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Hoffmann, R. A wiki for the life sciences where authorship matters. Nature Genetics (2008)
MeSH Review

Hydrogen Bonding

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Disease relevance of Hydrogen Bonding

  • This interaction is isosteric with the adenosine N1-2'-OH interaction in the related mRNA from beet western yellows virus (BWYV); however, the ScYLV and BWYV mRNA structures differ in their detailed L2-S1 hydrogen bonding and L2 stacking interactions [1].
  • Because the g-value anisotropy is an important indicator of the hydrogen bonding status of the tyrosyl radical, this result suggests that the mouse R2 radical has its tyrosylate oxygen hydrogen bonded with a D2O exchangeable proton, whereas this hydrogen bond is absent in the E. coli enzyme [2].
  • One has the glycosidic torsions of the third strand bases in the anti-conformation and Hoogsteen hydrogen-bonds to the purine strand of the duplex, the other has the third strand purines in the syn orientation and uses a reverse-Hoogsteen hydrogen-bonding pattern [3].
  • The structure, which occurred during dehydration, could be a transient in the alpha-helical to beta-sheet conversion, suggesting that formation of hydrogen bonding precedes the inter-sheet interaction and assembly into the amyloid of scrapie prion [4].
  • As it turned out, both oxygens in the bis-Thf ligands are involved in hydrogen-bonding interactions with Asp 29 and Asp 30 NH present in the S2 subsite of HIV-1 protease [5].

High impact information on Hydrogen Bonding

  • The formyl group is held by a novel hydrogen bonding network, involving His9 on the bottom of the groove, and the side chain of the P1 methionine is lodged in the B pocket [6].
  • Selectivity is achieved through a combination of hydrogen bonding to the sugar hydroxyl groups with van der Waals packing, often including packing of a hydrophobic sugar face against aromatic amino acid side chains [7].
  • The hydrogen bonding network formed among CBFalpha(Runt domain) and CBFbeta, and CBFalpha(Runt domain) and DNA revealed the allosteric regulation mechanism of CBFalpha(Runt domain)-DNA binding by CBFbeta [8].
  • Acetyl CoA recognition is mediated by a betaalpha structure derived from GNAT motif A, which presents an invariant Arg/Gln-X-X-Gly-X-Gly/Ala segment for hydrogen bonding with the cofactor [9].
  • Our data indicate that most of the water molecules exist as small hydrogen-bonded strings and clusters in a 'fluid' of close-packed methyl groups, with water clusters bridging neighbouring methanol hydroxyl groups through hydrogen bonding [10].

Chemical compound and disease context of Hydrogen Bonding

  • The complete hydrogen bonding patterns were determined by using deoxy and other synthetic derivatives of the receptor disaccharide, and the constructed models of the interactions were compared with that of Escherichia coli PapG396 adhesin [11].
  • While d(T4G4)2 is not a suitable substrate for quadruplex promotion by the beta subunit, the Raman spectra reveal other structural rearrangements of this DNA strand upon beta subunit binding, including changes in guanine glycosyl torsion angles from syn to anti and disruption of carbonyl hydrogen-bonding interactions [12].
  • N-3 of the imidazole ring participates in a novel hydrogen-bonding interaction with the bound water molecule, demonstrating the effectiveness of the imidazole ring as an isosteric replacement for the P1'--P2' amide bond in hydroxyethylene-based HIV-1 protease inhibitors [13].
  • The spectral properties of the indole quinones in H2O approach the corresponding values in Thiobacillus versutus MADH (C==O stretch at 1612 cm-1, lamdamax at 440mm) and are indicative of strongly hydrogen bonding of the C==O and NH groups of the cofactor in the native enzyme [14].
  • Ca2+ caused partial dehydration of the sulfate group and reduced hydrogen bonding of the sugar hydroxyls of both species [15].

Biological context of Hydrogen Bonding

  • Overall, these structures are very similar to each other, although the adenine and AMP complexes show different patterns of hydrogen-bonding to the base, and the active site pocket opens slightly to accommodate the larger AMP ligand [16].
  • The base specificity that makes netropsin bind preferentially to runs of four or more A X T base pairs is provided not by hydrogen bonding but by close van der Waals contacts between adenine C-2 hydrogens and CH groups on the pyrrole rings of the drug molecule [17].
  • These results provide evidence that alteration in substrate specificity of factitious thermophilic xylose isomerases can be achieved by designing reduced steric constraints and enhanced hydrogen-bonding capacity for glucose in the substrate-binding pocket of the active site [18].
  • In combination with mutagenesis results, a hydrogen-bonding network from the water molecule adjacent to the iron ligand to the protein surface of the distal pocket through the hydroxyl group of Ser 286 and the carboxyl group of Asp 393 can be assigned to a pathway for proton delivery during the NO reduction reaction [19].
  • Malonate semialdehyde is analogous to a beta-keto acid, and enzymes that catalyze the decarboxylation of these acids generally utilize metal ion catalysis, a Schiff base intermediate, or polarization of the carbonyl group by hydrogen bonding and/or electrostatic interactions [20].

Anatomical context of Hydrogen Bonding

  • Individual hybridoma proteins (all of which bind fluorescein with relatively high affinity) exhibited significant differences in the relative contribution of various forces (hydrophobicity, hydrogen bonding, ionic interactions) to binding and hence, affinity [21].
  • A cationic steroid with a hydrogen-bonding pocket that has an affinity for anionic phospholipid headgroups was synthesized and shown to strongly promote the translocation or flip-flop of a fluorescent, C(6)NBD-labeled phosphatidylserine probe (C(6)NBD-PS) across vesicle membranes [22].
  • This has led to a proposal that the capacity of hydroxylated ceramide moieties for intermolecular hydrogen bonding among themselves and with phosphoglycerides acts to stabilize the plasma membrane [23].
  • The results suggest that the main thermal transition in the purple membrane is due to a cooperative conformational change involving the disruption of the network of electrostatic and hydrogen-bonding interactions which originate from the protonated Schiff base [24].
  • Heparin thins sputum by decreasing the mucin molecule amino group negative charge, altering its intermolecular hydrogen bonding, and ionically shielding its polyionic moieties [25].

Associations of Hydrogen Bonding with chemical compounds

  • The guanine residues are held together by cyclic hydrogen bonding and an ion is located in the centre [26].
  • Evidence for hydrogen bonding of bound dioxygen to the distal histidine of oxycobalt myoglobin and haemoglobin [27].
  • The proximity of the imidazole side chain to the sixth coordination position, which is required for efficient hydrogen bonding, has been postulated to inhibit sterically the binding of CO and alkyl isocyanides [28].
  • This structure emphasizes the importance of specific hydrogen bonding between not only the nucleotide bases, but also the ribose hydroxyls, phosphate oxygens and tightly bound waters in stabilization of the intramolecular and intermolecular structures of double helical RNA [29].
  • The specific recognition of phosphotyrosine involves amino-aromatic interactions between lysine and arginine side chains and the ring system in addition to hydrogen-bonding interactions with the phosphate [30].

Gene context of Hydrogen Bonding


Analytical, diagnostic and therapeutic context of Hydrogen Bonding


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  15. Characterization of the interaction of Ca2+ with hydroxy and non-hydroxy fatty acid species of cerebroside sulfate by Fourier transform infrared spectroscopy and molecular modeling. Menikh, A., Nyholm, P.G., Boggs, J.M. Biochemistry (1997) [Pubmed]
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