09418nam 2200529 450 99646685230331620220718110650.04-431-56919-7(CKB)5340000000068386(MiAaPQ)EBC6792472(Au-PeEL)EBL6792472(OCoLC)1280461060(PPN)258298456(EXLCZ)99534000000006838620220718d2021 uy 0engurcnu||||||||txtrdacontentcrdamediacrrdacarrierHydration structures of proteins atomic details /Masayoshi NakasakoTokyo, Japan :Springer,[2021]©20211 online resource (321 pages)Soft and Biological Matter4-431-56917-0 Intro -- Preface -- Acknowledgements -- Contents -- About the Author -- Glossary of Symbols -- 1 Introduction -- 1.1 Water: The Cradle of Life -- 1.2 Structure and Interaction of Water Molecules -- 1.2.1 Structure of Water Molecules -- 1.2.2 Interactions Between Water Molecules -- 1.2.3 Hydrogen Bond Between Water Molecules -- 1.3 Phase Diagram of Water -- 1.3.1 Three Phases of Water -- 1.3.2 Hexagonal Ice and Amorphous Ice -- 1.4 Properties of Liquid Water -- 1.4.1 Unusual Physical Properties -- 1.4.2 Brownian Motion in Liquid Water -- 1.4.3 Structure of Liquid Water -- 1.5 Hydration -- 1.5.1 Solvation -- 1.5.2 Hydration -- 1.5.3 Hydration of Hydrophobic Molecules -- 1.6 Hydration Structures of Proteins -- 1.6.1 Proteins -- 1.6.2 Hydration Structures of Proteins -- 1.7 Scope of This Monograph -- References -- 2 Biophysical Methods to Investigate Hydration Structures of Proteins -- 2.1 Introduction -- 2.2 X-Ray Crystallography at Cryogenic Temperatures -- 2.2.1 Outline -- 2.2.2 Crystallographic Structure Refinement -- 2.2.3 Difference Fourier Map -- 2.2.4 X-Ray Crystallography at Cryogenic Temperatures -- 2.3 Cryogenic Electron Microscopy -- 2.3.1 Outline -- 2.3.2 Specimen Preparation and Image Collection -- 2.3.3 Image Processing and Single-Particle Analysis -- 2.4 Time-Resolved Fluorescence Measurement -- 2.4.1 Outline -- 2.4.2 Up-conversion Method -- 2.5 Molecular Dynamic Simulation -- 2.5.1 Outline -- 2.5.2 Force Field -- References -- 3 Hydration Structures Inside Proteins -- 3.1 Introduction -- 3.2 Water Molecules Inside Proteins -- 3.2.1 Tightly Bound Water Molecules -- 3.2.2 Water Molecules Confined Inside Proteins -- 3.3 Hydration Water Molecules as Glue in Protein Complexes -- 3.3.1 Hydration at the Subunit Interface of a Protein Complex -- 3.3.2 Hydration Sites Conserved in Protein Families.3.4 Hydration Water Molecules as Lubricant at the Protein Interface -- 3.5 Hydration Water Molecules in the Ligand-Binding Sites -- References -- 4 Hydration Layer Around Proteins -- 4.1 Introduction -- 4.2 Hydration Layer -- 4.2.1 First- and Second-Layer Classes -- 4.2.2 Distance Distribution and Positional Fluctuation -- 4.2.3 Monolayer Hydration -- 4.2.4 Contact Class -- 4.3 Local Patterns in Protein Hydration -- 4.3.1 Patterns on Hydrophilic Surfaces -- 4.3.2 Hydration Patterns on Hydrophobic Surfaces -- 4.3.3 Tetrahedral Hydrogen Bond Geometry of Water Molecules -- 4.4 Hydration Structures in Molecular Dynamics Simulation -- 4.4.1 Computation of Solvent Density -- 4.4.2 Characteristics of Solvent Density -- References -- 5 Structural Characteristics in Local Hydration -- 5.1 Introduction -- 5.2 Empirical Hydration Distribution Around Polar Atoms -- 5.2.1 Construction -- 5.2.2 