Download or read book Exploring Structure dynamics function Relationship in Proteins Protein written by Karan Pal Kapoor and published by . This book was released on 2015 with total page 227 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Introduction to Proteins written by Amit Kessel and published by CRC Press. This book was released on 2010-12-17 with total page 623 pages. Available in PDF, EPUB and Kindle. Book excerpt: As the tools and techniques of structural biophysics assume greater roles in biological research and a range of application areas, learning how proteins behave becomes crucial to understanding their connection to the most basic and important aspects of life. With more than 350 color images throughout, Introduction to Proteins: Structure, Function, and Motion presents a unified, in-depth treatment of the relationship between the structure, dynamics, and function of proteins. Taking a structural–biophysical approach, the authors discuss the molecular interactions and thermodynamic changes that transpire in these highly complex molecules. The text incorporates various biochemical, physical, functional, and medical aspects. It covers different levels of protein structure, current methods for structure determination, energetics of protein structure, protein folding and folded state dynamics, and the functions of intrinsically unstructured proteins. The authors also clarify the structure–function relationship of proteins by presenting the principles of protein action in the form of guidelines. This comprehensive, color book uses numerous proteins as examples to illustrate the topics and principles and to show how proteins can be analyzed in multiple ways. It refers to many everyday applications of proteins and enzymes in medical disorders, drugs, toxins, chemical warfare, and animal behavior. Downloadable questions for each chapter are available at CRC Press Online.

Download or read book Introduction to Proteins written by Amit Kessel and published by CRC Press. This book was released on 2018-03-22 with total page 1423 pages. Available in PDF, EPUB and Kindle. Book excerpt: Introduction to Proteins provides a comprehensive and state-of-the-art introduction to the structure, function, and motion of proteins for students, faculty, and researchers at all levels. The book covers proteins and enzymes across a wide range of contexts and applications, including medical disorders, drugs, toxins, chemical warfare, and animal behavior. Each chapter includes a Summary, Exercies, and References. New features in the thoroughly-updated second edition include: A brand-new chapter on enzymatic catalysis, describing enzyme biochemistry, classification, kinetics, thermodynamics, mechanisms, and applications in medicine and other industries. These are accompanied by multiple animations of biochemical reactions and mechanisms, accessible via embedded QR codes (which can be viewed by smartphones) An in-depth discussion of G-protein-coupled receptors (GPCRs) A wider-scale description of biochemical and biophysical methods for studying proteins, including fully accessible internet-based resources, such as databases and algorithms Animations of protein dynamics and conformational changes, accessible via embedded QR codes Additional features Extensive discussion of the energetics of protein folding, stability and interactions A comprehensive view of membrane proteins, with emphasis on structure-function relationship Coverage of intrinsically unstructured proteins, providing a complete, realistic view of the proteome and its underlying functions Exploration of industrial applications of protein engineering and rational drug design Each chapter includes a Summary, Exercies, and References Approximately 300 color images Downloadable solutions manual available at www.crcpress.com For more information, including all presentations, tables, animations, and exercises, as well as a complete teaching course on proteins' structure and function, please visit the author's website: http://ibis.tau.ac.il/wiki/nir_bental/index.php/Introduction_to_Proteins_Book. Praise for the first edition "This book captures, in a very accessible way, a growing body of literature on the structure, function and motion of proteins. This is a superb publication that would be very useful to undergraduates, graduate students, postdoctoral researchers, and instructors involved in structural biology or biophysics courses or in research on protein structure-function relationships." --David Sheehan, ChemBioChem, 2011 "Introduction to Proteins is an excellent, state-of-the-art choice for students, faculty, or researchers needing a monograph on protein structure. This is an immensely informative, thoroughly researched, up-to-date text, with broad coverage and remarkable depth. Introduction to Proteins would provide an excellent basis for an upper-level or graduate course on protein structure, and a valuable addition to the libraries of professionals interested in this centrally important field." --Eric Martz, Biochemistry and Molecular Biology Education, 2012

