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Are aromatic carbon donor hydrogen bonds linear in proteins?
Vikas Nanda1, Ann Schmiedekamp
1Department of Biochemistry, Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey, Piscataway, New Jersey 08854, USA. nanda@cabm.rutgers.edu
Weak hydrogen bonds involving aromatic carbons are crucial for protein structure. Only charged histidine sidechains strongly favor linear interactions, influencing protein modeling and design.
Area of Science:
- Biochemistry
- Structural Biology
- Computational Chemistry
Background:
- Proteins maintain structure via numerous weak, noncovalent interactions.
- Hydrogen bonds are vital forces acting over short distances.
- Weak carbon-donor hydrogen bonds are increasingly recognized for their role in protein structure and function.
Purpose of the Study:
- To investigate the geometric preferences of hydrogen bonds involving aromatic sidechain carbons.
- To determine if carbon-donor hydrogen bonds can enforce linear donor-hydrogen-acceptor geometry.
- To explore the role of histidine sidechains in directing hydrogen bond linearity.
Main Methods:
- Surveyed high-resolution protein structures to analyze hydrogen bond geometries.
- Categorized histidine sidechains into charged and neutral subsets.
- Performed computational optimizations (B3LYP/6-31G**) of imidazole and indole-water interactions.
Main Results:
- Most carbon-donor hydrogen bonds exhibited shorter-than-van-der-waals distances.
- Only histidine carbons showed a significant preference for linear geometry.
- Charged histidine sidechains, but not neutral ones, were found to participate in linear interactions.
Conclusions:
- While all aromatic carbons can engage in hydrogen bonding, only charged histidines enforce linearity against protein packing forces.
- This finding has implications for understanding protein structure and for protein modeling and design.
- Charged histidine interactions are key to directing hydrogen bond geometry in proteins.
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