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Fluorescent Methods for Molecular Motors / / edited by Christopher P. Toseland, Natalia Fili
| Fluorescent Methods for Molecular Motors / / edited by Christopher P. Toseland, Natalia Fili |
| Edizione | [1st ed. 2014.] |
| Pubbl/distr/stampa | Basel : , : Springer Basel : , : Imprint : Springer, , 2014 |
| Descrizione fisica | 1 online resource (306 p.) |
| Disciplina |
574.19245
572.64 |
| Collana | Experientia Supplementum |
| Soggetto topico |
Proteins
Cell biology Biophysics Biological physics Protein Science Cell Biology Biological and Medical Physics, Biophysics |
| ISBN | 3-0348-0856-9 |
| Formato | Materiale a stampa  |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto | Fluorescence and Labelling: How to choose and what to do -- Fluorescent biosensors: design and application to motor proteins -- Rapid Reaction Kinetic Techniques -- Fluorescence to study the ATPase mechanism of Motor Proteins -- Use of pyrene labelled actin to probe actin myosin interactions; kinetic and equilibrium studies -- Fluorescent methods to study transcription initiation and transition into elongation -- Single-molecule and single-particle imaging of molecular motors in vitro and in vivo -- Fluorescence methods in the investigation of the DEAD-box helicase mechanism -- Use of Fluorescent Techniques to Study the In Vitro Movement of Myosins -- Fluorescence Tracking of Motor proteins in vitro -- Measuring Transport of Motor Cargos -- Measuring two at the same time: Combining Magnetic Tweezers with Single-Molecule FRET -- Using fluorescence to study actomyosin in yeasts. |
| Record Nr. | UNINA-9910298329003321 |
| Basel : , : Springer Basel : , : Imprint : Springer, , 2014 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||
Mass spectrometry of protein interactions [[electronic resource] /] / edited by Kevin M. Downard
| Mass spectrometry of protein interactions [[electronic resource] /] / edited by Kevin M. Downard |
| Pubbl/distr/stampa | Hoboken, N.J., : Wiley-Interscience, c2007 |
| Descrizione fisica | 1 online resource (153 p.) |
| Disciplina |
543.65
572.64 572/.64 |
| Altri autori (Persone) | DownardK (Kevin) |
| Collana | Wiley-Interscience series in mass spectrometry |
| Soggetto topico |
Protein-protein interactions
Mass spectrometry |
| Soggetto genere / forma | Electronic books. |
| ISBN |
1-281-00190-2
9786611001902 0-470-14633-8 0-470-14632-X |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto | Direct characterization of protein complexes by electrospray ionization mass spectrometry and ion mobility analysis / Joseph A. Loo and Catherine S. Kaddis -- Softly, softly--detection of protein complexes by matrix-assisted laser desorption ionization mass spectrometry / Kevin M. Downard -- Probing protein interactions using hydrogen-deuterium exchange mass spectrometry / David D. Weis ... [et al.] -- Limited proteolysis mass spectrometry of protein complexes / Maria Monti and Piero Pucci -- Chemical cross-linking and mass spectrometry for investigation of protein-protein interactions / Andrea Sinz -- Genesis and application of radical probe mass spectrometry (RP-MS) to study protein interactions / Simin D. Maleknia and Kevin M. Downard. |
| Record Nr. | UNINA-9910144259003321 |
| Hoboken, N.J., : Wiley-Interscience, c2007 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||
Mass spectrometry of protein interactions [[electronic resource] /] / edited by Kevin M. Downard
| Mass spectrometry of protein interactions [[electronic resource] /] / edited by Kevin M. Downard |
| Pubbl/distr/stampa | Hoboken, N.J., : Wiley-Interscience, c2007 |
| Descrizione fisica | 1 online resource (153 p.) |
| Disciplina |
543.65
572.64 572/.64 |
| Altri autori (Persone) | DownardK (Kevin) |
| Collana | Wiley-Interscience series in mass spectrometry |
| Soggetto topico |
Protein-protein interactions
Mass spectrometry |
| ISBN |
1-281-00190-2
