bluuebunny/crossref_metadata_2025 huggingface dataset:
A time-dependent model for high-pressure discharges in narrow ablative capillaries
Authors: Zoler D. , Cuperman S. , Ashkenazy J. , Caner M. , Kaplan Z.
Published: March 2009

A time-dependent quasi-one-dimensional model is developed for studying high- pressure discharges in ablative capillaries used, for example, as plasma sources in electrothermal launchers. The main features of the model are (i) consideration of ablation effects in each of the continuity, momentum and energy equations; (ii) use of a non-ideal equation of state; and (iii) consideration of space- and time-dependent ionization.
Transport coefficients for an equal-mass plasma in a uniform magnetic field
Authors: Rassak-Abdul S. Y. , Laing E. W.
Published: March 2009

Cross–field transport coefficients for the electric current and heat flux have been calculated for an equal–mass plasma for various values of the Hall parameter Ωr in the range Ωr ≥ 1. Coefficients have also been calculated for parallel transport. These have been obtained using the linearized Fokker–Planck equations for both particle species, taking advantage of the mass symmetry, which leads to remarkable cancellations in the collision terms.
Outline of a theory of lower-hybrid wave absorption
Authors: Canobbio E. , Croci R.
Published: March 2009

This paper outlines a theory of absorption of lower-hybrid (LH) waves in an electron plasma that is based on the nonlinear relation between grad │E3│2, where E3is the electric field component parallel to the external homogeneous magnetic field, and the space dependent quasi-linear diffusion coefficient, and consequently between grad │E3│2and the absorption. A local absorption induces an increase of the value of the gradient in the neighbouring region and thereby extends the absorption domain. In this way virtually total ‘single-path’ absorption of the injected LH power is obtained. The theory also allows an explanation of the density limit in current drive.
Effect of collisions on the magnetization current in a plasma
Authors: Brodin G. , Stenflo L.
Published: March 2009

The generation of a quasi-stationary nonlinear magnetization current in a plasma in the presence of high-frequency electromagnetic waves is considered. A kinetic theory is developed that takes the velocity dependence of the collision frequency into account. The results show that even a small collision term can have a significant effect on the generation mechanism.
Short-wavelength ion Bernstein nonlinear waves and solitons
Authors: Davydova T. A. , Fishchuk A. I. , Lashkin V. M.
Published: March 2009

Short-wavelength coherent structures of ion Bernstein modes are studied on the basis of a nonlinear equation taking into account the effect of high-frequencey diamagnetism. Analytical solutions in the form of nonlinear periodic waves and envelope solitons are found, and their properties are discussed. The appearance of such structures may explain some phenomena observed in laboratory and space plasmas.
Obliquely propagating ion-acoustic solitons in a multi-component magnetized plasma with negative ions
Authors: Mishra M. K. , Chhabra R. S. , Sharma S. R.
Published: March 2009

Oblique propagation of ion-acoustic solitons in a magnetized low-β plasma consisting of warm positive and negative ion species along with hot electrons is studied. Using the reductive perturbation method, a KdV equation is derived for the system, which admits an obliquely propagating soliton solution. It is found that if the ions have finite temperatures then there exist two types of modes, namely slow and fast ion-acoustic modes. The parameter determining the nature of soliton (i.e. whether the system will support compressive or rarefactive solitons) is different for slow and fast modes. For the slow mode the parameter is the relative temperature of the two ion species, whereas for the fast mode it is the relative concentraion of the two ion species. For the fast mode it is found that there is a critical value of the negative-ion concentration below which only compressive solitons exist and above which rarefactive solitons exist. To discuss the soliton solution at the critical concentration, a modified KdV equation is derived. It is found that at the critical concentration of negative ions compressive and rarefactive solitons co-exist. The effects of temperature of different ion species, angle of obliqueness and magnetization on the characteristics of the solitons are discussed in detail.
Propagation of electromagnetic waves in inhomogeneous plasmas
Authors: Busatti E. , Ciucci A. , Rosa M. De , Palleschi V. , Rastelli S. , Lontano M. , Lunin† N.
Published: March 2009

The reflection and transmission coefficients for an electromagnetic beam propagating in an inhomogeneous plasma are calculated analytically using the Magnus approximation in different physical configurations. The theoretical predictions for such coefficients are expressed in simple analytical form, and are compared with the exact results obtained by numerical solution of the wave propagation equations, using the Berreman 4 × 4 matrix method. It is shown that the theoretical approach is able to reproduce the correct results for reflection and transmission coefficients over a wide range of physical parameters. The accuracy of the theoretical analysis, at different orders of approximation, is also discussed.
Effects of chronic and acute consumption of fruit- and vegetable-puree-based drinks on vasodilation, risk factors for CVD and the response as a result of theeNOSG298T polymorphism
Authors: George Trevor W. , Niwat Chutamat , Waroonphan Saran , Gordon Michael H. , Lovegrove Julie A.
Published: March 2009

