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PubMed1997

Proton and electron transfer to the secondary quinone (QB) in bacterial reaction centers: the effect of changing the electrostatics in the vicinity of QB by interchanging asp and glu at the L212 and L213 sites.

The bacterial reaction center (RC) plays a central role in photosynthetic energy conversion by facilitating the light induced double reduction and protonation of a bound quinone molecule, QB. Two carboxylic acid residues, Asp-L213 and Glu-L212, located near QB, were previously shown to be important for proton transfer to QB. In this work, the ability of Glu to substitute for Asp at L213 and Asp to substitute for Glu at L212 was tested by site-directed mutagenesis. Both single mutants and a double mutant in which Asp and Glu were exchanged between the two sites were constructed. The electron transfer rate constants kBD (D+QAQB- --> DQAQB), and kAB(2) (DQA-QB- + H+ --> DQA(QBH)-), that are known to be sensitive to the energy of the QB- state, were found to be altered by Asp/Glu substitutions. Both rates were fastest ( approximately 10-fold) in RCs with Asp at both sites, slowest with Glu at both sites ( approximately 50-fold) and relatively unchanged by the caboxylic acid exchange. These changes could be explained if Asp was predominantly ionized and Glu was predominantly protonated at both sites (pH 7.5). The charge recombination kBD suggests an observed approximately 5 pKa unit difference of Glu over Asp. Modeling of kBD by strong electrostatic interactions ( approximately 3-4 pKa units) among negatively charged acids and QB- indicated a lower intrinsic pKa for Asp compared to Glu at either site of approximately 2-3 units. The mechanism of the kAB(2) reaction was determined to be the same in all mutant RCs as for native RCs. A quantitative explanation of the effect of the electrostatic environment on kAB(2) was obtained using the two-step model proposed for native RCs [Graige, M. S., Paddock, M. L., Bruce, J. M., Feher, G., & Okamura, M. Y. (1996) J. Am. Chem. Soc. 118, 9005-9016] which involves fast protonation of the semiquinone followed by rate-limiting electron transfer. Using simple models for the quinone/quinol conversion rate, it is shown that the optimal electrostatic potential for the QB site is close to that found in native RCs.

Aspartic Acid↗
PubMed1997

Comparison of the physiologically equivalent proteins cytochrome c6 and plastocyanin on the basis of their electrostatic potentials. Tryptophan 63 in cytochrome c6 may be isofunctional with tyrosine 83 in plastocyanin.

The blue copper protein plastocyanin and the heme protein cytochrome c6 differ in composition and in structure but perform the same function in the photosynthetic electron-transport chain. We compare these two proteins on the basis of their electrostatic potentials in order to understand the structural basis of their functional equivalence. In the first approach, we use a monopole-dipole approximation of the electrostatic potentials to superimpose the proteins. The resulting alignment suggests that Tyr51 in cytochrome c6 corresponds to Tyr83 in plastocyanin. But since Tyr51 is not conserved in all known cytochrome c6 sequences, a physiological role of this residue is questionable. In a more sophisticated approach, we applied the recently-developed Fame (flexible alignment of molecule ensembles) algorithm, in which molecules are superimposed by optimizing the similarity of their electrostatic potentials with respect to the relative orientation of the molecules. On the basis of the Fame alignments of plastocyanin and cytochrome c6, we analyze the docking and the electron-transfer reactions of these two proteins with its physiological reaction partner cytochrome f. We derive functional analogies for individual amino acids in possible electron-transfer paths in the interprotein redox reactions. We identify two surface patches in cytochrome c6 that may be involved in electron-transfer paths. The hydrophobic patch with the exposed heme edge in cytochrome c6 may be equivalent to the hydrophobic patch with His87 in plastocyanin, whereas Trp63 in cytochrome c6 may be equivalent to Tyr83 in plastocyanin. An aromatic amino acid is present at the position of Trp63 in all known cytochrome c6 sequences. The electronic coupling between the heme and the copper site on the one side and several potentially important amino acid residues on the other is analyzed by the Pathways method. We have proposed recently that Lys65 of cytochrome f and Tyr83 of plastocyanin form a cation-pi system, which may be involved in a two-step mechanism of the electron-transfer reaction between these two proteins from higher plants. Now we corroborate this proposal by analyzing available amino acid sequences.

