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Hydration structures of proteins : atomic details / / Masayoshi Nakasako
Hydration structures of proteins : atomic details / / Masayoshi Nakasako
Autore Nakasako Masayoshi
Pubbl/distr/stampa Tokyo, Japan : , : Springer, , [2021]
Descrizione fisica 1 online resource (321 pages)
Disciplina 541.372
Collana Soft and Biological Matter
Soggetto topico Hydration
Proteins
Hydratation
ISBN 4-431-56919-7
Formato Materiale a stampa
Livello bibliografico Monografia
Lingua di pubblicazione eng
Nota di contenuto 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.
Record Nr. UNINA-9910506398103321
Nakasako Masayoshi  
Tokyo, Japan : , : Springer, , [2021]
Materiale a stampa
Lo trovi qui: Univ. Federico II
Opac: Controlla la disponibilità qui
Hydration structures of proteins : atomic details / / Masayoshi Nakasako
Hydration structures of proteins : atomic details / / Masayoshi Nakasako
Autore Nakasako Masayoshi
Pubbl/distr/stampa Tokyo, Japan : , : Springer, , [2021]
Descrizione fisica 1 online resource (321 pages)
Disciplina 541.372
Collana Soft and Biological Matter
Soggetto topico Hydration
Proteins
Hydratation
ISBN 4-431-56919-7
Formato Materiale a stampa
Livello bibliografico Monografia
Lingua di pubblicazione eng
Nota di contenuto 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.
Record Nr. UNISA-996466852303316
Nakasako Masayoshi  
Tokyo, Japan : , : Springer, , [2021]
Materiale a stampa
Lo trovi qui: Univ. di Salerno
Opac: Controlla la disponibilità qui
X-Ray Diffraction Imaging of Biological Cells [[electronic resource] /] / by Masayoshi Nakasako
X-Ray Diffraction Imaging of Biological Cells [[electronic resource] /] / by Masayoshi Nakasako
Autore Nakasako Masayoshi
Edizione [1st ed. 2018.]
Pubbl/distr/stampa Tokyo : , : Springer Japan : , : Imprint : Springer, , 2018
Descrizione fisica 1 online resource (XX, 228 p. 96 illus., 89 illus. in color.)
Disciplina 548.83
Collana Springer Series in Optical Sciences
Soggetto topico Lasers
Photonics
Materials science
Proteins 
Crystallography
Physical measurements
Measurement   
Optics, Lasers, Photonics, Optical Devices
Characterization and Evaluation of Materials
Protein Structure
Crystallography and Scattering Methods
Measurement Science and Instrumentation
ISBN 4-431-56618-X
Formato Materiale a stampa
Livello bibliografico Monografia
Lingua di pubblicazione eng
Nota di contenuto Introduction -- X-ray diffraction -- Theory of X-ray diffraction imaging -- Diffraction apparatus for X-ray diffraction imaging -- Specimen preparation for X-ray diffraction imaging experiments at cryogenic temperature -- Processing of diffraction patterns obtained from X-ray diffraction imaging experiments using X-ray free electron laser pulses -- Phase retrieval of diffraction patterns -- Projection structures of biological cells and organelles -- Three-dimensional structural analyses in cryogenic X-ray diffraction imaging -- Prospects for the structural analysis of biological specimens by X-ray diffraction imaging.
Record Nr. UNINA-9910300538303321
Nakasako Masayoshi  
Tokyo : , : Springer Japan : , : Imprint : Springer, , 2018
Materiale a stampa
Lo trovi qui: Univ. Federico II
Opac: Controlla la disponibilità qui