A Raman scattering study of the interactions of DNA with its water of hydration

Raman spectroscopy is used to probe the nature of the hydrogen bonds which hold the water of hydration to DNA. The ～ 3450?cm^?1 molecular O–H stretching mode shows that the first six water molecules per base pair of the primary hydration shell are very strongly bound to the DNA. The observed shift in the peak position of this mode permits a determination of the length of the hydrogen bonds for these water molecules. These hydrogen bonds appear to be about 0.3?Å shorter than the hydrogen bonds in bulk water. The linewidth of this mode shows no significant changes above water contents of about 15 water molecules per base pair. This technique of using a vibrational spectroscopy to obtain structural information about the hydration shells of DNA could be used to study the hydration shells of other biomolecules.     

Imaging mixed lipid monolayers by dynamic atomic force microscopy.

Phase imaging with tapping mode atomic force microscopy (AFM) and force modulation microscopy were used to probe the mechanical properties of phase-separated lipid monolayers made of a mixture (0.25:0.75) of the surface-active lipopeptide surfactin and of dipalmitoylphosphatidylcholine (DPPC). The pi-A isotherms and the result of a molecular modeling study revealed a loose, 2-D liquid-like organization for the surfactin molecules and a closely packed, 2-D solid-like organization for DPPC molecules. This difference in molecular organization was responsible for a significant contrast in height, tapping mode phase and force modulation amplitude images. Phase imaging at light tapping, i.e., with a ratio of the set-point tapping amplitude with respect to the free amplitude A(sp)/A(0) approximately 0.9, showed larger phase shifts on the solid-like DPPC domains attributed to larger Young's modulus. However, contrast inversion was observed for A(sp)/A(0)<0.7, suggesting that at moderate and hard tapping the image contrast was dominated by the probe-sample contact area. Surprisingly, force modulation amplitude images showed larger stiffness for the liquid-like surfactin domains, suggesting that the contrast was dominated by contact area effects rather than by Young's modulus. These data emphasize the complex nature of the contrast mechanisms of dynamic AFM images recorded on mixed lipid monolayers.     

Fluorescence depolarization and rotational modes of tyrosine in bovine pancreatic trypsin inhibitor

The fluorescence of bovine pancreatic trypsin inhibitor (BPTI) is due to one or more of its four tyrosine residues. Observations of the stationary polarization of the fluorescence over a large range of temperatures and viscosities permit the demonstration of at least three modes of tyrosine rotation, and perhaps an ultrafast fourth one. The slowest mode is one of motion of the whole molecule; the second, a much faster motion limited to an amplitude of 11 degrees, is not changed by quenching of the fluorescence through addition of citrate and is therefore ascribed to the motion of internal tyrosines of BPTI. The third mode of motion is faster still; it has an amplitude similar to that of the second and, being sensitive to citrate quenching, is attributed to the rotation of the external tyrosine residue. A residual depolarization corresponding to a rotational amplitude of 22 degrees is deduced by comparison of the polarizations of BPTI and tyrosine dissolved in 80% glycerol-water at -40 degrees C. It is in accord in amplitude with the picosecond tyrosine rotations predicted by Karplus and collaborators from molecular dynamics computer simulations, but it could also originate, in whole or in part, from electronic energy transfer among the tyrosines.     

Dynamic light-scattering studies of DNA. I. The coupling of internal modes with anisotropic translational diffusion in congested solutions

A model for the coupling between internal modes, or molecular rotation, and anisotropic translational diffusion in congested solutions is proposed to account for the anomalously slow component that has appeared ubiquitously in reported autocorrelation functions of Rayleigh scattered light from solutions of DNA's with molecular weights greater than about 10⁷. The predicted existence of an anomalously slow mode in addition to a faster “normal” mode, as well as the predicted relative amplitudes of both fast and slow components, are qualitatively in agreement with the observations. For sufficiently long-wavelength fluctuations all of the amplitude appears in the slower mode, which then exhibits an appropriately averaged translational diffusion coefficient. In support of the model it is shown in the Appendix that nonideal central interactions between macromolecules are by themselves insufficient to generate isolated internal mode relaxation terms in the autocorrelation function, unless translational ordering of the macromolecules extends over the illuminated observation region.     

Dynamics of electron transfer in the oxidation of water by chlorophyll a dimer

The observed temperature dependence of the rate constant for reduction of (Chl a.2H2O)2+. by water is fitted to a theoretical expression for the rate of an intramolecular electronic radiationless transition. The theory assumes a single effective mediating mode and the best-fit value for the frequency of this mode is omega(m) = 680 cm(-1), which corresponds to high-frequency, intermolecular librations in water. From an explicit calculation of the nonadiabatic-coupling matrix element, an average electron-transfer distance of 11 A is obtained, consistent with molecular dimensions available for this system.     

