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PubMed1978

Specific configurations of hydrogen bonding. I. Hydrogen bonding and conformational preferences of N-acylamino-acids, peptides and derivatives.

From a reexamination of the X-ray studies of the crystal structures of 27 N-acylamino acids, peptides and their derivatives and 30 linear peptides, it is concluded that specific formation of short intermolecular hydrogen bonds (2,5 to 2.6 A) from the carboxyl OH to the N-acyl oxygen is an important feature for N-acylamino acids. For N-acyl-N-amides, the formation of hydrogen bonds 2.7 to 2.9A long between N(acyl-H...O(amide) is strongly preferred. The dihedral angle delta between the N-acyl and carboxyl groups or adjacent amide groups shows a preference for values near 20 degrees or 90 degrees for N-acylamino acids and 90 degrees for N-acyl-N-amides.

Amino Acids↗

PubMed1978

Hydrogen bonding of flavoprotein. I. Effect of hydrogen bonding on electronic spectra of flavoprotein.

The effect of hydrogen bonding on the transition energy and the oscillator strength of the isoalloxazine nucleus of flavins was studied by the molecular orbital method. Among the possible hydrogen bondings examined, characteristic spectral shifts were found for the hydrogen bondings at N(1) and N(5) of the nucleus. The hydrogen bonding at N(1) resulted in the shift of the first absorption band towards blue and that of the second one towards red. On the other hand, the hydrogen bonding at N(5) resulted in the shifts of both the first and the second band towards red. The spectral characteristics reported on Clostridium MP and Desulfovibrio vulgaris flavodoxin coincided with the calculated results. The application of the calculated results to D-amino acid oxidase (D-amino acid: oxygen oxidoreductase (deaminating), EC 1.4.3.3) led to the conclusion that hydrogen bonding occurs at O(12), N(3)H, O(14) and N(5) of the isoalloxazine nucleus. The occurrence of hydrogen bondings at O(12), N(3)H, and O(14) is favorable for N(5) of the isoalloxazine nucleus to accept electron from an electron donor.

Clostridium↗

PubMed1979

Coupling between oxidation state and hydrogen bond conformation in heme proteins.

In all heme proteins for which crystal structures are available, the N(epsilon) of a histidyl residue is bonded to the heme iron and N(delta) is hydrogen bonded to a carbonyl oxygen of the peptide backbone. We investigate here the possibility that a change in oxidation state of the iron or a change in the geometry of this hydrogen bond might change the hydrogen bond strength in a functionally significant way. Dimerization energies obtained from ab initio molecular orbital calculations on the hydrogen-bonded dimer of imidazole and planar formamide are used to represent the strength of this hydrogen bond in heme proteins. The effect of a change in iron oxidation state is modeled by varying the positive charge on imidazole. The effect of a change in hydrogen bond geometry is studied by employing x-ray coordinates for reduced and oxidized cytochrome c, deoxy- and metmyoglobin, and deoxy- and methemoglobin. Our conclusions are that the strength of this hydrogen bond in heme proteins is sensitive to both the oxidation state of the iron atom and to geometry changes on the order of those obtained from the x-ray coordinates. We speculate that the changes in oxidation state may be functionally coupled with changes in hydrogen bond geometry and that this hydrogen bond represents a feasible pathway to link protein conformation with redox potential or reactivity of the iron atom.

Animals↗

PubMed1979

Hydrogen bonds in crystal structures of amino acids, peptides and related molecules.

The results of a survey of 439 hydrogen bonds in 95 recently determined crystal structures of amino acids, peptides and related molecules suggest that the following generalizations hold true for linear (angle X-H---Y greater than 150 degrees) hydrogen bonds. (1) The charge on the acceptor group does not influence the length of a hydrogen bond. (2) For a given acceptor group, the hydrogen bond lengths increase in the order imidazolium N--H less than ammonium N-H less than guanidinium N-H; this order holds true for oxygen anion acceptor groups. Cl-ions and the uncharged oxygen of water molecules. (3) The uncharged imidazole N-H group forms shorter hydrogen than the amide N-H GROUP. (4) The carboxyl O-H groups form shorter hydrogen bonds than other hydroxyl groups. (5) The hydrogen bonds involving a halogen ion are longer than hydrogen bonds with other acceptors when corrected for their longer van der Walls radii. The observed differences between the lengths of hydrogen bonds formed by different donor and acceptor groups in amino acids and peptides, imply differences in the energetics of their formation.