9786611001902 0-470-14633-8 0-470-14632-X |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto | Direct characterization of protein complexes by electrospray ionization mass spectrometry and ion mobility analysis / Joseph A. Loo and Catherine S. Kaddis -- Softly, softly--detection of protein complexes by matrix-assisted laser desorption ionization mass spectrometry / Kevin M. Downard -- Probing protein interactions using hydrogen-deuterium exchange mass spectrometry / David D. Weis ... [et al.] -- Limited proteolysis mass spectrometry of protein complexes / Maria Monti and Piero Pucci -- Chemical cross-linking and mass spectrometry for investigation of protein-protein interactions / Andrea Sinz -- Genesis and application of radical probe mass spectrometry (RP-MS) to study protein interactions / Simin D. Maleknia and Kevin M. Downard. |
| Record Nr. | UNINA-9910830173903321 |
| Hoboken, N.J., : Wiley-Interscience, c2007 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||
Pharmacology of the WNT signaling system / / Gunnar Schulte, Pawel Kozielewicz, editors
| Pharmacology of the WNT signaling system / / Gunnar Schulte, Pawel Kozielewicz, editors |
| Pubbl/distr/stampa | Cham, Switzerland : , : Springer, , [2021] |
| Descrizione fisica | 1 online resource (420 pages) |
| Disciplina | 572.64 |
| Collana | Handbook of experimental pharmacology |
| Soggetto topico |
Wnt proteins
Neuropharmacology Pharmacology Farmacologia |
| Soggetto genere / forma | Llibres electrònics |
| ISBN | 3-030-85499-X |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Record Nr. | UNINA-9910508448003321 |
| Cham, Switzerland : , : Springer, , [2021] | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||
Protein interactions : the molecular basis of interactomics / / edited by Volkhard Helms and Olga V. Kalinina
| Protein interactions : the molecular basis of interactomics / / edited by Volkhard Helms and Olga V. Kalinina |
| Pubbl/distr/stampa | Weinheim, Germany : , : Wiley-VCH, , [2023] |
| Descrizione fisica | 1 online resource (490 pages) |
| Disciplina | 572.64 |
| Soggetto topico |
Protein-protein interactions
Molecular biology Cell receptors |
| ISBN |
3-527-83050-2
3-527-83052-9 |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto |
Intro -- Table of Contents -- Title Page -- Copyright -- Preface -- 1 Protein Structure and Conformational Dynamics -- 1.1 Structural and Hierarchical Aspects -- 1.2 Conformational Dynamics -- 1.3 From Structure to Function -- 1.4 Summary -- References -- 2 Protein-Protein-Binding Interfaces -- 2.1 Definition and Properties of Protein-Protein Interfaces -- 2.2 Growing Number of Known Protein-Protein Interface Structures -- 2.3 Surface Areas of Protein-Protein Interfaces -- 2.4 Gap Volume of Protein-Protein Interfaces -- 2.5 Amino Acid Composition of Interfaces -- 2.6 Secondary Structure of Interfaces -- 2.7 Protein-Protein‐Binding Energy -- 2.8 Interfaces of Homo‐ and Hetero‐Dimeric Complexes -- 2.9 Interfaces of Non‐obligate and Obligate Complexes -- 2.10 Interfaces of Transient and Permanent Complexes -- 2.11 Biological vs. Crystal Interfaces -- 2.12 Type I, Type II, and Type III Interfaces -- 2.13 Conserved Residues and Hot Spots in Interfaces -- 2.14 Conclusion and Future Implications -- References -- 3 Correlated Coevolving Mutations at Protein-Protein Interfaces -- 3.1 Introduction -- 3.2 A Short Introduction into Biomolecular Modeling -- 3.3 Statistical Inference of Coevolution -- 3.4 Solving the Inverse Potts Model -- 3.5 Contact Guided Protein and RNA Structure Prediction -- 3.6 Inter‐Monomer Interaction and Signaling -- 3.7 Summary -- References -- Note -- 4 Computational Protein-Protein Docking -- 4.1 Introduction -- 4.2 Rigid Body Protein-Protein Docking Approaches -- 4.3 Accounting for Conformational Changes during Docking -- 4.4 Integration of Bioinformatics and Experimental Data for Protein-Protein Docking -- 4.5 Template‐Based Protein-Protein Docking -- 4.6 Flexible Refinement of Docked Complexes -- 4.7 Scoring of Docked Complexes -- 4.8 Conclusions and Future Developments -- Acknowledgments -- References.
