Quarterly Reviews of Biophysics

Although the importance of the polyelectrolyte character of DNA has been recognized for some time (Felsenfeld & Miles 1967), few of the implications have been explored, primarily because of a lag in translating the breakthroughs in polyelectrolyte theory of the last decade into a form that is well adapted to the analysis of the specialized problems of biophysical chemistry. Perhaps an analogous situation existed in the field of protein chemistry during the period after the formulation and confirmation of the Debye—Hückel theory of ionic solutions but before Scatchard's incorporation of the theory into his analysis of the binding properties of proteins. An achievement for polynucleotide solutions parallel to Scatchard's was recently presented by Record, Lohman, & de Haseth (1976) and further developed and reviewed by Record, Anderson & Lohman (1978).

1. Introduction 370

2. Infrared (IR) spectroscopy – general principles 372

2.1 Vibrations 372

2.2 Information that can be derived from the vibrational spectrum 372

2.3 Absorption of IR light 375

3. Protein IR absorption 376

3.1 Amino-acid side-chain absorption 376

3.2 Normal modes of the amide group 381

4. Interactions that shape the amide I band 382

4.1 Overview 382

4.2 Through-bond coupling 383

4.3 Hydrogen bonding 383

4.4 Transition dipole coupling (TDC) 383

5. The polarization and IR activity of amide I modes 387

5.1 The coupled oscillator system 387

5.2 Optically allowed transitions 388

5.3 The infinite parallel β-sheet 388

5.4 The infinite antiparallel β-sheet 389

5.5 The infinite α-helix 390

6. Calculation of the amide I band 391

6.1 Overview 391

6.2 Perturbation treatment by Miyazawa 393

6.3 The parallel β-sheet 394

6.4 The antiparallel β-sheet 395

6.5 The α-helix 396

6.6 Other secondary structures 398

7. Experimental analysis of protein secondary structure 398

7.1 Band fitting 398

7.2 Methods using calibration sets 401

7.3 Prediction quality 403

8. Protein stability 404

8.1 Thermal stability 404

8.2 ¹H/²H exchange 406

9. Molecular reaction mechanisms of proteins 408

9.1 Reaction-induced IR difference spectroscopy 408

9.2 The origin of difference bands 409

9.3 The difference spectrum seen as a fingerprint of conformational change 410

9.4 Molecular interpretation: strategies of band assignment 416

10. Outlook 419

11. Acknowledgements 420

12. References 420

This review deals with current concepts of vibrational spectroscopy for the investigation of protein structure and function. While the focus is on infrared (IR) spectroscopy, some of the general aspects also apply to Raman spectroscopy. Special emphasis is on the amide I vibration of the polypeptide backbone that is used for secondary-structure analysis. Theoretical as well as experimental aspects are covered including transition dipole coupling. Further topics are discussed, namely the absorption of amino-acid side-chains, ¹H/²H exchange to study the conformational flexibility and reaction-induced difference spectroscopy for the investigation of reaction mechanisms with a focus on interpretation tools.

Starting from known properties of non-specific salt effects on the surface tension at an air–water interface, we propose the first general, detailed qualitative molecular mechanism for the origins of ion-specific (Hofmeister) effects on the surfacepotential differenceat an air–water interface; this mechanism suggests a simple model for the behaviour of water at all interfaces (including water–solute interfaces), regardless of whether the non-aqueous component is neutral or charged, polar or non-polar. Specifically, water near an isolated interface is conceptually divided into three layers, each layer being 1 water-molecule thick. We propose that the solute determines the behaviour of the adjacent first interfacial water layer (I₁); that the bulk solution determines the behaviour of the third interfacial water layer (I₃), and that bothI₁andI₃compete for hydrogen-bonding interactions with the intervening water layer (I₂), which can be thought of as a transition layer. The model requires that a polar kosmotrope (polar water-structure maker) interact withI₁more strongly than would bulk water in its place; that a chaotrope (water-structure breaker) interact withI₁somewhat less strongly than would bulk water in its place; and that a non-polar kosmotrope (non-polar water-structure maker) interact withI₁much less strongly than would bulk water in its place.