Amino Acids↗

PubMed1979

Role of hydrogen bonding in red cell aggregation.

The role of hydrogen bonding in red cell aggregation induced by dextran was studied with the use of urea, an inhibitor for hydrogen bonding. In order to avoid hemolysis of red cells by the high concentration of urea, the studies were performed on human red cells hardened in glutaraldehyde. The degree of red cell aggregation at Hct = 45% was estimated by the use of a coaxial cylinder viscometer. The viscometric aggregation index (VAI) was calculated from viscosity values at shear rates of 52 sec-1 (eta H) and 0.05 sec-1 (eta L); VAI = (eta L - eta H)/eta H. Red cells with surface charge intact and with charge removal by neuraminidase treatment were studied. Urea at high concentrations, e.g., 6 M, significantly inhibited red cell aggregation induced by dextran. These findings indicate that hydrogen bonding plays an important role in dextran-induced red cell aggregation. An understanding of the nature of the forces involved in red cell aggregation serves to establish the physicochemical principles of cell-to-cell interactions induced by macromolecules.

Blood Viscosity↗

PubMed1977

Hydrogen-bonding parameter and its significance in quantitative structure--activity studies.

When the relative hydrogen-bonding effect of drugs on phases involved in the binding at the site of biological action differs from that in the 1-octanol-H2O partitioning phases used as the reference to estimate the hydrophobicity, a parameter (or parameters) which represents the "extra" hydrogen-bonding effect on the biological activity is required in the Hansch-type correlations. As a first approximation, the effect is analyzed in terms of the ratio of hydrogen-bonding association constants and the ratio of molarities of hydrogen-bonding species constituting the biological and organic phases. Sometimes, the association constants in both phases are so similar that they are not important in determining the extra hydrogen-bonding effect. The net result is that the effect is expressible by an indicator variable term the slope of which corresponds to the molarity ratio. The variable only applies to substituents having appreciable association capability in correlating a certain biological action exhibited by a series of congeners.

Acetylcholinesterase↗

PubMed1979

Stereochemical studies on cyclic peptides. Part X. Conformational analysis of hydrogen bonded cyclic pentapeptides.

Conformational aspects of 4 leads to 1 hydrogen bonded cyclic pentapeptides are considered in this paper from the point of view of "contact criteria" and potential energy calculations. Three types of such hydrogen bonded conformations, designated A1, A2 and B, are possible, involving some amount of strain on the bond angles. The energy of hydrogen bonded cyclopentaglycyl is somewhat less than that of the five-fold symmetrical conformation. The stereochemical feasibility of introducing L- and D-alanyl resudues in these structures has also been studied and the possible types for different sequences of alanyl residues have been determined. The results are discussed further in the light of the limited data available from crystal structure and nuclear magnetic resonance studies on cyclic pentapeptides.

Amino Acid Sequence↗

PubMed1976

A study of secondary and tertiary solution structure of yeast tRNA(Asp) by nuclear magnetic resonance. Assignment of G.U ring NH and hydrogen-bonded base pair proton resonances.