5 Identification of Putative Protein Complexes in Protein-Protein Interaction Networks -- 5.1 Protein-Protein Interaction Networks -- 5.2 Integration of Various PPI Resources in Public Data Repositories -- 5.3 Protein-Protein Interaction Networks of Model Organisms -- 5.4 Algorithms to Identify Protein Complexes in PPI Networks -- 5.5 Summary -- References -- 6 Structure, Composition, and Modeling of Protein Complexes -- 6.1 Protein Complex Structure -- 6.2 Methods for Automated Assignment of Biological Assemblies -- 6.3 Computational Approaches to Predicting 3D Structure of Protein Complexes -- 6.4 Conclusion and Outlook -- Acknowledgments -- References -- Notes -- 7 Live-Cell Structural Biology to Solve Molecular Mechanisms: Structural Dynamics in the Exocyst Function -- 7.1 Introduction -- 7.2 Structural Biology Using Light Microscopy Methods -- 7.3 Hybrid Methods: Integrative Structural Biology -- 7.4 Integrative Modeling: The Case of the Exocyst Complex -- 7.5 Comparing the In Situ Architecture of the Exocyst with a High‐Resolution Cryo‐EM Model -- 7.6 Discussion and Future Perspectives -- Acknowledgements -- References -- 8 Kinetics and Thermodynamics of Protein-Protein Encounter -- 8.1 Introduction -- 8.2 Thermodynamic Ensembles and Free Energy -- 8.3 Overview of Computational Methods to Determine Binding Free Energies -- References -- 9 Markov State Models of Protein-Protein Encounters -- 9.1 Introduction -- 9.2 Molecular Dynamics and Markov State Models -- 9.3 Strategies for MSM Estimation, Validation, and Analysis -- 9.4 The Connection to Experiments -- 9.5 Protein-Protein and Protein-Peptide Encounters -- 9.6 Emerging Technologies -- Acknowledgments -- References -- 10 Transcription Factor - DNA Complexes -- 10.1 Introduction -- 10.2 Principles of Sequence Recognition -- 10.3 Dimerization of Eukaryotic TFs. 10.4 Detection of Epigenetic Modifications -- 10.5 Detection of DNA Curvature/Bending -- 10.6 Modifications of Transcription Factors -- 10.7 Transcription Factor Binding Sites -- 10.8 Experimental Detection of TFBS -- 10.9 Position‐Specific Scoring Matrices -- 10.10 Molecular Modeling of TF-DNA Complexes -- 10.11 Cis‐Regulatory Modules -- 10.12 Relating Gene Expression to Binding of Transcription Factors -- 10.13 Summary -- References -- 11 The Chromatin Interaction System -- 11.1 Chromatin Is a Special Interaction Platform -- 11.2 Interaction of Proteins with Histone Posttranslational Modifications -- 11.3 Interaction of Proteins with Modified Nucleic Acids -- 11.4 UHRF1 as an Example of a Multidomain Reader/Writer Protein of Histone and DNA Modifications -- 11.5 Histone Chaperones and Chromatin Remodeling Complexes -- 11.6 Challenges in Chromatin Interactomics -- References -- 12 RNA-Protein Interactomics -- 12.1 Introduction -- 12.2 Interactions of Proteins with mRNA and ncRNA -- 12.3 The Basic Toolbox -- 12.4 RNA-Protein Interactomics -- 12.5 Outlook -- Notes -- References -- 13 Interaction Between Proteins and Biological Membranes -- 13.1 Introduction -- 13.2 The Plasma Membrane: Overview of Its Structure, Composition, and Function -- 13.3 Lipid‐Based and Protein‐Based Sorting of Plasma Membrane Components -- 13.4 Interaction of Peripheral Membrane Proteins with Membrane Lipids -- 13.5 Interactions and Conformations of Transmembrane Proteins in Lipid Membranes -- 13.6 Summary -- Acknowledgment -- References -- 14 Interactions of Proteins with Small Molecules, Allosteric Effects -- 14.1 Introduction -- 14.2 Modes of Binding to Proteins -- 14.3 Types of Interaction Between Protein and Ligand -- 14.4 Modeling Intermolecular Interactions by Force Fields and Docking Simulations -- 14.5 Entropic Aspects. 