Showing papers on "Hydrogen bond published in 1989"

New approach to mesophase stabilization through hydrogen-bonding molecular interactions in binary mixtures

Abstract: The authors report a new approach to novel liquid crystalline moieties having a greatly enhanced mesomorphic range through the formation of intermolecular hydrogen bonds between two dissimilar mesogens. In liquid crystals, mesomorphicity results from a proper combination of the shape of a molecule and the magnitude and direction of molecular interactions between molecules. While the importance of dipole-dipole interactions in the formation of mesophases has long been established, we have hypothesized that the occurrence of intermolecular hydrogen bonding should have great potential for ordering thermotropic liquid crystals because H-bonding is much stronger than dipole-dipole interactions.

The nature of the hydrophobic binding of small peptides at the bilayer interface: implications for the insertion of transbilayer helices.

Abstract: One method of obtaining useful information about the physical chemistry of peptide/bilayer interactions is to relate thermodynamic parameters of the interactions to structural parameters obtained by diffraction methods. We report here the results of the application of this approach to interactions of hydrophobic tripeptides of the form Ala-X-Ala-0-tert-butyl with lipid bilayers. The thermodynamic constants (ΔG_t> ΔH_1, and Δ1) for the transfer of the tripeptides from water into DMPC vesicles were determined for X = Leu, Phe, and Trp and found to be consistent with those expected for hydrophobic interactions above the phase transition of DMPC. Combining these results with the earlier ones of Jacobs and White [(1986) Biochemistry 25, 2605-2612], the favorable free energies of transfer with different amino acids in the -X- position increase in the order Gly

Capping and α-helix stability

Abstract: The first and last four residues of alpha-helices differ from the rest by not being able to make the intrehelical hydrogen bonds between the backbone greater than C=O groups of one turn and the greater than NH groups of the next Physico-chemical arguments and statistical analysis suggest that there is a preference for certain residues at the C and N termini (The C- and N-caps) that can fulfil the hydrogen bonding requirements We have tested this hypothesis by constructing a series of mutations in the two N-caps of barnase (Bacillus amyloliquefaciens ribonuclease, positions Thr 6 and Thr 26) and determining the change in their stability The N-cap is found to stabilize the protein by up to approximately 25 kcal mol(-1) The presence of a negative charge of the N-cap adds some 16 kcal mol(-1) of stabilization energy because of the interaction with the macroscopic electrostatic dipole of the helix

New hydrogen-bond potentials for use in determining energetically favorable binding sites on molecules of known structure.

Abstract: An empirical energy function designed to calculate the interaction energy of a chemical probe group, such as a carbonyl oxygen or an amine nitrogen atom, with a target molecule has been developed. This function is used to determine the sites where ligands, such as drugs, may bind to a chosen target molecule which may be a protein, a nucleic acid, a polysaccharide, or a small organic molecule. The energy function is composed of a Lennard-Jones, an electrostatic and a hydrogen-bonding term. The latter is dependent on the length and orientation of the hydrogen bond and also on the chemical nature of the hydrogen-bonding atoms. These terms have been formulated by fitting to experimental observations of hydrogen bonds in crystal structures. In the calculations, thermal motion of the hydrogen-bonding hydrogen atoms and lone-pair electrons may be taken into account. For example, in a alcoholic hydroxyl group, the hydrogen may rotate around the C-O bond at the observed tetrahedral angle. In a histidine residue, a hydrogen atom may be bonded to either of the two imidazole nitrogens and movement of this hydrogen will cause a redistribution of charge which is dependent on the nature of the probe group and the surrounding environment. The shape of some of the energy functions is demonstrated on molecules of pharmacological interest.

The structure of the saccharide-binding site of concanavalin A.

Abstract: A complex of concanavalin A with methyl alpha-D-mannopyranoside has been crystallized in space group P212121 with a = 123.9 A, b = 129.1 A and c = 67.5 A. X-ray diffraction intensities to 2.9 A resolution have been collected on a Xentronics/Nicolet area detector. The structure has been solved by molecular replacement where the starting model was based on refined coordinates of an I222 crystal of saccharide-free concanavalin A. The structure of the saccharide complex was refined by restrained least-squares methods to an R-factor value of 0.19. In this crystal form, the asymmetric unit contains four protein subunits, to each of which a molecule of mannoside is bound in a shallow crevice near the surface of the protein. The methyl alpha-D-mannopyranoside molecule is bound in the C1 chair conformation 8.7 A from the calcium-binding site and 12.8 A from the transition metal-binding site. A network of seven hydrogen bonds connects oxygen atoms O-3, O-4, O-5 and O-6 of the mannoside to residues Asn14, Leu99, Tyr100, Asp208 and Arg228. O-2 and O-1 of the mannoside extend into the solvent. O-2 is hydrogen-bonded through a water molecule to an adjacent asymmetric unit. O-1 is not involved in any hydrogen bond and there is no fixed position for its methyl substituent.