Download or read book Frontiers in Protein Structure Function and Dynamics written by Dev Bukhsh Singh and published by Springer Nature. This book was released on 2020-07-02 with total page 458 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book discusses a broad range of basic and advanced topics in the field of protein structure, function, folding, flexibility, and dynamics. Starting with a basic introduction to protein purification, estimation, storage, and its effect on the protein structure, function, and dynamics, it also discusses various experimental and computational structure determination approaches; the importance of molecular interactions and water in protein stability, folding and dynamics; kinetic and thermodynamic parameters associated with protein-ligand binding; single molecule techniques and their applications in studying protein folding and aggregation; protein quality control; the role of amino acid sequence in protein aggregation; muscarinic acetylcholine receptors, antimuscarinic drugs, and their clinical significances. Further, the book explains the current understanding on the therapeutic importance of the enzyme dopamine beta hydroxylase; structural dynamics and motions in molecular motors; role of cathepsins in controlling degradation of extracellular matrix during disease states; and the important structure-function relationship of iron-binding proteins, ferritins. Overall, the book is an important guide and a comprehensive resource for understanding protein structure, function, dynamics, and interaction.

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 Protein Structure Function Relationship written by D.L. Smith and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 291 pages. Available in PDF, EPUB and Kindle. Book excerpt: Although many pursue understanding of the relationship between protein structure and function for the thrill of pure science, the pay-off in a much broader sense is the ability to manipulate the Earth's chemistry and biology to improve the quality of life for mankind. Immediately goals of this area of research include identification of the life-supporting functions of proteins, and the fundamental forces that facilitate these functions. Upon reaching these goals, we shall have the understanding to direct and the tools required to implement changes that will dramatically improve the quality of life. For example, under standing the chemical mechanism of diseases will facilitate development of new therapeutic drugs. Likewise, understanding of chemical mechanisms of plant growth will be used with biotechnology to improve food production under adverse climatic conditions. The challenge to understand details of protein structure/function relationships is enormous and requires an international effort for success. To direct the chemistry and biology of our environment in a positive sense will require efforts from bright, imaginative scientists located throughout the world. Although the emergence of FAX, e-mail, and the World Wide Web has revolutionized international communication, there remains a need for scientists located in distant parts of the world to occasionally meet face to face.

Download or read book Protein Dynamics Function and Design written by Oleg Jardetzky and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 227 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume is a collection of articles from the proceedings of the International School of Structural Biology and Magnetic Resonance 3rd Course: Protein Dynamics, Function, and Design. This NATO Advance Study Institute was held in Erice at the Ettore Majorana Centre for Scientific Culture on April 16-28, 1997. The aim of the Institute was to bring together experts applyipg different physical methods to problems of macro molecular dynamics-notably x-ray diffraction, NMR and other forms of spectroscopy, and molecular dynamics simulations. Emphasis was placed on those systems and types of problems-such as mechanisms of allosteric control, signal transmission, induced fit to different ligands with its implications for drug design, and the effects of dynamics on structure determination-where a correlation of findings obtained by different methods could shed the most light on the mechanisms involved and stimulate the search for new approaches. The individual articles represent the state of the art in each of the areas cov ered and provide a guide to the original literature in this rapidly developing field. v CONTENTS 1. Determining Structures of ProteinlDN A Complexes by NMR Angela M. Gronenbom and G. Marius Clore 2. Fitting Protein Structures to Experimental Data: Lessons from before Your Mother Was Born . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15 Jeffrey C. Hoch, Alan S. Stem, and Peter J. Connolly 3. Multisubunit Allosteric Proteins. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27 William N. Lipscomb 4. Studying Protein Structure and Function by Directed Evolution: Examples with Engineered Antibodies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37 Andreas Pliickthun 5. High Pressure Effects on Protein Structure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

Download or read book Protein Structure and Function written by Gregory A. Petsko and published by New Science Press. This book was released on 2004 with total page 220 pages. Available in PDF, EPUB and Kindle. Book excerpt: Each title in the 'Primers in Biology' series is constructed on a modular principle that is intended to make them easy to teach from, to learn from, and to use for reference.