The 270-MHz spectra of yeast tRNA(Asp) in H2O solutions containing Mg2+ show clearly resolved resonances in the region from -15 to -9.5 ppm. Resonances between -15 and -11.5 ppm from the hydrogen-bonded protons of the acceptor stem and anticodon arm decrease in intensity with increasing temperature and disappear by 75 degrees C. Simultansously, four well-resolved resonances between -11.2 and -10.3 ppm also decrease in intensity and disappear. Because of this behavior and their positions these resonances have been assigned to the four ring NH protons of G.U base pairs 5 and 30 in the acceptor stem and anticodon arm which are thereby shown not to be hydrogen bonded by normal Watson-Crick hydrogen bonds. The five G.C base pair resonances of the T psi C arm remain visible above 70 degrees C after all other resonances have disappeared. The high-temperature tRNA spectrum agrees well with that of the isolated T psi C hairpin and CCA half-molecule fragments, each of which contains the same five hydrogen-bonded proton resonances. The root-mean-square error between the observed and calculated resonance positions for the hydrogen-bonded base pair protons of these three arms is 0.19 ppm. The dihydrouridine stem is expected to have two A.U Watson-Crick base pairs and no B.C base pairs. However, it does not contribute any hydrogen-bonded resonances to the nuclear magnetic resonance (NMR) spectrum below -11.5 ppm. This suggests that even at 35 degrees C this helix is not hydrogen bonded in a normal manner. In the region below -11.4 ppm there are three additional proton resonances melting earlier than the rest which cannot be assigned to a particular helix of the cloverleaf. We suggest that these resonances arise from hydrogen-bonded protons involved in stabilizing tertiary structure.

Binding Sites↗

PubMed1979

Model studies of interactions between nucleic acids and proteins: hydrogen bonding of amides with nucleic acid bases.

The formation of hydrogen bonded complexes between nucleic acid bases and acetamide has been studied by nuclear magnetic resonance in CDC13 at different temperatures. Pairs of hydrogen bonds are formed when acetamide binds to nucleic acid bases. Thermodynamic parameters have been computed and compared to those obtained for the association of carboxylic acids with nucleic acid bases. The role of hydrogen bonded complexes in the association of proteins with nucleic acids is discussed.

Acetamides↗

PubMed1979

Influence of hydrogen bonding in DNA and polynucleotides on reaction of nitrogens and oxygens toward ethylnitrosourea.

The reactivity of ethylnitrosourea toward hydrogen-bonded sites in double-stranded DNA or oly(rA).poly(rU) was compared with those sites in single-stranded DNA, RNA, or poly(rA). Alkylation of the N-1 of A in poly(rA).poly(rU) was almost suppressed at 5 degrees C but could be markedly increased by raining the reaction temperature to 25 degrees C, well below the Tm of 56 degrees C. In contrast, the N-7 and N-6 of A, which are not hydrogen bonded, reacted to the same extent at temperatures ranging from 5 to 65 degrees C. The extent of reaction at the N-3 of A varied inversely with the reactivity of the N-1 of A, indicating that of these two nitrogens the N-1 of A is the most reactive. The proportion of reaction at the various nitrogens in poly(rA) was not affected by temperature. Hydrogen-bonded oxygens in double-stranded DNA are the O-6 of G, the O-4 of T, and the O2 of C. All are equally reactive at 5, 25, and 51 degrees C. It is concluded that the observed temperature independence is due to these oxygens having an electron pair not involved in hydrogen bonding and, thus, available for reaction. In contrast, the electron pair of the N-1 of A (or the N-3 of C) is involved in hydrogen bonding, and the extent of their reactivity is dependent on thermal fluctuation providing transiently open base pairs at temperatures far below the Tm.

DNA↗

PubMedDate not supplied

[Number of hydrogen bonds in the structure of collagen].

The kinetics of hydrogen exchange of collagens from different animals was studied by the radioisotopic method (tritium) and infrared spectroscopy (deuterium). It has been shown that collagens from different animals (rat, pike, cod, carp, frogs) differ in amino acid composition and thermostability but are similar in the amount of slowly exchanged hydrogens. All the studied collagens have (1.00 +/- 0.05) very slowly exchanged hydrogens per triplet and (0.6 +/- 0.1) slowly exchanged hydrogens per triplet. Identifying the quantity of slowly exchanged hydrogens with the quantity of hydrogen bonds in the macromolecule, it can be concluded that collagens differing in stability do not differ by the quantity and composition of intramolecular hydrogen bonds.

Animals↗

PubMed1977

Accommodation of hydroxyl groups and their hydrogen bond system in a hydrocarbon matrix.