Tryptophan Raman bands sensitive to hydrogen bonding and side-chain conformation

Abstract: Raman Spectra of seven tryptophan derivatives in the crystalline state were examined to find Raman bands whose frequencies reflect the strength of hydrogen bonding at the N1H site of the indole ring or the conformation of the indole ring relative to the amino acid backbone. Two indole ring vibrations, W4 around 1490 cm−1 and W6 around 1430 cm−1, showed a correlation between their Raman frequencies and the infrared frequency of the N-1-H stretching mode, an indicator of hydrogen bond strength. W4 and W6 increase in frequency with increase in hydrogen bond strength and the frequency variation is particularly large for W6. On the other hand, another indole ring vibration, W3, observed around 1550 cm−1, changes in frequency as a function of the torsional angle, χ2,1, of the C-2C-3C-βC-α linkage. As the absolute value of χ2,1 becomes larger and the C-α atom moves away from the C-2 atom, the W3 frequency increases. In the Raman spectra of proteins excited with visible radiation, the W3 band is usually strong and can be used as a conformational marker, whereas the W4 band is very weak and the W6 band is overlapped by strog scattering due to C–H bending vibrations of aliphatic side-chains. In UV resonance Raman spectra, however, all these Raman bands are enhanced and may provide key information on the hydrogen bonding and conformation of tryptophan side-chains.

Substrate specificity and affinity of a protein modulated by bound water molecules

Abstract: Water molecules influence molecular interactions in all biological systems, yet it is extremely difficult to understand their effects in precise atomic detail. Here we present evidence, based on highly refined atomic structures of the complexes of the L-arabinose-binding protein with L-arabinose, D-fucose and D-galactose, that bound water molecules, coupled with localized conformational changes, can govern substrate specificity and affinity. The atoms common to the three sugars are identically positioned in the binding site and the same nine strong hydrogen bonds are formed in all three complexes. Two hydrogen-bonded water molecules in the site contribute further to tight binding of L-arabinose but create an unfavourable interaction with the methyl group of D-fucose. Equally tight binding of D-galactose is attained by the replacement of one of the hydrogen-bonded water molecules by its--CH2OH group, coordinated with localized structural changes which include a shift and redirection of the hydrogen-bonding interactions of the other water molecule. These observations illustrate how ordered water molecules can contribute directly to the properties of proteins by influencing their interaction with ligands.

Water-inserted alpha-helical segments implicate reverse turns as folding intermediates.

Abstract: Information relevant to the folding and unfolding of alpha helices has been extracted from an analysis of protein structures. The alpha helices in protein crystal structures have been found to be hydrated, either externally by a water molecule hydrogen bonding to the backbone carbonyl oxygen atom, or internally by inserting into the helix hydrogen bond and forming a hydrogen-bonded bridge between the backbone carbonyl oxygen and the amide nitrogen atoms. The water-inserted alpha-helical segments display a variety of reverse-turn conformations, such as type III, type II, type I, and opened out, that can be considered as folding intermediates that are trapped in the folding-unfolding process of alpha helices. Since the alpha helix, most turns, and the extended beta strand occupy contiguous regions in the conformational space of phi, psi dihedral angles, a plausible pathway can be proposed for the folding-unfolding process of alpha helices in aqueous solution.

Slow- and fast-binding inhibitors of thermolysin display different modes of binding: crystallographic analysis of extended phosphonamidate transition-state analogues.

