 1991 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Protein Ligand Interactions written by Hans-Joachim Böhm and published by John Wiley & Sons. This book was released on 2006-03-06 with total page 262 pages. Available in PDF, EPUB and Kindle. Book excerpt: The lock-and-key principle formulated by Emil Fischer as early as the end of the 19th century has still not lost any of its significance for the life sciences. The basic aspects of ligand-protein interaction may be summarized under the term 'molecular recognition' and concern the specificity as well as stability of ligand binding. Molecular recognition is thus a central topic in the development of active substances, since stability and specificity determine whether a substance can be used as a drug. Nowadays, computer-aided prediction and intelligent molecular design make a large contribution to the constant search for, e. g., improved enzyme inhibitors, and new concepts such as that of pharmacophores are being developed. An up-to-date presentation of an eternally young topic, this book is an indispensable information source for chemists, biochemists and pharmacologists dealing with the binding of ligands to proteins.

Download or read book Analysis and Prediction of Side chain Flexibility in Protein protein Recognition written by Kevin Wiehe and published by . This book was released on 2008 with total page 396 pages. Available in PDF, EPUB and Kindle. Book excerpt: Abstract: Protein-protein interaction is an essential mechanism in biological systems. It is fundamental to such diverse processes as the immunological response, signaling cascades and the function of enzymes. Understanding how proteins recognize and associate with each other has been a goal of biological research for decades. Currently, computational modeling of protein-protein interactions has become a common tool in the attempt to understand molecular recognition. Specifically, protein-protein docking algorithms which seek to predict the complexed protein structure from its unbound components have advanced rapidly in recent years. Most of the progress in protein-docking algorithms has come from the employment of a rigid-body approximation of the unbound proteins in order to reduce the complexity of the problem. Our own lab has demonstrated consistent success with such an approach utilizing our docking algorithm, ZDOCK, in the Critical Assessment of Protein Interactions (CAPRI), an international blind docking test. Recently, docking algorithms have begun to incorporate flexible proteins by modeling side-chain conformational change. Current attempts to predict side-chain rearrangement upon complexation do so using a brute-force methodology in which all interface residues are searched. Such an approach is computationally intensive and may be unnecessarily inaccurate because of the blind nature of the search. In order to address these flaws, we have created and analyzed a protein-protein docking benchmark dataset to discover the characteristics of side-chains that can best estimate the likelihood of a residue to exhibit conformational change. Our analysis shows that the majority of sidechains in the interface of protein complexes do not change position between the unbound and bound conformations. Additionally, the frequency of side-chain conformational change in interface residues is only slightly higher than other protein surface residues. Because of this small difference and the usually limited knowledge of the location of the interface prior to docking, we developed a support vector machine (SVM) approach that allows us to apply a probability of flexibility for all surface residues. Here we describe the accuracy of this predictive method and its potential for application to protein-protein docking.

Download or read book Protein protein Recognition written by Colin Kleanthous and published by Frontiers in Molecular Biology. This book was released on 2000 with total page 370 pages. Available in PDF, EPUB and Kindle. Book excerpt: The purpose of Protein-Protein Recognition is to bring together concepts and systems pertaining to protein-protein interactions in a single unifying volume. In the light of the information from the genome sequencing projects and the increase in structural information it is an opportune time totry to make generalizations about how and why proteins form complexes with each other. The emphasis of the book is on heteromeric complexes (complexes in which each of the components can exist in an unbound state) and will use well-studied model systems to explain the processes of formingcomplexes. After an introductory section on the kinetics, thermodynamics, analysis, and classification of protein-protein interactions, weak, intermediate, and high affinity complexes are dealt with in turn. Weak affinity complexes are represented by electron transfer proteins and integrincomplexes. Anti-lysozyme antibodies, the MHC proteins and their interactions with T-cell receptors, and the protein interactions of eukaryotic signal transduction are the systems used to explain complexes with intermediate affinities. Finally, tight binding complexes are represented by theinteraction of protein inhibitors with serine proteases and by nuclease inhibitor complexes. Throughout the chapters common themes are the technologies which have had the greatest impact, how specificity is determined, how complexes are stabilized, and medical and industrial applications.

Download or read book Protein Conformational Dynamics written by Ke-li Han and published by Springer Science & Business Media. This book was released on 2014-01-20 with total page 488 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Download or read book Investigating Molecular Recognition Through Large scale Analysis of Protein Sequences and Structures written by and published by . This book was released on 2000 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: The objective of this project is to study protein sequence-structure relationships through large-scale computational analysis of gene sequences and crystal structure in the databanks. The results of this analysis will be used to help better understand molecular recognition.