We introduce two simple new postulates to describe the behaviour ofI₁water molecules in aqueous solution. The first, the ‘relative competition’ postulate, states that anI₁water molecule, in maximizing its free energy (—δG), will favour those of its highly directional polar (hydrogen-bonding) interactions with its immediate neighbours for which the maximum pairwise enthalpy of interaction (—δH) is greatest; that is, it will favour the strongest interactions. We describe such behaviour as ‘compliant’, since anI₁water molecule will continually adjust its position to maximize these strong interactions. Its behaviour towards its remaining immediate neighbours, with whom it interacts relatively weakly (but still favourably), we describe as ‘recalcitrant’, since it will be unable to adjust its position to maximize simultaneously these interactions. The second, the ‘charge transfer’ postulate, states that the strong polar kosmotrope–water interaction has at least a small amount of covalent character, resulting in significant transfer of charge from polar kosmotropes to water–especially of negative charge from Lewis bases (both neutral and anionic); and that the water-structuring effect of polar kosmotropes is caused not only by the tight binding (partial immobilization) of the immediately adjacent (I₁) water molecules, but also by an attempt to distribute among several water molecules the charge transferred from the solute. When extensive, cumulative charge transfer to solvent occurs, as with macromolecular polyphosphates, the solvation layer (the layer of solvent whose behaviour is determined by the solute) can become up to 5- or 6-water-molecules thick.

We then use the ‘relative competition’ postulate, which lends itself to simple diagramming, in conjunction with the ‘charge transfer’ postulate to provide a new, startlingly simple and direct qualitative explanation for the heat of dilution of neutral polar solutes and the temperature dependence of relative viscosity of neutral polar solutes in aqueous solution. This explanation also requires the new and intriguing general conclusion that as the temperature of aqueous solutions is lowered towards o °C, solutes tend to acquire a non-uniform distribution in the solution, becoming increasingly likely to cluster 2 water molecules away from other solutes and surfaces (the driving force for this process being the conversion of transition layer water to bulk water). The implications of these conclusions for understanding the mechanism of action of general (gaseous) anaesthetics and other important interfacial phenomena are then addressed.

Membranes are the most common cellular structures in both plants and animals. They are now recognized as being involved in almost all aspects of cellular activity ranging from motility and food entrapment in simple unicellular organisms, to energy transduction, immunorecognition, nerve conduction and biosynthesis in plants and higher organisms. This functional diversity is reflected in the wide variety of lipids and particularly of proteins that compose different membranes. An understanding of the physical principles that govern the molecular organization of membranes is essential for an understanding of their physiological roles sincestructureandfunctionare much more interdependent in membranes than in, say, simple chemical reactions in solution. We must recognize, however, that the word ‘understanding’ means different things in different disciplines, and nowhere is this more apparent than in this multidisciplinary area where biology, chemistry and physics meet.

Though the structures presented in crystallographic models of macromolecules appear to possess rock-like solidity, real proteins and nucleic acids are not particularly rigid. Most structural work to date has centred upon the native state of macromolecules, the most probable macromolecular form. But the native state of a molecule is merely its most abundant form, certainly not its only form. Thermodynamics requires that all other possible structural forms, however improbable, must also exist, albeit with representation corresponding to the factor exp( —G_i/RT) for each state of free energyG_i(see Moelwyn-Hughes, 1961), and one appreciates that each molecule within a population of molecules will in time explore the vast ensemble ofpossiblestructural states.

Proton and carbon-13 nmr spectra of unsonicated lipid bilayers and biological membranes are generally dominated by strong proton–proton and proton–carbon dipolar interactions. As a result the spectra contain a large number of overlapping resonances and are rather difficult to analyse. Nevertheless, important information on the structure and dynamic behaviour of lipid systems has been provided by these techniques (Wennerström & Lindblom, 1977).

Alcohol based cosolvents, such as trifluoroethanol (TFE) have been used for many decades to denature proteins and to stabilize structures in peptides. Nuclear magnetic resonance spectroscopy and site directed mutagenesis have recently made it possible to characterize the effects of TFE and of other alcohols on polypeptide structure and dynamics at high resolution. This review examines such studies, particularly of hen lysozyme and β-lactoglobulin. It presents an overview of what has been learnt about conformational preferences of the polypeptide chain, the interactions that stabilize structures and the nature of the denatured states. The effect of TFE on transition states and on the pathways of protein folding and unfolding are also reviewed. Despite considerable progress there is as yet no single mechanism that accounts for all of the effects TFE and related cosolvents have on polypeptide conformation. However, a number of critical questions are beginning to be answered. Studies with alcohols such as TFE, and ‘cosolvent engineering’ in general, have become valuable tools for probing biomolecular structure, function and dynamics.