Algorithms↗
PubMed1998

Electrostatics and the membrane association of Src: theory and experiment.

The binding of Src to phospholipid membranes requires both hydrophobic insertion of its myristate into the hydrocarbon interior of the membrane and nonspecific electrostatic interaction of its N-terminal cluster of basic residues with acidic phospholipids. We provide a theoretical description of the electrostatic partitioning of Src onto phospholipid membranes. Specifically, we use molecular models to represent a nonmyristoylated peptide corresponding to residues 2-19 of Src [nonmyr-Src(2-19); GSSKSKPKDPSQRRRSLE-NH2] and a phospholipid bilayer, calculate the electrostatic interaction by solving the nonlinear Poisson-Boltzmann equation, and predict the molar partition coefficient using statistical thermodynamics. The theoretical predictions agree with experimental data obtained by measuring the partitioning of nonmyr-Src(2-19) onto phospholipid vesicles: membrane binding increases as the mole percent of acidic lipid in the vesicles is increased, the ionic strength of the solution is decreased, or the net positive charge of the peptide is increased. The theoretical model also correctly predicts the measured partitioning of the myristoylated peptide, myr-Src(2-19); for example, adding 33% acidic lipid to electrically neutral vesicles increases the partitioning of myr-Src(2-19) 100-fold. Phosphorylating either serine 12 (by protein kinase C) or serine 17 (by cAMP-dependent protein kinase) decreases the partitioning of myr-Src(2-19) onto vesicles containing acidic lipid 10-fold. We investigated the effect of phosphorylation on the localization of Src to biological membranes by expressing fusion constructs of Src's N terminus with a soluble carrier protein in COS-1 cells; phosphorylation produces a small shift in the distribution of the Src chimeras from the plasma membrane to the cytosol.

Amino Acid Sequence↗
PubMed1999

Crystal structure of Paracoccus denitrificans electron transfer flavoprotein: structural and electrostatic analysis of a conserved flavin binding domain.

The crystal structure of electron transfer flavoprotein (ETF) from Paracoccus denitrificans was determined and refined to an R-factor of 19.3% at 2.6 A resolution. The overall fold is identical to that of the human enzyme, with the exception of a single loop region. Like the human structure, the structure of the P. denitrificans ETF is comprised of three distinct domains, two contributed by the alpha-subunit and the third from the beta-subunit. Close analysis of the structure reveals that the loop containing betaI63 is in part responsible for conferring the high specificity of AMP binding by the ETF protein. Using the sequence and structures of the human and P. denitrificans enzymes as models, a detailed sequence alignment has been constructed for several members of the ETF family, including sequences derived for the putative FixA and FixB proteins. From this alignment, it is evident that in all members of the ETF family the residues located in the immediate vicinity of the FAD cofactor are identical, with the exception of the substitution of serine and leucine residues in the W3A1 ETF protein for the human residues alphaT266 and betaY16, respectively. Mapping of ionic differences between the human and P. denitrificans ETF onto the structure identifies a surface that is electrostatically very similar between the two proteins, thus supporting a previous docking model between human ETF and pig medium-chain acyl-CoA dehydrogenase (MCAD). Analysis of the ionic strength dependence of the electron transfer reaction between either human or P. denitrificans ETF and MCAD demonstrates that the human ETF functions optimally at low ( approximately 10 mequiv) ionic strength, while P. denitrificans ETF is a better electron acceptor at higher (>75 mequiv) ionic strength. This suggests that the electrostatic surface potential of the two proteins is very different and is consistent with the difference in isoelectric points between the proteins. Analysis of the electrostatic potentials of the human and P. denitrificans ETFs reveals that the P. denitrificans ETF is more negatively charged. This excess negative charge may contribute to the difference in redox potentials between the two ETF flavoproteins and suggests an explanation for the opposing ionic strength dependencies for the reaction of MCAD with the two ETFs. Furthermore, by analysis of a model of the previously described human-P. denitrificans chimeric ETF protein, it is possible to identify one region of ETF that participates in docking with ETF-ubiquinone oxidoreductase, the physiological electron acceptor for ETF.