The average UK adult consumes less than three portions of fruit and vegetables daily, despite evidence to suggest that consuming five portions daily could help prevent chronic diseases. It is recommended that fruit juice should only count as one of these portions, as juicing removes fibre and releases sugars. However, fruit juices contain beneficial compounds such as vitamin C and flavonoids and could be a useful source of dietary phytochemicals. Two randomised controlled cross-over intervention studies investigating the effects of chronic and acute consumption of commercially-available fruit- and vegetable-puree-based drinks (FVPD) on bioavailability, antioxidant status and CVD risk factors are described. Blood and urine samples were collected during both studies and vascular tone was measured using laser Doppler imaging. In the chronic intervention study FVPD consumption was found to significantly increase dietary carotenoids (P=0·001) and vitamin C (P=0·003). Plasma carotenoids were increased (P=0·001), but the increase in plasma vitamin C was not significant. There were no significant effects on oxidative stress, antioxidant status and other CVD risk factors. In the acute intervention study FVPD were found to increase total plasma nitrate and nitrite (P=0·001) and plasma vitamin C (P=0·002). There was no effect on plasma lipids or uric acid, but there was a lower glucose and insulin peak concentration after consumption of the FVPD compared with the sugar-matched control. There was a trend towards increased vasodilation following both chronic and acute FVPD consumption. All volunteers were retrospectively genotyped for theeNOSG298T polymorphism and the effect of genotype on the measurements is discussed. Overall, there was a non-significant trend towards increased endothelium-dependent vasodilation following both acute and chronic FVPD consumption. However, there was a significant time×treatment effect (P<0·05) of acute FVPD consumption in individuals with the GG variant of theeNOSgene.
A focus for biophysical research in energy problems
Authors: Moss Thomas H.
Published: March 2009

There is widespread agreement that solar energy is the most promising long-range energy source. However, contemporary technology for bulk energy storage is so primitive that full use of the inevitably erratic solar energy flux is severely limited. Biological systems have perfected methods of storing solar energy for later use in periods of darkness, and it is argued in this symposium presentation that there are many frontiers in biophysics related to the solar energy storage problem. Moreover, the conceivable biological storage systems span a wide range of technology, with appropriate applications in societies of widely varying degrees of industrial development. Use of biological systems to produce hydrogen from solar energy may be among the most versatile of these applications. The entire problem of bioconversion of solar energy presents an excellent example of how the needs for basic scientific understanding and application engineering can be very tightly interwoven.
Lipid conformation in model membranes and biological membranes
Authors: Seelig Joachim , Seelig Anna
Published: March 2009

Protein molecules in solution or in protein crystals are characterized by rather well-defined structures in which α-helical regions, β-pleated sheets, etc., are the key features. Likewise, the double helix of nucleic acids has almost become the trademark of molecular biology as such. By contrast, the structural analysis of lipids has progressed at a relatively slow pace. The early X-ray diffraction studies by V. Luzzati and others firmly established the fact that the lipids in biological membranes are predominantly organized in bilayer structures (Luzzati, 1968). V. Luzzati was also the first to emphasize the liquid-like conformation of the hydrocarbon chains, similar to that of a liquid paraffin, yet with the average orientation of the chains perpendicular to the lipid–water interface. This liquid–crystalline bilayer is generally observed in lipid–water systems at sufficiently high temperature and water content, as well as in intact biological membranes under physiological conditions (Luzzati & Husson, 1962; Luzzati, 1968; Tardieu, Luzzati & Reman, 1973; Engelman, 1971; Shipley, 1973). In combination with thermodynamic and other spectroscopic observations these investigations culminated in the formulation of the fluid mosaic model of biological membranes (cf. Singer, 1971). However, within the limits of this model the exact nature of lipid conformation and dynamics was immaterial, the lipids were simply pictured as circles with two squiggly lines representing the polar head group and the fatty acyl chains, respectively. No attempt was made to incorporate the well-established chemical structure into this picture. Similarly, membrane proteins were visualized as smooth rotational ellipsoids disregarding the possibility that protruding amino acid side-chains and irregularities of the backbone folding may create a rather rugged protein surface.
Regulation in macromolecules as illustrated by haemoglobin
Authors: Wyman Jeffries
Published: March 2009