14.6 Allosteric Effects: Conformational Changes Upon Ligand Binding -- 14.7 Aspects of Ligand Design Beyond Protein-Ligand Interactions -- 14.8 Conclusions -- References -- 15 Effects of Mutations in Proteins on Their Interactions -- 15.1 Introduction -- 15.2 Structural Annotation of Mutations in Proteins -- 15.3 Methods for Predicting Effect of Protein Mutations -- 15.4 Conclusion -- Acknowledgments -- References -- 16 Not Quite the Same: How Alternative Splicing Affects Protein Interactions -- 16.1 Introduction -- 16.2 Effects of Alternative Splicing on Individual Proteins -- 16.3 Effects of Alternative Splicing on Protein-Protein Interaction Networks -- 16.4 Conclusion and Future Work -- References -- Notes -- 17 Phosphorylation-Based Molecular Switches -- 17.1 Introduction -- 17.2 Reversible Protein Phosphorylation in Cellular Signaling: Writers, Readers, and Erasers -- 17.3 Protein Kinases as Molecular Switches and as Components of Signaling Cascades -- 17.4 Mechanisms of Phosphorylation Specificity: the Importance of Short Linear Motifs -- 17.5 Examples of Phospho‐Switch‐Based Biological Regulation -- 17.6 Conclusion -- Acknowledgments -- References -- 18 Summary and Outlook -- 18.1 Technical State of the Art -- 18.2 Role of Machine Learning -- 18.3 Challenges -- 18.4 What Picture(s) May Evolve? -- References -- Index -- End User License Agreement. |
| Record Nr. | UNINA-9910686761803321 |
| Weinheim, Germany : , : Wiley-VCH, , [2023] | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||
Protein Interactions / / edited by Jianfeng Cai, Rongsheng Wang
| Protein Interactions / / edited by Jianfeng Cai, Rongsheng Wang |
| Pubbl/distr/stampa | Rijeka, Croatia : , : InTech, , [2012] |
| Descrizione fisica | 1 online resource (vii, 464 pages) : illustrations |
| Disciplina | 572.64 |
| Soggetto topico | Protein-protein interactions |
| ISBN | 953-51-5242-4 |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Record Nr. | UNINA-9910137691303321 |
| Rijeka, Croatia : , : InTech, , [2012] | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||
Protein-Protein and Domain-Domain Interactions / / by Pandjassarame Kangueane, Christina Nilofer
| Protein-Protein and Domain-Domain Interactions / / by Pandjassarame Kangueane, Christina Nilofer |
| Autore | Kangueane Pandjassarame |
| Edizione | [1st ed. 2018.] |
| Pubbl/distr/stampa | Singapore : , : Springer Singapore : , : Imprint : Springer, , 2018 |
| Descrizione fisica | 1 online resource (216 pages) : illustrations |
| Disciplina | 572.64 |
| Soggetto topico |
Medical genetics
Bioinformatics Proteins Vaccines Gene Function Computational Biology/Bioinformatics Protein Science Vaccine |