Distribution Around Polar Protein Atoms -- 5.2.3 Hydration of Aromatic Acceptors -- 5.2.4 Characteristics and Benefits of the Empirical Hydration Distributions -- 5.2.5 Tetrahedral Hydrogen Bond Geometry -- 5.3 Assessment of Force Fields of Polar Protein Atoms -- 5.3.1 Models of Water Molecule Suitable for Simulation -- 5.3.2 Hydration of Deprotonated Polar Atoms in sp2-Hybridization -- 5.3.3 Hydration of Protonated Nitrogen Atoms in sp2- or sp3-Hybridization -- 5.3.4 Hydration of Protonated Oxygen Atoms in sp2- or sp3-Hybridization -- 5.3.5 Molecular Dynamics Simulation of Proteins Using Force Field with Lone-Pair Electrons -- References -- 6 Prediction of Hydration Structures -- 6.1 Introduction -- 6.2 Computation of Probability Distribution of Hydration Water Molecules [19] -- 6.3 Prediction for Soluble Protein [19] -- 6.3.1 On Solvent-Exposed Surfaces and in Cavities -- 6.3.2 At Interface in Protein Complex -- 6.4 Prediction for Membrane Proteins.6.4.1 For Surfaces of Membrane Proteins -- 6.4.2 For Channels in Transmembrane Regions -- 6.5 Accuracy of Prediction -- 6.6 Comparison of the Prediction with Theory of Liquids -- 6.7 Utilization of Probability Distribution in Structure Analysis -- 6.7.1 Assessment on Hydration Water Sites -- 6.7.2 Probability Distribution-Weighted Electron Density Map [55] -- 6.8 Prediction of Hydration Structures on Hydrophobic Surfaces -- References -- 7 Network of Hydrogen Bonds Around Proteins -- 7.1 Introduction -- 7.2 Network of Hydrogen Bonds -- 7.2.1 Chain Connection of Hydrogen Bonds -- 7.2.2 Percolation Property -- 7.3 Probability of Hydrogen Bond Formation -- 7.4 Network of Hydrogen Bonds in Simulation Trajectory -- 7.5 Influence of Networks of Hydrogen Bonds on Protein Motions -- References -- 8 Dipole-Dipole Interactions in Hydration Layer -- 8.1 Introduction -- 8.2 Orientational Ordering of Hydration Water Molecules -- 8.2.1 Coherent Patterns of Time-Averaged Water Dipoles -- 8.2.2 Solvent Dipole and Network of Hydrogen Bonds -- 8.2.3 Solvent Dipole in Drug Design -- 8.2.4 Poisson-Boltzmann Equation and Orientation Ordering of Water Molecules -- 8.3 Fluorescence from Tryptophan Side Chains Exposed to Solvent -- 8.3.1 Fluorescence from Photo-Excited Tryptophan of Protein -- 8.3.2 Interpretation of Dynamic Stokes Shift -- 8.3.3 Orientation Ordering of Water Molecules Around Tryptophan Side Chains -- 8.3.4 Origin of Dynamic Stokes Shift -- References -- 9 Hydration Structure Changes of Proteins at Work -- 9.1 Introduction -- 9.2 Experimental Evidence on Hydration-Regulated Protein Motion -- 9.2.1 Domain Motion in Glutamate Dehydrogenase -- 9.2.2 Hydration Structure Changes in Domain Motion -- 9.2.3 Model for Hydration Coupled Domain Motion -- 9.3 Molecular Mechanism in Hydration-Coupled Domain Motion -- 9.3.1 Domain Motion Observed in Simulation.9.3.2 Simultaneous Changes in Conformation and Hydration -- 9.3.3 Hydration Changes in the Hydrophobic Pocket -- 9.3.4 Drying Transition in the Hydrophobic Pocket -- 9.3.5 Hydration Changes in the Hydrophilic Crevice -- 9.3.6 Mechanism of Hydration Regulated Domain Motion -- 9.4 Manipulation of Conformation and