Mηδέν ἄγαν—nothing in excess. These words of the old Greek saying might well find a place in modern Biology. The maintenance of order and balance—homeostasis, as the physiologist would have it—is an attribute of all living things. At a molecular level the study of control and regulation, involving the conjugate concepts of structure and function is a central theme of Biophysics. How is it that an enzyme, by the braking effect of its end products, is prevented from going too far, or, alternatively, by the accumulation of other metabolic substances in its environment, is brought into play? How is it that a working respiratory protein like haemoglobin, by the reciprocal action of its metabolic opposite, carbon dioxide, is aided in the taking up of oxygen in the lungs and the giving it off in the tissues? These are problems of linkage. From one point of view they may be thought of in terms of information— the communication between ligand and macromolecule and between one part of the macromolecule and another. From a different point of view they may be thought of in terms of the storage and transfer of energy, of the way in which the work of introducing ligand, the same or different, at another. The analysis may be pitched either at the phenomenological, or at the mechanistic, level; but whatever the approach it profits cosiderably from the introduction of the concept of the binding potential.
The relation of microscopic structure to molecular structure
Authors: Bernal J. D.
Published: March 2009

What I shall try to do in this essay is not to produce a serious, accurate account of the immense amount of work in this field but, rather, to comment in a very general way on some of the new ideas in the advances of molecular biology, on the background of classical biological thought both histological and biochemical.
The stereochemical code and the logic of a protein molecule
Authors: Liquori A. M.
Published: March 2009

Like DNA and the various forms of RNA, a protein molecule is an information storage system. It contains in fact one or more polypeptide chains which may be regarded as linear sequences of twenty different types of monomer units. It is now clearly established that the chemical information corresponding to a given sequence of a polypeptide chain, containingnamino acid residues, is stored in a segment of one of the two strands of DNA containing 3nnucleotides. The transfer of such information from a gene to a polypeptide chain takes place according to the well-known process involving a transcription and a chemical translation step. This last step leads to a polymer which, in appropriate conditions, takes a three-dimensional conformation or tertiary structure which should correspond to a free-energy minimum of the molecule and its surrounding water solution.
Modification of memory systems: some neurobiological aspects
Authors: McGaugh James L. , Zornetzer Steven F. , Gold Paul E. , Landfield Philip W.
Published: March 2009

The findings of clinical and experimental studies conducted over the past 25 years provide extensive evidence that in both laboratory animals and man memory can be modified by treatments which affect the central nervous system. Patients with head injuries may suffer from retrograde amnesia, a loss of memory for experiences which occur just prior to the onset of the injury. Findings of laboratory studies using animal subjects indicate that retrograde amnesia can be produced by a wide variety of experimental treatments.
Ion transport across thin lipid membranes: a critical discussion of mechanisms in selected systems
Authors: Haydon D. A. , Hladky S. B.
Published: March 2009

There are now well-established examples of carriers and pores which facilitate the transfer of ions across thin lipid membranes. In the absence of such agents, lipid bilayer membranes are extremely impermeable to the common inorganic ions. Thus, the conductance of a pure lecithin + decane or glyceryl mono-oleate + decane membrane in M/10 NaCl is less than10−9Ω−1cm−2. However, on the addition of small lipid-soluble molecules such as valinomycin, or surface-active polypeptides such as gramicidin A, the conductance may become so high (> 10−1ω−lcm−2) that the resistance of the membrane merges into that of the aqueous phase. This review is concerned with the extent to which we now understand how these added substances transfer ions across lipid membranes. Attention has been concentrated on the simpler systems, i.e. the lipid-soluble ions, the 1–1 carriets, a simple pore and, with some loss of simplicity, a substance which prodeces interacting pores. Only molecules of known primary structure are discussed.
Image intersification applied to biological problems
Authors: Reynolds George T.
Published: March 2009

In many important types of observations in biological research, the information provided by the specimens is in the form of photons-quanta of visible light, u.v., or X-rays. The process of observation becomes one of recording this information in useful form, with as high an efficiency as possible. The problem becomes particularly important when for some reason or other the total number or rate of quanta provided by the specimen is small. Examples of such limitations are included in the following: (i) Processes permitting only low-intensity illumination in order not to interfere with the biological processes under observation. (ii) Processes changing very rapidly and requiring rapid sequence recording. (iii) Processes providing only a limited number of photons per event, such as bioluminescence. (iv) Processes in which radioactive tracers are utilized, and observation of radioactivity is desirable at low specific activity or within short time intervals. (v) X-ray diffraction processes where the specimen is weakly diffracting or where the X-ray intensity must be kept low in order not to damage the specimen. (vi) Processes involving the observation of fluorescence, where the intensity is low because of limitations on the amount of tagging material.
Antibody-induced conformational changes in proteins
Authors: Celada Franco , Strom Roberto
Published: March 2009

Several cases of modifications of functional properties of proteins upon specific interaction with antibodies have been reported in the last few years. The purpose of this paper is to discuss evidence that these effects may be due to conformational changes in the protein molecule.
The Theory of Multi-Stationary State Transitions and Biosynthetic Control Processes
Authors: Lavenda B. H.
Published: March 2009

