A role for CH...O interactions in protein-DNA recognition.

@article{MandelGutfreund1998ARF,
  title={A role for CH...O interactions in protein-DNA recognition.},
  author={Yael Mandel-Gutfreund and Hanah Margalit and Robert L. Jernigan and Victor B Zhurkin},
  journal={Journal of molecular biology},
  year={1998},
  volume={277 5},
  pages={
          1129-40
        }
}
The concept of CH...O hydrogen bonds has recently gained much interest, with a number of reports indicating the significance of these non-classical hydrogen bonds in stabilizing nucleic acid and protein structures. Here, we analyze the CH...O interactions in the protein-DNA interface, based on 43 crystal structures of protein-DNA complexes. Surprisingly, we find that the number of close intermolecular CH...O contacts involving the thymine methyl group and position C5 of cytosine is comparable… 
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TLDR
Analysis of available B-DNA type oligomeric crystal structures as well as protein-bound DNA fragments indicates that in both data sets, a majority of the (3'-Ade) H2..O2(3'-Thy/Cyt) distances in AA.TT and GA.TC dinucleotide steps, are considerably shorter than their values in a uniform fibre model, and are smaller than their optimum separation distance.
Three-centre C-H---O hydrogen bonds in the DNA minor groove: analysis of oligonucleotide crystal structures.
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  • Chemistry
    Acta crystallographica. Section D, Biological crystallography
  • 1999
TLDR
The analysis suggests that in addition to already documented features such as the large propeller twist of A.T base pairs and the hydration of the minor groove, these C2-H---O2 cross-strand interactions may also play a role in the narrowing of theMinor groove in A-tract regions of DNA and help explain the high structural rigidity and stability observed for poly(dA).poly(dT).
Contribution of unconventional C-H…O bonds to the structural stability of Antimicrobial peptides
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It is concluded that the C-H…O interaction can, indeed, be categorized as a true stabilizing force like hydrogen bond in Antimicrobial peptides.
C–H/O Interactions of Aromatic CH Donors within Proteins: A Crystallographic Study
C–H/O interactions of aromatic C–H donors within proteins have been studied by analyzing the data in the Protein Data Bank (PDB). The C–H/O interactions were studied between aromatic donors;…
The significant role of the intermolecular CH⋯O/N hydrogen bonds in governing the biologically important pairs of the DNA and RNA modified bases: a comprehensive theoretical investigation
TLDR
The studies reported here advance the understanding of the biological role of the weak CH⋯O/N H-bonds, that dictates the requirements for the structural and dynamical similarity of the canonical and mismatched pairs with Watson–Crick (WC) geometry, which facilitates their enzymatic incorporation into the DNA double helix during DNA replication.
CH···O Hydrogen Bonds at Protein-Protein Interfaces* 210
  • Lin Jiang, L. Lai
  • Chemistry, Biology
    The Journal of Biological Chemistry
  • 2002
TLDR
It is suggested that the weak CH···O H-bond makes an important contribution to the association and stability of protein complexes and needs more attention in protein-protein interaction studies.
Evaluation of C–H⋯O Hydrogen Bonds in Native and Misfolded Proteins
The role of water in protein-DNA recognition.
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  • 2004
TLDR
A survey of the current literature on water inprotein-DNA complexes and a critique of various interpretations of the data in the context of the role of water in protein- DNA binding and principles of protein-DNA recognition in general are presented.
Non-classical hydrogen bonds in interleukins: the role of C-H...O interactions.
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