The molecular electrostatic potential and steric accessibility of A-DNA.

The molecular electrostatic potential and steric accessibility of A-DNA are computed for base sequences (dG.dC)n and (dA.dT)n. An interpretation of the results in terms of the structure of A-DNA is provided and differences with respect to other forms of DNA, namely B-DNA and Z-DNA, are discussed.     

The electrostatic potential and steric accessibility of reactive sites within Z-DNA.

A theoretical study of indices potentially useful for investigation of the reactivity of the recently discovered Z-DNA double helix is presented. The electrostatic potential minima and the steric accessibility of reactive sites are calculated. The effect of screening the phosphate groups by metal cations is investigated. The results are compared with those for the B-DNA double helix.     

Theoretical studies of enzymic reactions: Dielectric,electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme

A general method for detailed study of enzymic reactions is presented. The method considers the complete enzyme-substrate complex together with the surrounding solvent and evaluates all the different quantum mechanical and classical energy factors that can affect the reaction pathway. These factors include the quantum mechanical energies associated with bond cleavage and charge redistribution of the substrate and the classical energies of steric and electrostatic interactions between the substrate and the enzyme. The electrostatic polarization of the enzyme atoms and the orientation of the dipoles of the surrounding water molecules is simulated by a microscopic dielectric model. The solvation energy resulting from this polarization is considerable and must be included in any realistic calculation of chemical reactions involving anything more than an isolated molecule in vacuo. Without it, acidic groups can never become ionized and the charge distribution on the substrate will not be reasonable. The same dielectric model can also be used to study the reaction of the substrate in solution. In this way the reaction in solution can be compared with the enzymic reaction.In this paper we study the stability of the carbonium ion intermediate formed in the cleavage of a glycosidic bond by lysozyme. It is found that electrostatic stabilization is an important factor in increasing the rate of the reaction step that leads to the formation of the carbonium ion intermediate. Steric factors, such as the strain of the substrate on binding to lysozyme, do not seem to contribute significantly.     

Relationship between catalytic properties, fixed charge concentration and electrostatic potential of polyelectrolyte-bound enzymes

An equation for the calculation of the electrostatic potentials of polyelectrolyte-enzyme supports from electrostatic parameters has been derived by relating two different theories which describe the catalytic behaviour of polyelectrolyte-bound enzymes. The electrostatic potentials of polyionic supports have been determined by use of experimental results, on the one hand, from the fixed charge concentration and the ionic strength, on the other hand, from pH- and Km-shifts of immobilized enzymes. The accordance of potentials calculated from electrostatic and kinetic parameters confirms the macroscopic carrier-enzyme model.     

pH dependent conformational changes and electrostatic effects in plastocyanin

Reduction of plastocyanin (PC) caused a change in the electric field at the surface of the molecule which resulted in a 0.3 pH unit increase in the pK_a of a nitrated derivative of Tyr 83. This change in electrical potential could alter the affinity for cytochrome f which is known to bind at this site. Conversely, properties of the copper center, including the pH dependence of the reduction potential, are regulated by the charge on the surface of the molecule. Both the reduction potential and conformation (as measured by near-UV circular dichroic spectra) were pH dependent. Thus the conformation and electrostatic behavior of PC are dependent on oxidiation state, pH and surface charge, raising the possibility that its redox activity is controlled by the pH gradient.     

Metabolic flux analysis of lactic acid fermentation: effects of pH and lactate ion concentration

A detailed metabolic flux analysis for lactic acid production by Streptococcus lactis has been carried out. A metabolic reaction set was constructed for the metabolism of S. lactis. Fluxes through these reactions were estimated by using accumulation rates of biomass, product and consumption rates of the substrate, which were obtained through experiments. The changes in the flux movement are shown for different pHs and initial lactate concentrations of the medium. The analysis indicated that pH only affected the uptake rates of lactose, whereas lactate ion concentration influenced the movement of flux through the network.     

