The basis of the hydrophobic effect

The property of a molecule that most reliably determines the magnitude of the hydrophobic effect that it will experience is the number of hydrogen–carbon bonds it contains not the accessible surface area of its nonpolar portions. This conclusion follows from an examination of the standard free energies of transfer of alkanes, alkenes, alkadienes, and arenes from water to hexadecane. When the standard free energies of transfer for hydrocarbons in these different classes are plotted as a function of the number of hydrogen–carbon bonds they contain, all of the data fall upon the same line. These standard free energies of transfer are also directly proportional to the number of hydrogen–carbon bonds the hydrocarbons contain. When the same standard free energies of transfer are plotted as a function of the accessible surface areas of the hydrocarbons, the data do not fall upon the same line nor are the standard free energies of transfer directly proportional to the accessible surface areas. An examination of the standard free energies of transfer for the different classes of hydrocarbons from the gas phase to water and from the gas phase to hexadecane reinforces the conclusion that the number of hydrogen–carbon bonds in a molecule rather than its accessible surface area is the basis of the hydrophobic effect. Consequently, estimates of the contribution of different functional groups to the hydrophobic effect providing the free energy of folding of a molecule of protein or providing the free energy of dissociation for the association of two proteins or the association of a ligand with a protein should be made by counting the number of hydrogen–carbon bonds excluded from water rather than computing the accessible surface areas excluded from water.     

Protein Linewidth and Solvent Dynamics in Frozen Solution NMR

Solid-state NMR of proteins in frozen aqueous solution is a potentially powerful technique in structural biology, especially if it is combined with dynamic nuclear polarization signal enhancement strategies. One concern regarding NMR studies of frozen solution protein samples at low temperatures is that they may have poor linewidths, thus preventing high-resolution studies. To learn more about how the solvent shell composition and temperature affects the protein linewidth, we recorded ¹H, ²H, and ¹³C spectra of ubiquitin in frozen water and frozen glycerol-water solutions at different temperatures. We found that the ¹³C protein linewidths generally increase with decreasing temperature. This line broadening was found to be inhomogeneous and independent of proton decoupling. In pure water, we observe an abrupt line broadening with the freezing of the bulk solvent, followed by continuous line broadening at lower temperatures. In frozen glycerol-water, we did not observe an abrupt line broadening and the NMR lines were generally narrower than for pure water at the same temperature. ¹H and ²H measurements characterizing the dynamics of water that is in exchange with the protein showed that the ¹³C line broadening is relatively independent from the arrest of isotropic water motions.     

The dynamics of protein hydration water: a quantitative comparison of molecular dynamics simulations and neutron-scattering experiments

We present results from an extensive molecular dynamics simulation study of water hydrating the protein Ribonuclease A, at a series of temperatures in cluster, crystal, and powder environments. The dynamics of protein hydration water appear to be very similar in crystal and powder environments at moderate to high hydration levels. Thus, we contend that experiments performed on powder samples are appropriate for discussing hydration water dynamics in native protein environments. Our analysis reveals that simulations performed on cluster models consisting of proteins surrounded by a finite water shell with free boundaries are not appropriate for the study of the solvent dynamics. Detailed comparison to available x-ray diffraction and inelastic neutron-scattering data shows that current generation force fields are capable of accurately reproducing the structural and dynamical observables. On the time scale of tens of picoseconds, at room temperature and high hydration, significant water translational diffusion and rotational motion occur. At low hydration, the water molecules are translationally confined but display appreciable rotational motion. Below the protein dynamical transition temperature, both translational and rotational motions of the water molecules are essentially arrested. Taken together, these results suggest that water translational motion is necessary for the structural relaxation that permits anharmonic and diffusive motions in proteins. Furthermore, it appears that the exchange of protein-water hydrogen bonds by water rotational/librational motion is not sufficient to permit protein structural relaxation. Rather, the complete exchange of protein-bound water molecules by translational displacement seems to be required.     

Metastable CO binding sites in the photoproduct of a novel cooperative dimeric hemoglobin.