Hydration of Proteins in the Crystals -- 9.4.1 Conformational Changes of Protein in Different Molecular Packing -- 9.4.2 Hydration Changes in Different Molecular Packing -- References -- 10 Energy Landscape and Hydration of Proteins -- 10.1 Introduction -- 10.1.1 Protein Conformation Manifold and Energy Landscape -- 10.2 X-Ray Diffraction Imaging -- 10.2.1 Structure Analysis Using X-Ray Diffraction Imaging -- 10.2.2 X-Ray Diffraction Imaging Using X-Ray Laser -- 10.3 Cryogenic Electron Microscopy -- 10.3.1 Classification of Protein Structures -- 10.3.2 Energy Landscape in Protein Motions -- 10.3.3 Prediction of Hydration Structures Using Neural Networks -- 10.4 Future Prospects -- References -- Appendix A -- Appendix B X-Ray Diffraction by a Crystal -- B.1 Thomson Scattering [B1] -- B.2 Interference of X-Rays Emitted by Electrons -- B.3 Diffraction From a Crystal [B3] -- B.4 The Ewald Sphere -- References -- Appendix C The Image Obtained by Electron Microscopy -- C1. Electron Scattering by a Weak-Phase Object [C1, C2] -- C2. Contrast Transfer Function [C1, C2] -- References -- Appendix D The Principle of the Up-Conversion Method -- D.1 Higher-Order Dielectric Polarization -- D.2 Radiation by Nonlinear Dielectric Polarization [D2, D3] -- D.3 The Phase-Matching Condition and Birefringence [D2, D3] -- References -- Appendix E The Symplectic Integrator -- Appendix F The Geometries of the Polar Groups in Amino Acid Residues -- Reference.Appendix G Examples of Force Field Parameters Incorporating Lone-Pair Electrons for Deprotonated Oxygen and Nitrogen Atoms in the sp2-Hybridization -- Reference -- Appendix H Energy Relaxation of Perturbed System -- Reference -- Appendix I Surface Topography of Protein Crystals by Atomic Force Microscopy -- References -- Appendix J The Phase Retrieval Algorithm Used in X-Ray Diffraction Imaging -- References -- Appendix K Derivation of the Formula to Determine Appearance Frequencies of Model Structures in Electron Micrographs -- Reference -- Index.Soft and biological matter.HydrationProteinsHydratationHydration.Proteins.Hydratation.541.372Nakasako Masayoshi835600MiAaPQMiAaPQMiAaPQBOOK996466852303316Hydration Structures of Proteins2568657UNISA01693nam0 22003853i 450 SBL056012520231121125827.0IT761373 20030128d1975 ||||0itac50 baitaitaitz01i xxxe z01nAutoritarismo, fascismo e classi socialiGino GermaniBolognaIl mulino1975306 p.19 cmUniversale paperbacks Il mulino31001CFI00000332001 Universale paperbacks Il mulino31Autoritarismo, fascismo e classi socialiUBO4730813RAVV031455648705TotalitarismoFIRRMLC077992I321.921Germani, GinoRAVV03145507032865Germani, G.UTOV554565Germani, GinoITIT-0120030128IT-RM1248 IT-FR0084 IT-RM0460 IT-FR0017 IT-RM0526 Biblioteca Della Fondazione Pietro NenniRM1248 Biblioteca Del Monumento Nazionale Di MontecassinoFR0084 Biblioteca Dell' Archivio Centrale Dello StatoRM0460 Biblioteca umanistica Giorgio ApreaFR0017 Biblioteca dell’Istituto Centrale per il Patrimonio ImmaterialeRM0526 NSBL0560125Biblioteca umanistica Giorgio Aprea 52MAG 12/2355 52MAG0000132255 VMN RS A 2013062520130625 23 25 27 52 58Autoritarismo, fascismo e classi sociali648705UNICAS