The internal equilibrium of the hairpin ribozyme: temperature, ion and pH effects

The hairpin ribozyme reversibly cleaves phosphodiesters of RNA substrates to generate products with 5' hydroxyl and 2',3'-cyclic phosphate termini. We previously found that the rate constant for ligation is tenfold faster than the rate constant for cleavage under standard conditions. The hammerhead ribozyme catalyzes the same reactions but is reported to favor cleavage relative to ligation by more than 100-fold under the same conditions. To explore the basis for this difference, we examined the influence of temperature, ions and pH on the hairpin ribozyme internal equilibrium. Under the same conditions, the loss of entropy associated with ligation is less for the hairpin than for the hammerhead ribozyme, consistent with the notion that a more rigid hairpin structure undergoes a smaller decrease in dynamics upon ligation than the more flexible hammerhead structure. Increased salt and reduced temperature shift the equilibrium toward ligation while pH has little effect, suggesting that conditions that stabilize RNA structure tend to promote ligation. The hairpin ribozyme appears to take up at least one tri- or divalent cation or two monovalent cations upon ligation. The efficiency with which different cations promote ligation depends strongly on valence and, less strongly, on ionic radius or electronegativity. This pattern of cation selectivity suggests that cations promote ligation through delocalized electrostatic shielding, perhaps interacting with a region of especially high charge density in the ligated ribozyme. Changes in ionic conditions produce large but compensating changes in enthalpy and entropy for cleavage and ligation. Thus, in addition to any increase in ribozyme dynamics associated with cleavage, re-organization of associated cations contributes significantly to hairpin ribozyme thermodynamics.     

Hydration effects on the electrostatic potential around tuftsin

The electrostatic potential and component dielectric constants from molecular dynamics (MD) trajectories of tuftsin, a tetrapeptide with the amino acid sequence Thr–Lys–Pro–Arg in water and in saline solution are presented. The results obtained from the analysis of the MD trajectories for the total electrostatic potential at points on a grid using the Ewald technique are compared with the solution to the Poisson–Boltzmann (PB) equation. The latter was solved using several sets of dielectric constant parameters. The effects of structural averaging on the PB results were also considered. Solute conformational mobility in simulations gives rise to an electrostatic potential map around the solute dominated by the solute monopole (or lowest order multipole). The detailed spatial variation of the electrostatic potential on the molecular surface brought about by the compounded effects of the distribution of water and ions close to the peptide, solvent mobility, and solute conformational mobility are not qualitatively reproducible from a reparametrization of the input solute and solvent dielectric constants to the PB equation for a single structure or for structurally averaged PB calculations. Nevertheless, by fitting the PB to the MD electrostatic potential surfaces with the dielectric constants as fitting parameters, we found that the values that give the best fit are the values calculated from the MD trajectories. Implications of using such field calculations on the design of tuftsin peptide analogues are discussed. © 1999 John Wiley & Sons, Inc. Biopoly 50: 133–143, 1999     

Drug-induced ion channel opening tuned by the voltage sensor charge profile

Polyunsaturated fatty acids modulate the voltage dependence of several voltage-gated ion channels, thereby being potent modifiers of cellular excitability. Detailed knowledge of this molecular mechanism can be used in designing a new class of small-molecule compounds against hyperexcitability diseases. Here, we show that arginines on one side of the helical K-channel voltage sensor S4 increased the sensitivity to docosahexaenoic acid (DHA), whereas arginines on the opposing side decreased this sensitivity. Glutamates had opposite effects. In addition, a positively charged DHA-like molecule, arachidonyl amine, had opposite effects to the negatively charged DHA. This suggests that S4 rotates to open the channel and that DHA electrostatically affects this rotation. A channel with arginines in positions 356, 359, and 362 was extremely sensitive to DHA: 70 µM DHA at pH 9.0 increased the current >500 times at negative voltages compared with wild type (WT). The small-molecule compound pimaric acid, a novel Shaker channel opener, opened the WT channel. The 356R/359R/362R channel drastically increased this effect, suggesting it to be instrumental in future drug screening.     