Download or read book Single molecule Force Manipulation and Nanoscopic Imaging of Protein Structure dynamics function Relationship written by Susovan Roy Chowdhury and published by . This book was released on 2021 with total page 141 pages. Available in PDF, EPUB and Kindle. Book excerpt: The anisotropic nature of the force fluctuation inside cells makes it very biologically relevant to study the dynamics of the structure-function relationship of protein molecules under force. The ability to manipulate individual molecules under near-physiological conditions makes the Atomic force microscope a very widely used technique. Force applied by AFM can be either compressive force or pulling force. Here in the thesis, we have explored the compressive force response of the protein molecules and the impact of the compressive force using AFM.The abrupt ruptures of protein native structures under compressive force were demonstrated by single-molecule AFM-FRET spectroscopic nanoscopy. The simultaneous measurement of the force curve and the FRET efficiency showed a temporal correlation between the compressive force drop and the FRET efficiency drop which indicated a spontaneous and abrupt rupture of the protein native tertiary structure.Furthermore, a similar compressive force experiment was done on targeted calmodulin molecules to characterize two different forms of CaM, the Ca2+-ligated activated form, and the Ca2+ free non-activated form (Apo-Calmodulin). A sudden and spontaneous rupture of Apo-CaM molecules was observed under the compressive force applied by an AFM tip, though no such events were recorded in the case of the Ca2+-ligated form.To further prove that this kind of compressive force rupture of Apo-CaM can trigger new chemistry inside the cell, a similar experiment was carried out where we observed compressive force rupture of apo-CaM molecules and successive binding of C28W peptide to the ruptured protein, a typical protein signaling activity that only a Ca2+-activated CaM has. This observation demonstrates that both chemical activation and force activation can play a vital role in biology, such as cell-signaling protein dynamics and function.Lastly, we further explored the entangled protein state formed following the events of the multiple and simultaneous tau protein ruptures under crowding. Crowded proteins simultaneously rupture and then spontaneously refold to an entangled folding state, different from either folded or unfolded states of the tau protein, which can be a plausible pathway for the tau protein aggregation that is related to several neurodegenerative diseases like Alzheimer's disease and Parkinson's disease.

Download or read book Biophysical Analysis of Membrane Proteins written by Eva Pebay-Peyroula and published by John Wiley & Sons. This book was released on 2008-06-25 with total page 368 pages. Available in PDF, EPUB and Kindle. Book excerpt: Meeting the need for a book on developing and using new methods to investigate membrane proteins, this is the first of its kind to present the full range of novel techniques in one resource. Top researchers from around the world focus on the physical principles exploited in the different techniques, and provide examples of how these can bring about important new insights. Following an introduction, further sections discuss structural approaches, molecular interaction and large assemblies, dynamics and spectroscopies, finishing off with an exploration of structure-function relationships in whole cells.

Download or read book Exploring the Physics of Proteins at Molecular Level by Neutron and X ray Scattering written by Utsab Raj Shrestha and published by . This book was released on 2017 with total page 207 pages. Available in PDF, EPUB and Kindle. Book excerpt: The protein structures revealed by the crystallographic studies have provided the valuable information over the years regarding their biological functions. However, such snapshots of protein fluctuations averaged over time may not be enough to fully capture the underlying biological phenomena. A deeper understanding of the protein dynamics is crucial for elucidating the structural pathways or the transition mechanism from the initial state to the final state necessary for regulating the physical and chemical processes. Hence, the biological activities and functions are mainly governed by the protein conformational dynamics. However, the direct correlation of a wide range of protein dynamics to function still remains unclear, posing a major challenge to biophysical community. In this dissertation, the relationships among the protein's conformation, dynamics and function are investigated using the state-of-the-art neutron and X-ray scattering techniques. Taking the advantage of comparable wavelength and momentum transfer of neutron and X-ray to that of the atoms, we studied the protein dynamics at molecular level over the timescale of few femtoseconds to nanoseconds regime, which provides the information regarding the conformational flexibility of protein. Interestingly, we observed that the protein dynamic behavior is similar to that of glass forming liquids, where the relaxation process is non-exponential and the collective excitations are highly damped. Specifically, picosecond to nanosecond dynamics, also known as beta-relaxation process decays logarithmically over the time. Remarkably, such dynamic phenomena revealed the direct experimental evidences of structure-dynamics-function relationship of a large variety of protein family such as a large hyperthermophilic protein, a membrane protein, and the native and denatured globular proteins.