Adenosine Monophosphate↗
PubMed1999

Electrostatic channeling of oxaloacetate in a fusion protein of porcine citrate synthase and porcine mitochondrial malate dehydrogenase.

Mitochondrial malate dehydrogenase and citrate synthase are sequential enzymes in the Krebs tricarboxylic acid cycle. We have shown [Lindbladh, C., Rault, M., Hagglund, C., Small, W. C., Mosbach, K., Bülow, L., Evans, C., and Srere, P.A (1994) Biochemistry 33, 11692-11698] that a fusion protein of yeast mitochondrial citrate synthase and yeast mitochondrial malate dehydrogenase channels oxaloacetate between the active sites. A Brownian dynamics simulation model of porcine mitochondrial enzymes of citrate synthase and malate dehydrogenase was used [Elcock, A. H., and McCammon, A. M. (1996) Biochemistry 35, 12652-12658], showing that a positive electrostatic surface potential between the active sites of the fusion protein could account for the channeling of oxaloacetate we observed with the yeast fusion protein. Since the data were established with a yeast fusion protein and the model was with porcine fusion protein, we have now prepared and studied the porcine fusion protein. The channeling of the oxaloacetate intermediate was the same for the porcine fusion protein as it was for the yeast fusion protein. This channeling behavior is eliminated at high ionic strength. A fusion protein of porcine citrate synthase and porcine cytosolic malate dehydrogenase does not exhibit any channeling of oxaloacetate. A model of the fusion protein with the cytosolic malate dehydrogenase shows no clear positive electrostatic potential surface between the two active sites, thus distinguishing it from the fusion protein with the mitochondrial malate dehydrogenase. These results establish the electrostatic nature of channeling in mitochondrial fusion proteins.

Animals↗
PubMed1999

Protonated 2'-aminoguanosine as a probe of the electrostatic environment of the active site of the Tetrahymena group I ribozyme.

We have probed the electrostatic environment of the active site of the Tetrahymena group I ribozyme (E) using protonated 2'-aminoguanosine (), in which the 2'-OH of the guanosine nucleophile (G) is replaced by an group. At low concentrations of divalent metal ion (2 mM Mg(2+)), binds at least 200-fold stronger than G or G(NH)()2, with a dissociation constant of </=1 microM from the ribozyme. oligonucleotide substrate. complex (). This strong binding suggests that the group interacts with negatively charged phosphoryl groups within the active site. Increasing the concentration of divalent metal ion weakens the binding of to E. S more than 10(2)-fold. The Mn(2+) concentration dependence suggests that M(C), the metal ion that interacts with the 2'-moiety of G in the normal reaction, is responsible for this effect. M(C) and compete for binding to the active site; this competition could arise from electrostatic repulsion between the positively charged and M(C) and, possibly, from their competition for interaction with active site phosphoryl groups. The reactive phosphoryl group of S increases the competition between M(C) and, consistent with a network of interactions involving M(C) that help position the reactive phosphoryl group and the guanosine nucleophile with respect to one another. The chemical step with bound is at least 10(4)-fold slower than with G or G(NH)()2. These results provide additional support for an integral role of M(C) in catalysis by the Tetrahymena ribozyme, and demonstrate the utility of the moiety as an electrostatic probe within a structured RNA.

Amines↗
PubMed1999

Molecular dynamics simulations of human prion protein: importance of correct treatment of electrostatic interactions.

