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A role for CH...O interactions in protein-DNA recognition
Y Mandel-Gutfreund1, H Margalit, R L Jernigan
1Department of Molecular Genetics and Biotechnology, The Hebrew University-Hadassah Medical School, Jerusalem, 91120, Israel.
Journal of Molecular Biology
|May 22, 1998
Summary
CH...O hydrogen bonds play a key role in protein-DNA interactions. These non-classical bonds, particularly involving thymine and cytosine, are as common as classical hydrogen bonds, enhancing recognition specificity.
Area of Science:
- Structural Biology
- Biochemistry
- Molecular Biology
Background:
- Non-classical CH...O hydrogen bonds are increasingly recognized for their role in stabilizing biomolecular structures.
- Understanding these interactions is crucial for deciphering the mechanisms of molecular recognition in biological systems.
Purpose of the Study:
- To investigate the role and prevalence of CH...O interactions at the protein-DNA interface.
- To compare the frequency and geometry of CH...O contacts with classical hydrogen bonds in protein-DNA complexes.
Main Methods:
- Analysis of 43 crystal structures of protein-DNA complexes.
- Geometrical analysis of intermolecular CH...O contacts involving specific DNA bases (thymine and cytosine) and amino acid residues.
Main Results:
- The number of CH...O contacts involving thymine methyl and cytosine C5 is comparable to classical protein-DNA hydrogen bonds.
- Geometries of these CH...O contacts are similar to those found in proteins, small molecules, and classical hydrogen bonds.
Conclusions:
- C5 of cytosine and C5-methyl of thymine form weak CH...O hydrogen bonds with specific amino acids (Asp, Asn, Glu, Gln, Ser, Thr).
- These interactions contribute to the specificity of protein-DNA recognition.
- Incorporating CH...O bonds provides a more complete understanding of amino acid-base recognition principles.