Abstract: The modes of binding to thermolysin of two phosphonamidate peptide inhibitors, carbobenzoxy-GlyP-L-Leu-L-Leu (ZGPLL) and carbobenzoxy-L-PheP-L-Leu-L-Ala (ZFPLA), have been determined by X-ray crystallography and refined at high resolution to crystallographic R-values of 17.7% and 17.0%, respectively. (GlyP is used to indicate that the trigonal carbon of the peptide linkage is replaced by the tetrahedral phosphorus of a phosphonamidate group.). These inhibitors were designed to be structural analogues of the presumed catalytic transition state and are potent inhibitors of thermolysin (ZGPLL, Ki = 9.1 nM; ZFPLA, Ki = 0.068 nM) [Bartlett, P. A., & Marlowe, C. K. (1987) Biochemistry (following paper in this issue)]. ZFPLA binds to thermolysin in the manner expected for the transition state and, for the first time, provides direct support for the presumed mode of binding of extended substrates in the S2 subsite. The mode of binding of ZFPLA displays all the interactions that are presumed to stabilize the transition state and supports the postulated mechanism of catalysis [Hangauer, D. G., Monzingo, A. F., & Matthews, B. W. (1984) Biochemistry 23, 5730-5741]. The two oxygens of the phosphonamidate moiety are liganded to the zinc to give overall pentacoordination of the metal. For the second inhibitor the situation is different. Although both ZFPLA and ZGPLL have similar modes of binding in the S1' and S2' subsites, the configurations of the carbobenzoxy-Phe and carbobenzoxy-Gly moieties are different. For ZFPLA the carbonyl group of the carbobenzoxy group is hydrogen bonded directly to the enzyme, whereas in ZGPLL the carbonyl group is rotated 117 degrees, and there is a water molecule interposed between the inhibitor and the enzyme. For ZGPLL only one of the phosphonamidate oxygens is liganded to the zinc. Correlated with the change in inhibitor-zinc ligation from monodentate in ZGPLL to bidentate in ZFPLA there is an increase in the phosphorus-nitrogen bond length of about 0.25 A, strongly suggesting that the phosphonamide nitrogen in ZFPLA is cationic, analogous to the doubly protonated nitrogen of the transition state. The observation that the nitrogen of ZFPLA appears to donate two hydrogen bonds to the protein also indicates that it is cationic. The different configurations adopted by the respective inhibitors are correlated with large differences in their kinetics of binding [Bartlett, P. A., & Marlowe, C. K. (1987) Biochemistry (following paper in this issue)]. These differences in kinetics are not associated with any significant conformational change on the part of the enzyme.(ABSTRACT TRUNCATED AT 250 WORDS)

Hydrogen-bond distances and angles in the structures of amino acids and peptides

Abstract: Determination des parametres de liaison hydrogene intermoleculaire (distance, angle de liaison) pour un certain nombre de peptides et d'aminoacides, les liaisons hydrogene existant entre chaines principales ou laterales

Ultrafast dynamics of hydrogen bonds directly observed by time‐resolved infrared spectroscopy

Abstract: Internal, hydrogen bonded OH groups of ethanol oligomers (solvent CCl4) are vibrationally excited by intense picosecond pulses at 3320 cm−1. The transient band shape observed in the OH stretching region (3000 to 3700 cm−1) is monitored by an independently tunable picosecond infrared pulse. The bands in this region are direct probes of hydrogen bridges. The time dependent growth and decay of these bands provides strong evidence for rapid bond breaking with a vibrational predissociation time of ≊5 ps, and for partial reassociation with a time constant of ≊20 ps.

Crystal structure of the carbon monoxide-substrate-cytochrome P-450CAM ternary complex

Abstract: The crystal structure of the ternary complex formed between carbon monoxide (CO), camphor, and ferrous cytochrome P-450CAM has been refined to an R value of 17.9% at 1.9-A resolution. To accommodate the CO molecule, the substrate, camphor, moves about 0.8 A while at the same time remaining in nonbonded contact with CO. The average temperature factor of the camphor atoms is about 50% higher in the CO complex, suggesting that the camphor is more loosely bound in this ternary complex. The Fe-C-O angle is about 166 degrees, and thus, CO appears to be bent from the heme normal, as it is in various CO-globin complexes, due to steric interactions with active site groups. The oxygen atom of the CO molecule is nestled into a groove formed by an unusual helical hydrogen bond in the distal helix between the highly conserved Thr 252 and Gly 248 residues. In the transition from the ferric camphor-bound binary complex to the ferrous CO-camphor-bound ternary complex, the heme iron atom moves into the plane defined by the pyrrole nitrogens by about 0.41 A. Although the axial Cys ligand also moves toward the heme, the S-Fe bond stretches from about 2.20 A in the absence of CO to about 2.41 A once CO has bound.

