Copper is a redox–active transition metal ion required for the function of many essential human proteins. For biosynthesis of proteins coordinating copper, the metal may bind before, during or after folding of the polypeptide. If the metal binds to unfolded or partially folded structures of the protein, such coordination may modulate the folding reaction. The molecular understanding of how copper is incorporated into proteins requires descriptions of chemical, thermodynamic, kinetic and structural parameters involved in the formation of protein–metal complexes. Because free copper ions are toxic, living systems have elaborate copper-transport systems that include particular proteins that facilitate efficient and specific delivery of copper ions to target proteins. Therefore, these pathways become an integral part of copper protein folding in vivo. This review summarizes biophysical-molecular in vitro work assessing the role of copper in folding and stability of copper-binding proteins as well as protein–protein copper exchange reactions between human copper transport proteins. We also describe some recent findings about the participation of copper ions and copper proteins in protein misfolding and aggregation reactions in vitro.

Most biological processes require the production and degradation of proteins, a task that weighs heavily on the cell. Mutations that compromise the conformational stability of proteins place both specific and general burdens on cellular protein homeostasis (proteostasis) in ways that contribute to numerous diseases. Efforts to elucidate the chain of molecular events responsible for diseases of protein folding address one of the foremost challenges in biomedical science. However, relatively little is known about the processes by which mutations prompt the misfolding of α-helical membrane proteins, which rely on an intricate network of cellular machinery to acquire and maintain their functional structures within cellular membranes. In this review, we summarize the current understanding of the physical principles that guide membrane protein biogenesis and folding in the context of mammalian cells. Additionally, we explore how pathogenic mutations that influence biogenesis may differ from those that disrupt folding and assembly, as well as how this may relate to disease mechanisms and therapeutic intervention. These perspectives indicate an imperative for the use of information from structural, cellular, and biochemical studies of membrane proteins in the design of novel therapeutics and in personalized medicine.

Antibody molecules secreted by B-lymphocytes play a central role in the immune defense systems of higher organisms. The major function of the antibody molecule is to bind specifically to foreign molecules (antigens) and to effect their inactivation and/or removal. Antibody molecules exist in millions of different forms, each with a unique amino acid sequence and combining site structure. Collectively called immunoglobulins (abbreviated as Ig), they form one of the major classes of proteins present in the blood, constituting 20% of the total plasma protein by weight.

Very early in the era of isotopic tracers it became apparent that tracer fluxes did not always come out as one had predicted from classical measurements of transport by osmosis or diffusion. Thus Hevesy, Hofer & Krogh (1935) determined the water permeability of frog skin from osmotic uptake of water as well as from measurements of its permeability to heavy water. They found the first method to give values some 4–5 times higher than the latter. Although this result at first seemed disappointing, it was soon realized that the two types of experiments provided more information about the nature of osmosis through real membranes than had been available before. Thus it was shown that the results might be explained in terms of interaction between water molecules moving in bulk, possibly through pores in the membrane (Ussing, 1952; Koefoed-Johnsen & Ussing, 1953; Andersen & Ussing, 1957).

Glycolipid transfer proteins (GLTPs) originally were identified as small (~24 kDa), soluble, amphitropic proteins that specifically accelerate the intermembrane transfer of glycolipids. GLTPs and related homologs now are known to adopt a unique, helically dominated, two-layer ‘sandwich’ architecture defined as the GLTP-fold that provides the structural underpinning for the eukaryotic GLTP superfamily. Recent advances now provide exquisite insights into structural features responsible for lipid headgroup selectivity as well as the adaptability of the hydrophobic compartment for accommodating hydrocarbon chains of differing length and unsaturation. A new understanding of the structural versatility and evolutionary premium placed on the GLTP motif has emerged. Human GLTP-motifs have evolved to function not only as glucosylceramide binding/transferring domains for phosphoinositol 4-phosphate adaptor protein-2 during glycosphingolipid biosynthesis but also as selective binding/transfer proteins for ceramide-1-phosphate. The latter, known as ceramide-1-phosphate transfer protein, recently has been shown to form GLTP-fold while critically regulating Group-IV cytoplasmic phospholipase A2 activity and pro-inflammatory eicosanoid production.

Ribonuclease P is among the first ribozymes discovered, and is the only ubiquitously occurring ribozyme besides the ribosome. The bacterial RNase P RNA is catalytically active without its protein subunit and has been studied for over two decades as a model system for RNA catalysis, structure and folding. This review focuses on the thermodynamic, kinetic and structural frameworks derived from the folding studies of bacterial RNase P RNA.

