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[null,"1.","Record Nr.",null,"UNINA9910971322703321"]
[null,null,"Titolo",null,"Molecular machines / / editor, Benoît Roux"]
[null,null,"Pubbl/distr/stampa",null,"Singapore ; ; Hackensack, N.J., : World Scientific, c2011"]
[null,null,"ISBN",null,"9786613433749"]
[{"$nulls":4},"9781283433747"]
[{"$nulls":4},"1283433745"]
[{"$nulls":4},"9789814343466"]
[{"$nulls":4},"9814343463"]
[null,null,"Edizione",null,"[1st ed.]"]
[null,null,"Descrizione fisica",null,"1 online resource (288 p.)"]
[null,null,"Disciplina",null,"572.8"]
[{"$nulls":4},"579"]
[null,null,"Soggetti",null,"Molecular biology"]
[{"$nulls":4},"Bioenergetics"]
[{"$nulls":4},"Biomolecules"]
[{"$nulls":4},"Cell interaction"]
[{"$nulls":4},"Cytology"]
[{"$nulls":4},"Microbiology"]
[null,null,"Lingua di pubblicazione",null,"Inglese"]
[null,null,"Formato",null,"Materiale a stampa"]
[null,null,null,"Livello bibliografico","Monografia"]
[null,null,null,"Note generali","Description based upon print version of record."]
[null,null,null,"Nota di bibliografia","Includes bibliographical references and index."]
[null,null,"Nota di contenuto",null,"Intro -- Contents -- Preface -- About the Authors -- Chapter 1 Molecular Behavior in Biological Cells: The Bacterial Cytoplasm as a Model System Adrian H. Elcock and Andrew S. Thomas -- 1. Introduction -- 2. A Simple Analogy for Molecular Behavior in vivo -- 3. Macromolecular Crowding Effects -- 4. The Bacterial Cytoplasm as a Model System -- 5. A Structural Model of the Bacterial Cytoplasm -- 6. Some Issues in Simulating Such a System -- 7. A Dynamic Model of the Bacterial Cytoplasm -- 8. Quantifying Protein Diffusion in the Bacterial Cytoplasm -- 9. Thermodynamic Stability of Proteins in the Bacterial Cytoplasm -- 10. Conclusion -- Acknowledgments -- Suggested Additional Reading Material -- References -- Chapter 2 The Light-Harvesting Apparatus in Purple Photosynthetic Bacteria: Introduction to a Quantum Biological Device Johan Strümpfer, Jen Hsin, Melih Şener, Danielle Chandler and Klaus Schulten -- 1. Introduction -- 2. Components of a Chromatophore Vesicle -- 2.1 The light-harvesting complex LH2 -- 2.2 The RC-LH1 core complex -- 2.2.1 Organization "]
[{"$nulls":4},"of RC-LH1 -- 2.2.2 Structures of LH1 and RC -- 2.3 Spatial organization of the chromatophore -- 3. Energy Harvesting and Transfer -- 3.1 Excitons -- 3.2 Excitation transfer -- 3.3 Chromatophore-wide exciton transfer -- 4. Discussion -- Acknowledgments -- References -- Appendix -- Chapter 3 DNA Polymerases: Structure, Function, and Modeling Tamar Schlick -- 1. Introduction -- 1.1 Venerable task -- 1.2 Replication and repair fidelity -- 1.3 Polymerase structure and function -- 2. Modeling Studies -- 2.1 Need for modeling -- 2.2 Conformational pathways in pol β, pol λ, pol X, and pol µ -- 2.3 Pol β's closing pathway -- 2.4 Pol β's chemical mechanism for G:C vs. G:A systems -- 2.5 Pol λ's pathway and slippage tendency -- 2.6 Dpo4's handling of 8-oxoG -- 2.7 Pol X mispair incorporation -- 3. Conclusion."]