Hydrogen bond cooperativity in simulated water: Time dependence analysis of pair interactions

Abstract: Hydrogen bonding in water systems is investigated by introducing a new method to analyze the time dependence of pair‐interaction data obtained from a molecular dynamics simulation of 216 ST2 [F. H. Stillinger and A. Rahman, J. Chem. Phys. 60, 1545 (1974)] water molecules at 280 K. This approach avoids the use of cutoff values and yields a more realistic bond population, whose distributions of geometric and energetic properties are reported as a function of the bond lifetimes. For the fraction of long‐lived bonds, correlation among bond stability, molecular mobility, and local structure is elecited. Percolation analysis of HB network evidences cooperativity in the spatial distribution of bonds, which does not originate from proton polarizability of HB and/or from many‐body terms of the interaction potentials since a rigid water model and pair potentials are used. These features can play a role in the anomalous properties of liquid water.

Structure-properties relationships for densely cross-linked epoxide-amine systems based on epoxide or amine mixtures

Abstract: The solubility and diffusivity of water at 100° C, 95% relative humidity were studied for 14 stoichiometric epoxide-amine networks based on epoxide or amine mixtures Neither the packing density nor the glass transition temperature nor the crosslink density seemed to play a significant role The water absorption is essentially linked to the concentration of polar structures, but also decreases with the extent of intramolecular hydrogen bonding This can be accurately predicted using a simple additive relationship The diffusivity decreases with the hydrophilicity and packing density, but in a complex way probably involving the nature of hydrogen bonds between the water and the substrate

Further studies of the helix dipole model: Effects of a free α‐NH3+ or α‐COO− group on helix stability

Abstract: Interactions between the α-helix peptide dipoles and charged groups close to the ends of the helix were found to be an important determinant of α-helix stability in a previous study.1 The charge on the N-terminal residue of the C-peptide from ribonuclease A was varied chiefly by changing the α-NH2 blocking group, and the correlation of helix stability with N-terminal charge was demonstrated. An alternative explanation for some of those results is that the succinyl and acetyl blocking groups stabilize the helix by hydrogen bonding to an unsatisfied main-chain NH group. The helix dipole model is tested here with peptides that contain either a free α-NH α-COO− groups, and no other charged groups that would titrate with similar pKa's. This model predicts that α-NH3α-COO- groups are helix-destabilizingand that the destabilizing interactions are electrostatic in origin. The hydrogen bonding model predicts that α-NH3 and α-COO- groups are not themselves helix-destabilizing, but that an acetyl or amide blocking group at the N- or C- terminus, respectively, stabilizes the helix by hydrogen bonding to an unsatisfied main-chain NH or CO group. The results are as follows: (1) Removal of the charge from α-NH3 and α-COO- groups by pH titration stabilizes an α-helix. (2) The increase in helix stability on pH titration of these groups is close to the increase produced by adding an acetyl or amide blocking group. (3) The helix-stabilizing effect of removing the charge from α-NH3 and α-COO- groups by pH titration is screened by increasing the NaCl concentration, and therefore the effect is electrostatic in origin. (4) Replacing the C-terminal amide blocking group with a methylester blocking group, which cannot donate a hydrogen bond, causes little change in helix stability.

Refined crystal structure of cytoplasmic malate dehydrogenase at 2.5-A resolution.