Branchial and renal ion fluxes and transepithelial electrical potential differences in rainbow trout,Oncorhynchus mykiss: effects of aluminium at low pH

Synopsis Adult rainbow trout, Oncorhynchus mykiss, were acutely exposed for 4 hours to low pH (4.4) and elevated Al-concentrations (300 µgI^–1) in soft water (Ca²⁺ + Mg²⁺ = 25 µmolI^–1). Comparison of branchial and renal ion fluxes (Na⁺, Cl^–, Mg²⁺, Ca²⁺ and NH₄ ⁺) gave evidence that pH and Al effects were primarily localized at the gill site. The negative whole body ion balance seemed to be caused by stimulatory effects on Na and Cl efflux especially under Al stress and to a lesser extent by inhibition of influx. Measurements of gill potentials indicated positive shifts, which were similar in response to increasing levels of H⁺ ions and Al. It is suggested that Al-induced changes of branchial potentials causes high diffusable loss of ions through interference with membrane-bound Ca²⁺ at the gill site.     

The intrinsic electrostatic potential and the intermediate ring of charge in the acetylcholine receptor channel

A ring of aligned glutamate residues named the intermediate ring of charge surrounds the intracellular end of the acetylcholine receptor channel and dominates cation conduction (Imoto et al. 1988). Four of the five subunits in mouse-muscle acetylcholine receptor contribute a glutamate to the ring. These glutamates were mutated to glutamine or lysine, and combinations of mutant and native subunits, yielding net ring charges of -1 to -4, were expressed in Xenopus laevis oocytes. In all complexes, the alpha subunit contained a Cys substituted for alphaThr244, three residues away from the ring glutamate alphaGlu241. The rate constants for the reactions of alphaThr244Cys with the neutral 2-hydroxyethyl-methanethiosulfonate, the positively charged 2-ammonioethyl-methanethiosulfonate, and the doubly positively charged 2-ammonioethyl-2'-ammonioethanethiosulfonate were determined from the rates of irreversible inhibition of the responses to acetylcholine. The reagents were added in the presence and absence of acetylcholine and at various transmembrane potentials, and the rate constants were extrapolated to zero transmembrane potential. The intrinsic electrostatic potential in the channel in the vicinity of the ring of charge was estimated from the ratios of the rate constants of differently charged reagents. In the acetylcholine-induced open state, this potential was -230 mV with four glutamates in the ring and increased linearly towards 0 mV by +57 mV for each negative charge removed from the ring. Thus, the intrinsic electrostatic potential in the narrow, intracellular end of the open channel is almost entirely due to the intermediate ring of charge and is strongly correlated with alkali-metal-ion conductance through the channel. The intrinsic electrostatic potential in the closed state of the channel was more positive than in the open state at all values of the ring charge. These electrostatic properties were simulated by theoretical calculations based on a simplified model of the channel.     

An unusual functional group interaction and its potential to reproduce steric and electrostatic features of the transition states of peptidolysis

The donor-acceptor interaction between a tertiary amine and an aldehyde, first observed among a select class of alkaloids, was deliberately established in a peptidomimetic (1a-c) to mimic features of the two principal transition states of peptide hydrolysis. Compounds 1a-c show preferential adoption in methanol and water of a 'folded' conformation displaying the interaction. Proportions of the folded form in MeOH range from 45% to 70% and can reach 84% in buffer. Significantly, three tendencies for the folded/unfolded equilibrium are observed: increasing solubility and polarity of the medium and decreasing temperature results in a higher extent of folding. In the absence of any parameter set available for this weak bond, no modeling studies were conducted to aid in the design of 1a-c. The successful straightforward synthesis of 1 and its folding and inhibition results with HIV-1 peptidase using FRET technology encourage studies to further pre-organize candidate molecules and to screen the structure space by modeling and parallel combinatorial chemistry.     

