Showing papers on "Hydrogen bond published in 1990"
4,107 citations
TL;DR: A mechanism for GTP hydrolysis involving mainly Gln61 and Glu63 as activating species for in‐line attack of water as well as a mechanism for rate enhancement by GAP is proposed.
Abstract: The crystal structure of the H-ras oncogene protein p21 complexed to the slowly hydrolysing GTP analogue GppNp has been determined at 1.35 A resolution. 211 water molecules have been built into the electron density. The structure has been refined to a final R-factor of 19.8% for all data between 6 A and 1.35 A. The binding sites of the nucleotide and the magnesium ion are revealed in high detail. For the stretch of amino acid residues 61-65, the temperature factors of backbone atoms are four times the average value of 16.1 A2 due to the multiple conformations. In one of these conformations, the side chain of Gln61 makes contact with a water molecule, which is perfectly placed to be the nucleophile attacking the gamma-phosphate of GTP. Based on this observation, we propose a mechanism for GTP hydrolysis involving mainly Gln61 and Glu63 as activating species for in-line attack of water. Nucleophilic displacement is facilitated by hydrogen bonds from residues Thr35, Gly60 and Lys16. A mechanism for rate enhancement by GAP is also proposed.
1,042 citations
1,018 citations
TL;DR: This study demonstrates that, in horse cytochrome c, the side-chain of Phe82 is positioned in a co-planar fashion next to the heme in a conformation comparable to that found in other cytochromes c, and strongly implicates this internal water molecule as having a functional role in the mechanism of action of cy tochrome c.
992 citations
TL;DR: The crystal structure of thioredoxin from Escherichia coli has been refined by the stereochemically restrained least-squares procedure to a crystallographic R-factor of 0.165 at 1.68 A resolution.
571 citations
TL;DR: Gooday et al. as discussed by the authors showed that the (1→4)-β-linked homopolymer of N-acetyl-D-glucosamine can be stabilised as a rigid ribbon by a statistical mixture of CH2OH orientations, equivalent to half oxygens on each residue.
Abstract: Chitin is the (1→4)-β-linked homopolymer of N-acetyl-D-glucosamine (Fig. 1). The individual polymer chains can be thought of as helices, as each sugar unit is inverted with respect to its neighbors. This leads to their stabilization as rigid ribbons by 03—H … 05 and 06—H … 07 hydrogen bonds. The commonest form of chitin is α-chitin. Its unit cell is of two N,N‵-diacetylchitobiose units of two chains in an antiparallel arrangement. Thus, adjacent polymer chains run in opposite directions, held together by 06—H … 06 hydrogen bonds, and the chains are held in sheets by 07 … H—N hydrogen bonds (Minke and Blackwell, 1978). This gives a statistical mixture of CH2OH orientations, equivalent to half oxygens on each residue, each forming inter- and intramolecular hydrogen bonds. This results in two types of amide groups; all are involved in the interchain C=O … H—N bonds, while half of the groups also serve as acceptors for 06—H … O=C intramolecular bonds. This extensive intermolecular hydrogen bonding leads to a very stable structure, the individual polymer chains eventually giving rise to microfibrils if allowed to crystallize (Gooday, 1983). A less common form of chitin is β-chitin, in which the unit cell is of one N,N‵diacetylchitobiose unit, giving a polymer stabilized as a rigid ribbon, as for α-chitin, by 03—H … 05 intramolecular bonds (Gardner and Blackwell, 1975). Chains are then held together in sheets by C=O … H—N hydrogen bonding of the amide groups and by the CH2OH side chains, forming intersheet hydrogen bonds to the carbonyl oxygens on the next chains (06—H … 07). This gives a structure of parallel poly-N-acetylglucosamine chains with no intersheet hydrogen bonds.