The infrared absorption spectrum of the CO-photoproduct from Scapharca inaequivalvis hemoglobin (Hbl) at 10 K yields only a single line in the "B" state region at 2132 cm-1. This is the same frequency as the B1 line observed in photodissociated vertebrate HbCO and MbCO. No evidence was found for the B2 line detected in vertebrate hemoglobins and myoglobin in the 2118-2120 cm-1 region. These data demonstrate that the protein does not have the same conformationally accessible ligand-binding sites as do vertebrate hemoglobins and myoglobins. The absence of the B2 line indicates that only a single weak site is accessible to the photolyzed CO molecule. These results are in accord with geminate rebinding experiments and ligand escape pathway calculations which have shown that the distal properties of Hbl are distinct from those of tetrameric hemoglobins and vertebrate myoglobins.     

Microwave dielectric studies on proteins,tissues, and heterogeneous suspensions

We summarize the results of several of our recent studies on the dielectric properties of protein solutions, tissues, and nonionic microemulsions at microwave frequencies extending to 18 GHz. The data in all cases are analyzed using the Maxwell mixture theory to determine the dielectric properties of the suspending water and the amount and dielectric properties of the water of hydration associated with the suspended phase. The dielectric data from the protein solutions and tissues are broadly consistent with the results of previous studies at UHF frequencies; they indicate hydration values in the range of 0.4–0.6 g water/g protein. There is evidence of a dielectric relaxation process occurring at low-GHz frequencies that can be attributed in part to dielectric relaxation of the “bound” water in the system. The remaining solvent water appears to have dielectric properties close to, if not precisely the same as, those of pure water. The average relaxation frequency of the suspending water in the microemulsions is reduced from that of pure water, evidently reflecting an average of that of the water of hydration (～5–6 GHz) and that of pure water. This reduced average relaxation frequency implies an increased average viscosity of the water and (by Walden's rule) accounts for the unexpectedly low ionic conductivity of the preparations.     

转SOD基因对烟草抗旱性和相关生理指标的影响

以近等基因系烟草(非转基因品系、转Fe-SOD基因品系和转Mn-SOD基因品系)为材料,研究了盆栽条件下转SOD基因对烟草抗旱性的影响。结果显示:外源Mn-SOD基因的导入能切实提高烟草抗旱能力,而导入的Fe-SOD基因虽能提高烟草体内的SOD活性水平,但不能提高烟草的抗旱性,说明Mn-SOD可能与烟草的抗旱性关系较大;当遭受干旱胁迫时,所导入的2种SOD基因可能在某种程度上影响了植物体内MDA、蛋白质、光合作用以及脯氨酸等的正常生理代谢;脯氨酸、MDA、蛋白质等生理指标的变化在抗旱与不抗旱品系之间并没有表现出明显的规律性,因此能否作为抗旱育种的重要指标应该通过更多的试验来确定。     

Lateral line-mediated rheotactic behavior in tadpoles of the African clawed frog (<Emphasis Type="Italic">Xenopus laevis</Emphasis>)

Tadpoles (Xenopus laevis) have a lateral line system whose anatomical structure has been described, but whose functional significance has not been closely examined. These experiments tested the hypothesis that the lateral line system is involved in rheotaxis. Tadpoles in developmental stages 47–56 oriented toward the source of a water current. Orientation was less precise after treatment with cobalt chloride or streptomycin, but was similar to that of untreated animals after exposure to gentamicin. In no current conditions, tadpoles exhibited a characteristic head-down posture by which they held themselves in the water column at an angle around 45°. This body posture became significantly less tilted in the presence of water current. Treatment with cobalt chloride or streptomycin increased the angle of tilt close to that seen in no current conditions, while gentamicin treatment tended to decrease tilt angle. The data are consistent with anatomical and physiological findings that tadpole neuromasts are similar to superficial, but not canal, neuromasts in fishes, and they suggest that the lateral line system is involved in both directional current detection and current-related postural adjustments in Xenopus.     

