Protein interactions : the molecular basis of interactomics / / edited by Volkhard Helms and Olga V. Kalinina

• Pubblicazione: Weinheim, Germany : , : Wiley-VCH, , [2023]; ©2023
• Descrizione fisica: 1 online resource (490 pages)
• Disciplina: 572.64
• Soggetto topico: Protein-protein interactions; Molecular biology; Cell receptors
• Persona (resp. second.): HelmsVolkhard; KalininaOlga V.
• Nota di bibliografia: Includes bibliographical references and index.
• 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.
• Titolo autorizzato: Protein Interactions
• ISBN: 3-527-83050-2; 3-527-83052-9
• Formato: Materiale a stampa
• Livello bibliografico: Monografia
• Lingua di pubblicazione: Inglese
• Record Nr.: 9910686761803321
• Lo trovi qui: Univ. Federico II