Biological interactions are ‘processes’ 331

Intermolecular forces involved 332

Synergy between different forces occurring at different locations 333

Non-equilibrium, rate and time-dependent interactions 335

Reversible and irreversible interactions 337

The interaction forces between biological molecules and surfaces are much more complex than those between non-biological molecules or surfaces, such as colloidal particle surfaces. This complexity is due to a number of factors: (i) the simultaneous involvement of many different molecules and different non-covalent forces – van der Waals, electrostatic, solvation (hydration, hydrophobic), steric, entropic and ‘specific’, and (ii) the flexibility of biological macromolecules and fluidity of membranes. Biological interactions are better thought of as ‘processes’ that evolve in space and time and, under physiological conditions, involve a continuous input of energy. Such systems are, therefore, not at thermodynamic equilibrium, or even tending towards equilibrium. Recent surface forces apparatus (SFA) and atomic force microscopy (AFM) measurements on supported model membrane systems (protein-containing lipid bilayers) illustrate these effects. It is suggested that the major theoretical challenge is to establish manageable theories or models that can describe the spatial and time evolution of systems consisting of different molecules subject to certain starting conditions or energy inputs.

As a consequence of the activities of modern industry and agriculture, many made-made organic compounds have found their way into our environment, and by persisting there for varying periods of time have caused concern to society. Why do some chemicals persist while others disappear? Detailed answers to this question require an understanding of the degradative segment of the earth's carbon cycle, most of the reactions of which are catalysed by enzymes used by microbes. These organisms owe much of their degradative expertise to their ability to render oxygen gas chemically reactive. This is a process that would be extremely dangerous for any living organism if it were carried out in a haphazard or accidental fashion; but when catalysed and cantrolled by enzymes (oxygenases) of micro-organisms, reaction sequences are started that result in biodegradation of compounds that resist the enzymes of all other living forms.

Detailed understanding of the action of biological molecular machines must overcome the challenge of gaining a clear knowledge of the corresponding free-energy landscape. An example for this is the elucidation of the nature of converting chemical energy to torque and work in the rotary molecular motor of F1-ATPase. A major part of the challenge involves understanding the rotary–chemical coupling from a non-phenomenological structure/energy description. Here we focused on using a coarse-grained model of F1-ATPase to generate a structure-based free-energy landscape of the rotary–chemical process of the whole system. In particular, we concentrated on exploring the possible impact of the position of the catalytic dwell on the efficiency and torque generation of the molecular machine. It was found that the experimentally observed torque can be reproduced with landscapes that have different positions for the catalytic dwell on the rotary–chemical surface. Thus, although the catalysis is undeniably required for torque generation, the experimentally observed position of the catalytic dwell at 80° might not have a clear advantage for the force generation by F1-ATPase. This further implies that the rotary–chemical couplings in these biological motors are quite robust and their efficiencies do not depend explicitly on the position of the catalytic dwells. Rather, the specific positioning of the dwells with respect to the rotational angle is a characteristic arising due to the structural construct of the molecular machine and might not bear any clear connection to the thermodynamic efficiency for the system.

In this paper, a structure-function analysis of B-DNA self-fitting is reviewed in the light of recent oligonucleotide crystal structures. Their crystal packings provided a high-resolution view of B-DNA helices closely and specifically fitted by groove-backbone interaction, a natural and biologically relevant manner to assemble B-DNA helices. In revealing that new properties of the DNA molecule emerge during condensation, these crystallographic studies have pointed to the biological importance of DNA—DNA interactions.

The large ribosomal subunit has a distinct feature, the stalk, extending outside the ribosome. In bacteria it is called the L12 stalk. The base of the stalk is protein uL10 to which two or three dimers of proteins bL12 bind. In archea and eukarya P1 and P2 proteins constitute the stalk. All these extending proteins, that have a high degree of flexibility due to a hinge between their N- and C-terminal parts, are essential for proper functionalization of some of the translation factors. The role of the stalk proteins has remained enigmatic for decades but is gradually approaching an understanding. In this review we summarise the knowhow about the structure and function of the ribosomal stalk till date starting from the early phase of ribosome research.

The main advantage of high voltage in electron microscopy is greater penetration. When using an aperture of optimum size the thickness of specimen that can be imaged increases almost linearly with applied voltage in the case of light elements, both when the criterion is image intensity and when it is resolution. For heavy elements the increase is less rapid. With a small aperture the increase in observable thickness is still less rapid, and ‘saturates’ towards I MV. For a specimen of given thickness, image definition increases nearly linearly with voltage owing to the decrease in chromatic aberration. Although ultimate resolving power improves with voltage, the gain is slight and is offset by a fall in contrast. The optimum voltage for very high resolution is probably between 200 and 300 kV. Radiation damage arising from ionization decreases with rising voltage, making easier the examination of sensitive materials such as polymers. On the other hand, ejection of atoms by head-on collision increases rapidly above a threshold voltage, causing observable defects in metals.