Molecular dynamics simulations have been used to investigate the dynamical and structural behavior of a homology model of human prion protein HuPrP(90-230) generated from the NMR structure of the Syrian hamster prion protein ShPrP(90-231) and of ShPrP(<90-231) itself. These PrPs have a large number of charged residues on the protein surface. At the simulation pH 7, HuPrP(90-230) has a net charge of -1 eu from 15 positively and 14 negatively charged residues. Simulations for both PrPs, using the AMBER94 force field in a periodic box model with explicit water molecules, showed high sensitivity to the correct treatment of the electrostatic interactions. Highly unstable behavior of the structured region of the PrPs (127-230) was found using the truncation method, and stable trajectories could be achieved only by including all the long-range electrostatic interactions using the particle mesh Ewald (PME) method. The instability using the truncation method could not be reduced by adding sodium and chloride ions nor by replacing some of the sodium ions with calcium ions. The PME simulations showed, in accordance with NMR experiments with ShPrP and mouse PrP, a flexibly disordered N-terminal part, PrP(90-126), and a structured C-terminal part, PrP(127-230), which includes three alpha-helices and a short antiparallel beta-strand. The simulations showed some tendency for the highly conserved hydrophobic segment PrP(112-131) to adopt an alpha-helical conformation and for helix C to split at residues 212-213, a known disease-associated mutation site (Q212P). Three highly occupied salt bridges could be identified (E146/D144<-->R208, R164<-->D178, and R156<-->E196) which appear to be important for the stability of PrP by linking the stable main structured core (helices B and C) with the more flexible structured part (helix A and strands A and B). Two of these salt bridges involve disease-associated mutations (R208H and D178N). Decreased PrP stability shown by protein unfolding experiments on mutants of these residues and guanidinium chloride or temperature-induced unfolding studies indicating reduced stability at low pH are consistent with stabilization by salt bridges. The fact that electrostatic interactions, in general, and salt bridges, in particular, appear to play an important role in PrP stability has implications for PrP structure and stability at different pHs it may encounter physiologically during normal or abnormal recycling from the pH neutral membrane surface into endosomes or lysomes (acidic pHs) or in NMR experiments (5.2 for ShPrP and 4.5 for mouse PrP).

Amino Acid Sequence↗
PubMed2002

Electrostatic sampler for semivolatile aerosols: chemical artifacts.

Electrostatic precipitators (ESPs) show promise as an alternative sampling method for semivolatile aerosols because they are less susceptible to adsorptive and evaporative artifacts than filter based methods. However, the corona discharge may after the chemical composition of a sampled aerosol. Chemical artifacts associated with electrostatic precipitation of semivolatile aerosols were investigated in the laboratory. ESPs and filters sampled both particles and vapors of alkanes, polycyclic aromatic hydrocarbons, and alkenes across varying concentrations. Gravimetric measurements between the two sampling methods were well correlated. Ozone generated by the ESP corona was the primary cause of alkene reactions in the gas phase. Particles collected within the corona region were vulnerable to irradiation by corona ions overtime. Particles collected outside the corona region did not react. Vapors passing through the corona reacted to a lesser extent. Vapors captured after passing through the ESP reacted with ozone that was not removed by the vapor trap. Chemical speciation of highly reactive compounds (i.e., alkenes or other compounds with relatively short half-lives outdoors) is not appropriate with ESPs. Electrostatic precipitation of these compounds is appropriate, however, when total organic carbon is of interest as the ESP does not alter the amount of mass measured gravimetrically. ESPs can make accurate measurements of more persistent semivolatile compounds, such as alkanes and PAHs.

Aerosols↗
PubMed2004

Influence of electrostatics on the oxidation rates of organic compounds in heterogeneous Fenton systems.

Electrostatic effects influence the oxidation rates of charged dissolved organic compounds in systems where the hydroxyl radical (*OH) is produced by the iron oxide-catalyzed decomposition of hydrogen peroxide (H2O2). Experiments were performed using goethite and the *OH probes 14C-labeled formic acid, 2-chlorophenol (2-CP), and nitrobenzene. At pH 4 and an ionic strength of 0.01 M, formic acid (pKa = 3.745) detected a steady-state concentration of *OH ([*OH]ss, calculated as a solution average) approximately 50 times higher than the two neutral probes did in the same systems, indicating significant enrichment of formate at the surface of the positively charged iron oxide where the *OH is being produced. Increasing the pH and ionic strength decreased formic acid oxidation rates by factors consistent with predicted decreases in electrostatic effects. In the presence of high 2-CP concentrations, the [*OH]ss measured by formic acid decreased with time, and goethite coagulation increased, due to loss of positive charge on the oxide surface as the oxidation products of 2-CP complexed surface Fe species. The [*OH]ss detected by 2-CP did not change significantly, indicating that neither goethite coagulation nor surface complexation of 2-CP oxidation products interfered with the rate of *OH generation; however, such an effect could have occurred in experiments using dissolved Fe instead of goethite. Model predictions of organic compound oxidation rates in mineral-catalyzed Fenton-like systems were improved by taking electrostatic effects into account.