Factors involved in genetic control of protein synthesis can be classified according to their structural and regulatory roles. The structural constitution of the genetic locus determines the ordering of amino acids in the protein primary structure while regulatory factors influence the rates of protein synthesis. The genetic scheme, proposed by Jacob & Monod (1961), groups genes according to their structural and regulatory functions. This genetic classification alone is insufficient to explain the dynamics of regulatory behaviour. Basic questions such as why cells with the same complement of genes synthesize more of one protein than another are left unanswered. The answers to such questions would shed some light on the dynamical mechanism of tissue differentiation and embryological development. Regulation of protein synthesis should be the result of a combination of structural genetic factors and dynamic biochemical processes. It will be shown in this article that the interaction of structural and dynamic factors leads to a coherent and efficient control mechanism of biosynthesis.
Recent advances and applications of diffuse X-ray small-angle scattering on biopolymers in dilute solutions
Authors: Kratky O. , Pilz I.
Published: March 2009

In all scattering phenomena the scattering angles are inversely related to the dimensions of the scattering particles. As macromolecules are giant compared with the normally used CuKαwavelength λ = 1·54 Å, we find the scattering of the particle as a whole at Correspondingly small angles.
A new probe for reaction kinetics—the spectrum of scattered light
Authors: Yeh Yin , Keeler R. N.
Published: March 2009

The rates of reaction and reaction mechanisms in biological systems are the controlling factors in the metabolism and life cycles of all living organisms. Nevertheless, very little is known today about the details of these processes, particularly in more complicated life forms. For example, addition of certain metallic ions to an enzymic matrix can cause gross changes in enzymic activity (Brewer & Weber, 1966); just how these ions specifically enter into enzymic reactions is a subject of intense interest. The nature of the kinetics of bonding in nucleic acids is also the subject of much research (Eigen, 1967).
Integrated gas chromatography-mass spectrometry
Authors: Ryhage Ragnar
Published: March 2009

Mass spectrometric analysis of organic compounds was in the early 1950s done mostly for quantitative determination of petroleum products. The use of the mass spectrometer for qualitative analysis of solid organic material samples was shown by O'Neil & Wier (1951) and since then a continuous increase in mass spectrometric studies of different classes of organic compounds has been noted. After the gas chromatograph was developed by James & Martin (1952) the quantitative analysis of complex mixtures of organic compounds was possible and after a few years the gas chromatographic method was considered as routine. The first connection of a gas chromatograph (GC) to a mass spectrometer (MS) was made by Holmes & Morell (1957). They studied gases using a splitter system where only a small part or less than 1% of the effluent from a packed column was transferred to the ion source of the mass spectrometer. The next step in GC—MS development was made by Gohlke (1959), who studied compounds of low molecular weight using capillary column directly connected to a time-of-flight mass spectrometer. This was possible due to the fact that the carrier gas flow rate could be limited to about 1 ml/min. To avoid the sample loss resulting from using a packed column with the splitter system a jet molecular separator was constructed as an interphase between the packed column and a mass spectrometer with magnetic sector analyser (Ryhage, 1964). Mixtures of fatty acids and of hydrocarbons with a molecular weight of up to about 420 were studied. In this study spectra were taken at irregular intervals.
Effects of Metal Binding on Protein Structure
Authors: Friedberg Felix
Published: March 2009

A distinction has been made between ‘metalloproteins’ and ‘metal-protein complexes’. The former exhibit high metal-ligand stability constants (the metal is not removed during the isolation of the protein), while the latter bind metal ions only loosely (Vallee, 1955). Actually, all proteins can be considered as existing as metal-protein complexes. Selectivity, however, among proteins in their tendency to combine with inorganic ions (both with regard to the type of ion as well as number of ions) suggests that particular configurations produce specific reactive sites. In turn, binding of ions to these sites alters the electronic and consequently the steric conformation of the protein. Thus, effects on macromolecular conformation may not only be due to structural changes of the solvent induced by ions, which modifies solvent-macromole interaction, but also to specific ligation of the ions to the protien which alters local molecular arrangement.
Isolation and characterization of the components of the sodium pump
Authors: Jørgensen Peter Leth
Published: March 2009

A satisfactory understanding of the functions of the sodium pump, the system responsible for the active transport of sodium and potassium, require the isolation and characterization of its protein and lipid components which are integrated in the structure of the cell membrane. The enzyme system (Na++ K+)-ATPase, is located in membrane fragments and behaves in the test tube like the transport system in the intact cell membrane (Skou,1957) Purified preparations of this enzyme will contain some, if not all, of the components of the sodium pump.
The (Na++K+) activated enzyme system and its relationship to transport of sodium and potassium
Authors: Skou Jens Chr.
Published: March 2009

It seems to be the membrane bound (Na++K+)-activated enzyme system which transforms the energy from a hydrolysis of ATP into a vectorial movement of sodium out and potassium into the cell against electrochemical gradients, i.e. this systems seems to be the transport system for sodium and potassium (see, for example, review by Skou, 1972; Hokin & Dahl, 1972).
New Paths in the Molecular Orbital Approach to Solvation of Biological Molecules
Authors: Pullman Alberte , Pullman Bernard
Published: March 2009