In construction, a high-voltage microscope differs from the normal type only in size and in having an accelerator instead of a simple electron gun. In operation it differs little, apart from precautions to avoid fiashover in the accelerator. A decrease in response of viewing screens and photographic emulsions is more than compensated by higher brightness of the electron gun. The chief applications so far of the high-voltage microscope have been for studying thick films of metals, magnetic materials, ceramics and polymers. Improved preparation techniques should make it possible to study sections of biological tissues up to 5 μ thick. The observation of micro-organisms and other specimens in the wet state can be carried out in double-walled cells, but only at poor resolution. Still higher voltages, up to 3 or MV coupled with the use of an energy analyser or an image intensifier, should improve further the microscopy of such thick specimens.

The initial act for visual perception is the absorption of light in the photo-pigment of the receptor end-organs. Since both light and the nervous message have a quantal structure, any theory of visual information processing should in principle be a digital processing theory. And not only in principle, since we know for certain that in many situations the number of quanta is rather restricted, so that an over-all thermodynamic theory cannot but fail to adequately describe visual facts.

The purpose of this review is to summarize the present status of preparative zonal centrifugation and to indicate where the remaining problems, in the reviewer's opinion, may lie. The field is sufficiently new for interest in practical separartions to be uppermost. However, a number of theoretical problems relating to gradient capacity, zonal rotor configuration and particle—particle interactions remain to be fully explored.

This paper consists of three parts. The first describes theoretically a general strategy for fragmentation and separation of membranes which can be used in the elucidation of their structure and function. The second part describes a practical separation method, partition in liquid aqueous polymer two-phase systems, which can be used for separation of macromolecules and membrane particles of biological origin. The third part gives examples of the application of this method to membrane vesicles, and how this separation in combination with the strategy described in the first part can be used for analysis of the structure of biological membranes.

It has become clear that there is no simple ‘code’ for protein–DNA recognition and that selecting an optimal binding sequence along the DNA double helix corresponds to more than simply forming a set of specific hydrogen bonds or steric interactions. However, it has been difficult to characterize the so-called indirect components of recognition. While DNA deformation certainly underlies indirect recognition, it is not easy to determine how local fine structure and deformability depend on base sequence or exactly what percentage of recognition should be attributed to such factors. Molecular modelling can help to develop these ideas into a quantitative model, provided the calculations can be carried out fast enough to enable a comprehensive survey of base-sequence effects. I present here some recent results from our group and their consequences for improving our understanding of protein–DNA binding, and their potential for predicting, and eventually modulating, protein–DNA binding.

Lead is probably the oldest and most widely distributed environmental intoxicant, but unlike many of the synthetic agents which cause the greatest concern in industrial societies today, it occurs naturally at low levels in the environment and was present during evolutionary times. Galena (PbS), the most important lead-bearing mineral, is abundant and it is readily smelted. The metal is easily shaped and does not corrode and its compounds have found innumerable uses, particularly as pigments. This explains, in brief, why lead has had great economic importance since ancient times and why lead disease has plagued civilized societies for thousands of years and continues to be a serious concern to health authorities today. (Grandjean, 1975; Eisinger, 1977).

Biophysical studies have a very high impact on the understanding of internalization, molecular mechanisms, interactions, and localization of CPPs and CPP/cargo conjugates in live cells or in vivo. Biophysical studies are often first carried out in test-tube set-ups or in vitro, leading to the complicated in vivo systems. This review describes recent studies of CPP internalization, mechanisms, and localization. The multiple methods in these studies reveal different novel and important aspects and define the rules for CPP mechanisms, hopefully leading to their improved applicability to novel and safe therapies.

This review represents a personal view of membrane thermodynamics. I do not intend to deal at all with the irreversible thermodynamics of membrane mass transfer processes. This aspect has been covered far more competently and completely by other people (Bittar, 1970; Paterson, 1970; Rottenberg, Caplan & Essig, 1970; Mitchell, 1970; Rothschild et al. 1980; Oster, Perelson & Katchalsky, 1973; Kedem & Katchalsky, 1958; Schwartz, 1971). The recent review on osmosis by Hill (1979) is a particularly succinct appraisal of a facet of irreversible membrane thermodynamics. Arata & Nishimura (1980) have considered the coupling of electron transfer to vectorial processes in biological membranes.