Hydrogen Peroxide↗
PubMed2005

Why are carborane acids so acidic? An electrostatic interpretation of Brønsted acid strengths.

Acidity of Brønsted acids is explained in terms of the electrostatic potentials of the corresponding conjugate bases. The electrostatic potential distribution on the zero-flux surface of the strongest isolable carborane anions is seen to provide a good measure of their acidities. Increasing value of the lowest minimum in the electrostatic potential is observed to be a signature of increasing acidity.

Journal Article↗
PubMed2001

Electrostatics of cell membrane recognition: structure and activity of neutral and cationic rigid push-pull rods in isoelectric, anionic, and polarized lipid bilayer membranes.

Design, synthesis, and structural and functional studies of rigid-rod ionophores of different axial electrostatic asymmetry are reported. The employed design strategy emphasized presence of (a) a rigid scaffold to minimize the conformational complexity, (b) a unimolecular ion-conducting pathway to minimize the suprastructural complexity and monitor the function, (c) an extended fluorophore to monitor structure, (d) variable axial rod dipole, and (e) variable terminal charges to create axial asymmetry. Studies in isoelectric, anionic, and polarized bilayer membranes confirmed a general increase in activity of uncharged rigid push-pull rods in polarized bilayers. The similarly increased activity of cationic rigid push-pull rods with an electrostatic asymmetry comparable to that of alpha-helical bee toxin melittin (positive charge near negative axial dipole terminus) is shown by fluorescence-depth quenching experiments to originate from the stabilization of transmembrane rod orientation by the membrane potential. The reduced activity of rigid push-pull rods having an electrostatic asymmetry comparable to that in alpha-helical natural antibiotics (a positive charge near the positive axial dipole terminus) is shown by structural studies to originate from rod "ejection" by membrane potentials comparable to that found in mammalian plasma membranes. This structural evidence for cell membrane recognition by asymmetric rods is unprecedented and of possible practical importance with regard to antibiotic resistance.

Amino Acid Sequence↗
PubMed2002

Measurement of electrostatic interactions in protein folding with the use of protein charge ladders.

This paper describes a new method for the measurement of the role of interactions between charged groups on the energetics of protein folding. This method uses capillary electrophoresis (CE) and protein charge ladders (mixtures of protein derivatives that differ incrementally in number of charged groups) to measure, in a single set of electrophoresis experiments, the free energy of unfolding (DeltaG(D-N)) of alpha-lactalbumin (alpha-LA) as a function of net charge. These same data also yield the hydrodynamic radius, R(H), and net charge measured by CE, Z(CE), of the folded and denatured proteins. Alpha-LA unfolds to a compact denatured state under mildly alkaline conditions; a small increase in R(H) (11%, 2 A) coincides with a large increase in Z(CE) (71%, -4 charge units), relative to the folded state. The increase in Z(CE), in turn, predicts a large pH dependence of free energy of unfolding (-22 kJ/mol per unit increase in pH), due to differences in proton binding in the folded and denatured states. The free energy of unfolding correlates with the square of net charge of the members of the charge ladder. The differential dependence of DeltaG(D-N) on net charge for holo-alpha-LA, (partial differential) DeltaG(D-N)/(partial differential)Z = -0.14Z kJ/mol per unit of charge. This dependence of DeltaG(D-N) on net charge is a result of a net electrostatic repulsion among charge groups on the protein. These results, together with data from pH titrations, show that both the effects of electrostatic repulsion and differences in proton binding in the folded and denatured states can play an important role in the pH dependence of this protein; the relative magnitude of these effects varies with pH. The combination of charge ladders and CE is a rapid and efficient tool that measures the contributions of electrostatics to the energetics of protein folding, and the size and charge of proteins as they unfold. All this information is obtained from a single set of electrophoresis experiments.

