(I) Aims and function of the Union

(1) The objects of the International Union for Pure and Applied Biophysics are advancement of education in theScience of Biophysics. In furtherance of this aim the Council may exercise the following powers:

(a) to organize international cooperation in Biophysics and to promote communication between the variousbranches of Biophysics and allied subjects;

to encourage within each adhering body cooperation between the societies that represent the interests ofBiophysics;

to contribute to the advancement of Biophysics in all its aspects.

(2) For these purposes it shall have power:

(a) to set up commissions or bodies for special purposes;

(b) to organize international meetings and conferences;

(c) to collaborate with other scientific organizations;

(d) to act in all ways as a constituent union of the International Council of Scientific Unions in accordance with thestatutes of that body;

(e) to develop any lawful activity deemed helpful to the forwarding of its declared objects.

1. INTRODUCTION 195

2. THE PROTEIN SYNTHESIS SYSTEM 199

2.1 Aminoacyl-tRNA synthetases 199

2.1.1 Glutaminyl-tRNA synthetase 202

2.1.2 Glutamyl-tRNA synthetase 206

2.1.3 Tyrosyl- and tryptophanyl-tRNA synthetases 207

2.1.4 Methionyl-tRNA synthetase 208

2.1.5 Aspartyl-tRNA synthetase 208

2.1.6 Lysyl-tRNA synthetase 209

2.1.7 Seryl-tRNA synthetase 210

2.1.8 Glycyl- and histidyl-tRNA synthetases 210

2.1.9 Phenylalanyl-tRNA synthetase 211

2.2 Ribosomal proteins 211

2.2.1 L7/L12 212

2.2.2 L30 214

2.2.3 S5 215

2.2.4 S17 215

2.2.5 L6 215

2.2.6 L9 216

2.2.7 S6 217

2.2.8 L1 217

2.2.9 L14 217

2.2.10 S8 217

2.3 Elongation factors 218

2.3.1 EF-Tu 218

2.3.2 EF-G 219

3. SPLICEOSOMAL PROTEINS 221

3.1 U1 snRNP protein A 222

4. PROTEINS FROM RNA VIRUSES 223

4.1 Viral enzymes and regulatory proteins 224

4.1.1 Reverse transcriptase 224

4.1.2 Tat 224

4.1.3 Rev 225

4.2 Viral capsid proteins 225

4.2.1 Tobacco Mosaic Virus 226

4.2.2 Satellite Tobacco Mosaic Virus 226

4.2.3 Bean-Pod Mottled Virus 226

4.2.4 Black Beetle Virus and Flock House Virus 228

4.2.5 Bacteriophage MS2 228

5. OTHER RNA-BINDING PROTEINS 230

5.1 tRNA-guanine transglycosylase 230

5.2 Major cold-shock protein 230

5.3 Rop 231

5.4 Ricin 231

6. CONCLUSION 232

7. ACKNOWLEDGEMENTS 233

1. INTRODUCTION 2

2. OVERALL STRUCTURE AND SUBSTRUCTURES 5

2.1 Overall structure and components 5

2.2 Bidirectional rotary motor 5

2.3 Drive shaft 8

2.4 Bushing 8

2.5 Universal joint 9

2.6 Helical propeller 9

2.7 Axial junction 10

2.8 Capping structure 11

3. ASSEMBLY PROCESS OF THE FLAGELLUM 11

3.1 Step by step assembly 11

3.2 Flagellum-specific export apparatus and the channel 12

4. UNIQUE CHARACTERISTICS OF THE FLAGELLAR MOTOR DYNAMICS 13

5. STRUCTURAL DESIGN OF FLAGELLIN FOR ASSEMBLY REGULATION AND POLYMORPHISM 14

5.1 Domain organization and terminal disorder of flagellin 15