| ISBN | 981-10-7347-3 |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto | Module 1. Preface -- Module 2. Introduction to protein complexes -- Module 3. Historical advancement -- Module 4. Databases for protein complexes -- Module 5. Types of protein complexes -- Module 6. Hetero dimer protein complexes -- Module 7. Homo dimer protein complexes -- Module 8. Multimer protein complexes -- Module 9. Interfaces in protein complexes -- Module 10. Principles of protein-protein binding -- Module 11. Homodimer folding and binding -- Module 12. Gene fusion and protein complexes -- Module 13. Domain-domain interactions -- Module 14. Protein docking: Methods, software tools and servers -- Module 15. Protein complexes, pathways and networks -- Module 16. Protein complexes and biological functions -- Module 17. Protein complexes in diseases -- Module 18. Protein complexes in drug discovery & vaccine development -- Module 19. Protein complexes in genome and proteome analysis -- Module 20. Conclusions & challenges. |
| Record Nr. | UNINA-9910298416703321 |
Kangueane Pandjassarame
|
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| Singapore : , : Springer Singapore : , : Imprint : Springer, , 2018 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||
Protein-protein complexes [[electronic resource] ] : analysis, modeling and drug design / / edited by Martin Zacharias
| Protein-protein complexes [[electronic resource] ] : analysis, modeling and drug design / / edited by Martin Zacharias |
| Pubbl/distr/stampa | London, : Imperial College Press, 2010 |
| Descrizione fisica | 1 online resource (400 p.) |
| Disciplina |
572.6
572.64 |
| Altri autori (Persone) | ZachariasMartin |
| Soggetto topico |
Protein-protein interactions
Protein-protein interactions - Computer simulation Protein-protein interactions - Mathematical models Proteins - Structure Drugs - Design |
| Soggetto genere / forma | Electronic books. |
| ISBN |
1-282-75984-1
9786612759840 1-84816-340-1 |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Record Nr. | UNINA-9910456211303321 |
| London, : Imperial College Press, 2010 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||
Protein-protein complexes [[electronic resource] ] : analysis, modeling and drug design / / edited by Martin Zacharias
| Protein-protein complexes [[electronic resource] ] : analysis, modeling and drug design / / edited by Martin Zacharias |
| Pubbl/distr/stampa | London, : Imperial College Press, 2010 |
| Descrizione fisica | 1 online resource (400 p.) |
| Disciplina |
572.6
572.64 |
| Altri autori (Persone) | ZachariasMartin |
| Soggetto topico |
Protein-protein interactions
Protein-protein interactions - Computer simulation Protein-protein interactions - Mathematical models Proteins - Structure Drugs - Design |
| ISBN |
1-282-75984-1
9786612759840 1-84816-340-1 |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Record Nr. | UNINA-9910780878003321 |
| London, : Imperial College Press, 2010 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||
Protein-protein complexes : analysis, modeling and drug design / / edited by Martin Zacharias
| Protein-protein complexes : analysis, modeling and drug design / / edited by Martin Zacharias |
| Edizione | [1st ed.] |
| Pubbl/distr/stampa | London, : Imperial College Press, 2010 |
| Descrizione fisica | 1 online resource (400 p.) |
| Disciplina |
572.6
572.64 |
| Altri autori (Persone) | ZachariasMartin |
| Soggetto topico |