From data of a single crystal analysis of 12-D-hydroxyoctadecanoic acid methyl ester principles for the incorporation of hydroxyl groups into a hydrocarbon chain matrix can be deduced. In the crystalline compound infinite hydrogen bond systems are accommodated in an orthorhombic perpendicular chain arrangement. The orthorhombic perpendicular hydrocarbon subcell is expanded towards a hexagonal packing pattern, allowing more space and optimal geometry for the hydrogen bond system. The arrangement of the bond system in the orthorhombic perpendicular subcell requires that hydrogen bonded carbon chains carry alternatingly hydroxyl groups with opposite configuration. For the enantiomeric compound this requirement is met by a head to tail packing of molecules in a single layer arrangement. The corresponding racemates on the other hand pack head to head in double layers as confirmed by X-ray powder and IR studies. In monolayers both enantiomers and racemates behave identically. The hydrogen bonding of the hydroxyl groups apparently leads to the formation of lipid clusters, in which the geometric conditions for both a close packing of hydrocarbon chains and the formation of an extensive hydrogen bond system do not exist.

Chemical Phenomena↗

PubMed1977

1H NMR studies of transfer RNA III: the observed and the computed spectra of the hydrogen-bonded NH resonances of baker's yeast transfer-RNA Phe.

The hydrogen-bonded NH resonances of Baker's yeast tRNAphe in H2O solution with Mg++ have been measured by a 360 MHz spectrometer at 23 degrees C. Totally, fifteen peaks and one shoulder can be resolved which represent 25 +/- 1 protons. Based on the refined atomic coordinates of the tRNAphe in the orthorhombic crystal, on the recent advances in the distance dependence of the ring-current magnetic field effects and on the adopted values for the isolated hydrogen-bonded NH resonances, a computed spectrum consisting of 23 protons was constructed. A quantitative comparison by computer was made between the computed spectrum and the spectrum simulated from the observed spectrum. These two spectra are closely similar but not identical. We suggest that the conformation of yeast tRNAphe in aqueous solution is closely similar but not identical to that found in the crystal, especially in the T psi C region and D region. Also the NH resonances in 3-4 proposed hydrogen bonds (most likely for tertiary structure) may exchange very rapidly in aqueous solution.

Binding Sites↗

PubMedDate not supplied

1H-NMR investigations on the hydrogen bond formation between the tranquilizers diazepam and nitrazepam and some nucleobases.

The formation of hydrogen bonds between the minor tranquilizers diazepam and nitrazepam and a few nucleobases was studied in deuterochloroform solution by means of proton magnetic resonance spectroscopy. The thermodynamic and spectroscopic data of the associations were evaluated on the basis of a dimer model, using the concentration dependent shifts of the protons involved in hydrogen bonds. The interactions of nitrazepam (deltaH0=-10 to -21 kJ/mol; deltaG025 -0.2 to -7.4 kJ/mol) were found to be stronger than those of diazepam (deltaH0=-10 to -13 kJ/mol; deltaG025=6.0 to 6.4 kJ/mol). The various binding sites of the benzodiazepines for hydrogen bonds are discussed.

Adenine↗

PubMed1977

Intramolecular hydrogen bonding and molecular conformations of nucleosides. N (6)-dimethyl-2',3'-isopropylidene adenosine.

The physical properties of an adenosine derivative, N(6)-dimethyl-2',3'-O-isopropylidene adenosine, Derivative 1, which is capable of intramolecular hydrogen bond formation between base-ring and sugar exocyclic hydroxymethyl group, have been studied in solution by infrared, circular dichroic and nuclear magnetic resonance spectroscopy. Analysis of the 220 MHZ 1H NMR spectrum of Derivative 1 in C2HCl2 solution indicated an overwhelming preference for the gg conformation for rotation about the C(4')--C5') bond and a predominant conformation for rotation about the C(5')--O(5') bond in which OH(5') projects towards the base ring. The purine base ring was shown to be in a predominant syn conformation with respect to the sugar ring by 100 MHZ 1H nuclear Overhauser experiments, by analysis of 3J(13C,H1') magnitudes observed in proton-coupled 13C NMR experiments and by CD measurements. Combination of each conformation feature of Derivative 1 in non-polar solvents is consistent with the overall molecular conformation observed in the solid state in which intramolecular hydrogenbonding exists between purine N(3) and the sugar CH2OH group; the presence of a strong intramolecular hydrogen bond was observed by infrared spectroscopy. The sugar ring conformations of 2',3'-O-isopropylidene ribonucleosides were analysed in terms of the pseudorotational properties of the ring; the N and S conformations tend toward to C(2')-exo and C(3')-'exo conformations, respectively, compared to normal ribonucleosides (C(3')-endo and C(2')-endo, respectively). The presence of the hydrogen bond in the derivative is sufficient to promote the S-type conformations (approx. 80%--90%) compared to cases where such a strong hydrogen bond is unlikely to be present approx. 40--50%).