This review is devoted to the presentation of recent developments in a field of theoretical molecular biophysics which seem to open large possibilities for progress in a hitherto relatively unexplored although very important direction. It is concerned with the establishment of a new methodology in the molecular orbital approach to the problem of the solvation of biological molecules. The methodology is still in an initial stage, susceptible of many refinements and its practical applications may also be considered as being in their beginnings. Nevertheless the successes obtained so far and the interest which they aroused in a number of laboratories incite us to present already now the general principles and the available results so as to offer a possibility of evaluating the advantages, present-day limitations and future potentialities of the procedure, which could then be explored by all those interested. This review may thus be said to be to a large extent oriented towards the future, with the acknowledged aim of producing an acceleration and widening of researches in this field. Possible progress in this respect is interesting from a double point of view.
Cytochromecoxidase: some current biochemical and biophysical problems
Authors: Malmström Bo G.
Published: March 2009

Few fields of biochemistry have seen such widespread applications of physical theories and techniques as that of biological oxidation. There are obvious reasons for this. Oxidation-reduction reactions form the foundations of bioenergetics, an area which can only be understood in terms of thermodynamic theory. Most components of the mitochondrial respiratory chain contain transition metals, and these elements and their chemical environment can often be studied by modern spectroscopic methods, such as electron-paramagnetic resonance (EPR). The relation between spectroscopic properties and chemical structure of metallo-proteins, e.g. haem proteins, represents one of the few branches of present-day biochemistry to which quantum mechanical calculations can profitably be applied (see, for example, Zerner, Gouterman & Kobayashi, 1966).
Excited electronic states in dark biological process
Authors: Cilento G.
Published: March 2009

It is well known that excited states may be generated chemically in biological systems as evidencex and by the phenomenon of bioluminescence and it is natural to suspect that they may also be generated and used in dark processes (Szent-Györgyi, 1941; Steele, 1963; Cilento, 1965; White & Wei, 1970; Whiteet al.1971). Förster (1967) has pointed out that electronic excitation and subsequent transfer processes may occur in biological dark systems despite the fact that the energy available from enzymic processes is too low to excite aromatic amino acids and other biochemical structures. Hastings (1968) suggests that in some organisms light emission is just an alternative to the formation of an active species.
Physical principles of membrane organization
Authors: Israelachvili J. N. , Marčelja S. , Horn R. G.
Published: March 2009

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.
Similarities of protein topologies: evolutionary divergence, functional convergence or principles of folding?
Authors: Ptitsyn O. B. , Finkelstein A. V.
Published: March 2009

(A)Evolutionary similarities of protein structuresTwo decades have passed from the time that the three dimensional structure of the first globular protein, sperm whale myoglobin, was decoded (Kendrewet al.1960). Its structure, which now looks so simple and habitual, then seemed to be unusually complicated. The decoding of the subsequent proteins, lysozyme (Blakeet al.1965), ribonuclease (Kartha, Bello & Harker, 1967), chymotrypsin (Matthewset al.1967), carboxypeptidase (Lipscombet al.1969) redoubled the feeling of amazement and even of some confusion before the extremely complicated, intricate and, above all, absolutely unlike protein structures. Some consolation against this background was the evident and far-reaching similarity between the three-dimensional structures of myoglobin and hemoglobin subunits (Perutz, Kendrew & Watson, 1965) and an analogous similarity between the structures of chymotrypsin and other serine proteases, elastase (Shotton & Watson, 1970) and trypsin (Stroud, Kay & Dickerson, 1972). However this similarity was easily explained by the far-reaching homology between the primary structures of myoglobin and hemoglobin and between the primary structures of serine proteases.
Molecular aspects of photoreceptor function
Authors: Ebrey Thomas G. , Honig Barry
Published: March 2009

The description of the molecular processes which underlie visual excitation is the fundamental problem in understanding vision at the level of a single photoreceptor. Thus far only a general outline of photoreceptor function has emerged with little known about actual biochemical and biophysical mechanisms.
Phase transitions and fluidity characteristics of lipids and cell membranes
Authors: Chapman D.
Published: March 2009

The concept that the liquid crystalline or mesomorphic condition was of importance to biological systems is a relatively old idea. Thus Bernal (1933) when discussing the different types of arrangements of molecules in liquid crystals commented ‘Such structures belong to the liquid crystal as a unit and not to its molecules which may be replaced by others without destroying them and they persist in spite of the complete fluidity of the substance. These are just the properties to be required for a degree of organization between that of the continuous substance, liquid or crystalline solid and even the simplest living cell.’ Stewart (1961) some thirty years later also stated that ‘It is this property – the combination of flow and lability with a preferred and relatively stable molecular orientation – that makes the mesomorphic (i.e. liquid crystal) phase uniquely appropriate to the structure of protoplasm and living tissue.’
Biophysics of cell separations
Authors: Mel H. C. , Ross D. W.
Published: March 2009