Protein-protein interactions
Protein-protein interactions - Computer simulation Protein-protein interactions - Mathematical models Proteins - Structure Drugs - Design |
| ISBN |
1-282-75984-1
9786612759840 1-84816-340-1 |
| Formato | Materiale a stampa |
| Livello bibliografico | Monografia |
| Lingua di pubblicazione | eng |
| Nota di contenuto |
Intro -- CONTENTS -- Preface -- 1. X-ray Study of Protein-Protein Complexes and Analysis of Interfaces Joel Janin -- 1.1 Introduction -- 1.2 Preparing Proteins for Structural Studies -- 1.3 Preparing Protein-Protein Complexes and Multi-component Assemblies -- 1.4 Crystallization and X-ray Studies -- 1.5 The Geometric Analysis of Protein-Protein Interfaces -- 1.6 Types and Sizes of Protein-Protein Interfaces -- 1.7 Chemical and Physical Chemical Properties of the Interfaces -- 1.8 Atomic Packing and Interface Topology -- 1.9 Conclusions and Outlook -- Acknowledgements -- References -- 2. A Structural Perspective on Protein-Protein Interactions in Macromolecular Assemblies Ranjit P. Bahadur -- 2.1 Introduction -- 2.2 The Icosahedral Viruses -- 2.3 The Structure of the Icosahedral Virus Capsids -- 2.4 Structural and Chemical Features of the Protein-Protein Interfaces -- 2.4.1 Symmetry and Size of Interfaces -- 2.4.2 Chemical Composition and Hydrogen Bonds -- 2.4.3 Atomic Packing of the Interfaces -- 2.4.4 Interface Patches and Segments -- 2.4.5 Residue Conservation -- 2.5 Comparison with Binary Interfaces -- 2.6 Mechanism of the Capsid Assembly -- 2.7 Conclusions and Outlook -- Acknowledgements -- References -- 3. Energetics of Protein-Protein Interactions Ilian Jelesarov -- 3.1 Introduction -- 3.2 Thermodynamic Formalism Describing the Energetics of Binding Reactions -- 3.2.1 Determination of the Binding Affinity -- 3.2.1.1 Heterologous Binding -- 3.2.1.2 Homologous Binding (Self-association) -- 3.2.2 Free Energy, Enthalpy and Entropy of Association -- 3.2.3 Determination of Energetic Changes -- 3.3 Experimental Methods to Measure the Energetics of Protein- Protein Association -- 3.3.1 Methods utilising Physical Separation of Species -- 3.3.2 Indirect Spectroscopic Methods -- 3.3.3 Methods Based on Refractive Phenomena -- 3.3.4 Kinetic Approaches.
3.3.5 Isothermal Titration Calorimetry (ITC) -- 3.4 Energetics of Protein-Protein Interactions -- 3.4.1 Calculation of Binding Affinities -- 3.4.2 Structure-based Prediction of Binding Parameters -- 3.4.3 Understanding Binding: Are there Structure-Energy Relationships? -- 3.5 Conclusions and Outlook -- Acknowledgements -- References -- 4. Kinetics of Biomacromolecular Complex Formation: Theory and Experiment Georgi V. Pachov, Razif R. Gabdoulline and Rebecca C. Wade -- 4.1 Introduction -- 4.1.1 Bimolecular Association -- 4.1.1.1 Diffusional Encounter Complex -- 4.1.1.2 Bound Complex -- 4.1.2 Molecular Transport -- 4.1.2.1 Diffusion -- 4.1.2.2 Viscosity -- 4.1.3 Molecular Interactions -- 4.1.3.1 Electrostatics -- 4.1.3.2 Hydrodynamics -- 4.1.3.3 Hydrophobicity -- 4.1.4 Reaction Rates -- 4.2 Experimental Techniques -- 4.2.1 Crystallography -- 4.2.2 Nuclear Magnetic Resonance (NMR) -- 4.2.3 Stopped-flow Methods (SF) -- 4.2.4 Fluorescence Recovery After Photobleaching (FRAP) -- 4.2.5 Fluorescence Resonance Energy Transfer (FRET) -- 4.2.6 Fluorescence