Abstract: The molecular structure of cytoplasmic malate dehydrogenase from pig heart has been refined by alternating rounds of restrained least-squares methods and model readjustment on an interactive graphics system. The resulting structure contains 333 amino acids in each of the two subunits, 2 NAD molecules, 471 solvent molecules, and 2 large noncovalently bound molecules that are assumed to be sulfate ions. The crystallographic study was done on one entire dimer without symmetry restraints. Analysis of the relative position of the two subunits shows that the dimer does not obey exact 2-fold rotational symmetry; instead, the subunits are related by a 173 degrees rotation. The structure results in a R factor of 16.7% for diffraction data between 6.0 and 2.5 A, and the rms deviations from ideal bond lengths and angles are 0.017 A and 2.57 degrees, respectively. The bound coenzyme in addition to hydrophobic interactions makes numerous hydrogen bonds that either are directly between NAD and the enzyme or are with solvent molecules, some of which in turn are hydrogen bonded to the enzyme. The carboxamide group of NAD is hydrogen bonded to the side chain of Asn-130 and via a water molecule to the backbone nitrogens of Leu-157 and Asp-158 and to the carbonyl oxygen of Leu-154. Asn-130 is one of the corner residues in a beta-turn that contains the lone cis peptide bond in cytoplasmic malate dehydrogenase, situated between Asn-130 and Pro-131. The active site histidine, His-186, is hydrogen bonded from nitrogen ND1 to the carboxylate of Asp-158 and from its nitrogen NE2 to the sulfate ion bound in the putative substrate binding site. In addition to interacting with the active site histidine, this sulfate ion is also hydrogen bonded to the guanidinium group of Arg-161, to the carboxamide group of Asn-140, and to the hydroxyl group of Ser-241. It is speculated that the substrate, malate or oxaloacetate, is bound in the sulfate binding site with the substrate 1-carboxyl hydrogen bonded to the guanidinium group of Arg-161.

Hydrogen bonding and diffusion in crystalline silicon.

Abstract: The nature of hydrogen bonding and diffusion in crystalline Si was investigated using an ab initio self-consistent pseudopotential method. The relative energies of interstitial atomic hydrogen, diatomic hydrogen complexes, and shallow dopant-hydrogen complexes were examined. We present a mechanism for hydrogen diffusion which involves a new metastable diatomic complex with a much lower activation barrier for diffusion than molecular hydrogen. The effects on diffusion of diatomic-complex dissociation or its conversion to molecular hydrogen are discussed. The influence of temperature, hydrogen concentration, and dopant (n or p type) on hydrogen diffusion are examined. Metastable diatomic-complex formation is proposed to be highly likely at low temperatures and at high hydrogen concentrations, particularly in n-type Si. Diffusion through an ionized ${\mathrm{H}}^{+}$ form is most likely to occur in p-type Si.

Molecular imprinting by noncovalent interactions: enantioselectivity and binding capacity of polymers prepared under conditions favoring the formation of template complexes

Abstract: A molecular imprinting procedure based on electrostatic and hydrogen bonding interactions was developed, resulting in polymers of high selectivity for complexing of L-phenylalanine anilide. The polymerization conditions were chosen in such a way that the formation of solution complexes between methacrylic acid (MAA) and the template (L-phenylalanine anilide) prior to polymerization would be favored. Thus, by increasing the ratio of MAA to the crosslinker (ethylene dimethacrylate, EDMA), polymers of a higher enantioselectivity and binding capacity were obtained. In the chromatographic mode, a high chiral separation factor (a = 3,4) was observed even for polymers prepared in presence of nearly 50 mol-% MAA in the monomer mixture. However, the use of polymers prepared by initiating at a lower temperature (40 instead of 60°C) and polymers prepared using porogens of lower polarity (benzene instead of acetonitrile) only resulted in higher capacity factors (K'). The association constant for the binding of L-phenylalanine anilide to the sites of an imprinted polymer as well as the number of accessible sites of the latter were estimated from a binding study using a batch and a chromatographic procedure.

Effects of hydrogen bonding on the tyrosine Raman bands in the 1300-1150 cm-1 region

Abstract: Raman spectra of p-cresol, a model compound for tyrosine, were measured in solutions of various solvents, paying special attention to the effects of hydrogen bonding on the Raman bands in the 1300–1150 cm−1 region. The frequency of the ν7a (CO stretch) band was found to be sensitive to the state of hydrogen bonding at the phenolic hydroxyl group. It occurs at 1275–1265 cm−1 in proton-donating states, 1240–1230 cm−1 in proton-accepting states and around 1255 cm−1 in weakly or non-hydrogen-bonding states. This relationship between the ν7a′ frequency and hydrogen bonding was verified in the Raman spectra of L-tyrosine and its derivatives in the crystalline state. Analysis of the crystal Raman spectra further suggested that the ν7a (CC stretch) frequency also serves as a marker, though less sensitive, of hydrogen bonding and the ν9a (CH bend) frequency reflects the displacement of the OH hydrogen atom from the plane of benzene ring, which may be induced by hydrogen bonding. These Raman bands are strong with UV excitation and are expected to be useful in characterizing tyrosine side-chains in peptides and proteins by UV resonance Raman spectroscopy.