5.2 The role of terminal disorder in filament formation and polymorphism 17

5.3 Common structural motif for regulation of self-assembly 21

6. STRUCTURAL DESIGN OF FLAGELLAR FILAMENTS FOR POLYMORPHISM 22

6.1 Polymorphic mechanism 23

6.2 Structures of the filaments deduced by electron microscopy 25

6.2.1 Overview of the electron microscopic studies 25

6.2.2 Helical image reconstruction procedure 27

6.2.3 Structural details of the filament 28

6.3 X-ray fibre diffraction studies 32

6.3.1 Overview of the X-ray studies 32

6.3.2 Orientation of liquid crystalline sols and diffraction patterns 33

6.3.3 Equatorial analysis 35

6.3.4 A preliminary map refined at 11 resolution 37

6.4 Overall chain folding of the subunit in the filament 38

6.4.1 Mapping out the terminal and central regions 38

6.4.2 The chain folding and role of each domain 42

6.5 Polymorphic nature of flagellar filament 43

6.5.1 Comparison of the L- and R-type 43

6.5.2 New helical symmetry Lt-type 46

6.5.3 Direct comparison of the Lt-type lattice to the other two 48

6.5.4 Plausible conformational changes involved in polymorphism 51

7. PERSPECTIVE 55

8. ACKNOWLEDGEMENTS 55

9. REFERENCES 55

Most advances in biology can usually be traced back to the development of a new technique: the recent explosion in sequence information in the databases arose from the pioneering work on separation methods by Frederick Sanger which paved the way for the development of protein (Sanger, 1945) and DNA/RNA (Maxam & Gilbert, 1977; Sanger, 1981) sequencing and culminated in the receipt of two Nobel prizes by Sanger. The initial phase of sequence database expansion was slow due to the tedious and slow nature of protein sequencing. Peptide sequencing was carried out manually and the complete analysis of a protein was tiresome, requiring the isolation of sufficient peptides from several digests of the target protein using proteases of different specialities to collect an overlapping set of fragments which cover the whole sequence. Protein sequencing gained momentum when the phenylisothiocyanate sequencing chemistry developed by Edman in 1949 was automated (Edman & Begg, 1967) and a commercial instrument requiring lower amounts (nanomoles) of sample was put on the market. Further technical advances such as novel valves to deal with small volumes of aggressive chemicals, the introduction of high pressure liquid chromatography (HPLC), and novel supports for sample immobilization, were all combined in the first gas phase sequencers, greatly increasing the sensitivity and allowing automated data collection (Hewick et al. 1981) and analysis. The new instruments with a sensitivity in the low picomole range appeared as rapid advances in DNA technology such as the development of restriction mapping (Danna et al. 1973), cloning (Cohen et al. 1973) and the dideoxynucleotide sequencing chemistry were threatening to make protein chemistry a relic of the past (Malcolm, 1978).

