Ebook: Structure, Dynamics and Function of Biomolecules: The First EBSA Workshop A Marcus Wallenberg Symposium

This is a collection of papers presented and discussed at the first EBSA workshop held at Saltsj6baden outside stockholm in Sweden, July 6-10, 1986. The common theme of these papers is dynamics of biomolecules, and how the dynamics depends on the molecular structure and organi­ zation, and connects to and determines the biological function. This is a rapidly expanding field of research which combines many different aspects of molecular bio­ physics. Much material is new and presented for the first time. Even if the work so far has been of the kind that is usually called basic research, practical applications are clearly indicated in some articles, and are waiting around the corner in several other cases. At the workshop only one third of the time was used for the formal presentations and two thirds for discussion. To this should also be added discussions during the poster sessions. During these lively and unrecorded discussions fresh viewpoints emerged and new ideas were created. Ad­ mittedly, our knowledge at present is only fragmentary but when pieces of the puzzle are brought together at a workshop or in a publication of this kind more extended and sometimes unexpected contours and shapes become vi­ sible. It is our hope that this rapid publication of camera-ready manuscripts will transfer some of the spi­ rit at the workshop to the reader, and in his or her institute or laboratory initiate further discussions, bring forward more ideas and start new experimental ap­ roaches.

---

---

Content:
Front Matter....Pages I-XVI
The Nature of Mechanical Devices in Biological Systems....Pages 1-4
Physical Chemistry and Biological Strategy of Antigen Recognition....Pages 5-9
Heme Protein Reactions: Models, Concepts, and Problems....Pages 10-14
Multiple Conformational States of Myoglobin: A Molecular Dynamics Analysis....Pages 15-19
Dynamics of Structural Changes in Hemoglobin....Pages 20-24
Structure and Dynamics of Photodissociated Myoglobin....Pages 25-29
Structural Fluctuations in Myoglobin....Pages 30-33
Glass Transition of Hydration Water and Structural Flexibility of Myoglobin....Pages 34-38
Pressure Studies of Large-Scale Protein Motions....Pages 39-42
Viscosity and Glycerol Effects on Dynamics of Cytochrome c....Pages 43-46
Kinetics of Geminate Recombination Following Photodissociation of Mutant (Carbonmonoxy)Hemoglobins....Pages 47-50
Thermodynamics of Enzyme Folding and Activity: Theory and Experiment....Pages 51-55
Progress and Problems in the Study of Protein Dynamics by X-Ray Diffraction....Pages 56-60
Activation Free Energies of Enzymatic Reactions; Simulations and Experiments....Pages 61-64
Simple Models for the Dynamics of Biomolecules: How Far Can We Go?....Pages 65-69
Condensed Matter Biophysics: Structure and Dynamics of Large Biomolecules....Pages 70-74
Molecular Dynamics Simulation of Parvalbumin in Aqueous Solution....Pages 75-81
Cooperative Ion Binding to Proteins. A Statistical Mechanical Approach....Pages 82-85
Single Step Kinetics of Enzyme Dynamics....Pages 86-92
Low Frequency Dynamics of BPTI Studied by Inelastic Neutron Scattering....Pages 93-97
Trans-Cis Isomerizations in Biology....Pages 98-103
A NMR View of Proteins in Solution....Pages 104-107
Determination of 3D-Structures of Macromolecules by Restrained Molecular Dynamics on the Basis of Interproton Distances....Pages 108-112
The Structure of the tRNA Anticodon Arm as Determined by Restrained Molecular Dynamics in Combination with NMR Interproton Distance Data....Pages 113-117