Correlation Spectroscopy (FCS) -- 4.2.7 Force Probe Methods -- 4.2.8 Electrophoresis -- 4.2.9 Surface Plasmon Resonance (SPR) Biosensor -- 4.3 Theoretical and Computational Approaches -- 4.3.1 Computation of Bimolecular Rate Constants -- 4.3.2 Estimation of Rate Enhancements due to Electrostatic Interactions -- 4.4 Recent Advances in Computational Approaches -- 4.4.1 Protein-Protein Interactions -- 4.4.1.1 Computation of Rates -- 4.4.1.2 Determinants of Binding -- 4.4.1.3 Encounter Complex Quantification -- 4.4.1.4 Induced Fit Phenomena -- 4.4.1.5 Crowding Phenomena -- 4.4.2 Protein-nucleic Acid Interactions -- 4.4.2.1 Computation of Rates -- 4.4.2.2 Specificity and Nonspecificity -- 4.4.2.3 Chromatin Models -- 4.5 Conclusions and Outlook -- Acknowledgements -- References. 5. Evolutionary Trace of Protein Functional Determinants Olivier Lichtarge -- 5.1 Introduction -- 5.2 Evolutionary Trace Basics: Which Amino Acids are Important in a Protein? -- 5.3 Validation Through Prospective Case Studies -- 5.3.1 Separation of Function -- 5.3.2 Rewiring Functions -- 5.3.3 Redirecting Protein Binding Specificity to DNA -- 5.3.4 Other Case Studies -- 5.4 Proteomics Properties of Evolutionary Important Residues -- 5.5 Molecular Determinants of GPCR Signal Transduction -- 5.6 Protein Function Prediction -- References -- 6. Protein-Protein Docking Adrien Saladin and Chantal Prevost -- 6.1 Introduction -- 6.2 Definition and Goals of Macromolecular Docking -- 6.2.1 Protein-Protein Docking Terminology -- 6.2.2 Goals and Strategies -- 6.3 Protein-Protein Docking Methods -- 6.3.1 Systematic Search Methods -- 6.3.1.1 Discrete Sampling: The Correlation Methods -- 6.3.1.2 Geometric Surface Matching -- 6.3.2 Guided Search Methods -- 6.3.2.1 Example of a Guided Search Programme: ICM-DISCO -- 6.3.2.2 Speeding up the Calculation -- 6.3.2.3 Data-driven Methods -- 6.3.3 Refinement -- 6.3.3.1 Increasing the Resolution -- 6.3.3.2 Accounting for Side Chain Conformational Change -- 6.3.3.3 Explicit Solvation -- 6.3.3.4 Hierarchical Approaches -- 6.3.4 Scoring the Predictions -- 6.4 Evaluation of the Docking Methods -- 6.4.1 The CAPRI Experience -- 6.4.2 Docking Benchmarks -- 6.4.3 Challenges -- 6.5 Conclusions and Outlook -- Acknowledgements -- References -- 7. Data-driven Docking: Using External Information to Spark the Biomolecular Rendez-vous Adrien S.J. Melquiond and Alexandre M.J.J. Bonvin -- 7.1 Introduction -- 7.2 Stoichiometry and Composition -- 7.3 Shape of a Biomolecular Complex -- 7.4 Nature of the Interface: Which Residues are Engaged in a Date? -- 7.5 Orientation and Symmetry Problems. 7.6 Flexibility: How to Cope with Conformational Changes Occurring upon Complex Formation? -- 7.7 How to Implement Data-driven Docking, the HADDOCK Example -- 7.8 Conclusions and Outlook -- Acknowledgements -- References -- 8. High-resolution Protein-Protein Docking Nir London and Ora Schueler-Furman -- 8.1 Introduction -- 8.1.1 From Molecules to Networks: Making Sense of Large-scale Data, Starting from the Atomic Details of Protein-Protein Interactions -- 8.1.2 Docking - The Creation of Protein Complex Structures Starting from the Monomers -- 8.1.3 Explicit Modelling of the Atomic Details of the Protein-Protein Interface Allows Distinguishing the Correct