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Author : Hui Yang
Publisher :
ISBN 13 :
Total Pages : 137 pages
Book Rating : 4.:/5 (773 download)
Download or read book Theoretical Studies of Molecular Recognition in Protein-ligand and Protein-protein Complexes written by Hui Yang and published by . This book was released on 2010 with total page 137 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Author : Natasja Brooijmans
Publisher :
ISBN 13 :
Total Pages : 510 pages
Book Rating : 4.:/5 (82 download)
Download or read book Theoretical Studies of Molecular Recognition written by Natasja Brooijmans and published by . This book was released on 2003 with total page 510 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Author : Hans-Joachim Böhm
Publisher : John Wiley & Sons
ISBN 13 : 3527605517
Total Pages : 262 pages
Book Rating : 4.5/5 (276 download)
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.
Author : Andrey Dyachenko
Publisher :
ISBN 13 :
Total Pages : 163 pages
Book Rating : 4.:/5 (892 download)
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.
Author : G. Ulrich Nienhaus
Publisher : Humana
ISBN 13 : 9781617375255
Total Pages : 0 pages
Book Rating : 4.3/5 (752 download)
Download or read book Protein'Ligand Interactions written by G. Ulrich Nienhaus and published by Humana. This book was released on 2010-11-19 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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 BiologyTM 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.
Author : Holger Gohlke
Publisher : John Wiley & Sons
ISBN 13 : 3527645977
Total Pages : 359 pages
Book Rating : 4.5/5 (276 download)
Download or read book Protein-Ligand Interactions written by Holger Gohlke and published by John Wiley & Sons. This book was released on 2012-04-06 with total page 359 pages. Available in PDF, EPUB and Kindle. Book excerpt: Innovative and forward-looking, this volume focuses on recent achievements in this rapidly progressing field and looks at future potential for development. The first part provides a basic understanding of the factors governing protein-ligand interactions, followed by a comparison of key experimental methods (calorimetry, surface plasmon resonance, NMR) used in generating interaction data. The second half of the book is devoted to insilico methods of modeling and predicting molecular recognition and binding, ranging from first principles-based to approximate ones. Here, as elsewhere in the book, emphasis is placed on novel approaches and recent improvements to established methods. The final part looks at unresolved challenges, and the strategies to address them. With the content relevant for all drug classes and therapeutic fields, this is an inspiring and often-consulted guide to the complexity of protein-ligand interaction modeling and analysis for both novices and experts.
Author : Natalya Kurochkina
Publisher : Springer
ISBN 13 : 9811366012
Total Pages : 276 pages
Book Rating : 4.8/5 (113 download)
Download or read book Protein Structure and Modeling written by Natalya Kurochkina and published by Springer. This book was released on 2019-06-04 with total page 276 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book will consider principles of the organization of protein molecules, the relationships between primary, secondary, and tertiary structure, the determinants of protein conformation, and the applications of structure determination and structure modeling in biomedical research.
Author : Irena Roterman-Konieczna
Publisher : Springer Science & Business Media
ISBN 13 : 9400752849
Total Pages : 173 pages
Book Rating : 4.4/5 (7 download)
Download or read book Identification of Ligand Binding Site and Protein-Protein Interaction Area written by Irena Roterman-Konieczna and published by Springer Science & Business Media. This book was released on 2012-10-19 with total page 173 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume presents a review of the latest numerical techniques used to identify ligand binding and protein complexation sites. It should be noted that there are many other theoretical studies devoted to predicting the activity of specific proteins and that useful protein data can be found in numerous databases. The aim of advanced computational techniques is to identify the active sites in specific proteins and moreover to suggest a generalized mechanism by which such protein-ligand (or protein-protein) interactions can be effected. Developing such tools is not an easy task – it requires extensive expertise in the area of molecular biology as well as a firm grasp of numerical modeling methods. Thus, it is often viewed as a prime candidate for interdisciplinary research.