Download or read book Protein Interactions Computational Methods Analysis And Applications written by M Michael Gromiha and published by World Scientific. This book was released on 2020-03-05 with total page 424 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book is indexed in Chemical Abstracts ServiceThe interactions of proteins with other molecules are important in many cellular activities. Investigations have been carried out to understand the recognition mechanism, identify the binding sites, analyze the the binding affinity of complexes, and study the influence of mutations on diseases. Protein interactions are also crucial in structure-based drug design.This book covers computational analysis of protein-protein, protein-nucleic acid and protein-ligand interactions and their applications. It provides up-to-date information and the latest developments from experts in the field, using illustrations to explain the key concepts and applications. This volume can serve as a single source on comparative studies of proteins interacting with proteins/DNAs/RNAs/carbohydrates and small molecules.

Download or read book Protein Modules and Protein Protein Interactions written by and published by Elsevier. This book was released on 2002-11-24 with total page 343 pages. Available in PDF, EPUB and Kindle. Book excerpt: Protein modules engage in a multitude of interactions with one another and with other cellular components, notably with DNA. These interactions are a central aspect of protein function of great relevance in the post-genomic era. This volume describes a panel of approaches for analyzing protein modules and their interactions, ranging from bioinformatics to physical chemistry, to biochemistry, with an emphasis on the structure-function relationship in protein-protein complexes involved in cellular processes including signal transduction. Comprehensive overview of different facets of macromolecule interactions Computational and bioinformatics aspects of analyzing protein modules and their interactions Emphasis on structure-function relationship in protein-protein complexes involved in cellular processes

Download or read book Protein protein Complexes written by Martin Zacharias and published by World Scientific. This book was released on 2010 with total page 401 pages. Available in PDF, EPUB and Kindle. Book excerpt: Given the immense progress achieved in elucidating protein-protein complex structures and in the field of protein interaction modeling, there is great demand for a book that gives interested researchers/students a comprehensive overview of the field. This book does just that. It focuses on what can be learned about protein-protein interactions from the analysis of protein-protein complex structures and interfaces. What are the driving forces for protein-protein association? How can we extract the mechanism of specific recognition from studying protein-protein interfaces? How can this knowledge be used to predict and design protein-protein interactions (interaction regions and complex structures)? What methods are currently employed to design protein-protein interactions, and how can we influence protein-protein interactions by mutagenesis and small-molecule drugs or peptide mimetics?The book consists of about 15 review chapters, written by experts, on the characterization of protein-protein interfaces, structure determination of protein complexes (by NMR and X-ray), theory of protein-protein binding, dynamics of protein interfaces, bioinformatics methods to predict interaction regions, and prediction of protein-protein complex structures (docking and homology modeling of complexes, etc.) and design of protein-protein interactions. It serves as a bridge between studying/analyzing protein-protein complex structures (interfaces), predicting interactions, and influencing/designing interactions.

Download or read book Protein Protein Interactions written by Weibo Cai and published by BoD – Books on Demand. This book was released on 2012-03-30 with total page 488 pages. Available in PDF, EPUB and Kindle. Book excerpt: Proteins are indispensable players in virtually all biological events. The functions of proteins are coordinated through intricate regulatory networks of transient protein-protein interactions (PPIs). To predict and/or study PPIs, a wide variety of techniques have been developed over the last several decades. Many in vitro and in vivo assays have been implemented to explore the mechanism of these ubiquitous interactions. However, despite significant advances in these experimental approaches, many limitations exist such as false-positives/false-negatives, difficulty in obtaining crystal structures of proteins, challenges in the detection of transient PPI, among others. To overcome these limitations, many computational approaches have been developed which are becoming increasingly widely used to facilitate the investigation of PPIs. This book has gathered an ensemble of experts in the field, in 22 chapters, which have been broadly categorized into Computational Approaches, Experimental Approaches, and Others.

Download or read book MOLECULAR RECOGNITION BIOTECHNOLOGY CHEMICAL ENGINEERING AND MATERIALS APPLICATIONS written by JASON A. MCEVOY and published by Lulu.com. This book was released on 2011 with total page 322 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Recent Trends in Molecular Recognition written by F. Diederich and published by Springer Science & Business Media. This book was released on 2013-04-17 with total page 274 pages. Available in PDF, EPUB and Kindle. Book excerpt: Reasoning in terms of molecular recognition may be traced back to Emil Fischer, who practiced the art of chemistry at Humboldt University in Prussian Berlin a century ago. Today, it is clearly recognized that molecular recognition impacts and determines all life processes. It has become a key research field in both chemistry and biology and the emerging interface of what now is being called "chemical biology". The technological advances derived from this knowledge are particularly important, diverse, and directly evident in the pharmaceutical industry. Under the auspices of the Ernst Schering Research Foundation, a workshop held in Berlin in February 1998 addressed novel basic developments of potential relevance to drug research efforts. A balance of timely research topics in molecular recognition is presented in the lectures delivered by a multidisciplinary international panel of renowned scholars and documented in this volume.