Dynamics of Protein and its Hydration Water: Neutron Scattering Studies on Fully Deuterated GFP

We present a detailed analysis of the picosecond-to-nanosecond motions of green fluorescent protein (GFP) and its hydration water using neutron scattering spectroscopy and hydrogen/deuterium contrast. The analysis reveals that hydration water suppresses protein motions at lower temperatures (<∼200 K), and facilitates protein dynamics at high temperatures. Experimental data demonstrate that the hydration water is harmonic at temperatures <∼180–190 K and is not affected by the proteins’ methyl group rotations. The dynamics of the hydration water exhibits changes at ∼180–190 K that we ascribe to the glass transition in the hydrated protein. Our results confirm significant differences in the dynamics of protein and its hydration water at high temperatures: on the picosecond-to-nanosecond timescale, the hydration water exhibits diffusive dynamics, while the protein motions are localized to <∼3 Å. The diffusion of the GFP hydration water is similar to the behavior of hydration water previously observed for other proteins. Comparison with other globular proteins (e.g., lysozyme) reveals that on the timescale of 1 ns and at equivalent hydration level, GFP dynamics (mean-square displacements and quasielastic intensity) are of much smaller amplitude. Moreover, the suppression of the protein dynamics by the hydration water at low temperatures appears to be stronger in GFP than in other globular proteins. We ascribe this observation to the barrellike structure of GFP.     

Deuterium NMR of water in immobilized protein systems.

Deuterium NMR spectra are reported for lysozyme crystals, powders, and frozen solutions. At high water contents the spectrum is a superposition of a narrow central component and a quadrupole doublet. The quadrupole splitting and the relaxation rates of both components, monitored as a function of water content and temperature, are discussed in terms of models for the water-protein interaction. The anisotropy of the water molecule motion is clearly demonstrated by the deuterium quadrupole splitting observed in the protein single crystal, but such splittings were not found in protein powders and frozen protein solutions. We therefore suggest that the most useful view of such data is to consider the water-protein interactions at the surface to be mixed rapidly and that a distribution of interactions be invoked rather than an oversimplified view often taken of a two or n-site mixing where n is small.     

Replica exchange simulation of reversible folding/unfolding of the Trp-cage miniprotein in explicit solvent: on the structure and possible role of internal water

We simulate the folding/unfolding equilibrium of the 20-residue miniprotein Trp-cage. We use replica exchange molecular dynamics simulations of the AMBER94 atomic detail model of the protein explicitly solvated by water, starting from a completely unfolded configuration. We employ a total of 40 replicas, covering the temperature range between 280 and 538 K. Individual simulation lengths of 100 ns sum up to a total simulation time of about 4 micros. Without any bias, we observe the folding of the protein into the native state with an unfolding-transition temperature of about 440 K. The native state is characterized by a distribution of root mean square distances (RMSD) from the NMR data that peaks at 1.8A, and is as low as 0.4A. We show that equilibration times of about 40 ns are required to yield convergence. A folded configuration in the entire extended ensemble is found to have a lifetime of about 31 ns. In a clamp-like motion, the Trp-cage opens up during thermal denaturation. In line with fluorescence quenching experiments, the Trp-residue sidechain gets hydrated when the protein opens up, roughly doubling the number of water molecules in the first solvation shell. We find the helical propensity of the helical domain of Trp-cage rather well preserved even at very high temperatures. In the folded state, we can identify states with one and two buried internal water molecules interconnecting parts of the Trp-cage molecule by hydrogen bonds. The loss of hydrogen bonds of these buried water molecules in the folded state with increasing temperature is likely to destabilize the folded state at elevated temperatures.     