Author : A.D. Buckingham
Publisher : Springer Science & Business Media
ISBN 13 : 9401121680
Total Pages : 213 pages
Book Rating : 4.4/5 (11 download)
Download or read book Principles of Molecular Recognition written by A.D. Buckingham and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 213 pages. Available in PDF, EPUB and Kindle. Book excerpt: The importance of molecular recognition in chemistry and biology is reflected in a recent upsurge in relevant research, promoted in particular by high-profile initiatives in this area in Europe, the USA and Japan. Although molecular recognition is necessarily microscopic in origin, its consequences are de facto macroscopic. Accordingly, a text that starts with intermolecular interactions between simple molecules and builds to a discussion of molecular recognition involving larger scale systems is timely. This book was planned with such a development in mind. The book begins with an elementary but rigorous account of the various types of forces between molecules. Chapter 2 is concerned with the hydrogen bond between pairs of simple molecules in the gas phase, with particular reference to the preferred relative orientation of the pair and the ease with which this can be distorted. This microscopic view continues in chapter 3 wherein the nature of interactions between solute molecules and solvents or between two or more solutes is examined from the experimental standpoint, with various types of spectroscopy providing the probe of the nature of the interactions. Molecular recognition is central to the catalysis of chemical reactions, especially when bonds are to be broken and formed under the severe con straint that a specific configuration is to result, as in the production of enan tiotopically pure compounds. This important topic is considered in chapter 4.
Author : Rui Qi (Ph. D.)
Publisher :
ISBN 13 :
Total Pages : 372 pages
Book Rating : 4.:/5 (124 download)
Download or read book Computational Studies of Protein-ligand Recognition written by Rui Qi (Ph. D.) and published by . This book was released on 2018 with total page 372 pages. Available in PDF, EPUB and Kindle. Book excerpt: Molecular recognition between biomolecules and ligands is very specific in living cells. The functions of all biochemical processes and cell mechanisms are dependent upon complex but specific non-covalent intermolecular interactions. As essential building blocks in protein and nucleic acid, phosphate groups are commonly found in nucleic acids, proteins, and lipids. Nearly half of known proteins have been shown to interact with ligands containing a phosphate group. Binding of a phosphoryl group is fundamental to a range of biological processes including metabolism, biosynthesis, gene regulation, signal transduction, muscle contraction, and antibiotic resistance. Phosphorylation is one of the most common forms of reversible posttranslational modification of protein and, nearly 30% of all proteins are phosphorylated on at least one residue in cells. However, phosphate binding sites are less well defined and fundamental principles of why and how proteins recognize phosphate groups are not yet fully understood. Molecular modeling is a common tool for studying biomolecular structure, dynamics, interaction and function. Due to the complex electrostatics, high concentration of ions and intricate interactions with environment, however, the modeling and designing of highly charged drug-like molecules and nucleic acid derivatives are extremely difficult. This thesis will focus on the highly charged phosphate, including its different protonation states, and energetic and thermodynamic driving forces behind protein-phosphate recognition. This thesis work will also discuss the development of more sophisticated computational models, AMOEBA+, that are necessary for a better understanding and prediction of the physical properties of small organic molecules. Four projects will be discussed in this dissertation: two projects on force field development, and two on applying molecular dynamic simulations to understand biological processes. These projects have led to new insights into understanding of physical and chemical principles and mechanisms underlying highly protein-phosphate binding and nucleic acid stability. In addition, this thesis work will enhance the capability to develop and apply computational and theoretical frameworks to model, predict and design proteins, therapeutics, and diagnostic strategies targeting phosphates, phosphate-containing biomolecules
Author : Sibo Feng
Publisher :
ISBN 13 :
Total Pages : 340 pages
Book Rating : 4.:/5 (377 download)
Download or read book Molecular Recognition of Protein-ligand Complexes written by Sibo Feng and published by . This book was released on 1997 with total page 340 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Author : Olgun Guvench
Publisher :
ISBN 13 :
Total Pages : 436 pages
Book Rating : 4.:/5 (763 download)
Download or read book Theoretical Studies of Proteins and Protein-ligand Complexes written by Olgun Guvench and published by . This book was released on 2005 with total page 436 pages. Available in PDF, EPUB and Kindle. Book excerpt: Part I . Toward the development of an efficient all-atom implicit-solvent model for use in protein structure prediction. An efficient implicit-solvent model that includes the hydrophobic effect, hydrogen bonding, volume exclusion, bonded interactions, and aromatic-aromatic interactions was developed and applied to protein structure prediction. A new efficient approximate surface area method for modeling the hydrophobic effect was formulated, and the importance of electrostatic interactions between aromatic sidechains in conferring the geometry of inter-strand aromatic-aromatic interactions in the "trpzip" [beta]-hairpin was shown. The developed model was applied to the folding of the 20 amino-acid stable designed mini-protein "Trp-cage". Using replica-exchange molecular dynamics, Trp-cage was folded to its native state with near-experimental stability. The model predicts the folded structure Trp-cage as the global free-energy minimum while being two orders of magnitude faster than explicit-solvent simulation of this protein.
