Structural And Dynamic Aspects Of Protein Function And Allostery
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Structural And Dynamic Aspects Of Protein Function And Allostery
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Author : George Lisi
language : en
Publisher: Frontiers Media SA
Release Date : 2022-03-28
Structural And Dynamic Aspects Of Protein Function And Allostery written by George Lisi and has been published by Frontiers Media SA this book supported file pdf, txt, epub, kindle and other format this book has been release on 2022-03-28 with Science categories.
Biomolecular Simulations In Structure Based Drug Discovery
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Author : Francesco L. Gervasio
language : en
Publisher: John Wiley & Sons
Release Date : 2019-04-29
Biomolecular Simulations In Structure Based Drug Discovery written by Francesco L. Gervasio and has been published by John Wiley & Sons this book supported file pdf, txt, epub, kindle and other format this book has been release on 2019-04-29 with Medical categories.
A guide to applying the power of modern simulation tools to better drug design Biomolecular Simulations in Structure-based Drug Discovery offers an up-to-date and comprehensive review of modern simulation tools and their applications in real-life drug discovery, for better and quicker results in structure-based drug design. The authors describe common tools used in the biomolecular simulation of drugs and their targets and offer an analysis of the accuracy of the predictions. They also show how to integrate modeling with other experimental data. Filled with numerous case studies from different therapeutic fields, the book helps professionals to quickly adopt these new methods for their current projects. Experts from the pharmaceutical industry and academic institutions present real-life examples for important target classes such as GPCRs, ion channels and amyloids as well as for common challenges in structure-based drug discovery. Biomolecular Simulations in Structure-based Drug Discovery is an important resource that: -Contains a review of the current generation of biomolecular simulation tools that have the robustness and speed that allows them to be used as routine tools by non-specialists -Includes information on the novel methods and strategies for the modeling of drug-target interactions within the framework of real-life drug discovery and development -Offers numerous illustrative case studies from a wide-range of therapeutic fields -Presents an application-oriented reference that is ideal for those working in the various fields Written for medicinal chemists, professionals in the pharmaceutical industry, and pharmaceutical chemists, Biomolecular Simulations in Structure-based Drug Discovery is a comprehensive resource to modern simulation tools that complement and have the potential to complement or replace laboratory assays for better results in drug design.
Molecular Biology Of The Cell
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Author :
language : en
Publisher:
Release Date : 2004
Molecular Biology Of The Cell written by and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 2004 with Cells categories.
Understanding Protein Dynamics Binding And Allostery For Drug Design
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Author : Guang Hu
language : en
Publisher: Frontiers Media SA
Release Date : 2021-06-08
Understanding Protein Dynamics Binding And Allostery For Drug Design written by Guang Hu and has been published by Frontiers Media SA this book supported file pdf, txt, epub, kindle and other format this book has been release on 2021-06-08 with Science categories.
Sublinear Computation Paradigm
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Author : Naoki Katoh
language : en
Publisher: Springer Nature
Release Date : 2021-10-19
Sublinear Computation Paradigm written by Naoki Katoh and has been published by Springer Nature this book supported file pdf, txt, epub, kindle and other format this book has been release on 2021-10-19 with Computers categories.
This open access book gives an overview of cutting-edge work on a new paradigm called the “sublinear computation paradigm,” which was proposed in the large multiyear academic research project “Foundations of Innovative Algorithms for Big Data.” That project ran from October 2014 to March 2020, in Japan. To handle the unprecedented explosion of big data sets in research, industry, and other areas of society, there is an urgent need to develop novel methods and approaches for big data analysis. To meet this need, innovative changes in algorithm theory for big data are being pursued. For example, polynomial-time algorithms have thus far been regarded as “fast,” but if a quadratic-time algorithm is applied to a petabyte-scale or larger big data set, problems are encountered in terms of computational resources or running time. To deal with this critical computational and algorithmic bottleneck, linear, sublinear, and constant time algorithms are required. The sublinear computation paradigm is proposed here in order to support innovation in the big data era. A foundation of innovative algorithms has been created by developing computational procedures, data structures, and modelling techniques for big data. The project is organized into three teams that focus on sublinear algorithms, sublinear data structures, and sublinear modelling. The work has provided high-level academic research results of strong computational and algorithmic interest, which are presented in this book. The book consists of five parts: Part I, which consists of a single chapter on the concept of the sublinear computation paradigm; Parts II, III, and IV review results on sublinear algorithms, sublinear data structures, and sublinear modelling, respectively; Part V presents application results. The information presented here will inspire the researchers who work in the field of modern algorithms.