1. COSOLVENTS: OLD HAT? 298

2. HOW DOES TFE WORK? 299

2.1 Effect on hydrogen bonding 300

2.2 Effect on non-polar sidechains 301

2.3 Effect on solvent structure 302

3. EFFECTS OF TFE ON (UN-)FOLDING TRANSITIONS 303

3.1 Pretransition 303

3.2 Transition 304

3.3 Posttransition 305

3.4 Far UV CD spectroscopic detection of structure 306

3.5 Effect with temperature 306

3.6 Effect with additional denaturants 306

4. THERMODYNAMIC PARAMETERS FROM STRUCTURAL TRANSITIONS OF PEPTIDES AND PROTEINS IN TFE 307

5. ADVANCES IN NMR SPECTROSCOPY 310

5.1 Chemical shifts 310

5.2 ³[Jscr ]_HNHαcoupling constants 311

5.3 Amide hydrogen exchange 312

5.4 Nuclear Overhauser Effects (NOEs) 312

6. α-HELIX – EVERYWHERE? 313

6.1 Intrinsic helix propensity equals helix content? 313

6.2 A helix propensity scale for the amino acids in TFE 314

6.3 Capping motifs and stop signals 315

6.4 Limits and population of helices as seen by CD and NMR 316

7. TURNS 317

8. β-HAIRPINS AND SHEETS 317

9. ‘CLUSTERS’ OF SIDECHAINS 320

10. THE TFE DENATURED STATE OF β-LACTOGLOBULIN 321

11. THE TFE DENATURED STATE OF HEN LYSOZYME 324

12. TERTIARY STRUCTURE, DISULPHIDES, DYNAMICS AND COMPACTNESS 327

13. PROSPECTS FOR STRUCTURE CALCULATION 328

14. EFFECT OF TFE ON QUATERNARY STRUCTURE 329

15. EFFECT ON TFE ON UN- AND REFOLDING KINETICS 330

16. OTHER USES 336

16.1 Mimicking membranes and protein receptors 336

16.2 Solubilizing peptides and proteins 336

16.3 Cosolvents as helpers for protein folding? 338

16.4 Modifying protein dynamics and catalysis 338

16.5 Effects on nucleic acids 339

16.6 Effects on lipid bilayers and micelles 339

16.7 Future applications 339

17. CONCLUSIONS: TFE – WHAT IS IT GOOD FOR? 340

18. ACKNOWLEDGMENTS 340

19. REFERENCES 340

The inner membranes of mitochondria contain three multi-subunit enzyme complexes that act successively to transfer electrons from NADH to oxygen, which is reduced to water (Fig. I). The first enzyme in the electron transfer chain, NADH:ubiquinone oxidoreductase (or complex I), is the subject of this review. It removes electrons from NADH and passes them via a series of enzyme-bound redox centres (FMN and Fe-S clusters) to the electron acceptor ubiquinone. For each pair of electrons transferred from NADH to ubiquinone it is usually considered that four protons are removed from the matrix (see section 4.1 for further discussion of this point).

To proceed at a high rate, phosphorylating respiration requires ADP to be available. In the resting state, when the energy consumption is low, the ADP concentration decreases so that phosphorylating respiration ceases. This may result in an increase in the intracellular concentrations of O₂as well as of one-electron O₂reductants such asThese two events should dramatically enhance non-enzymatic formation of reactive oxygen species, i.e. of, and OHׁ, and, hence, the probability of oxidative damage to cellular components. In this paper, a concept is put forward proposing that non-phosphorylating (uncoupled or non-coupled) respiration takes part in maintenance of low levels of both O₂and the O₂reductants when phosphorylating respiration fails to do this job due to lack of ADP.

In particular, it is proposed that some increase in the H⁺leak of mitochondrial membrane in State 4 lowers, stimulates O₂consumption and decreases the level ofwhich otherwise accumulates and serves as one-electron O₂reductant. In this connection, the role of natural uncouplers (thyroid hormones), recouplers (male sex hormones and progesterone), non-specific pore in the inner mitochondrial membrane, and apoptosis, as well as of non-coupled electron transfer chains in plants and bacteria will be considered.

In a living cell membrane-bound compartments are continuously either separated or united through fusion reactions, and literally thousands of such reactions take place every minute. The formation of membrane vesicles from pre-existing membranes, and their fusion with specific acceptor membranes, constitute a prerequisite for the transport of most impermeant molecules and macromolecules into the cell by endocytosis, out of the cell by exocytosis, and between the cellular organelles (Palade, 1975; Silverstein, 1978; Evered & Collins, 1982). Less frequent, but equally crucial, are fusion events in fertilization, cell division, polykaryon formation, enucleation, etc. (for reviews see Poste & Nicholson, 1978). Although a great deal is known about the properties and consequences of individual forms of membrane fusion in cellular systems, and about fusion in artificial lipid membranes, the molecular basis for the reactions remain largely unclear.