Author : Yaohua Han
Publisher :
ISBN 13 :
Total Pages : 161 pages
Book Rating : 4.:/5 (867 download)
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:
Author : Alberte Pullman
Publisher : Springer Science & Business Media
ISBN 13 : 9780792331025
Total Pages : 518 pages
Book Rating : 4.3/5 (31 download)
Download or read book Modelling of Biomolecular Structures and Mechanisms written by Alberte Pullman and published by Springer Science & Business Media. This book was released on 1995 with total page 518 pages. Available in PDF, EPUB and Kindle. Book excerpt: Gathering together a number of experts in the world, the 27th Jerusalem Symposium was devoted to the theme of the modelling of biomolecular structures and mechanisms. As a result of recent growth in both importance and audience, the papers contained in this volume present an evaluation of the status of the present knowledge in this field. The main topics covered by this year's Symposium include nucleic acids and their interactions, proteins and their interaction, membranes and their interactions, enzymatic processes and the pharmacological and medical aspects of these subjects. Readers should benefit from the interdisciplinary approach which provides coverage of both theoretical and experimental advances.
Author : Benedikt Frieg
Publisher :
ISBN 13 :
Total Pages : pages
Book Rating : 4.:/5 (113 download)
Download or read book Integrative Modeling of Function-associated Molecular Recognition in Protein-ligand, Protein-peptide, and Protein-protein Complexes written by Benedikt Frieg and published by . This book was released on 2020 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Author : Hans-Joachim Böhm
Publisher : Wiley-VCH
ISBN 13 : 9783527305216
Total Pages : 262 pages
Book Rating : 4.3/5 (52 download)
Download or read book Protein-Ligand Interactions written by Hans-Joachim Böhm and published by Wiley-VCH. This book was released on 2003-05-06 with total page 262 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Author : Yat T. Tang
Publisher :
ISBN 13 :
Total Pages : 125 pages
Book Rating : 4.:/5 (756 download)
Download or read book Examination of Molecular Recognition in Protein-ligand Interactions written by Yat T. Tang and published by . This book was released on 2010 with total page 125 pages. Available in PDF, EPUB and Kindle. Book excerpt: This dissertation is a compilation of two main projects that were investigated during my thesis research. The first project was a prospective study which identified and characterized drug-like inhibitors of a prototype of bacterial two-component signal transduction response regulator using computational and experimental methods. The second project was the development and validation of a scoring function, PHOENIX, derived using high-resolution structures and calorimetry measurements to predict binding affinities of protein-ligand interactions. Collectively, my thesis research aimed to better understand the underlying driving forces and principles which govern molecular recognition and molecular design. A prospective study coupled computational predictions with experimental validation resulted in the discovery of first-in-class inhibitors targeting a signal transduction module important for bacterial virulence. Development and validation of the PHOENIX scoring function for binding affinity prediction derived using high-resolution structures and calorimetry measurements should guide future molecular recognition studies and endeavors in computer-aided molecular design.