Solving Solution Structural Problems by Combining 2-D NMR Data with Known Substructures from a Protein Database....Pages 118-121
Molecular Graphics and Molecular Dynamics....Pages 122-126
Study of the Dynamics of Hydrated Proteins and Protein-Bound Water by Rayleigh Scattering of Mossbauer Radiation (RSMR)....Pages 127-131
Fluorescence Lifetime Distributions of Single Tryptophan Proteins: A Protein Dynamics Approach....Pages 132-135
Time Domain Spectroscopy of Molecular Dynamics....Pages 136-139
Detection of Time-Resolved Microsecond Molecular Dynamics by Optical and Magnetic Resonance Spectroscopy....Pages 140-144
Linear Dichroism — A Potential Method for Studying DNA-Protein Interaction....Pages 145-147
Microtubule Structure and Assembly Studied by Time-Resolved X-Ray Scattering and Cryo-Electron Microscopy....Pages 148-151
Polymerisation of Fibrinogen to Fibrin Studied by Time-Resolved Small Angle Neutron Scattering....Pages 152-158
Internal Dynamics of Aromatic Residues in Subtilisin BPN’ and Subtilisin Carlsberg: Time-Resolved Fluorescence Properties....Pages 159-164
Time-Resolved Fluorescence Anisotropy Decay Studies in Proteins....Pages 165-170
Study of Single Cycles of the Direct and Back Enzyme Reactions Catalyzed by Malatedehydrogenase....Pages 171-175
Dynamics of Iron in Ferritin....Pages 176-179
Structure, Dynamics and Function of Serine Proteases....Pages 180-182
Intramolecular Proton Transfer in Bacteriorhodopsin (bR)....Pages 183-186
ATP Synthesis by the Membrane Bound and Isolated H+ ATPases After Jump-Like pH Increase....Pages 187-190
Structural Aspects on Energy Transfer in Light-Harvesting Complexes....Pages 191-195
Imino-Proton Exchange and Base-Pair Kinetics of Nucleic Acids....Pages 196-200
NMR and Time Resolved Fluorescence Studies of a 2-Aminopurine Substituted Eco RI Restriction Site....Pages 201-207
Local Flexibility in Recognition Processes Between Macromolecules....Pages 208-211
Conformational Aspects of Hairpin Loops in DNA Oligonucleotides....Pages 212-216
The Cruciform Extrusion Transition in Supercoiled DNA Molecules....Pages 217-223
Left-Handed DNA: Energetic and Dynamic Aspects....Pages 224-228
Z-DNA Dynamic Structure: A Hydrogen Exchange Study....Pages 229-233
Induction of the Z Conformation in DNAs Studied by I.R. Spectroscopy....Pages 234-237
The B > Z Transition in Poly[d(G-C)·d(G-C)] After Covalent Binding of Anti-Benzo(a)Pyrenediolepoxide....Pages 238-241
Effects of Hydration on the DNA Base Motion....Pages 242-246
Structure and Dynamics of DNA and DNA-Adduct Complexes Studied with Polarized Light Spectroscopy....Pages 247-250
Calculation of Electrostatic Interactions Between Hexagonally Oriented DNA-Molecules....Pages 251-254
Structure of the DNA-EcoRI Endonuclease Recognition Complex....Pages 255-259
Ribonuclease T1: Interaction with 2’GMP and 3’GMP as Studied by Time-Resolved Fluorescence Spectroscopy....Pages 260-265
Ultrasonic Absorption Evidence for Enhanced Volume Fluctuations in the Tobacco-Mosaic-Virus-Protein Helical Aggregate....Pages 266-269
3-D Image Reconstruction of a Specific Premessenger RNP Particle....Pages 270-274
Molecular Dynamics of a Bilayer Membrane with Atomic Detail....Pages 275-280
Time-Resolved X-Ray Diffraction on Lipid Bilayer Interactions Using Synchrotron Radiation....Pages 281-284
Molecular Dynamics Studies of Model Membranes with Alfa Helices....Pages 285-288
Orientational Fluctuations of Melittin in Lipid Membranes as Detected by Time-Resolved Fluorescence Anisotropy Measurements....Pages 289-294
Structure Predictions for Membrane Proteins....Pages 295-298
The Temperature Peaks of Cell Membrane Permeability....Pages 299-302
Back Matter....Pages 303-303