[{"$nulls":4},"Acknowledgment -- Suggested Additional Reading Materials -- References -- Chapter 4 Information Processing by Nanomachines: Decoding by the Ribosome Karissa Y. Sanbonmatsu, Scott C. Blanchard and Paul C. Whitford -- 1. Introduction -- 2. Overview of Protein Synthesis and Elongation -- 3. Decoding by the Ribosome -- 4. Dynamic Regions of the Ribosomal Complex -- 4.1 Dynamic regions of the ribosome -- 4.2 tRNA as an active player in decoding: Flexible tRNAs -- 5. Computational Studies of Decoding by the Ribosome -- 5.1 Early simulations of decoding and tRNA selection -- 5.2 REMD simulations of the decoding center produce exhaustive sampling -- 5.3 High performance computing systems are required to simulate the intact ribosome -- 5.4 Simulations of large-scale conformational changes of tRNAs -- 6. Towards Energy Landscapes of Decoding -- Suggested Additional Reading Materials -- References -- Chapter 5 Chaperonins: The Machines Which Fold Proteins Del Lucent, Martin C Stumpe and Vijay S Pande -- 1. Introduction -- 2. GroEL -- 3. How Do Chaperonins Work? -- 3.1. The Anfinsen cage hypothesis -- 3.2. Iterative annealing -- 3.3. The landscape modulation hypothesis: Confinement -- 3.4. The landscape modulation hypothesis: Chaperonin-enhanced hydrophobic effect -- 4. Other Chaperonins -- 5. Conclusions -- Suggested Additional Reading Materials -- References -- Chapter 6 Muscle and Myosin Ronald S. Rock -- 1. A Structural Basis for Motion -- 2. Coupling of Motion to ATP Hydrolysis -- 3. In Vitro Motility Assays Reconstitute Motion from a Minimal Set of Components -- 4. The Stepsize Controversy and Single Molecule Motility -- 5. From Swinging Crossbridges to Sliding Filaments -- 6. The Regulation of Contraction -- 7. New Frontiers in Motility Research: Nonmuscle Myosins and the Evolution of Eukaryotic Motility -- Suggested Additional Reading Material."]
[{"$nulls":4},"References -- Chapter 7 Protein Kinases: Phosphorylation Machines Elaine E. Thompson, Susan S. Taylor and J. Andrew McCammon -- 1. Introduction -- 2. Activation Loop -- 3. DFG Loop -- 4. C-helix -- 5. Kinase Spines -- 6. Processive Phosphorylation -- 7. Conclusion -- Acknowledgments -- Suggested Additional Reading Materials -- References -- Chapter 8 Computational Studies of Na /H  Antiporter: Structure, Dynamics and Function Assaf Ganoth, Raphael Alhadeff and Isaiah T. Arkin -- 1. Introduction -- 2. Structure of the Na /H  Antiporter -- 3. The Dynamics of the Na /H  Antiporter -- 3.1 The influence of protonation states on the NhaA -- 3.2 Mechanism of Na /H antiporting -- 3.3 The unique Na  /H   electrostatic organization -- 4. Models for the Na /H  Proteins -- 4.1 Model structure of the vibrio parahaemolyticus NhaA -- 4.2 Model structure of NHE1 - A human Na /H  exchanger -- 4.3 Model structure of NHA2 - A human Na /H  antiporter -- 5. Concluding Remarks -- Acknowledgments -- Suggested Additional Reading Materials -- References -- Chapter 9 "]
[{"$nulls":4},"Membrane Transporters: Molecular Machines Coupling Cellular Energy to Vectorial Transport Across the Membrane Zhijian Huang, Saher A. Shaikh, Po-Chao Wen, Giray Enkavi, Jing Li and Emad Tajkhorshid -- 1. Introduction -- 2. ATP-Driven Transport in ABC Transporters -- 3. Ion-Coupled Neurotransmitter Uptake by the Glutamate Transporter -- 4. Substrate-Induced Rocker-Switch Motion in an Antiporter -- 5. Alternating Access Model in Leucine Transporter -- 6. Interconversion of the Open and Occluded States in Na -Coupled Galactose Transporter -- 7. Concluding Remarks -- Acknowledgment -- Suggested Additional Reading Materials -- References -- Chapter 10 ABC Transporters E. P. Coll and D. P. Tieleman -- 1. Introduction -- 2. Structure of ABC Transporters -- 2.1 NBD structure -- 2.2 TMD structure -- 2.2.1 Importers."]