Taurine depletion increases phosphorylation of a specific protein in the rat retina

Summary Partial depletion of the taurine content in the rat retina was accomplished for up to 22 weeks by introduction of 1.5% guanidinoethanesulfonate (GES) in the drinking water. Taurine levels decreased by 50% after 1 week of GES treatment and by 80% at 16 weeks. Replacement of GES by taurine to the GES-treated rats from week 16 to 22 returned their taurine content to the control value. Whereas addition of taurine (1.5%) to the drinking water of control rats from week 16 to 22 elevated the retinal taurine content to 118% of the control value, the administration of untreated water to GES-treated animals for the 16 to 22 week time period increased the retinal taurine content to only 76% of the control value.The amplitude of the electroretinogram (ERG) b-wave was decreased by 60% after GES-treatment for 16 weeks and maintained this reduced level for up to 22 weeks. Administration of taurine in the drinking water from week 16 to 22 returned the b-wave amplitude to a range not statistically different from the control values whereas the administration of untreated water produced less improvement.After 6 weeks of GES treatment when the retinal taurine content was reduced by 70% and the amplitude of the b-wave was reduced by 50% (extrapolated from Figure 1), phosphorylation of a specific protein with an approximate molecular weight of 20K was increased by 94%. The increased phosphorylation of the ~20K protein observed after GES treatment was reversed when the animals were treated with taurine (1 1/2%) in the drinking water for an additional 6 weeks. There was no change in the phosphorylation of the ~20K protein when animals were treated with taurine for 6 weeks. The data obtained support the theory that taurine may have a regulatory effect on retinal protein phosphorylation.     

On the importance of van der Waals interaction in the groove binding of DNA with ligands: restrained molecular dynamics study

Comparison of interaction energy between an oligonucleotide and a DNA-binding ligand in the minor and major groove modes was made by use of restrained molecular dynamics. Distortion in DNA was found for the major groove mode whereas less significant changes for both ligand and DNA were detected for the minor groove binding after molecular dynamics simulation. The conformation of the ligand obtained from the major groove mode resembles that computed with the ligand soaked in water. The van der Waals contact energy was found to be as significant as electrostatic energy and more important for difference in binding energy between these two binding modes. The importance of van der Waals force in groove binding was supported by computations on the complex formed by the repressor peptide fragment from the bacteriophage 434 and its operator oligonucleotide.     

A preferred amplitude of calcium sparks in skeletal muscle

In skeletal and cardiac muscle, calcium release from the sarcoplasmic reticulum, leading to contraction, often results in calcium sparks. Because sparks are recorded by confocal microscopy in line-scanning mode, their measured amplitude depends on their true amplitude and the position of the spark relative to the scanned line. We present a method to derive from measured amplitude histograms the actual distribution of spark amplitudes. The method worked well when tested on simulated distributions of experimental sparks. Applied to massive numbers of sparks imaged in frog skeletal muscle under voltage clamp in reference conditions, the method yielded either a decaying amplitude distribution (6 cells) or one with a central mode (5 cells). Caffeine at 0.5 or 1 mM reversibly enhanced this mode (5 cells) or induced its appearance (4 cells). The occurrence of a mode in the amplitude distribution was highly correlated with the presence of a mode in the distribution of spark rise times or in the joint distribution of rise times and spatial widths. If sparks were produced by individual Markovian release channels evolving reversibly, they should not have a preferred rise time or amplitude. Channel groups, instead, could cooperate allosterically or through their calcium sensitivity, and give rise to a stereotyped amplitude in their collective spark.     

Dehydration affects synaptic transmission at flexor muscle in acute lead-treated mice.

The effect of 24 hrs. water deprivation on spontaneous and evoked transmitter release was studied at flexor nerve terminals of control and lead-treated male C57BL mice. Miniature endplate potentials (MEPPs) and endplate potentials (EPPs) were recorded intracellularly from urethane-anesthetized (2 mg/g, i.p.) control and lead exposed mice in both hydrated and dehydrated conditions. Exposure to lead was made by i.p. injection of lead acetate (1.0 mg/kg) dissolved in a 5% glucose solution 24 hrs. prior to the experiment. Unimodal and bimodal MEPP frequencies decreased with dehydration, while small mode MEPPs remained unchanged and large mode MEPPs increased in frequency. EPP amplitude and quantal content were unchanged by dehydration. Lead treatment by itself reduced the frequency of unimodal and bimodal MEPPs but had no effect on the amplitude of EPPs or of quantal content. However a combination of dehydration and acute lead treatment reduced the frequency of unimodal, bimodal and large mode MEPPs and significantly reduced both EPP amplitude and quantal content. Dehydration apparently reveals an underlying neurotoxic action of lead at the neuromuscular junction. This raises a health concern that people subjected to both lead pollution and dehydration are at greater risk to lead poisoning of the neuromuscular junction.     