Cytochrome c Group↗
PubMed2003

Are the enolates of amides and esters stabilized by electrostatics?

The fact that amides and esters form less stable enolates than ketones might be seen as evidence that electrostatic stabilization is unimportant in these anions. However, ab initio molecular orbital calculations show that electrostatic stabilization does in fact lie beneath the competing resonance effect that causes the decrease in acidity. The electrostatic contribution is revealed by examining torsionally twisted amide and ester structures in which the pi resonance interactions are largely inhibited. These twisted amides and esters have greater enolate acidity than the corresponding ketones. Qualitatively similar behavior is observed with respect to protonation, such that twisted amides and esters are generally less basic than the reference ketones, in striking contrast to their behavior in the normal geometries.

Journal Article↗
PubMed2004

Electrostatic study of the proton pumping mechanism in bovine heart cytochrome C oxidase.

Cytochrome c oxidase (CcO) is the terminal enzyme of the cell respiratory chain in mitochondria and aerobic bacteria. It catalyzes the reduction of oxygen to water and utilizes the free energy of the reduction reaction for proton pumping across the inner-mitochondrial membrane, a process that results in a membrane electrochemical proton gradient. Although the structure of the enzyme has been solved for several organisms, the molecular mechanism of proton pumping remains unknown. In the present paper, continuum electrostatic calculations were employed to evaluate the electrostatic potential, energies, and protonation state of bovine heart cytochrome c oxidase for different redox states of the enzyme along its catalytic cycle. Three different computational models of the enzyme were employed to test the stability of the results. The energetics and pH dependence of the P-->F, F-->O, and O-->E steps of the cycle have been investigated. On the basis of electrostatic calculations, two possible schemes of redox-linked proton pumping are discussed. The first scheme involves His291 as a pump element, whereas the second scheme involves a group linked to propionate D of heme a(3). In both schemes, loading of the pump site is coupled to ET between the two hemes of the enzyme, while transfer of a chemical proton is accompanied by ejection of the pumped H(+). The two models, as well as the energetics results are compared with recent experimental kinetic data. The proton pumping across the membrane is an endergonic process, which requires a sufficient amount of energy to be provided by the chemical reaction in the active site. In our calculations, the conversion of OH(-) to H(2)O provides 520 meV of energy to displace pump protons from a loading site and overall about 635 meV for each electron passing through the system. Assuming that the two charges are translocated per electron against the membrane potential of 200 meV, the model predicts an overall efficiency of 63%.

Animals↗
PubMed2006

Electrostatic-gated transport in chemically modified glass nanopore electrodes.

Electrostatic-gated transport in chemically modified glass nanopore electrodes with orifice radii as small as 15 nm is reported. A single conical-shaped nanopore in glass, with a approximately 1 microm radius Pt disk located at the pore base, is prepared by etching the exposed surface of a glass-sealed Pt nanodisk. The electrochemical response of the nanopore electrode corresponds to diffusion of redox-active species through the nanopore orifice to the Pt microdisk. Silanization of the exterior glass surface with Cl(Me)(2)Si(CH(2))(3)CN and the interior pore surface with EtO(Me)(2)Si(CH(2))(3)NH(2) introduces pH-dependent ion selectivity at the pore orifice, a consequence of the electrostatic interactions between the redox ions and protonated surface amines. Nanopore electrodes with very small pore orifice radii (< approximately 50 nm) display anion permselectively at pH < 4, as demonstrated by electrochemical measurement of transport through the pore orifice. Ion selective transport vanishes at pH > 6 or when the pore radius is significantly larger than the Debye screening length, consistent with the observed ion selectivity resulting from electrostatic interactions. The ability to introduce different surface functionalities to the interior and exterior surfaces of glass nanopores is demonstrated using fluorescence microscopy to monitor the localized covalent attachment of 5- (and 6)-carboxytetramethylrhodamine succinimidyl ester to interior pore surfaces previously silanized with EtO(Me)(2)Si(CH(2))(3)NH(2).