---

Content:
Front Matter....Pages I-XVI
The Nature of Mechanical Devices in Biological Systems....Pages 1-4
Physical Chemistry and Biological Strategy of Antigen Recognition....Pages 5-9
Heme Protein Reactions: Models, Concepts, and Problems....Pages 10-14
Multiple Conformational States of Myoglobin: A Molecular Dynamics Analysis....Pages 15-19
Dynamics of Structural Changes in Hemoglobin....Pages 20-24
Structure and Dynamics of Photodissociated Myoglobin....Pages 25-29
Structural Fluctuations in Myoglobin....Pages 30-33
Glass Transition of Hydration Water and Structural Flexibility of Myoglobin....Pages 34-38
Pressure Studies of Large-Scale Protein Motions....Pages 39-42
Viscosity and Glycerol Effects on Dynamics of Cytochrome c....Pages 43-46
Kinetics of Geminate Recombination Following Photodissociation of Mutant (Carbonmonoxy)Hemoglobins....Pages 47-50
Thermodynamics of Enzyme Folding and Activity: Theory and Experiment....Pages 51-55
Progress and Problems in the Study of Protein Dynamics by X-Ray Diffraction....Pages 56-60
Activation Free Energies of Enzymatic Reactions; Simulations and Experiments....Pages 61-64
Simple Models for the Dynamics of Biomolecules: How Far Can We Go?....Pages 65-69
Condensed Matter Biophysics: Structure and Dynamics of Large Biomolecules....Pages 70-74
Molecular Dynamics Simulation of Parvalbumin in Aqueous Solution....Pages 75-81
Cooperative Ion Binding to Proteins. A Statistical Mechanical Approach....Pages 82-85
Single Step Kinetics of Enzyme Dynamics....Pages 86-92
Low Frequency Dynamics of BPTI Studied by Inelastic Neutron Scattering....Pages 93-97
Trans-Cis Isomerizations in Biology....Pages 98-103
A NMR View of Proteins in Solution....Pages 104-107
Determination of 3D-Structures of Macromolecules by Restrained Molecular Dynamics on the Basis of Interproton Distances....Pages 108-112
The Structure of the tRNA Anticodon Arm as Determined by Restrained Molecular Dynamics in Combination with NMR Interproton Distance Data....Pages 113-117
Solving Solution Structural Problems by Combining 2-D NMR Data with Known Substructures from a Protein Database....Pages 118-121
Molecular Graphics and Molecular Dynamics....Pages 122-126
Study of the Dynamics of Hydrated Proteins and Protein-Bound Water by Rayleigh Scattering of Mossbauer Radiation (RSMR)....Pages 127-131
Fluorescence Lifetime Distributions of Single Tryptophan Proteins: A Protein Dynamics Approach....Pages 132-135
Time Domain Spectroscopy of Molecular Dynamics....Pages 136-139
Detection of Time-Resolved Microsecond Molecular Dynamics by Optical and Magnetic Resonance Spectroscopy....Pages 140-144
Linear Dichroism — A Potential Method for Studying DNA-Protein Interaction....Pages 145-147
Microtubule Structure and Assembly Studied by Time-Resolved X-Ray Scattering and Cryo-Electron Microscopy....Pages 148-151
Polymerisation of Fibrinogen to Fibrin Studied by Time-Resolved Small Angle Neutron Scattering....Pages 152-158
Internal Dynamics of Aromatic Residues in Subtilisin BPN’ and Subtilisin Carlsberg: Time-Resolved Fluorescence Properties....Pages 159-164
Time-Resolved Fluorescence Anisotropy Decay Studies in Proteins....Pages 165-170
Study of Single Cycles of the Direct and Back Enzyme Reactions Catalyzed by Malatedehydrogenase....Pages 171-175
Dynamics of Iron in Ferritin....Pages 176-179
Structure, Dynamics and Function of Serine Proteases....Pages 180-182
Intramolecular Proton Transfer in Bacteriorhodopsin (bR)....Pages 183-186
ATP Synthesis by the Membrane Bound and Isolated H+ ATPases After Jump-Like pH Increase....Pages 187-190
Structural Aspects on Energy Transfer in Light-Harvesting Complexes....Pages 191-195
Imino-Proton Exchange and Base-Pair Kinetics of Nucleic Acids....Pages 196-200
NMR and Time Resolved Fluorescence Studies of a 2-Aminopurine Substituted Eco RI Restriction Site....Pages 201-207
Local Flexibility in Recognition Processes Between Macromolecules....Pages 208-211
Conformational Aspects of Hairpin Loops in DNA Oligonucleotides....Pages 212-216
The Cruciform Extrusion Transition in Supercoiled DNA Molecules....Pages 217-223
Left-Handed DNA: Energetic and Dynamic Aspects....Pages 224-228
Z-DNA Dynamic Structure: A Hydrogen Exchange Study....Pages 229-233
Induction of the Z Conformation in DNAs Studied by I.R. Spectroscopy....Pages 234-237
The B > Z Transition in Poly[d(G-C)·d(G-C)] After Covalent Binding of Anti-Benzo(a)Pyrenediolepoxide....Pages 238-241
Effects of Hydration on the DNA Base Motion....Pages 242-246
Structure and Dynamics of DNA and DNA-Adduct Complexes Studied with Polarized Light Spectroscopy....Pages 247-250
Calculation of Electrostatic Interactions Between Hexagonally Oriented DNA-Molecules....Pages 251-254
Structure of the DNA-EcoRI Endonuclease Recognition Complex....Pages 255-259
Ribonuclease T1: Interaction with 2’GMP and 3’GMP as Studied by Time-Resolved Fluorescence Spectroscopy....Pages 260-265
Ultrasonic Absorption Evidence for Enhanced Volume Fluctuations in the Tobacco-Mosaic-Virus-Protein Helical Aggregate....Pages 266-269
3-D Image Reconstruction of a Specific Premessenger RNP Particle....Pages 270-274
Molecular Dynamics of a Bilayer Membrane with Atomic Detail....Pages 275-280
Time-Resolved X-Ray Diffraction on Lipid Bilayer Interactions Using Synchrotron Radiation....Pages 281-284
Molecular Dynamics Studies of Model Membranes with Alfa Helices....Pages 285-288
Orientational Fluctuations of Melittin in Lipid Membranes as Detected by Time-Resolved Fluorescence Anisotropy Measurements....Pages 289-294
Structure Predictions for Membrane Proteins....Pages 295-298
The Temperature Peaks of Cell Membrane Permeability....Pages 299-302
Back Matter....Pages 303-303
....