Characterization of bacterial polysaccharide capsules and detection in the presence of deliquescent water by atomic force microscopy

We detected polysaccharide capsules from Zunongwangia profunda SM-A87 with atomic force microscopy (AFM). The molecular organization of the capsules at the single-polysaccharide-chain level was reported. Furthermore, we found that with ScanAsyst mode the polysaccharide capsules could be detected even in the presence of deliquescent water covering the capsule.     

A pulsed H NMR study of the hydration properties of extruded maize-sucrose mixtures

The molecular mobility in maize and maize-sucrose extudates was studied as a function of the degree of hydration (up to 35% w/w dry basis) using proton spin-spin relaxation NMR. The extrusion of maize systems was found to enhance the molecular mobility of the constituents generating the rigid ‘solid-like’ and the mobile ‘liquid-like’ components of the NMR free induction decay signal.

As the moisture content was increased, the amplitude of the normalised NMR signal arising from the rigid component decreased dramatically for the samples containing sucrose, suggesting an increased mobility and thus a solution type behaviour of the sugar. This hypothesis was supported by the observation of shorter T₂ values for the liquid component of the signal recorded for the samples containing sugar. Sucrose was found to be miscible with the polysaccharide at moisture contents below 15%, but progressively dissolved into the additional water at higher moisture contents. This suggested the occurrence of phase separation over a short distance scale as the water content of the maize-sucrose system was modified. The results are discussed in terms of unequal water partitioning between the maize and the sugar components.     

Effect of various physical factors on oscillations of light-dispersion in water and aqueous biopolymer solutions

Study of the dependence of light scattering fluctuation on temperature, mechanic perturbation and magnetic field in water and water hemoglobin and DNA solution has shown that an increase in temperature results in the decline of long-term fluctuation amplitude and in the increase of short-term fluctuation amplitude. Mechanical mixing removes long-term fluctuations and over 10 hours are spent for their recovery. Regular fluctuations appear when the constant magnetic field above 240 A/m is applied; the fluctuations are retained for many hours after the removal of the field (when the field is off). It was supposed that maintenance of long-range correlation of molecular rotation-translation fluctuation by the effect of long-range forces and external fields underlies the mechanism of long-term light scattering fluctuations.     

Nuclear-magnetic-resonance studies of carboxypeptidase B. Binding of inhibitors to the manganese enzyme.

Longitudinal and transverse proton relaxation rates of water in solutions of porcine manganese carboxypeptidase B have been measured in the presence of various competitive inhibitors by pulse nuclear magnetic resonance (NMR) spectrometry. The inhibition constant of Mn-carboxypeptidase activity by L-argininic acid and acetyl-L-arginine was in agreement with the equilibrium constant obtained by the NMR method, indicating similar and specific binding of the inhibitors to the active site of the manganese enzyme. Titration of the water boound to the metal ion revealed the presence of one water molecular which could be displaced from the sphere of the managenese ion by various inhibitors. The structural features of the inhibitors required for this displacement as well as the mode of interaction is described.     

The coding of frequency-modulated signals by the presynaptic control system

Mechanism of presynaptic inhibition transforms frequency-modulated sensory signals amplitude-frequency-modulated reaction of potentials of dorsal side of spinal cord. Frequency regulation is characterized by a wide threshold range which is several times higher than amplitude regulation mode. Neuromuscular system of motor apparatus is a kind of impulse-frequency detector. The system isolates analogous amplitude changes of mechanic movements by demodulation of frequency-modulated dorsal potentials. The detection mode is facilitated by preliminary transformation.     

Quasielastic light-scattering study of polyadenylic acid solutions. II

Quasielastic light scattering is used to study saline solutions of polyadenylic acid with varying polymer concentrations and molecular masses. These experiments clearly show the existence of two relaxation times. For dilute solutions, when the chains are mutually independent, the fast mode is due to the free diffusion of the polymer chains. For concentrations above the overlap concentration C*, the fast mode is due to the propagation of collective excitations of the pseudolattice of polymer chains. The slow modes are observed when the polymer concentration is in the vicinity of the overlap concentration C*. A series of experiments shows that both their relaxation time and amplitude depend only on the polymer concentration and not on the polymer molecular mass. This result rules out any previous explanation based on individual chain motion. Furthermore, since the amplitudes depend on the time elapsed from the preparation of the solution, the slow modes are due to the diffusion of concentration inhomogeneities in the pseudolattice.     

Water-coupled low-frequency modes of myoglobin and lysozyme observed by inelastic neutron scattering.