Biosensing Techniques↗
PubMed2006

Electrostatic, steric, and hydration interactions favor Na(+) condensation around DNA compared with K(+).

Condensation of monovalent counterions around DNA influences polymer properties of the DNA chain. For example, the Na(+) ions show markedly stronger propensity to induce multiple DNA chains to assemble into compact structures compared with the K(+) ions. To investigate the similarities and differences in the sodium and potassium ion condensation around DNA, we carried out a number of extensive all-atom molecular dynamics simulations of a DNA oligomer consisting of 16 base pairs, [d(CGAGGTTTAAACCTCG)](2), in explicit water. We found that the Na(+) ions penetrate the DNA interior and condense around the DNA exterior to a significantly larger degree compared with the K(+) ions. We have provided a microscopic explanation for the larger Na(+) affinity toward DNA that is based on a combination of steric, electrostatic, and hydration effects. Unexpectedly, we found that the Cl(-) co-ions provide more efficient electrostatic screening for the K(+) ions than for the Na(+) ions, contributing to the larger Na(+) condensation around DNA. To examine the importance of the discrete nature of water and ions, we also computed the counterion distributions from the mean-field electrostatic theory, demonstrating significant disagreements with the all-atom simulations. Prior experimental results on the relative extent of the Na(+) and K(+) condensation around DNA were somewhat contradictory. Recent DNA compaction experiments may be interpreted to suggest stronger Na(+) condensation around DNA compared to K(+), which is consistent with our simulations. We also provide a simple interpretation for the experimentally observed increase in DNA electrophoretic mobility in the alkali metal series, Li(+) < Na(+) < K(+) < Rb(+). We compare the DNA segment conformational preferences in various buffers with the proposed NMR models.

DNA↗
PubMed1992

A steric and electrostatic comparison of three models for the agonist/antagonist binding site on the adenosine A1 receptor.

Several models have been described in the literature to explain the similarity of interaction of adenosine receptor agonists and antagonists with the binding site of the receptor. Besides the superposition of the nitrogen atoms of adenosine and xanthine (the "standard" model), two other models have been described: one in which xanthine is rotated around its "horizontal" axis before superposition ("flipped") and one in which the adenosine N6-region and the xanthine C8-region are superimposed ("N6-C8"). In this study we compared the steric and electrostatic properties of these models. The flipped model tends to show higher percentages of overlap for the positive electrostatic potentials and the N6-C8 model yielded predominantly a slightly higher overlap for the negative electrostatic potentials, although these differences were rather small. Since the N6-region in adenosine and the C8-region in xanthine are coinciding in this model, the N6-C8 model yielded a much larger overlap in van der Waals volume than the other two models. The N6-C8 model seems therefore to be the more probable model, also because the interactive groups point in the same direction for both adenosine and xanthine analogues. We determined the geometries of both the adenosine N6-substituents and the xanthine 8-substituents in earlier studies. The N6-C8 model causes a coincidence of these separately determined conformations.

Adenosine↗
PubMed1988

Ab initio molecular electrostatic potentials of perillartine analogues: implications for sweet-taste receptor recognition.

A model for the recognition of the perillartine analogues has been determined from a consideration of the molecular electrostatic potentials calculated at the ab initio 3-21G level for a select set of biologically active analogues. The model stresses the importance of two regions of negative electrostatic potential. One region, near the oxime moiety, does not vary in shape or value with substitution in the hydrocarbon domain. A second region in the hydrocarbon domain varies in depth, extension, orientation, and shape, depending on the nature of the substituent. The depth, relative position, and orientation of this latter region in the most potent systems (the 1,4-cyclohexadiene analogue and its p-methyl derivative) serve as the basis for the optimum recognition pattern of these analogues. The rank order of taste potencies is in general agreement with predictions based on this model. In addition, some conclusions are drawn concerning the receptor-analogue interaction as well as the electrostatic features of the receptor.

Cyclohexenes↗