Download or read book Molecular Biology of The Cell written by Bruce Alberts and published by . This book was released on 2002 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Molecular Recognition in Gas Phase written by Andrey Dyachenko and published by . This book was released on 2013 with total page 163 pages. Available in PDF, EPUB and Kindle. Book excerpt: In the present thesis we have explored different factors that impede accurate quantitative description of non-covalent protein-protein and protein-ligand interactions and design of new potent and specific binders from the scratch. Firstly, we addressed the role of solvent in the mechanism of non-covalent interactions. Secondly, we tackled the question about the intrinsic conformational flexibility of the protein molecules and the part it plays in weak interactions between proteins. In the first part of the thesis we studied the interactions of vascular endothelial growth factor (VEGF) protein with five cyclic peptides in solution and gas phase. The results showed that affinities of five ligands to VEGF in solution and gas phase are ranked in inversed order. That is, the that has the highest affinity in solution (as shown by chemical shift perturbation NMR and isothermal titration calorimetry) forms the weakest complex with VEGF in gas phase, and vice versa. We compared gas-phase and solution binding affinities of of five peptides and made qualitative conclusions about the role of the solvent in protein-ligand interactions. In order to obtain more quantitative information about the gas-phase behavior of non-covalent complexes we have developed a combined experimental/theoretical approach to study the energetics of collisional activation of the ion prior to dissociation. We applied developed strategy to model CID in traveling wave ion guide (TWIG) collision cell. We validated the model on the CID of leu-enkephalin peptide and then applied developed strategy to five non-covalent protein-peptide complexes and found activation energies of their dissociation reactions. Next we applied ESI native MS to study the allosteric interactions between the molecular chaperonin GroEL and ATP. The obtained data allowed to construct a scheme of conformational transition of GroEL upon binding of ATP and distinguish between two different cooperativity models, providing strong arguments in favor of Monod-Wyman-Changeux (MWC) model. Finally, be studied the backbone dynamics of VEGF with a combination of NMR relaxation and all-atom force-field based normal mode analysis (NMA). We showed that combination of experimental and computational approach allows to identify flexible zones with higher level of confidence. We also found out that residues, that are involved VEGF-receptor interactions, reside in or close to the flexible zones, suggesting the critical role conformational plasticity plays in the non-covalent protein-protein interactions.

Download or read book Quantum Chemical Study of Molecular Recognition in Protein ligand Complexes written by Yaohua Han and published by . This book was released on 2013 with total page 161 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Protein Engineering written by Raghupathy Sarma and published by Elsevier. This book was released on 2012-12-02 with total page 441 pages. Available in PDF, EPUB and Kindle. Book excerpt: Protein Engineering: Applications in Science, Medicine, and Industry deals with the scientific, medical, and industrial applications of protein engineering. Topics range from protein structure and design to mutant analysis and complex systems. Applications such as production of novel antibiotics, genetic transformation of plants, and genetic engineering of bioinsecticides are described. This book is comprised of 25 chapters and begins with an overview of trends and developments in protein chemistry and their relevance to protein engineering, followed by a discussion on protein sequence data banks. Subsequent chapters explore the design and construction of biologically active peptides, including hormones; structural and functional analysis of thermophile proteins; the conformation of diphtheria toxin; and applications of surface-simulation synthesis in protein molecular recognition. The use of oligonucleotide-directed site-specific mutagenesis in functional analysis of the signal peptide for protein secretion is also considered. The results of studies on the mechanism of membrane fusion are presented. This monograph will serve as a useful guide for those who are already working on protein engineering and those who are about to start research in this field.

Download or read book Spectroscopy and Modeling of Biomolecular Building Blocks written by Jean-Pierre Schermann and published by Elsevier. This book was released on 2007-10-16 with total page 499 pages. Available in PDF, EPUB and Kindle. Book excerpt: Spectroscopy and Modeling of Biomolecular Building Blocks presents an overview of recent advances in the intertwining of the following research fields: photon and electron spectroscopy, quantum chemistry, modelling and mass-spectrometry. The coupling of these disciplines offers a new point of view to the understanding of isolated elementary building blocks of biomolecules and their assemblies. It allows the unambiguous separation between intrinsic properties of biomolecular systems and those induced by the presence of their environment. The first chapters provide background in modelling (I), frequency-resolved spectroscopy using microwave, infrared and UV photons, time-resolved spectroscopy in the femtosecond domain and energy-resolved electron spectroscopy (II) and production of gas-phase neutral and ionic biomolecular species, mass-spectrometry, ion mobility and BIRD techniques (III). Chapter IV is devoted to case studies of gas-phase experimental investigations coupled to quantum or classical calculations. The topics are structural studies of nucleobases and oligonucleotides, peptides and proteins, sugars; neuromolecules; non-covalent complexes; chiral systems, interactions of low-energy electrons with biomolecules in the radiation chemistry context and very large gas-phase biomolecular systems. The fifth chapter concerns the link between gas-phase and liquid-phase. Different treatments of solvation are illustrated through examples pointing out the influence of progressive addition of water molecules upon properties of nucleobases, peptides, sugars and neuromolecules. Offer a new perspective to the understanding of isolated elementary building blocks of bio molecules Includes case studies of experimental investigations coupled to quantum or classical calculations