To the Chemist, it has long been second nature to work with separate, purified substances. Biochemists and molecular biologists have now largely achieved the same working position, with their powerful separation techniques of ultracentrifugation, electrophoresis, chromatography and the like. For the cell biologists, it is a much more recent phenomenon that widespread attention is being directed towards quantitative measurement of properties in isolated, homogeneous cell types. The richness and diversity of cell systems beg for cleverness on the part of the experimenter.
Thermodynamic analysis of ion effects on the binding and conformational equilibria of proteins and nucleic acids: the roles of ion association or release, screening, and ion effects on water activity
Authors: Record M. Thomas , Anderson Charles F. , Lohman Timothy M.
Published: March 2009

The purpose of this review is to examine the various effects of low- molecular-weight electrolytes on the associations and interactions of proteins and nucleic acids. Our primary interest is in general electrostatic effects, rather than chemical effects (specific interactions) of particular ions (e.g. transition metals, protons). We consider those interactions in which a variation in salt concentration has a significant effect on the macromolecular equilibrium, and analyse the effects of salt in these situations in terms of (i) direct participation of ions in the biopolymer reaction, (ii) Debye—Hückel screening by salt ions of the charge interactions on the biopolymers, and (iii) the reduction in water activity brought about at high salt concentrations.
Chemical Kinetics and Fluorescence Correlation Spectroscopy
Authors: Magde D.
Published: March 2009

The dynamics of macromolecules, the subject of this symposium, are most directly studied by simply looking through a microscope and observing the molecular motion. With a microscope, we can resolve the size and shape of large particles, as well as monitor dynamic motion. For smaller particles, particularly single macromolecules, we cannot resolve the size or shape; but it is still possible to observe the motion, if we can make the particles appear as bright points of light sprinkled dilutely over a dark background. Siedentopf & Zsigmondy (1903) demonstrated this fact with a device which came to be called the ultramicroscope.
Fluorescence correlation spectroscopy applied to rotational diffusion of macromolecules
Authors: Ehrenberg Måns , Rigler Rudolf
Published: March 2009

A quantitative relationship between polarization properties of fluorescence light and molecular rotational diffusion was first derived by Perrin (1926). His results, which concerned spherical particles, have later been refined to the more complex rotational motion of asymmetric bodies (Memming, 1961; Chuang & Eisenthal, 1972; Ehrenberg & Rigler, 1972; Belford, Belford & Weber, 1972).
Forward scattering of light, X-rays and neutrons
Authors: Eisenberg Henryk
Published: March 2009

The central points of this paper can now be summarized. We consider here, for simplicity only, vanishing particle concentration. In equilibrium sedimentation equation (6) applies. The density increment is a measurable quantity. It can either be introduced into equation (6) to calculateM2, or it can be analysed by equations (7) and (8) to provide additional information on specific volumes and solute interactions.

Light scattering is determined by the analogous equation (20). The refractive index increment is also experimentally accessible and its structure (not considered here) is similar to that of the density increment. Small angle X-ray scattering is determined by equation (31) and the electron density increment which appears in this equation cannot be directly determined by experiment. Yet it can be obtained in straightforward fashion from the mass density increment, by equation (34). Similarly, in the case of neutron scattering (equation (38)), the scattering length density increment is obtained from the mass density increment by equation (40), or it may now be directly evaluated by neutron interferometry.
Resonance Raman spectroscopy in biochemistry and biology
Authors: Carey P. R.
Published: March 2009

Resonance Raman (RR) spectroscopy provides detailed information on the vibrational and electronic properties of biochemical and biological chromophores. The analysis of RR spectra, using for example model compounds or a group frequency approach, enables us to form an accurate structural picture of the chromophore in its natural biological site. Moreover, the insight gained into the electronic states of a biological chromophore can be crucial to our understanding of its function. Thus the RR technique represents a powerful means of eliciting precise structural and electronic data from a coloured species and of focusing upon key aspects of its function. It has even been possible to obtain RR spectra from some natural chromophores invivo, giving spectra detailed and informative enough to please a spectroscopist from a system complex enough to satisfy a biologist.
Molecular electrostatic potential of the nucleic acids
Authors: Pullman Alberte , Pullman Bernard
Published: March 2009

It is generally acknowledged that geometrical and conformational properties of biopolymers have an important effect on their biochemical behaviour. It is less easily recognized that these properties depend also on their macromolecular electronic characteristics.