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.

Download or read book Exploring Protein Structure Principles and Practice written by Tim Skern and published by Springer. This book was released on 2018-07-04 with total page 255 pages. Available in PDF, EPUB and Kindle. Book excerpt: This textbook introduces the basics of protein structure and logically explains how to use online software to explore the information in protein structure databases. Readers will find easily understandable, step-by step exercises and video-trainings to support them in grasping the fundamental concepts. After reading this book, readers will have the skills required to independently explore and analyze macromolecular structures, will be versed in extracting information from protein databases and will be able to visualize protein structures using specialized software and on-line algorithms. This book is written for advanced undergraduates and PhD students wishing to use information from structural biology in their assignments and research and will be a valuable source of information for all those interested in applied and theoretical aspects of structural biology.

Download or read book Computational Approaches to Protein Dynamics written by Monika Fuxreiter and published by CRC Press. This book was released on 2014-12-24 with total page 458 pages. Available in PDF, EPUB and Kindle. Book excerpt: The Latest Developments on the Role of Dynamics in Protein FunctionsComputational Approaches to Protein Dynamics: From Quantum to Coarse-Grained Methods presents modern biomolecular computational techniques that address protein flexibility/dynamics at all levels of theory. An international contingent of leading researchers in chemistry, physics, an

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 Proteins written by Charles L. Brooks and published by John Wiley & Sons. This book was released on 2009-09-08 with total page 278 pages. Available in PDF, EPUB and Kindle. Book excerpt: Presenting a wide-ranging view of current developments in protein research, the papers in this collection, each written by highly regarded experts in the field, examine various aspects of protein structure, functions, dynamics, and experimentation. Topics include dynamical simulation methods, the biological role of atom fluctuations, protein folding, influences on protein dynamics, and a variety of analytical techniques, such as X-ray diffraction, vibrational spectroscopy, photodissociation and rebinding kinetics. This is part of a series devoted to providing general information on a wide variety of topics in chemical physics in order to stimulate new research and to serve as a text for beginners in a particular area of chemical physics.