Conformational changes of proteins often involve the relative motion of rigid structural domains. Normal mode analysis and molecular dynamics simulations of small globular proteins predict delocalized vibrations with frequencies below 20 cm(-1), which may be overdamped in solution due to solvent friction. In search of these modes, we have studied deuterium-exchanged myoglobin and lysozyme using inelastic neutron scattering in the low-frequency range at full and low hydration to modify the degree of damping. At room temperature, the hydrated samples exhibit a more pronounced quasielastic spectrum due to diffusive motions than the dehydrated samples. The analysis of the corresponding lineshapes suggests that water modifies mainly the amplitude, but not the characteristic time of fast protein motions. At low temperatures, in contrast, the dehydrated samples exhibit larger motional amplitudes than the hydrated ones. The excess scattering, culminating at 16 cm(-1), is suggested to reflect water-coupled librations of polar side chains that are depressed in the hydrated system by strong intermolecular hydrogen bonding. Both myoglobin and lysozyme exhibit ultra-low-frequency modes below 10 cm(-1) in the dry state, possibly related to the breathing modes predicted by harmonic analysis.     

Protein folding and wring resonances

The polypeptide chain of a protein is shown to obey topological constraints which enable long range excitations in the form of wring modes of the protein backbone. Wring modes of proteins of specific lengths can therefore resonate with molecular modes present in the cell. It is suggested that protein folding takes place when the amplitude of a wring excitation becomes so large that it is energetically favorable to bend the protein backbone. The condition under which such structural transformations can occur is found, and it is shown that both cold and hot denaturation (the unfolding of proteins) are natural consequences of the suggested wring mode model. Native (folded) proteins are found to possess an intrinsic standing wring mode.     

The impairing effects of chaetochromin D on mitochondrial respiration and structure

Chaetochromin D, a toxic secondary metabolite ofChaetomlum graclle, was examined for impairing effects on mitochondrial respiration and structure (swelling-induction) using isolated rat liver mitochondria to gain Insight into the molecular mechanism for Its cytotoxicity. Chaetochromin D exerted similar mode of effects to those of chaetochromin A, cephalochromin, and ustilaginoldin A on mitochondrial reactions, causing uncoupling of oxidative phosphorylation, depression of state 3 respiration, and induction of drastic swelling In mitochondria. Chaetochromin D induced the same style of swelling as that induced by chaetochromin A, being characterized by a very high rate and small amplitude of swelling. The swelling terminated In the middle and the amplitude was about half of the full swelling. Once the quick swelling ceased in the middle, subsequent swelling could not be elicited by the second addition of chaetochromin D at any of the concentrations tested.     

Photosynthetic flexibility and ecophysiological plasticity: questions and lessons from Clusia, the only CAM tree, in the neotropics

The discovery of crassulacean acid metabolism (CAM) in the trees of Clusia: arrival in the limelight of international research 8 II. Phylogeny 8 III. Photosynthetic physiotypes 10 IV. Metabolic flexibility: organic acid variations 12 V. The environmental control of photosynthetic flexibility 13 VI. Phenotypic plasticity: physiotypes and morphotypes 16 VII. Ecological amplitude and habitat impact 16 VIII. Conclusions and outlook 21 Acknowledgements 22 References 22 Summary It is the aim of this review to present a monographic survey of the neotropical genus Clusia on scaling levels from molecular phylogeny, metabolism, photosynthesis and autecological environmental responses to ecological amplitude and synecological habitat impact. Clusia is the only dicotyledonous genus with real trees performing crassulacean acid metabolism (CAM). By way of introduction, a brief historical reminiscence describes the discovery of CAM in Clusia and the consequent increase in interest in studying this particular genus of tropical shrubs and trees. The molecular phylogeny of CAM in the genus is compared with that in Kalancho? and the Bromeliaceae. At the level of metabolism and photosynthesis, the great plasticity of expression of photosynthetic physiotypes, i.e. (i) C(3) photosynthesis, (ii) CAM including CAM idling, (iii) CAM cycling and (iv) C(3)/CAM-intermediate behaviour, as well as metabolic flexibility in Clusia is illustrated. At the level of autecology, the factors water, irradiance and temperature, which control photosynthetic flexibility, are assessed. The phenotypic plasticity of physiotypes and morphotypes is described. At the level of synecology, the ecological amplitude of Clusia in the tropics and the relations to habitat are surveyed.     

Docking studies on PARP-1 inhibitors: insights into the role of a binding pocket water molecule

The binding mode of a series of competitive PARP-1 inhibitors was investigated employing a molecular docking approach by using Autodock 3.0. A particular attention was given to the role played by a water molecule present in some but not all the so far available crystal structures of the catalytic domain of PARP-1. Good correlation between calculated binding energies and experimental inhibitory activities was obtained either by including (r2=0.87) or not (r2=0.84) the structural water molecule. Closer inspection of our results suggested that this water molecule should be considered part of the hydration shell of polar inhibitors and not as a structural water.