The aim of this review is to demonstrate the significance of such macromolecular electronic effects. Particularly useful for this sake is the recently much developed concept of ‘molecular electrostatic potential’ (MEP) (Scrocco & Tomasi, 1973, 1978) by which is defined the electrostatic (Coulomb) potential created in the neighbouring space by the nuclear charges and the eletronic distribution of a molecule.
Kinetic Analysis of ATPase Mechanisms
Authors: Trentham D. R. , Eccleston J. F. , Bagshaw C. R.
Published: March 2009

At even the simplest level we can expect an ATPase mechanism to comprise the following four steps: the binding of ATP, the reaction of ATP with water on the enzyme, and the release of the products ADP and P1. So at the outset techniques are needed to investigate these four processes. The range of techniques needed is soon extended once questions are asked about the role of protons and metal ions, the possibility of a multistep hydrolytic process, multistep substrate and product binding processes, and protein–lipid or protein–protein interactions. Since ATPases and ATP synthases are almost universally involved in some form of energy transduction there is a particular need in an ATPase or ATP synthase reaction to evaluate the equilibrium constants of the steps in the mechanism and to investigate the possibility of alternate reaction pathways. The nature of the coupling process by the protein of the chemical reactions of ATP to the other energetic process, be it muscle contraction, active transport, respiration or photosynthesis, is likewise of profound interest. Finally we would like to know as much as possible about the ATPase or ATP synthase mechanism during the period when the various forms of energy transduction are occurring.
Free radicals and the action of inhibitors of radical processes under pathological states and ageing in living organisms and in man
Authors: Emanuel N. M.
Published: March 2009

The concept of processes in a living organism as of a most complex enzyme-catalysed system of coupled chemical conversions following both physical and chemical laws, opens up new possibilities of cognizance and control of vital processes.
Determination of the Mass of Viruses by Quantitative Electron Microscopy
Authors: Bahr G. F. , Engler W. F. , Mazzone H. M.
Published: March 2009

In general the characterization of a virus particle depends upon a number of known and independently acquired parameters, all of which require a great deal of time. As a direct method of measurement, the mass of viruses has been largely ignored in virus characterization studies. Where the molecular weight of viruses has been determined by sedimentation and diffusion, sedimentation equilibrium, light scattering, or the electron microscopy-counting procedure, the relationship between this property and mass has been arrived at by employing Avogadro's number. In the present report it will be demonstrated that the disadvantages found in these usual methods of determining molecular weight, such as experimentation, calculation of virus size, and purification of virus preparation, are not present in the quantitative electron microscopy method for determination of mass and molecular weight.
Kinetics of Channel Gating in Excitable Membranes
Authors: Goldman L.
Published: March 2009

To a certain degree, the events underlying the action potential are understood. For each ion to which the membrane is permeable, there exists an equilibrium potential, whose physical origin is in the activity gradient for that ion. The membrane potential is then the summation of these individual ionic batteries each weighted according to the membrane permeability to that ion. In nerve fibres at rest the potassium permeability is relatively high and the membrane potential is near to the equilibrium potential for potassium. During excitation there is a transitory increase in the permeability to sodium and a slower transitory increase in the potassium permeability also. The membrane potential, therefore, temporarily moves to a value near to the sodium equilibrium potential and then returns to its resting value. Less well understood are the molecular mechanisms responsible for these selective changes in membrane permeability, i.e. how it is that a channel (pathway bywhich an ion traverses the membrane) changes its availability for ion passage as a response to a change in the membrane potential. This is the gating process.
Structure and function of channel-forming peptaibols
Authors: Sansom M. S. P.
Published: March 2009

Transport of ions through channels is fundamental to a number of physiological processes, especially the electrical properties of excitable cells (Hille, 1992). To understand this process at a molecular level requires atomic resolution structures of channel proteins.
Voltage gating of ion channels
Authors: Sigworth F. J.
Published: March 2009

Voltage-gated ion channels are membrane proteins that play a central role in the propagation and transduction of cellular signals (Hille, 1992). Calcium ions entering cells through voltage-gated calcium channels serve as the trigger for neurotransmitter release, muscle contraction, and the release of hormones. Voltage-gated sodium channels initiate the nerve action potential and provide for its rapid propagation because the ion fluxes through these channels regeneratively cause more channels to open.
Protein folding
Authors: Némethy George , Scheraga Harold A.
Published: March 2009

This review describes recent advances in studies on the stabilities of the three-dimensional structures of proteins and on the processes leading to the formation of these structures. The term ‘protein folding’ will be used here to denote the process of the conversion of an open polypeptide chain into the unique three-dimensional conformation of the native protein. Experimental and theoretical aspects of protein folding have been reviewed by anfinsen & Scheraga (1975). In the present article, we emphasize advances made since the writing of that review, together with a brief summary of the background of recent studies.
DNA–carcinogen interaction: covalent DNA-adducts of benzo(a)pyrene 7, 8-dihydrodiol 9, 10-epoxides studied by biochemical and biophysical techniques
Authors: Gräslund Astrid , Jernström Bengt
Published: March 2009