from Alternative Conformations -- 8.1.4 The Scope of this Chapter -- 8.2 High-resolution Docking, as Defined by CAPRI -- 8.3 Accounting for Conformational Changes of Monomers is Crucial to High-resolution Modelling -- 8.3.1 Modelling Side Chain Flexibility -- 8.3.2 Taking it to the Next Step: Modelling Backbone Flexibility -- 8.3.2.1 Ensemble Docking -- 8.3.2.2 Refinement and Minimization -- 8.3.2.3 Modelling Hinge Motion -- 8.4 The High-resolution RosettaDock Protocol - Explicit Modelling of Full Side Chain Flexibility (and Beyond) Allows Accurate Modelling of Protein Complexes -- 8.4.1 Adding Backbone Conformational Flexibility to the RosettaDock Protocol -- 8.4.2 Ensemble Docking with RosettaDock -- 8.5 Additional High-resolution Docking Approaches -- 8.5.1 High-accuracy Modelling with Rigid Body Docking -- 8.5.2 A New Generation of Docking Protocols: Combining Successful Approaches of Low-resolution and High-resolution Searches -- 8.6 The Contribution of High-resolution Docking to the Understanding of Interactions of Biological Interest -- 8.6.1 Entry Mechanism of Anthrax Toxin -- 8.6.2 Antitumor Monoclonal Antibody 806 (mAb806) and the Epidermal Growth Factor Receptor (EGFR). 8.6.3 High-resolution Docking in the Service of Biochemistry -- 8.6.4 Applications of High-resolution Docking: Structure-based Prediction of Binding Specificity -- 8.7 Conclusions and Outlook -- 8.7.1 Impact of Docking on the Modelling Field -- Acknowledgements -- References -- 9. Scoring and Refinement of Predicted Protein-Protein Complexes Martin Zacharias -- 9.1 Introduction -- 9.2 Generation of Protein-Protein Complexes by Docking Methods -- 9.3 Protein-Protein Complexes Based on Homology to Known Complexes -- 9.4 Structural Refinement of Modelled Protein-Protein Complexes -- 9.4.1 Force Field Description of Proteins and Protein Complexes -- 9.4.2 Optimization Based on Energy Minimization -- 9.4.3 Accounting for Global Conformational Changes -- 9.4.4 Molecular Dynamics Simulation of Protein-Protein Complexes -- 9.4.5 Refinement of Docked Complexes by Molecular Dynamics Simulation -- 9.4.6 Monte Carlo and Brownian Dynamics Refinement of Docked Complexes -- 9.5 Scoring of Modelled Protein-Protein Complexes -- 9.5.1 Driving Forces for Molecular Association and the Scoring Problem -- 9.5.2 Scoring Based on Physical Force Fields -- 9.5.2.1 Scoring Based on Ensembles of Structures -- 9.5.3 Knowledge-based Scoring of Docked Complexes -- 9.5.3.1 Principles of Statistical Potentials to Score Predicted Complexes -- 9.5.3.2 Application of Statistical Potentials to Score Predicted Complexes -- 9.6 Conclusions and Outlook -- Acknowledgements -- References -- 10. Motif-mediated Protein Interactions and their Role in Disease Holger Dinkel and Heinrich Sticht -- 10.1 Introduction -- 10.2 Protein Interaction Domains -- 10.2.1 SH3 Domains -- 10.2.2 SH2 Domains -- 10.2.3 Signalling Adaptors: Proteins Containing Multiple Interaction Domains -- 10.3 Properties and Regulation of Motif-mediated Interactions -- 10.3.1 Inducible Interactions -- 10.3.2 Cooperative Effects. 10.3.3 Mutually Exclusive Interactions. |
| Record Nr. | UNINA-9910819748603321 |
| London, : Imperial College Press, 2010 | ||
| Materiale a stampa | ||
| Lo trovi qui: Univ. Federico II | ||
| ||