SUMMARY 241

1. INTRODUCTION 242

1.1 Milestones in the history of HS 244

1.2 Solvation forces 245

2. PHENOMENOLOGY OF THE HOFMEISTER SERIES 246

2.1 Extension of the properties of HS from inorganic to organic cosolutes 246

2.2 Effect of salts on the stability of biomolecules 247

2.3 Effect on enzyme activity 248

2.4 Influence of salts on the crystallization of biological macromolecules 249

2.5 Effects of salts on DNA–protein interactions 250

2.6 Interactions at receptor sites and effects on ion channels 251

2.7 Water-coordinating properties of salts as determined by gel chromatographic behaviour 254

3. INTERFACIAL FREE ENERGY 254

3.1 Types of forces 254

3.2 Distance dependence of the interactions 257

4. THE NATURE OF SURFACES AND LIQUIDS 259

4.1 Proteins 259

4.2 Adsorbing surfaces 260

4.3 Water 261

5. THE EFFECT OF COSOLUTES ON WATER 263

5.1 Electrochemistry 263

5.2 Neutron scattering 264

5.3 Vibrational spectroscopy 265

5.4 Nuclear magnetic resonance 265

6. COSOLUTE EXCLUSION FROM SURFACES 266

6.1 Cosolute enrichment 268

7. CONCLUSIONS AND OUTLOOK 268

8. ACKNOWLEDGEMENTS 269

9. REFERENCES 269

A. GLOSSARY 276

B. LIST OF PRINCIPAL SYMBOLS 276

Advances in experimental and computational methodologies have led to a recent renewed interest in the Hofmeister series and its molecular origins. New results are surveyed and assessed. Insights into the underlying mechanisms have been gained, although deeper molecular understanding still seems to be elusive. The principal reason appears to be that the Hofmeister series emerges from a combination of a general effect of cosolutes (salts, etc.) on solvent structure, and of specific interactions between the cosolutes and the solute (protein or other biopolymer). Hence every system needs to be studied individually in detail, a state of affairs which is likely to continue for some time. A deeper understanding of the Hofmeister series can be an extraordinarily valuable guide to designing experiments, including not only those probing the series per se, but also those designed to elucidate the adsorption, aggregation and stabilization phenomena which underlie so many biological events. The aim of this review is to provide an up-to-date framework to guide such understanding, consolidating recent advances in the many fields on which the Hofmeister series impinges.

The mechanism of energy transduction in biological membranes is a fascinating unsolved problem in biology. It has been recognized for some time that the driving force for a variety of seemingly unrelated phenomena (e.g. secondary active transport, oxidative phosphorylation, rotation of the bacterial flagellar motor) is a bulk-phase, transmembrane electrochemical ion gradient. However, insight into the molecular mechanisms by which free energy stored in such gradients is transduced into work or into chemical energy is just beginning. Nonetheless, gene sequencing and analyses of deduced amino-acid sequences suggest that many biological machines involved in energy transduction, secondary transport proteins in particular (Henderson, 1990; Marger & Saier, 1993), fall into families encompassing proteins from archaea to the mammalian central nervous system, thereby raising the possibility that the members may have common basic structural features and mechanisms. In addition, many of these proteins play important roles in human disease (e.g. diabetes mellitus, glucose/galactose malabsorption, some forms of drug abuse, stroke, antibiotic resistance), as well as the mechanism of action of certain psychotropic drugs.

The focus of this review is on recent observations with a specific secondary transport protein, the lactose permease (lac permease) of Escherichia coli, as a representative of a huge number of proteins that catalyse similar reactions in virtually all biological membranes.

1. INTRODUCTION 107

2. ORGANIZATION 108

3. THE MAIN GOALS 108

4. SCIENTIFIC ACTIVITIES 109

5. CONNECTION AND COOPERATION WITH OTHER ORGANIZATIONS 109

6. PUBLICATIONS 110

7. CLOSING REMARKS 110

8. HISTORICAL TABLES 111

9. APPENDIX: IUPAB STATUTES (as modified in Amsterdam, 1996) 115

The IUPAB was founded on 2 August 1961 in Stockholm as the International Organization of Pure and Applied Biophysics. The main goal of the Organization was to promote and organize international cooperation in biophysics and molecular biology and to encourage its development and practical application all over the world. Some detailed information on the foundation of the Union was published by A. K. Solomon (first Secretary General) in Quarterly Review of Biophysics.Another summary of the activity of IUPAB was prepared by R. D. Keynes(second Secretary General) in 1976.