543 citations
459 citations
TL;DR: The role of hydrogen bonding in catalysis has been discussed in this article, although mainly in terms of the salicylate ion as a leaving group, and it seems likely that this will herald other systems where the role of a strong hydrogen bond may serve as the key step in a catalytic process.
Abstract: Publisher Summary This chapter discusses the hydrogen bonding, which has been recognized as the single most important intermolecular interaction, The chapter presents the hypothesis that there are three kinds of hydrogen bond: weak, strong, and very strong. These are determined by the shape of the potential energy well and the respective positions of hydrogen and deuterium within the well, which can be used to provide information about the well that applies in a particular example. The role of hydrogen bonding in catalysis has been discussed, although mainly in terms of the salicylate ion as a leaving group. With its strong intramolecular hydrogen bond playing an essential part in the reaction mechanism, it seems likely that this will herald other systems where the role of a strong hydrogen bond may serve as the key step in a catalytic process.
454 citations
TL;DR: In this paper, effective pairpotential models, parametrized to the properties of pure liquids, have been used in molecular-dynamics simulations of aqueous (binary) mixtures containing methanol, ammonia, or acetone.
Abstract: Effective pair‐potential models, parametrized to the properties of the pure liquids, have been used in molecular‐dynamics simulations of aqueous (binary) mixtures containing methanol, ammonia, or acetone. Results are reported for thermodynamic and structural properties, self‐diffusion coefficients, and reorientational correlation times. There is fair agreement with a wide variety of experimental data. The pattern of hydrogen bonding and the distribution of hydrogen‐bond lifetimes in the simulated mixtures have been investigated. The observed anomalous behavior of methanol and acetone solutions appears to be related to specific features of the hydrogen bonding—namely, the ability of these molecules to exhibit enhanced acceptor character. As a consequence of the assumed intermolecular potentials, the balance between the competing effects of hydrophobic hydration of methyl groups and hydrogen bonding to oxygen atoms is tipped towards the latter. A number of interesting structural effects have been noted. In ...
385 citations
TL;DR: Comparison of the structure of yeast iso-1-cytochrome c with those of tuna and rice cytochromes c shows that these three molecules have very high structural similarity, with the atomic packing in the heme crevice region being particularly highly conserved.
366 citations
TL;DR: In this paper, the results of the mass action law analysis of part 1 are combined with the results from spectroscopic studies to analyze chemical interactions involved in the complexation of carboxylic acids with amine extractants in various diluents.
Abstract: The results of the mass action law analysis of part 1 are combined with the results from spectroscopic studies to analyze chemical interactions involved in the complexation of carboxylic acids with amine extractants in various diluents. Infrared spectroscopic studies were performed on anhydrous solutions of succinic, maleic, and fumaric acids to compare the effect of rigidity and configuration on complex stoichioletry. Dicarboxylic acids that form intramolecular hydrogen bonds are inhibited from forming (1,2) and (2,2) complexes. (The notation (p,q) denotes p, the number of acid molecules, and q, the number of amine molecules, in the complex.) The results from the mass action law analysis and spectroscopic studies of previous investigators indicate that formation of the (1,1) complex involves ion-pair or hydrogen-bond formation between the acid and the amine, while (2,1) complex formation involves hydrogen bonding between the carboxyl of the second acid and the carboxylate of the first
TL;DR: The H-exchange results suggest that the major helices of cytochrome c and their common hydrophobic domain are largely preserved in the globular acidic form while the loop region of the native structure is flexible and partly disordered.