Advances In Phosphotransferases Phosphate Group Acceptor Research And Application 2011 Edition
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Author :
language : en
Publisher: ScholarlyEditions
Release Date : 2012-01-09
Advances In Phosphotransferases Phosphate Group Acceptor Research And Application 2011 Edition written by and has been published by ScholarlyEditions this book supported file pdf, txt, epub, kindle and other format this book has been release on 2012-01-09 with Medical categories.
Advances in Phosphotransferases (Phosphate Group Acceptor) Research and Application: 2011 Edition is a ScholarlyPaper™ that delivers timely, authoritative, and intensively focused information about Phosphotransferases (Phosphate Group Acceptor) in a compact format. The editors have built Advances in Phosphotransferases (Phosphate Group Acceptor) Research and Application: 2011 Edition on the vast information databases of ScholarlyNews.™ You can expect the information about Phosphotransferases (Phosphate Group Acceptor) in this eBook to be deeper than what you can access anywhere else, as well as consistently reliable, authoritative, informed, and relevant. The content of Advances in Phosphotransferases (Phosphate Group Acceptor) Research and Application: 2011 Edition has been produced by the world’s leading scientists, engineers, analysts, research institutions, and companies. All of the content is from peer-reviewed sources, and all of it is written, assembled, and edited by the editors at ScholarlyEditions™ and available exclusively from us. You now have a source you can cite with authority, confidence, and credibility. More information is available at http://www.ScholarlyEditions.com/.
On Protein Structure Function And Modularity From An Evolutionary Perspective
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Author : Robert Pilstål
language : en
Publisher: Linköping University Electronic Press
Release Date : 2018-05-23
On Protein Structure Function And Modularity From An Evolutionary Perspective written by Robert Pilstål and has been published by Linköping University Electronic Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2018-05-23 with categories.
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.
Protein Allostery In Drug Discovery
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Author : Jian Zhang
language : en
Publisher: Springer Nature
Release Date : 2019-11-09
Protein Allostery In Drug Discovery written by Jian Zhang and has been published by Springer Nature this book supported file pdf, txt, epub, kindle and other format this book has been release on 2019-11-09 with Medical categories.
The book focuses on protein allostery in drug discovery. Allosteric regulation, ʹthe second secret of lifeʹ, fine-tunes virtually most biological processes and controls physiological activities. Allostery can both cause human diseases and contribute to development of new therapeutics. Allosteric drugs exhibit unparalleled advantages compared to conventional orthosteric drugs, rendering the development of allosteric modulators as an appealing strategy to improve selectivity and pharmacodynamic properties in drug leads. The Series delineates the immense significance of protein allostery—as demonstrated by recent advances in the repertoires of the concept, its mechanistic mechanisms, and networks, characteristics of allosteric proteins, modulators, and sites, development of computational and experimental methods to predict allosteric sites, small-molecule allosteric modulators of protein kinases and G-protein coupled receptors, engineering allostery, and the underlying role of allostery in precise medicine. Comprehensive understanding of protein allostery is expected to guide the rational design of allosteric drugs for the treatment of human diseases. The book would be useful for scientists and students in the field of protein science and Pharmacology etc.