1. INTRODUCTION 68

1.1 Receptor patterns in the plasma membrane 68

1.2 Different types of receptor patterns 71

2. METHODS TO INVESTIGATE NON-RANDOM RECEPTOR CLUSTERING 73

2.1 Fluorescence resonance energy transfer 73

2.2 Flow cytometric energy transfer measurement 78

2.3 Fluorescence anisotropy and energy transfer 79

2.4 Photobleaching energy transfer on single cells 81

2.5 Two-dimensional mapping of receptor superstructures 82

2.6 Detecting single receptor molecules 85

2.7 Chemical identification of receptor clusters 86

2.8 Electron microscopy 87

2.9 Scanning force microscopy 88

3. CONFORMATIONAL STATES OF RECEPTORS 90

3.1 Multi-subunit receptor structures 90

3.2 Physical parameters influencing conformational states 91

3.3 Chemical interactions and receptor conformations 92

4. ON THE ORIGIN OF NATURALLY OCCURRING RECEPTOR CLUSTERS 93

4.1 Synthesis of receptors and their localization in the plasma membrane 93

4.2 Lipid domain structure of the plasma membrane 94

4.3 The validity of the SingerNicolson model 94

5. CONCLUSIONS 96

6. ACKNOWLEDGEMENTS 96

7. REFERENCES 97

Infrared spectroscopy is a useful technique for the determination of conformation and orientation of membrane-associated proteins and lipids. The technique is especially powerful for detecting conformational changes by recording spectral differences before and after perturbations in physiological solution. Polarized infrared measurements on oriented membrane samples have revealed valuable information on the orientation of chemical groupings and substructures within membrane molecules which is difficult to obtain by other methods. The application of infrared spectroscopy to the static and dynamic structure of proteins and peptides in lipid bilayers is reviewed with some emphasis on the importance of sample preparation. Limitations of the technique with regard to the absolute determination of secondary structure and orientation and new strategies for structural assignments are also discussed.

Whenever fundamental features of living systems and their molecular basis are reviewed, the problem of timing, of time setting or free open-end running times is only marginally on the desk of research agendas, although the finite ageing as one of the features resulting from time markers is known since long. With the discovery of cellular and most important of cellfree oscillatory processes new concepts and experimental techniques were designed to approach these questions more directly leading not only to a better understanding of timing but strongly contributed to concepts for spatial pattern generation. As given in the list of contents major items in the field of intracellular and intercellular periodic reactions are reviewed in Sections 2–7 in terms of specific properties of various systems and in Section 8 in summing important features common to all oscillatory stems in chemistry and biology. Section 9 draws attention to the problem of patterning in the mesoscopic domains of living systems, which is so basic in terms of the volume dimensions specific for the cellular and subcellular reaction compartments in biology. The last chapter sets some marks on urgent problems currently approached by the combined methods of molecular genetics, biochemistry and computer technologies.

1. INTRODUCTION AND HISTORY 122

2. PERIODIC GLYCOLYSIS: TEMPORAL AND SPATIAL OSCILLATIONS 123

2.1 Cell-free glycolysis 123

2.2 Intact cells 128

2.2.1 Yeast 128

2.2.2 Myocytes 130

2.2.3 β-Cells of the islets of pancreas 131

3. CALCIUM OSCILLATIONS 131

3.1 Temporal oscillations 131

3.2 Calcium waves 136

3.3 Physiology 138

4. MICROTUBULE OSCILLATIONS 140

5. THE MITOTIC OSCILLATOR 141

6. DICTYOSTELIUM DISCOIDEUM 144

7. CARDIOMUSCULAR NETWORK 150

8. GENERAL PROPERTIES OF DYNAMIC SPATIAL PATTERNS 152

9. MICROSCOPIC PATTERNS 156

10. PERSPECTIVES 162

11. ACKNOWLEDGEMENTS 163

12. REFERENCES 163

Most working proteins, including metabolic enzymes, transcription regulators, and membrane receptors, transporters, and ion channels, share the property of allosteric coupling. The term ‘allosteric’ means that these proteins mediate indirect interactions between sites that are physically separated on the protein. In the example of ligand-gated ion channels, the binding of a suitable ligand elicits local conformational changes at the binding site, which are coupled to further conformational changes in regions distant from the binding site. The physical motions finally arrive at the site of biological activity: the ion-permeating pore. The conformational changes that lead from the ligand binding to the actual opening of the pore comprise ‘gating’. In 1956, del Castillo and Katz suggested that the competition between different ligands at nicotinic acetylcholine receptors (nAChRs) could be explained by formation of an intermediate, ligand-bound, yet inactive state of the receptor, which separates the active state of the receptor from the initial binding of the ligand (del Castillo & Katz, 1957). This ‘binding-then-gating’, two-step model went beyond the then-prevailing drug-receptor model that assumes a single bimolecular binding reaction, and paralleled Stephenson's conceptual dichotomy of ‘affinity’ and ‘efficacy’ (Stephenson, 1956). In 1965 Monod, Wyman and Changeux presented a simple allosteric model (the MWC model) (Monod et al. 1965) that explained the cooperative binding of oxygen to haemoglobin; it was adopted as an important paradigm for ligand-gated channels soon after its initial formulation (Changeux et al. 1967; Karlin, 1967; Colquhoun, 1973).