The molecular electrostatic potential and steric accessibility of poly (dA-dT). poly (dA-dT) in various conformations: B-DNA, D-DNA and 'alternating-B' DNA.

The influence of conformational changes on the molecular electrostatic potential and the steric accessibility of the double stranded polynucleotide poly (dA-dT). poly (dA-dT) are investigated by calculating these properties for three different conformations : B-DNA, D-DNA and alternating-B DNA.     

The influence of a surface charge on the electronic and steric structure of a high potential iron-sulfur protein

The recombinant high-potential iron-sulfur protein (HiPIP) iso-I from Ectothiorhodospira halophila has been mutated at position 68. The αC of Val 68 is within a 0.6-nm sphere from the closest iron ion of the cluster. The valine residue has been replaced by a negatively charged glutamate residue (V68E) and by a positively charged lysine residue (V68K). With respect to the recombinant wild-type protein the reduction potentials of the V68E and V68K variants are –21±2 and +29±2?mV respectively (200?mM NaCl, pH?7, 25??°C). The solution structure of the V68E mutant was solved up to a pairwise RMSD of 66?pm for backbone atoms and 138?pm for all heavy atoms. The structure of the variant is very similar to that of recombinant wild type, indicating that the observed changes in reduction potentials are largely due to the effect of the introduced charges. It is proposed that the valence distribution within the oxidized iron-sulfur cluster is affected only slightly by the change in charge at position 68, but consistently with a simple electrostatic model.     

Carnosine binding: characterization of steric and charge requirements for ligand recognition.

The steric and charge requirements for binding of l-carnosine (β-alanyl-l-histidine) by bovine serum albumin were investigated with proton magnetic resonance (¹HMR) spectrometry. The histidinyl side chain of the dipeptide is responsible for primary recognition by the binding site. Furthermore, recognition is specific to a particular orientation of the histidinyl side chain that is determined by the other amino acid residue of the dipeptide. It was found that, although salts do not have a great effect on the binding of carnosine to bovine serum albumin, this binding cannot be measured by equilibrium dialysis in the presence of salt because of formation of a complex Donnan equilibrium. Carnosine, which has been postulated to have a role in olfaction, binds to the crude particulate fraction of nasal olfactory epithelium in the same steric orientation as it does to bovine serum albumin. Therefore, we have used the binding of carnosine to bovine serum albumin as a model system to test potential competitive inhibitors of carnosine binding that ultimately could be tested for activity in the olfactory pathway. It was found that the binding of carnosine to bovine serum albumin is a good model of nonspecific binding of carnosine to tissue preparations but not of the specific binding of carnosine to the nasal olfactory epithelium. In addition to requiring the proper conformation of the histidinyl residue, the binding to olfactory epithelium also appears to require recognition of the β-alanyl residue and of substituents on the imidazole ring. Evidence is provided that the carnosine binding by the nasal olfactory epithelium demonstrated by ¹HMR spectroscopy does not occur with the mature olfactory receptor neurons.     

Spectropotentiometric analysis of metal binding to structural zinc-binding sites: accounting quantitatively for pH and metal ion buffering effects

Studies of the metal-binding affinity of protein sites are ubiquitous in bioinorganic chemistry and are valuable for the information that they can provide about metal speciation and exchange in biological systems. The potential for error in these studies is high, however, since many competing equilibria are present in solution and must be taken into consideration. Here, we report a new spectropotentiometric titration apparatus that allows pH and UV-vis absorption to be monitored simultaneously on small samples under inert atmosphere. In addition, we explain how data obtained from the complex equilibria can be combined with tabulated information about the protonation and metal-binding constants for common buffers to provide detailed, quantitative information about metal-protein interactions. Application of this approach to the investigation of metal binding to structural zinc-binding domains and common pitfalls encountered when performing these experiments are also discussed. We have used this approach to reevaluate the metal-binding constants of the N-terminal zinc-binding peptide from the HIV-1 nucleocapsid protein (10(-8)M相似文献