Different effects of TPA on two skin-derived cell lines: murine (HEL-30) and human (NCTC) epidermal cells

12-O-tetradecanoylphorbol-13-acetate (TPA) caused a rapid activation of protein kinase C in a murine (HEL-30) and in a human (NCTC) epidermal cell line. In HEL-30 cells, protein kinase C activation is followed by ornithine decarboxylase stimulation and cell proliferation, events inhibited by H-7, a specific inhibitor of protein kinase C. TPA in NCTC cells inhibited the basal ornithine decarboxylase activity and cell growth, whereas H-7 did not modify TPA effect. The response of NCTC cells was not due to direct toxicity of TPA. These data confirm that in murine epidermal cells, the proliferation induced by TPA is mediated by protein kinase C, whereas in a human skin-derived cell line these events are not or inversely associated.     

Zero-field M?ssbauer studies of diferric human transferrin

Diferric transferrin samples labelled with 57Fe at the N- or the C-terminal binding sites are compared by M?ssbauer spectroscopy at 15 K and in zero magnetic field. The spectra of the samples are similar but the fitting of single Lorenzian lines to the data shows that some of the line positions differ in the two cases. According to this we can not exclude a difference between the chemical structures of the binding sites that can arise for example from the participation of different forms of the anion and/or water in the two lobes of transferrin. All other line parameters (line-width, intensity) are the same within the limits of errors.     

Continuum electrostatic analysis of preferred solvation sites around proteins in solution

To understand water-protein interactions in solution, the electrostatic field is calculated by solving the Poisson-Boltzmann equation, and the free energy surface of water is mapped by translating and rotating an explicit water molecule around the protein. The calculation is applied to T4 lysozyme with data available on the conservation of solvent binding sites in 18 crystallographically independent molecules. The free energy maps around the ordered water sites provide information on the relationship between water positions in crystal structure and in solution. Results show that almost all conserved sites and the majority of nonconserved sites are within 1.3 A of local free energy minima. This finding is in sharp contrast to the behavior of randomly placed water molecules in the boundary layer, which, on the average, must travel more than 3 A to the nearest free energy minimum. Thus, the solvation sites are at least partially determined by protein-water interactions rather than by crystal packing alone. The characteristic water residence times, obtained from the free energies at the local minima, are in good agreement with nuclear magnetic resonance experiments. Only about half of the potential sites show up as ordered water in the 1.7 A resolution X-ray structure. Crystal packing interactions can stabilize weak or mobile potential sites (in fact, some ordered water positions are not close to free energy minima) or can prevent water from occupying certain sites. Apart from a few buried water molecules that are strong binders, the free energies are not very different for conserved and nonconserved sites. We show that conservation of a water site between two crystals occurs if the positions of protein atoms, primarily contributing to the free energy at the local minimum, do not substantially change from one structure to the other. This requirement can be correlated with the nature of the side chain contacting the water molecule in the site.     

Interleukin 2 activates a receptor-associated protein kinase

The interleukin 2 (IL 2) receptor complex has been shown to consist of at least two IL 2 binding molecules, one of 55 to 57 kd (gp57Tac) and one of 75 to 78 kd apparent m.w. The data presented here indicate that a protein of m.w. 78,000 (pp78) co-immunoprecipitates with gp57Tac when a monoclonal antibody against gp57Tac is used. The 78 kd molecule is phosphorylated in vitro within the immune complex only in the presence of exogenously added IL 2, whereas the 57 kd molecule is phosphorylated equally in the presence or absence of IL 2. Phosphorylation in vitro of pp78 was demonstrated in extracts of human peripheral blood T cells (PBL-T) and the human T cell line Jurkat, but not in extracts of the human macrophage line U937 or the murine T cell line 2.8.2. Metabolic phosphorylation in intact cells reflects results observed in vitro; both pp78 and gp57Tac are phosphorylated in PBL-T and Jurkat, but not in U937. These data demonstrate that the IL 2 receptor complex contains an IL 2 responsive protein kinase activity and may signal the cell through a phosphorylation event.     