Abstract: Hydrogen exchange and two-dimensional nuclear magnetic resonance (2D NMR) techniques were used to characterize the structure of oxidized horse cytochrome c at acid pH and high ionic strength. Under these conditions, cytochrome c is known to assume a globular conformation (A state) with properties resembling those of the molten globule state described for other proteins. In order to measure the rate of hydrogen-deuterium exchange for individual backbone amide protons in the A state, samples of oxidized cytochrome c were incubated at 20 {degree}C in D{sub 2}O buffer for time periods ranging from 2 min to 500 h. The exchange reaction was then quenched by transferring the protein to native conditions. The extent of exchange for 44 amide protons trapped in the refolded protein was measured by 2D NMR spectroscopy. The results show that this approach can provide detailed information on H-bonded secondary and tertiary structure in partially folded equilibrium forms of a protein. All of the slowly exchanging amide protons in the three major helices of native cytochrome c are strongly protected from exchange at acid pH, indicating that the A state contains native-like elements of helical secondary structure. By contrast, a number of amide protons involved in irregular tertiarymore » H-bonds of the native structure are only marginally protected in the A state, indicating that these H-bonds are unstable or absent. The H-exchange results suggest that the major helices of cytochrome c and their common hydrophobic domain are largely preserved in the globular acidic form while the loop region of the native structure is flexible and partly disordered.« less
TL;DR: Crystallographic analyses of the mutant lysozyme structures suggest that the stabilization is due to electrostatic interaction and does not require precise hydrogen bonding between the substituted amino acid and the end of the α-helix.
Abstract: Two different genetically engineered amino-acid substitutions designed to interact with α-helix dipoles in T4 lysozyme are shown to increase the thermal stability of the protein. Crystallographic analyses of the mutant lysozyme structures suggest that the stabilization is due to electrostatic interaction and does not require precise hydrogen bonding between the substituted amino acid and the end of the α-helix.
TL;DR: The crystal structure of flavocytochrome b2 has been solved at 3.0 A resolution by the method of multiple isomorphous replacement with anomalous scattering by using a combination of maps both averaged and not averaged about the molecular symmetry axis.
TL;DR: Comparison of this structure with a reduced peptide bond inhibitor-protease complex indicates that these contacts confer the exceptional binding strength of JG-365.
Abstract: The structure of a crystal complex of the chemically synthesized protease of human immunodeficiency virus 1 with a heptapeptide-derived inhibitor bound in the active site has been determined. The sequence of the inhibitor JG-365 is Ac-Ser-Leu-Asn-Phe-psi[CH(OH)CH2N]-Pro-Ile-Val-OMe; the Ki is 0.24 nM. The hydroxyethylamine moiety, in place of the normal scissile bond of the substrate, is believed to mimic a tetrahedral reaction intermediate. The structure of the complex has been refined to an R factor of 0.146 at 2.4-A resolution by using restrained least squares with rms deviations in bond lengths of 0.02 A and bond angles of 4. The bound inhibitor diastereomer has the S configuration at the hydroxyethylamine chiral carbon, and the hydroxyl group is positioned between the active site aspartate carboxyl groups within hydrogen bonding distance. Comparison of this structure with a reduced peptide bond inhibitor-protease complex indicates that these contacts confer the exceptional binding strength of JG-365.
TL;DR: The three-dimensional structure of horse heart metmyoglobin has been refined to a final R-factor of 15.5% and the backbone conformation is very similar to sperm whale met myoglobin, with significant differences in secondary structure occurring only near residues 119 and 120.
TL;DR: Preference hydrogen bond stereochemistry is described for the side-chains of glutamate and aspartate (carboxylate), glutamine and asparagine ( carboxamide), arginine (guanidinium), histidine (imidazole/IMidazolium), tryptophan (indole), tyrosine (phenolic hydroxyl), lysine (ammonium), serine and threonine (alkylhydroxyl)
TL;DR: In this article, high levels of ab initio molecular orbital theory were used to examine rearrangement processes in the water dimer corresponding to the interchange of various hydrogen atoms, and the most reliable calculations involve MP4/6•311+G(2df,2p) energy evaluations at MP2/6−311+g(d,p) optimized structures.