Download or read book On protein structure function and modularity from an evolutionary perspective written by Robert Pilstål and published by Linköping University Electronic Press. This book was released on 2018-05-31 with total page 77 pages. Available in PDF, EPUB and Kindle. Book excerpt: We are compounded entities, given life by a complex molecular machinery. When studying these molecules we have to make sense of a diverse set of dynamical nanostructures with wast and intricate patterns of interactions. Protein polymers is one of the major groups of building blocks of such nanostructures which fold up into more or less distinct three dimensional structures. Due to their shape, dynamics and chemical properties proteins are able to perform a plethora of specific functions essential to all known cellular lifeforms. The connection between protein sequence, translated into protein structure and in the continuation into protein function is well accepted but poorly understood. Malfunction in the process of protein folding is known to be implicated in natural aging, cancer and degenerative diseases such as Alzheimer's. Protein folds are described hierarchically by structural ontologies such as SCOP, CATH and Pfam all which has yet to succeed in deciphering the natural language of protein function. These paradigmatic views centered on protein structure fail to describe more mutable entities, such as intrinsically disordered proteins (IDPs) which lack a clear defined structure. As of 2012, about two thirds of cancer patients was predicted to survive past 5 years of diagnosis. Despite this, about a third do not survive and numerous of successfully treated patients suffer from secondary conditions due to chemotherapy, surgery and the like. In order to handle cancer more efficiently we have to better understand the underlying molecular mechanisms. Elusive to standard methods of investigation, IDPs have a central role in pathology; dysfunction in IDPs are key factors in cellular system failures such as cancer, as many IDPs are hub regulators for major cell functions. These IDPs carry short conserved functional boxes, that are not described by known ontologies, which suggests the existence of a smaller entity. In an investigation of a pair of such boxes of c-MYC, a plausible structural model of its interacting with Pin1 emerged, but such a model still leaves the observer with a puzzle of understanding the actual function of that interaction. If the protein is represented as a graph and modeled as the interaction patterns instead of as a structural entity, another picture emerges. As a graph, there is a parable from that of the boxes of IDPs, to that of sectors of allosterically connected residues and the theory of foldons and folding units. Such a description is also useful in deciphering the implications of specific mutations. In order to render a functional description feasible for both structured and disordered proteins, there is a need of a model separate from form and structure. Realized as protein primes, patterns of interaction, which has a specific function that can be defined as prime interactions and context. With function defined as interactions, it might be possible that the discussion of proteins and their mechanisms is thereby simplified to the point rendering protein structural determination merely supplementary to understanding protein function. Människan byggs upp av celler, de i sin tur består av än mindre beståndsdelar; livets molekyler. Dessa fungerar som mekaniska byggstenar, likt maskiner och robotar som sliter vid fabrikens band; envar utförandes en absolut nödvändig funktion för cellens, och hela kroppens, fortsatta överlevnad. De av livets molekyler som beskrivs centralt i den här avhandling är proteiner, vilka i sin tur består utav en lång kedja, med olika typer av länkar, som likt garn lindar upp sig i ett nystan av en (mer eller mindre...) bestämd struktur som avgör dess roll och funktion i cellen. Intrinsiellt oordnade proteiner (IDP) går emot denna enkla åskådning; de är proteiner som saknar struktur och beter sig mer likt spaghetti i vatten än en maskin. IDP är ändå funktionella och bär på centrala roller i cellens maskineri; exempel är oncoproteinet c-Myc som agerar "gaspedal" för cellen - fel i c-Myc's funktion leder till att cellerna löper amok, delar sig hejdlöst och vi får cancer. Man har upptäckt att c-Myc har en ombytlig struktur vi inte kan se; studier av punktvisa förändringar, mutationer, i kedjan av byggstenar hos c-Myc visar att många länkar har viktiga roller i funktionen. Detta ger oss bättre förståelse om cancer men samtidigt är laboratoriearbetet både komplicerat och dyrt; här kan evolutionen vägleda oss och avslöja hemligheterna snabbare. Molekylär evolution studeras genom att beräkna variation i proteinkedjan mellan besläktade arter som finns lagrade i databaser; detta visar snabbt, via nätverksanalys och grafteori, vilka delar av proteinet som är centrala och kopplade till varandra av nödvändighet för artens fortlevnad. På så vis hjälper evolutionen oss att förstå proteinfunktioner via modeller baserade på proteinernas interaktioner snarare än deras struktur. Samma modeller kan nyttjas för att förstå dynamiska förlopp och skillnader mellan normala och patologiska varianter av proteiner; mutationer kan uppstå i vår arvsmassa som kan leda till sjukdom. Genom analys av proteinernas kopplingsnätverk i grafmodellerna kan man bättre förutsäga vilka mutationer som är farligare än andra. Dessutom har det visat sig att en sådan representation kan ge bättre förståelse för den normala funktionen hos ett protein än vad en proteinstruktur kan. Här introduceras även konceptet proteinprimärer, vilket är en abstrakt representation av proteiner centrerad på deras interaktiva mönster, snarare än på partikulär form och struktur. Det är en förhoppning att en sådan representation skall förenkla diskussionen anbelangande proteinfunktion så till den grad att strukturbestämmelse av proteiner, som är en mycket kostsam och tidskrävande process, till viss mån kan anses vara sekundär i betydelse jämfört med funktionellt modellerande baserat på evolutionära data extraherade ur våra sekvensdatabaser.