Reaction of alpha-actinin from renal inner medulla on prolonged dehydration

A western-blot analysis using monoclonal antibodies revealed that a reduction of alpha-actinin occurred in the renal inner medulla under the long-lasting dehydration. The ratio between protein content measured in rats of WAG line being hydrated or after 3-days water deprivation consisted of 52.7+/-6.2 against 23.9+/-3.3 as evaluated in relative units. The alpha-actinin level changes similarly in mutant rats of Brattleboro line not capable of synthesizing vasopressin. It was 57.5+/-4.6 in hydrated animals, and statistically lower in rats being under 3-day water deprivation--26.4+/-5.7 in relative units of protein.     

Orientational ordering and dynamics of the hydrate and exchangeable hydrogen atoms in crystalline crambin

Deuterium nuclear magnetic resonance studies of crambin crystals grown from deuterated solvent (2H2O/CH3CH2O2H or H2O/C2H3CH2OH) are reported. The extent to which the hydrate and exchangeable hydrogen atoms are dynamically disordered are then determined from the size of the residual deuterium quadrupole couplings, qcc. Rapid molecular reorientation (tau c-1 greater than 10(5) s-1) reduces the magnitude of the quadrupole coupling from its static value (216 kHz for solid water). We find that the room temperature spectrum of crambin is dominated by two features: a sharp line with very small residual quadrupolar coupling less than 3 kHz, and a broad pattern with a quadrupolar coupling in the range 185 to 195 kHz. The former is indicative of very nearly isotropically reorienting deuterons, whereas the latter is somewhat narrower than that observed for the amide deuterons of poly-gamma-benzyl-L-glutamate and thus indicative of deuterons that are almost but not completely stationary. By considering the nuclear magnetic resonance spectrum intensities along with the amino acid sequence, X-ray structure and the manner in which quadrupole couplings are reduced by dynamics, we conclude that the nuclear magnetic resonance signal from most of the water molecules of hydration are contained in the sharp line, i.e. reorient nearly isotropically in the crystalline protein. Unlike bulk water, which freezes abruptly in the manner of a phase transition, the water of hydration in crambin has a broad freezing range from 180 to 250K, as evidenced by the decreasing intensity of the sharp line that disappears at 180K. At temperatures between 150 and 200K, a typical hydrate molecule reorients at a rate comparable to the quadrupole coupling, 10(4) s-1 to 10(5) s-1, a process that occurs in hexagonal ice in the range of 240 to 270K. At 140K, the hydrate is stationary, tau c-1 less than 10(3) s-1. Studies of the protein crystallized from solvent deuterated only at the non-exchangeable methyl group of ethanol confirm that ethanol is in the lattice and show that this solvate behaves in much the same way as the hydrate. The refined X-ray structure has identified four ethanol solvate molecules. The deuterium spectrum at room temperature has a well-defined residual pattern with qcc = 2.2 kHz, i.e. a small-order parameter consistent with nearly isotropically reorienting molecules. The spectrum width broadens substantially only at temperatures below 200K and achieves the characteristic spectrum of a rotating methyl group with stationary C-C axis at 140K.(ABSTRACT TRUNCATED AT 400 WORDS)     

Structure of hen egg-white lysozyme solvated in TFE/water: a molecular dynamics simulation study based on NMR data

Various experimental studies of hen egg white lysozyme (HEWL) in water and TFE/water clearly indicate structural differences between the native state and TFE state of HEWL, e.g. the helical content of the protein in the TFE state is much higher than in the native state. However, the available detailed NMR studies were not sufficient to determine fully a structure of HEWL in the TFE state. Different molecular dynamics (MD) simulations, i.e. at room temperature, at increased temperature and using proton–proton distance restraints derived from NMR NOE data, have been used to generate configurational ensembles corresponding to the TFE state of HEWL. The configurational ensemble obtained at room temperature using atom-atom distance restraints measured for HEWL in TFE/water solution satisfies the experimental data and has the lowest protein energy. In this ensemble residues 50–58, which are part of the β-sheet in native HEWL, adopt fluctuating α-helical secondary structure.     