Exposure to various chemicals, either due to occupation or lifestyle, is considered to be a major contributing factor to tumour formation in man (Higginson, 1969; Doll and Peto, 1981). An important and prevalent class of potent carcinogenic compounds present in he environment is polycyclic aromatic hydrocarbons (PAHs), which are found in various petroleum and combustion products derived from heat and power generation and motor vehicle exhausts (Baum, 1978). Furthermore, since PAHs are generally formed by pyrolysis of organic matters such as tobacco smoking and certain procedures of food preparation, the PAH exposure to humans is extensive.
Oligonucleotide structure: a decade of results from single crystal X-ray diffraction studies
Authors: Kennard Olga , Hunter William N.
Published: March 2009

Writing a review gives authors a splendid opportunity to view developments in a particular area of science from a very personal angle. They are at liberty to select material, emphasize aspects of direct interest to their own work and air speculations which, wisely or not, referees have caused to have removed from their publications. Such personal accounts often make good reading, but may be somewhat misleading especially for readers seeking an introduction to the field. One remedy is to aim at a comprehensive review with equal weight given to all publications but boredom, if not bias, is then likely to creep in.
Decoding neuronal firing and modelling neural networks
Authors: Abbott L. F.
Published: March 2009

Biological neural networks are large systems of complex elements interacting through a complex array of connexions. Individual neurons express a large number of active conductances (Connors et al. 1982; Adams & Gavin, 1986; Llinás, 1988; McCormick, 1990; Hille, 1992) and exhibit a wide variety of dynamic behaviours on time scales ranging from milliseconds to many minutes (Llinás, 1988; Harris-Warrick & Marder, 1991; Churchland & Sejnowski, 1992; Turrigiano et al. 1994).
Diffuse scattering in protein crystallography
Authors: Benoit Jean-Pierre , Doucet Jean
Published: March 2009

The understanding of flexibility and deformability in proteins is one of the current major challenges of structural molecular biology. The knowledge of the average atomic positions of three-dimensional folding of proteins, which is obtained either by X-ray diffraction or n.m.r. spectroscopy, is generally not sufficient to explain their functional mechanisms. Very often it is necessary to consider the existence of other concerted atomic motions as, for example, in the well-known case of the CO molecule fixation at the active site of myoglobin which requires the concerted displacement of a large number of atoms in order to open a channel down to this site. This opening, which depends on the physico-chemical conditions, plays the role of a regulator in the biochemical reactions (Janin & Wodak, 1983; Tainer et al. 1984; Westhof et al. 1984; Ormos et al. 1988).
The potential and limitations of neutrons, electrons and X-rays for atomic resolution microscopy of unstained biological molecules
Authors: Henderson Richard
Published: March 2009

Radiation damage is the main problem which prevents the determination of the structure of a single biological macromolecule at atomic resolution using any kind of microscopy. This is true whether neutrons, electrons or X-rays are used as the illumination. Forneutrons, the cross-section for nuclear capture and the associatedenergy deposition and radiation damage could be reduced by using samples that are fully deuterated and15N-labelled and by using fast neutrons, but single molecule biological microscopy is still not feasible. For naturally occurring biological material,electronsat present provide the most information for a given amount of radiation damage. Using phase contrast electron microscopy on biological molecules and macromolecular assemblies of ˜ 105molecular weight and above, there is in theory enough information present in the image to allow determination of the position and orientation of individual particles: the application of averaging methods can then be used to provide an atomic resolution structure. The images of approximately 10000 particles are required. Below 105molecular weight, some kind of crystal or other geometrically ordered aggregate is necessary to provide a sufficiently high combined molecular weight to allow for the alignment. In practice, the present quality of the best images still falls short of that attainable in theory and this means that a greater number of particles must be averaged and that the molecular weight limitation is somewhat larger than the predicted limit. ForX-rays, the amount of damage per useful elastic scattering event is several hundred times greater than for electrons at all wavelengths and energies and therefore the requirements on specimen size and number of particles are correspondingly larger. Because of the lack of sufficiently bright neutron sources in the foreseeable future, electron microscopy in practice provides the greatest potential for immediate progress.
Neutron scattering studies of biological macromolecules in solution
Authors: Kneale G. G. , Baldwin J. P. , Bradbury E. M.
Published: March 2009

Small-angle neutron scattering studies of biological macromolecules have developed rapidly in recent years due to the advent of high neutron-flux reactors,† efficient position-sensitive area detectors for neutrons (Allemand et al. 1975) and novel design of instruments (Ibel, 1976). At the same time position-sensitive detectors for X-rays (Gabriel & Dupont, 1972) have revitalized the small-angle X-ray scattering field (Kratky & Pilz, 1972; Luzzati et al. 1976) and it is now becoming clear that neutrons and X-rays can provide complementary structural information on biological complexes.