[{"$nulls":4},"2.2.2 Type I importers -- 2.2.3 Type II importers -- 2.2.4 Exporters -- 3. Transport Cycle -- 4. Methods of Study -- 5. Conclusions -- Acknowledgments -- References -- Chapter 11 Sodium-coupled Secondary Transporters: Insights from Structure-based Computations Elia Zomot, Ahmet Bakan, Indira H. Shrivastava, Jason DeChancie, Timothy R. Lezon and Ivet Bahar -- 1. Introduction: Biological Function and Classification -- 2. Na -Coupled Mechanism of Transport: A Macroscopic View -- 2.1 Transport cycle and alternate access mechanism -- 2.2. Balance of forces/potentials across the membrane favors Na inward flow -- 2.3 Sodium ion co-transport as a driving potential for the transmembrane translocation of solutes by secondary transporters -- 3. Structural Information -- 3.1 Structure and topology -- 3.2 Substrate and sodium binding -- 4. Molecular Mechanisms Revealed by Structure-Based Modeling and Computations -- 4.1 Local Motions and Substrate/Sodium Interactions in Glutamate Transporters -- 4.1.1 Gate opening in the outward-facing state of Glt -- 4.1.2 Role of Na   ions in stabilizing the closed conformation of the EC gate in the substrate-bound outward-facing Glt -- 4.1.3 Na  and substrate release by Glt   in the inward-facing state -- 4.2 Conformational dynamics of NSS family members and their structural homologs -- 4.2.1 Molecular dynamics of transporters that share the LeuT fold -- 4.2.2 Spontaneous release of Na  and dislodging of substrate observed in MD simulations of galactose transporter vSGLT -- 5. Transitions between Inward- and Outward-Facing States Explored by Computational Analyses -- 5.1 Structure prediction via homology modeling based on structural symmetry -- 5.1.1 Modeling of Glt    in the inward-facing state based on the outward-facing structure -- 5.1.2 Modeling of LeuT in the inward-facing state based on known outward-facing structure."]
[{"$nulls":4},"5.2 Results from elastic network models -- 6. Conclusion -- References -- Chapter 12 Voltage-Gated Ion Channels: The Machines Responsible for the Nerve Impulse Benoît Roux and Francisco Bezanilla -- 1. Introduction -- 2. Biological Membranes and Channels -- 3. The Nernst Potential -- 4. Selective Channels and the Action Potential -- 5. Channel Function at the Atomic Level -- 5.1 Fast ion conduction and selectivity -- 5.2 Channel gating and membrane voltage -- 5.3 The functional implications of a focused field -- 6. Future Outlook -- Suggested Additional Reading Materials -- References -- Chapter 13 Voltage-Gated Channels and the Heart Jonathan R. Silva and Yoram Rudy -- 1. Introduction -- 2. Cardiac Electrophysiology Background -- 2.1 Organ level physiology -- 2.2 Cellular level electrophysiology -- 2.2.1 The Hodgkin-Huxley model -- 2.2.2 Modeling the cardiac ventricular action potential -- 2.2.3 Rate dependence -- 2.2.4 β-adrenergic regulation -- 2.2.5 The long QT syndrome -- 3. I   as a Molecular Machine -- 3.1 Structure and kinetics -- 3.2 Kinetic modeling of I -- 3.3 Molecular modeling of I -- Conclusion -- Further "]
[{"$nulls":4},"Reading -- References -- Index."]
[null,null,null,"Sommario/riassunto","Molecular machines are complex biomolecules, proteins, nucleic acids, and carbohydrates that consume energy in order to perform specific functions. The concerted action of all those machines underlies all the activities of the living cell. To understand how such molecular machines are able to perform their function, it is necessary to identify the different moving parts and understand how they act together. Breaking new ground with these difficult problems is likely to require novel paradigms permitting a seamless integration of structural, dynamical and functional data from experiments and theory.The goal of this volume is to provide an introduction to the world of biological molecular machines to a broad audience of students and researchers in biosciences. Each chapter is written by leading experts to cover results from cutting-edge research, while remaining broadly accessible. The volume presents the current state of knowledge for several important systems, ranging from polymerases, the ribosome, chaperonins, the chromatophore, kinases, actin and myosin, membrane transporters, and voltage-gated ion channels, thus giving students and researches in biosciences a pedagogically integrated picture of this exciting and rapidly expanding field."]