Abstract: High levels of ab initio molecular orbital theory were used to examine rearrangement processes in the water dimer corresponding to the interchange of various hydrogen atoms. Our most reliable calculations involve MP4/6‐311+G(2df,2p) energy evaluations at MP2/6‐311+G(d,p) optimized structures. The lowest energy rearrangement pathway corresponds to the interchange of hydrogen atoms of the acceptor molecule within the Cs water dimer structure (1). This proceeds via a transition structure of C1 symmetry (2) and requires an energy of 0.59 kcal mol−1. The interchange of donor and acceptor molecules can be achieved via a transition structure with Ci symmetry (4) and requires an energy of 0.87 kcal mol−1. Finally, the interchange of hydrogen atoms of the donor molecule, via a C2v transition structure (9), requires 1.88 kcal mol−1. The rearrangements via 2 and 4 lead to complete scrambling of hydrogen atoms within the individual H2O moieties at a cost of 0.87 kcal mol−1; the transition structure 9 is not necessary...
TL;DR: In this paper, the mean lifetime of hydrogen bonds was calculated and found to be 5-7 ps at 300 K, through the results depend on the averaging time used in the hydrogen bond definition.
Abstract: Molecular‐dynamics simulations of liquid methanol have been carried out at two temperatures (T=300 and 200 K) to investigate the dynamics of hydrogen bonding. The mean lifetime of hydrogen bonds (defined in terms of a time‐averaged pair energy) is calculated and found to be 5–7 ps at 300 K, through the results depend on the averaging time used in the hydrogen bond definition. At 200 K the lifetime becomes much longer, by one order of magnitude or more. A bonding state is defined for each molecule according to the number of hydrogen bonds, and the mean lifetime of the states and the rate constants of transition between states are calculated. Molecules with two hydrogen bonds have much longer lifetimes than expected from the assumption that forming and breaking of hydrogen bonds occur randomly. Bonding autocorrelation and state autocorrelation functions are calculated, which enable us to have another definition of lifetimes and to discuss the way in which local diffusion occurs near molecules.
TL;DR: In this paper, trans-PdR(OR')(HOR')L 2 (R'=CH(CF 3 )Ph,C 6 H 5, p-CH 3 C 6 H 4, p-Ch 3 OC 6H 4, P-BrC 6H4, p -FC 6H 5 ) respectivement.
Abstract: Le trans-PdR 2 L 2 (R=CH 3 ,C 2 H 5 ; L=PMe 3 ,PEt 3 ) et le trans-NiMe 2 (PMe 3 ) 2 ) reagissent avec 2 equivalents d'alcools fluores et de phenols para-substitues pour donner des complexes de formules: trans-PdR(OR')(HOR')L 2 (R'=CH(CF 3 )Ph,C 6 H 5 , p-CH 3 C 6 H 4 , p-CH 3 OC 6 H 4 , p-ClC 6 H 4 , p-BrC 6 H 4 , p-FC 6 H 4 ) et trans-NiMe(OR')(HOR')(PMe 3 ) 2 (R'=CH(CF 3 )Ph, C 6 H 5 ) respectivement. Diverses reactions de ces complexes sont examinees. Les complexes alcoolates (phenolates) catalysent la transesterification des alcools avec les esters. Des implications mecanistiques pour la transesterification sont presentees
TL;DR: Electron microscopy is employed to examine DNA aggregates produced by three tripositively charged condensing agents, finding that ligand charge seems to be the major factor in predicting condensing power, ligand structure influences the morphology and dimensions of the particles produced.
Abstract: Electron microscopy is employed to examine DNA aggregates produced by three tripositively charged condensing agents. Spermidine, hexammine cobalt (III), and me8spermidine (in which the amine groups of spermidine are exhaustively methylated) all produce condensates. The predominant form of condensate observed is toroidal; however, me8spermidine produces a large fraction of rodlike condensates. Distributions of toroidal radii and estimated volumes suggest that the size of condensates depends on the condensing agent employed, its concentration, and the time elapsed after addition of condensing agent. While ligand charge seems to be the major factor in predicting condensing power, ligand structure influences the morphology and dimensions of the particles produced. The ability to form hydrogen bonds is not required to promote condensation, since me8spermidine has no NHs. There may be a kinetic barrier to condensation at low me8spermidine concentrations. The relative proportions of toroids and rods may depend on the energetic compensation between bending and binding in cyclic structures, or on rate-limiting formation of sharply bent or kinked regions in rods.
