Structure, Dynamics and Function of Biomolecules

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.

Section I. Introductory Keynotes.- The Nature of Mechanical Devices in Biological Systems.- Physical Chemistry and Biological Strategy of Antigen Recognition.- Section II. Structure and Dynamics of Heme Proteins.- Heme Protein Reactions: Models, Concepts, and Problems.- Multiple Conformational States of Myoglobin: A Molecular Dynamics Analysis.- Dynamics of Structural Changes in Hemoglobin.- Structure and Dynamics of Photodissociated Myoglobin.- Structural Fluctuations in Myoglobin.- Glass Transition of Hydration Water and Structural Flexibility of Myoglobin.- Pressure Studies of Large-Scale Protein Motions.- Viscosity and Glycerol Effects on Dynamics of Cytochrome c.- Kinetics of Geminate Recombination Following Photodissociation of Mutant (Carbonmonoxy) Hemoglobins.- Section III. Physical Aspects of Biomolecular Dynamics and Kinetics.- Thermodynamics of Enzyme Folding and Activity: Theory and Experiment.- Progress and Problems in the Study of Protein Dynamics by X-Ray Diffraction.- Activation Free Energies of Enzymatic Reactions; Simulations and Experiments.- Simple Models for the Dynamics of Biomolecules: How Far Can We Go?.- Condensed Matter Biophysics: Structure and Dynamics of Large Biomolecules.- Molecular Dynamics Simulation of Parvalbumin in Aqueous Solution.- Cooperative Ion Binding to Proteins. A Statistical Mechanical Approach.- Single Step Kinetics of Enzyme Dynamics.- Low Frequency Dynamics of BPTI Studied by Inelastic Neutron Scattering.- Trans-Cis Isomerizations in Biology.- Section IV. Determination of Biomolecular Structure and Dynamics in Solution.- A NMR View of Proteins in Solution.- Determination of 3D-Structures of Macromolecules by Restrained Molecular Dynamics on the Basis of Interproton Distances.- The Structure of the tRNA Anticodon Arm as Determined by Restrained Molecular Dynamics in Combination with NMR Interproton Distance Data.- Solving Solution Structural Problems by Combining 2-D NMR Data with Known Substructures from a Protein Database.- Molecular Graphics and Molecular Dynamics.- Study of the Dynamics of Hydrated Proteins and Protein-Bound Water by Rayleigh Scattering of Mössbauer Radiation (RSMR).- Fluorescence Lifetime Distributions of Single Tryptophan Proteins: A Protein Dynamics Approach.- Time Domain Spectroscopy of Molecular Dynamics.- Detection of Time-Resolved Microsecond Molecular Dynamics by Optical and Magnetic Resonance Spectroscopy.- Linear Dichroism ― A Potential Method for Studying DNA-Protein Interaction.- Section V. Experimental Studies of Protein Dynamics and Kinetics.- Microtubule Structure and Assembly Studied by Time-Resolved X-Ray Scattering and Cryo-Electron Microscopy.- Polymerisation of Fibrinogen to Fibrin Studied by Time-Resolved Small Angle Neutron Scattering.- Internal Dynamics of Aromatic Residues in Subtilisin BPN’ and Subtilisin Carlsberg: Time-Resolved Fluorescence Properties.- Time-Resolved Fluorescence Anisotropy Decay Studies in Proteins.- Study of Single Cycles of the Direct and Back Enzyme Reactions Catalyzed by Malatedehydrogenase.- Dynamics of Iron in Ferritin.- Structure, Dynamics and Function of Serine Proteases.- Section VI. Proton and Energy Transfer.- Intramolecular Proton Transfer in Bacteriorhodopsin (bR).- ATP Synthesis by the Membrane Bound and Isolated H+ ATPases After Jump-Like pH Increase.- Structural Aspects on Energy Transfer in Light Harvesting Complexes.- Section VII. Nucleic Acid Dynamics.- Imino-Proton Exchange and Base-Pair Kinetics of Nucleic Acids.- NMR and Time Resolved Fluorescence Studies of a 2-Aminopurine Substituted Eco RI Restriction Site.- Local Flexibility in Recognition Processes Between Macromolecules.- Conformational Aspects of Hairpin Loops in DNA Oligonucleotides.- The Cruciform Extrusion Transition in Supercoiled DNA Molecules.- Left-Handed DNA: Energetic and Dynamic Aspects.- Z-DNA Dynamic Structure: A Hydrogen Exchange Study.- Induction of the Z Conformation in DNAs Studied by I.R. Spectroscopy.- The B ? Z Transition in Poly[d(G-C)·d(G-C)] After Covalent Binding of Anti-Benzo(a)Pyrenediolepoxide.- Effects of Hydration on the DNA Base Motion.- Structure and Dynamics of DNA and DNA-Adduct Complexes Studied with Polarized Light Spectroscopy.- Calculation of Electrostatic Interactions Between Hexagonally Oriented DNA-Molecules.- Section VIII. Nucleic Acid-Protein Interactions.- Structure of the DNA-EcoRI Endonuclease Recognition Complex.- Ribonuclease T1: Interaction with 2’GMP and 3’GMP as Studied by Time-Resolved Fluorescence Spectroscopy.- Ultrasonic Absorption Evidence for Enhanced Volume Fluctuations in the Tobacco-Mosaic-Virus-Protein Helical Aggregate.- 3-D Image Reconstruction of a Specific Premessenger RNP Particle.- Section IX. Membranes and Membrane Proteins.- Molecular Dynamics of a Bilayer Membrane with Atomic Detail.- Time-Resolved X-Ray Diffraction on Lipid Bilayer Interactions Using Synchrotron Radiation.- Molecular Dynamics Studies of Model Membranes with Alfa Helices.- Orientational Fluctuations of Melittin in Lipid Membranes as Detected by Time-Resolved Fluorescence Anisotropy Measurements.- Structure Predictions for Membrane Proteins.- The Temperature Peaks of Cell Membrane Permeability.