Continued Fascination A Tribute To A Giant In Immunology Dr William E Paul
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Author : Jinfang Zhu
language : en
Publisher: Frontiers Media SA
Release Date : 2019-06-19
Continued Fascination A Tribute To A Giant In Immunology Dr William E Paul written by Jinfang Zhu and has been published by Frontiers Media SA this book supported file pdf, txt, epub, kindle and other format this book has been release on 2019-06-19 with categories.
Dr. William E. Paul (1936–2015) was the leader of the National Institutes of Health (NIH) immunology community and his career is without parallel in the field of immunology. He was the Chief of the Laboratory of Immunology, National Institute of Allergy and Infectious Diseases (NIAID), from 1970 at the age of 34 until his death. His groundbreaking contributions to the field of immunology, including the discovery of interleukin (IL)-4, led to more than 600 publications over half a century. He also played an important role in the establishment of the NIH Vaccine Research Center while he was the Director of the NIH Office of AIDS Research. Furthermore, Dr. Paul was a shining icon and an international giant of contemporary immunology. He was a genius and a living encyclopedia of immunology: the author of the textbook "Fundamental Immunology" since its inception to the 7th edition in 2013; and the editor of the “Annual Review of Immunology” from its inaugural issue in 1983 until 2011. In his last book "Immunity", he discussed the three laws of immunology: universality, tolerance and appropriateness. These capture the essence of Dr. Paul as well as the field. Dr. Paul had an enormous impact on the research career of his trainees, many of whom became leaders in the field of immunology, including Drs. Charles Janeway, Ronald Schwartz, Laurie Glimcher and Mark Davis. Dr. Paul was an intelligent, generous, humble but optimistic man. He was also an inspirational and thoughtful leader, colleague and friend; he inspired and encouraged people around him in every possible way. As his trainees and/or colleagues, we miss him greatly and dedicate this special Research Topic to his memory. We thank all the authors who participated in this collection as well as other colleagues and friends of Dr. Paul's who have supported us in a series of events after Dr. Paul's passing. Finally, we would like to thank the Frontiers in Immunology for providing such a wonderful platform for remembering Dr. Paul's remarkable life.
New Experimental Probes For Enzyme Specificity And Mechanism
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Author :
language : en
Publisher: Elsevier
Release Date : 2023-05-26
New Experimental Probes For Enzyme Specificity And Mechanism written by and has been published by Elsevier this book supported file pdf, txt, epub, kindle and other format this book has been release on 2023-05-26 with Science categories.
New Experimental Probes for Enzyme Specificity and Mechanism, Volume 685, the latest release in the Methods of Enzymology series, highlights new advances in the field with this new volume presenting interesting chapters on a variety of topics including Subverting Hedgehog Protein Autoprocessing by Chemical Induction of Paracatalysis, New Mechanistic Probes to Identify Novel Substrates for N-Myristoyltransferases, Phosphonate and α Fluorophosphonate Analogues of D Glucose 6 Phosphate as Active-Site Probes of 1L-Myo-Inositol 1 phosphate Synthase, Kinetic Mechanism of Nicotine-Degrading Enzyme Probed by Stopped-Flow Kinetic Analyses, Kinetics and Mechanism for Enzyme-Catalyzed Reactions of Substrate Pieces, and more. Additional chapters cover Kinetics and Mechanism for Reactions of Enzyme Pieces, Evaluation of allostery for the bienzyme assembly of a 3-deoxy-D-arabino heptulosonate-7-phosphate synthase and chorismate mutase, Recognition and Catalysis of Reactions of Chiral Substrates by Mandelate Racemase, Innovative and emerging modalities of EGFR kinase inhibitors, Characterization of the Aminoacrylate Intermediate of Tyrosine Phenol-Lyases, and much more. - Provides the authority and expertise of leading contributors from an international board of authors - Presents the latest release in Methods in Enzymology serials - Updated release includes the latest information on New Experimental Probes for Enzyme Specificity and Mechanism