Correlation of the hydrogen-bond acceptor properties of nitrogen with the geometry of the Nsp
 
 2
 →Nsp
 
 3
 transition in R
 1(X=)C–NR
 2
 R
 3 substructures: reaction pathway for the protonation of nitrogen

Allen, Frank H.; Bird, C. M.; Rowland, R. Scott; Harris, S.E.; Schwalbe, Carl H.

doi:10.1107/s0108768195004800

Cited by 21 publications

(7 citation statements)

References 8 publications

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“…In this study, it has been shown that histidine's interaction with metal ions is the strongest followed by cation-π and π-π interactions. Histidine is also found to be more frequently 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 22 those between two amino groups [55][56] When all histidine residues with the respective imidazole nitrogen atoms participating in N-H…Nδ/Nε type of HBs were examined, we found that 9% of them are also simultaneously involved in another hydrogen bond. In almost half of them, the second HB is also N-H…Nδ/Nε type.…”

Section: Discussionmentioning

confidence: 90%

N–H···N Hydrogen Bonds Involving Histidine Imidazole Nitrogen Atoms: A New Structural Role for Histidine Residues in Proteins

Deepak

Sankararamakrishnan

2016

Biochemistry

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The amino acid histidine can play a significant role in the structure and function of proteins. Its various functions include enzyme catalysis, metal binding activity, and involvement in cation-π, π-π, salt-bridge, and other types of noncovalent interactions. Although histidine's imidazole nitrogens (Nδ and Nε) are known to participate in hydrogen bond (HB) interactions as an acceptor or a donor, a systematic study of N-H···N HBs with the Nδ/Nε atom as the acceptor has not been conducted. In this study, we have examined two data sets of ultra-high-resolution (data set I) and very high-resolution (data set II) protein structures and identified 28 and 4017 examples of HBs of the N-H···Nδ/Nε type from both data sets involving histidine imidazole nitrogen as the acceptor. In nearly 70% of them, the main-chain N-H bond is the HB donor, and a majority of the examples are from the N-H group separated by two residues (Ni+2-Hi+2) from histidine. Quantum chemical calculations using model compounds were performed with imidazole and N-methylacetamide, and they assumed conformations from 19 examples from data set I with N-H···Nδ/Nε HBs. Basis set superposition error-corrected interaction energies varied from -5.0 to -6.78 kcal/mol. We also found that the imidazole nitrogen of 9% of histidine residues forming N-H···Nδ/Nε interactions in data set II participate in bifurcated HBs. Natural bond orbital analyses of model compounds indicate that the strength of each HB is mutually influenced by the other. Histidine residues involved in Ni+2-Hi+2···Nδi/Nεi HBs are frequently observed in a specific N-terminal capping position giving rise to a novel helix-capping motif. Along with their predominant occurrence in loop segments, we propose a new structural role for histidines in protein structures.

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Section: Discussionmentioning

confidence: 90%

N–H···N Hydrogen Bonds Involving Histidine Imidazole Nitrogen Atoms: A New Structural Role for Histidine Residues in Proteins

Deepak

Sankararamakrishnan

2016

Biochemistry

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“…Allen, B.F.L. & Z.S., unpublished results; for a discussion of amino group contacts and geometry, see Allen et al (1995)). The N-H vector of the donor amino group tends to become more aligned with the normal to the plane of the acceptor amino group as the N ± H distance becomes shorter.…”

Section: Discussionmentioning

confidence: 91%

X-ray and solution studies of DNA oligomers and implications for the structural basis of A-tract-dependent curvature 1 1Edited by T. Richmond

Shatzky-Schwartz

Arbuckle²,

Eisenstein

et al. 1997

Journal of Molecular Biology

110

113

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“…Analysis of the energy-minimized structure suggests that this counterintuitive NH 2 distortion is a result of stabilizing CH---N contacts with the aromatic ring of a third molecule. Indeed, such contacts (d H--N ) 2.57 Å) are increasingly considered to be weak hydrogen bonds, 45 with structure-directing capabilities. densest structuressclearly, optimization of hydrogen-bonding interactions results in less efficient packing.…”

Section: Discussionmentioning

confidence: 99%

Amide Pyramidalization in Carbamazepine: A Flexibility Problem in Crystal Structure Prediction?

Cruz‐Cabeza

Day

Motherwell

et al. 2006

Crystal Growth & Design

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Carbamazepine is known to exist in various polymorphic forms. Here we report on crystal structure prediction calculations for carbamazepine in an attempt to examine the predictability and relative stability of the various polymorphs. Hypothetical crystal structures generated in 10 of the most common space groups were compared to the observed polymorphs. Particular attention has been given to the influence of amide pyramidalization on the relative energies of the predicted structures. While the actual generation of possible crystal structures was found to be independent of the degree of deformation of the amide group, their final ranking in energy was greatly affected by pyramidalization of the amide nitrogen. This effect was examined in detail through systematic variation of the NH 2 geometry for each of the low-energy crystal structures; different amide geometries were favored in the various low-energy crystal structures. The results demonstrate that energetically feasible deformation of the amide group may occur in order to optimize hydrogen-bond interactions, and we conclude that neglect of amide pyramidalization introduces significant errors in crystal structure prediction for carbamazepine and similar molecules.

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Correlation of the hydrogen-bond acceptor properties of nitrogen with the geometry of the Nsp ²→Nsp ³ transition in R ₁(X=)C–NR ₂ R ₃ substructures: reaction pathway for the protonation of nitrogen

Cited by 21 publications

References 8 publications

N–H···N Hydrogen Bonds Involving Histidine Imidazole Nitrogen Atoms: A New Structural Role for Histidine Residues in Proteins

N–H···N Hydrogen Bonds Involving Histidine Imidazole Nitrogen Atoms: A New Structural Role for Histidine Residues in Proteins

X-ray and solution studies of DNA oligomers and implications for the structural basis of A-tract-dependent curvature 1 1Edited by T. Richmond

Amide Pyramidalization in Carbamazepine: A Flexibility Problem in Crystal Structure Prediction?

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Correlation of the hydrogen-bond acceptor properties of nitrogen with the geometry of the Nsp 2 →Nsp 3 transition in R 1(X=)C–NR 2 R 3 substructures: reaction pathway for the protonation of nitrogen

Cited by 21 publications

References 8 publications

N–H···N Hydrogen Bonds Involving Histidine Imidazole Nitrogen Atoms: A New Structural Role for Histidine Residues in Proteins

N–H···N Hydrogen Bonds Involving Histidine Imidazole Nitrogen Atoms: A New Structural Role for Histidine Residues in Proteins

X-ray and solution studies of DNA oligomers and implications for the structural basis of A-tract-dependent curvature 1 1Edited by T. Richmond

Amide Pyramidalization in Carbamazepine: A Flexibility Problem in Crystal Structure Prediction?

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Product

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Correlation of the hydrogen-bond acceptor properties of nitrogen with the geometry of the Nsp ²→Nsp ³ transition in R ₁(X=)C–NR ₂ R ₃ substructures: reaction pathway for the protonation of nitrogen