Adenosine↗

PubMed1976

Enthalpies of hydrogen bonding in psychotropic drugs.

The enthalpy of hydrogen bonding of some antipsychotic, antidepressant, anticonvulsant, and antianxiety agents with phenol, as determined from IR and NMR spectroscopic measurements, was shown not to be responsible for differences in activity within the drug classes. These results support a theoretical prediction advanced for anticonvulsant activity.

Antidepressive Agents↗

PubMed2025

Single-Molecule Nanopore Detection of Non-Canonical Thymine-Melamine Hydrogen Bonding Base Pair in DNA Abasic Site.

The binding of small molecules to DNA may represent a mutagenic process capable of inducing genomic structural alterations and functional impairment. Melamine (MA), a toxic small molecule, exhibits a hydrogen-bonding interface structurally analogous to adenine, enabling to form non-canonical thymine-melamine (T-MA) base pairs like Watson-Crick pairing. This property allows MA to program DNA nanostructure formation. Given MA's documented biological consequences, such as kidney disease, reproductive toxicity, and central nervous system dysfunction, sensitive detection of MA-DNA interactions has become critically important. However, such subtle structural changes remain challenging to identify because of the paucity of effective detection approaches in a high-resolution manner. To overcome this limitation, nanopore measurement is employed to identify T-MA hydrogen bonding base pairing in DNA. Results demonstrate that nanopore enables unambiguous identification of T-MA hydrogen bonding via mechanically unzipping thymine-melamine-thymine (T-MA-T) triplets in DNA structures. The approach achieves single-base-pair resolution, as evidenced by nucleotide substitutions flanking the abasic site in complex DNA structures. In addition, nanopore-based kinetic analysis reveals an enhanced intramolecular stability in MA-binding DNA compared to those consisting of complete canonical DNA pairs. This research establishes a powerful platform for high-resolution interrogation of DNA-small molecule interactions and quantitative biophysical characterization of mutagenic modifications at the nanoscale.

Single Molecule Imaging↗

PubMed1979

Biofunctional evaluation of a hydrogen bond linking the ring and tail beta-turns of oxytocin.

Deamino-[8-N-methylleucine]oxytocin and deamino-[8-alpha-hydroxyisocaproic acid]oxytocin were synthesized to study the importance of hydrogen bonding between the carboxamide carbonyl of asparagine and the peptide N-H of leucine in stabilizing the biologically active conformation of oxytocin. The analogs were synthesized by coupling deaminotocinoic acid with Pro-Leu(Me)-Gly-NH2 and Pro-HyIc-Gly-NH2, respectively. (HyIc is alpha-hydroxyisocaproic acid). Deamino-[8-N-methylleucine]oxytocin was found to possess 48 +/- 7 units of uterotonic activity, 33 +/- 5 units of avian vasodepressor activity, and 3.15 +/- 1.5 units of antidiuretic activity per mg; deamino-[8-alpha-hydroxyisocaproic acid]oxytocin possessed 134 +/- 12 units of uterotonic activity, 31 +/- 3 units of avian vasodepressor activity, 9.6 +/- 3.0 units of antidiuretic activity, and 0.26 +/- 0.02 unit of pressor activity per mg. Neither of the analogs possesses the peptide N-H at residue 8 required for the formation of a hydrogen bond with the asparagine carboxamide; however, both can assume the conformation needed to evoke the characteristic biological activities of oxytocin although in lower potency. It is concluded that such a hydrogen bond does not constitute a conformational constraint that is essential for hormone action.

Animals↗