TL;DR: The crystal structure of emerimicin-(1-9) benzyl ester reported here shows essentially pure alpha-helical character, whereas other similar compounds show predominantly 3(10)-helical structures.
Abstract: The presence of multiple alpha,alpha-dialkyl amino acids such as alpha-methylalanine (alpha-aminoisobutyric acid, Aib) leads to predominantly helical structures, either with alpha-helical or 3(10)-helical hydrogen bonding patterns. The crystal structure of emerimicin-(1-9) benzyl ester (Ac-Phe-Aib-Aib-Aib-Val-Gly-Leu-Aib-Aib-OBzl) reported here shows essentially pure alpha-helical character, whereas other similar compounds show predominantly 3(10)-helical structures. The factors that govern helical preference include the inherent relative stability of the alpha-helix compared with the 3(10)-helix, the extra hydrogen bond seen with 3(10)-helices, and the enhanced electrostatic dipolar interaction of the 3(10)-helix when packed in a crystalline lattice. The balance of these forces, when combined with the steric requirements of the amino acid side chains, determines the relative stability of the two helical conformations under a given set of experimental conditions.
TL;DR: The binding of four inhibitors—mercuric ion, 3‐acetoxymercuri‐4‐aminobenzenesulfonamide (AMS), acetazolamide (Diamox), and thiocyanate ion—to human carbonic anhydrase II (HCA II) has been studied with X‐ray crystallography.
Abstract: The binding of four inhibitors--mercuric ion, 3-acetoxymercuri-4-aminobenzenesulfonamide (AMS), acetazolamide (Diamox), and thiocyanate ion--to human carbonic anhydrase II (HCA II) has been studied with X-ray crystallography The binding of mercury to HCA II at pH 70 has been investigated at 31 A resolution Mercuric ions are observed at both nitrogens in the His-64 ring One of these sites is pointing toward the zinc ion The only other binding site for mercury is at Cys-206 The binding of the two sulfonamide inhibitors AMS and Diamox, has been reinvestigated at 20 and 30 A, respectively Only the nitrogen of the sulfonamide group binds to the zinc ion replacing the hydroxyl ion The sulfonamide oxygen closest to the zinc ion is 31 A away Thus the tetrahedral geometry of the zinc is retained, refuting earlier models of a pentacoordinated zinc The structure of the thiocyanate complex has been investigated at pH 85 and the structure has been refined at 19 A resolution using the least-squares refinement program PROLSQ The crystallographic R factor is 176% The zinc ion is pentacoordinated with the anion as well as a water molecule bound in addition to the three histidine residues The nitrogen atom of the SCN- ion is 19 A from the zinc ion but shifted 13 A with respect to the hydroxyl ion in the native structure and at van der Waals' distance from the O gamma l atom of Thr-199 This is due to the inability of the O gamma l atom of Thr-199 to serve as a hydrogen bond donor, thus repelling the nonprotonated nitrogen The SCN- molecule reaches into the deep end of the active site cavity where the sulfur atom has displaced the so-called "deep" water molecule of the native enzyme The zinc-bound water molecule is 22 A from the zinc ion and 24 A from the SCN- nitrogen In addition, this water is hydrogen bonded to the O gamma l atom of Thr-199 and to another water molecule We have observed that solvent and inhibitor molecules have three possible binding sites on the zinc ion and their significance for the catalysis and inhibition of HCA II will be discussed All available crystallographic data are consistent with a proposed catalytic mechanism in which both the OH moiety and one oxygen of the substrate HCO3- ion are ligated to the zinc ion
TL;DR: The results presented represent a substantial widening of the scope of molecular imprinting in that it may now be possible to prepare molecular imprints against a very large number of compounds.
