Protein-protein complexes : analysis, modeling and drug design / / edited by Martin Zacharias

• Pubblicazione: London, : Imperial College Press, 2010
• Edizione: 1st ed.
• Descrizione fisica: 1 online resource (400 p.)
• Disciplina: 572.6; 572.64
• Soggetto topico: Protein-protein interactions; Protein-protein interactions - Computer simulation; Protein-protein interactions - Mathematical models; Proteins - Structure; Drugs - Design
• Altri autori: ZachariasMartin
• Note generali: Description based upon print version of record.
• Nota di bibliografia: Includes bibliographical references and index.
• 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.
• Titolo autorizzato: Protein-protein complexes
• ISBN: 1-282-75984-1; 9786612759840; 1-84816-340-1
• Formato: Materiale a stampa
• Livello bibliografico: Monografia
• Lingua di pubblicazione: Inglese
• Record Nr.: 9910819748603321
• Lo trovi qui: Univ. Federico II