Genetic selection, sex and feeding treatment affect the whole-body chemical composition of sheep

Hypotheses on total body chemical composition were tested using data from 350 Suffolk sheep grown to a wide range of live weights, and fed in a non-limiting way, or with reduced amounts of feed, or ad libitum on feeds of reduced protein content. The sheep were from an experiment where selection used an index designed to increase the lean deposition rate while restricting the fat deposition rate. Ultrasound muscle and fat depths were the only composition measurements in the index. The animals were males and females from a selection (S) line and its unselected control (C). The protein content of the lipid-free dry matter was unaffected by live weight, sex or feeding treatment with only a very small effect of genetic line (0.762 kg/kg in S and 0.753 kg/kg in C; P < 0.05). The form of the relationship between water and protein was not affected by any of the factors; in the different kinds of sheep it was consistent with no effect other than through differences in mature protein weight. The water : protein ratio at maturity was estimated as 3.45. Over the whole dataset, lipid weight (L) increased with protein weight (P) according to L = 0.3135 × P1.850. Allowing for this scaling, fatness increased on low-protein feeds, was greater in females than in males and in C than in S (P < 0.001). Lipid content (g/kg fleece-free empty body weight) was reduced by restricted feeding only in males at the highest slaughter weight (114 kg). The lines differed in lipid content (P < 0.001) with means of 265.1 g/kg for C and 237.3 g/kg for S. Importantly, there was no interaction between line and feeding treatments. A higher proportion of total body protein was in the carcass in S than in C (0.627 v. 0.610; P < 0.001). For lipid, the difference was reversed (0.736 v. 0.744; P < 0.05). The total energy content increased quadratically with slaughter weight. At a particular weight, the energy content of gain was higher in females than in males and in C than in S. Genetic selection affected body composition at a weight favouring the distribution of protein to the carcass and lipid to the non-carcass. Once allowing for effects of genetic selection, sex and feeding treatment on fatness, simple rules can be used to generate the chemical composition of sheep.     

Nuclear magnetic resonance study of the conformation and dynamics of beta-casein at the oil/water interface in emulsions.

A (13)C and (31)P nuclear magnetic resonance (NMR) study has been carried out on beta-casein adsorbed at the interface of a tetradecane/water emulsion. (13)C NMR spectra show signals from the carbonyl, carboxyl, aromatic, and C alpha carbons in beta-casein, well resolved from solvent resonances. Only a small fraction of all carbon atoms in beta-casein contribute to detectable signals; intensity measurements show that the observable spectrum is derived from about 30 to 40 amino acid residues.(31)P NMR spectra show signals from the five phosphoserines on the hydrophilic N-terminal part of the protein. Analysis of T(1) relaxation times of these nuclei, using the model free approach for the spectral density function and the line shape of the alpha-carbon region, indicates that a large part of the protein is in a random coil conformation with restricted motion and a relatively long internal correlation time. The NMR results show that the conformation and dynamics of the N-terminal part of beta-casein are not strongly altered at the oil/water interface, as compared to beta-casein in micelle-like aggregates in aqueous solution.     

Responses to dipole stimuli of anterior lateral line nerve fibres in goldfish, <Emphasis Type="Italic">Carassius auratus</Emphasis>, under still and running water conditions

We investigated how fibres in the anterior lateral line nerve of goldfish, Carassius auratus, respond to sinusoidal water motions in a background of still or running water. Two types of fibres were distinguished: type I fibres, which most likely innervate superficial neuromasts, were stimulated by running water (10 cm s⁻¹) while type II fibres, which most likely innervate canal neuromasts, were not stimulated by running water. The responses of type I fibres to sinusoidal water motions were masked in running water whereas responses of type II fibres were not masked. These findings are in agreement with previous data obtained from the posterior lateral line nerve of goldfish. Furthermore, we demonstrate here that for type I fibres the degree of response masking increased with increasing flow velocity. Finally, the ratio between responses that were masked in running water (type I) and those that were not masked (type II) increases with increasing flow velocity. Flow fluctuations that were generated by a cylinder in front of the fish did not affect ongoing activity in the flow, nor the dipole-evoked responses. The findings are discussed with respect to particle image velocimetry data of the water motions generated in the experiments.