TL;DR: Two crystal (A and B) of the 29,500 Da Class A β‐lactamase (penicillinase) from Bacillus licheniformis 749/C have been examined crystallographically and the structure suggests the binding of β‐ lactam substrates is facilitated by interactions with Lys‐234, Tyhr‐235, and Ala‐237 in a conserved β‐strand peptide.
Abstract: Two crystal forms (A and B) of the 29,500 Da Class A beta-lactamase (penicillinase) from Bacillus licheniformis 749/C have been examined crystallographically. The structure of B-form crystals has been solved to 2 A resolution, the starting model for which was a 3.5 A structure obtained from A-form crystals. The beta-lactamase has an alpha + beta structure with 11 helices and 5 beta-strands seen also in a penicillin target DD-peptidase of Streptomyces R61. Atomic parameters of the two molecules in the asymmetric unit were refined by simulated annealing at 2.0 A resolution. The R factor is 0.208 for the 27,330 data greater than 3 sigma (F), with water molecules excluded from the model. The catalytic Ser-70 is at the N-terminus of a helix and is within hydrogen bonding distance of conserved Lys-73. Also interacting with the Lys-73 are Asn-132 and the conserved Glu-166, which is on a potentially flexible helix-containing loop. The structure suggests the binding of beta-lactam substrates is facilitated by interactions with Lys-234, Thr-235, and Ala-237 in a conserved beta-strand peptide, which is antiparallel to the beta-lactam's acylamido linkage; an exposed cavity near Asn-170 exists for acylamido substituents. The reactive double bond of clavulanate-type inhibitors may interact with Arg-244 on the fourth beta-strand. A very similar binding site architecture is seen in the DD-peptidase.
TL;DR: In this paper, the authors derived rules describing hydrogen bond preferences of 2-aminopyrimidine from the crystal structure and stoicheiometries of cocrystals with mono- or di-carboxylic acids.
Abstract: Rules describing hydrogen bond preferences of 2-aminopyrimidine were derived from the crystal structure of 2-aminopyrimidine, stoicheiometries of cocrystals of 2-aminopyrimidine with mono- or di-carboxylic acids, and the crystal structure of the 1 : 1 2-aminopyrimidine/succinic acid cocrystal.
TL;DR: Refinement has allowed accurate assessment of the contact distances for four hydrogen bonds, a strong buried non-polar contact with the acetamido CH3 group and a large number of van der Waals' interactions with the three aromatic side-chains.
TL;DR: The crystal structures of a series of ureylenedicarboxylic acids have been determined as part of a project directed toward the design of molecular solids as mentioned in this paper.
Abstract: The crystal structures of a series of ureylenedicarboxylic acids have been determined as part of a project directed toward the design of molecular solids. The ureylenedicarboxylic acids were chosen for study because they were predicted to form a two-dimensional hydrogen-bonded network. This two-dimensional network is the result of two orthogonal linear arrays of self-complementary hydrogen-bonded functionalities, the dicarboxylic acids and N,N{prime}-disubstituted ureas, being present in the same molecule. The simplest molecules of the series, 2,2{prime}-ureylenediacetic acid (1), 3,3{prime}-ureylenedipropionic acid (2), and 4,4{prime}-ureylenedibutyric acid (3) as well as the simplest ureylene derived from a dipeptide, N,N{prime}-carbonylbisglycylglycine (4) were synthesized and studied by using x-ray crystallographic techniques. Each molecule was found to crystallize to give the predicted solid-state structure.
TL;DR: The crystal structure of the type III enzyme from Escherichia coli with chloramphenicol bound has been determined and refined at 1.75 A resolution, using a restrained parameter reciprocal space least squares procedure.