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Evaluating Unexpectedly Short Non-covalent Distances in X-ray Crystal Structures of Proteins with Electronic Structure Analysis

preprint
submitted on 20.01.2019 and posted on 21.01.2019 by Helena W. Qi, Heather Kulik

We investigate unexpectedly short non-covalent distances (< 85% of the sum of van der Waals radii) in atomically resolved X-ray crystal structures of proteins. We curate over 13,000 high quality protein crystal structures and an ultra-high resolution (1.2 Å or better) subset containing > 1,000 structures. Although our non-covalent distance criterion excludes standard hydrogen bonds known to be essential in protein stability, we observe over 82,000 close contacts in the curated protein structures. Analysis of the frequency of amino acids participating in these interactions demonstrates some expected trends (i.e., enrichment of charged Lys, Arg, Asp, and Glu) but also reveals unexpected enhancement of Tyr in such interactions. Nearly all amino acids are observed to form at least one close contact with all other amino acids, and most interactions are preserved in the much smaller ultra high-resolution subset. We quantum-mechanically characterize the interaction energetics of a subset of > 6,000 close contacts with symmetry adapted perturbation theory to enable decomposition of interactions. We observe the majority of close contacts to be favorable. The shortest favorable non-covalent distances are under 2.2 Å and are very repulsive when characterized with classical force fields. This analysis reveals stabilization by a combination of electrostatic and charge transfer effects between hydrophobic (i.e., Val, Ile, Leu) amino acids and charged Asp or Glu. We also observe a unique hydrogen bonding configuration between Tyr and Asn/Gln involving both residues acting simultaneously as hydrogen bond donors and acceptors. This work confirms the importance of first-principles simulation in explaining unexpected geometries in protein crystal structures.

Funding

Burroughs-Wellcome Fund Career Award at the Scientific Interface

Department of Energy Computational Science Graduate Fellowship

History

Email Address of Submitting Author

hjkulik@mit.edu

Institution

Massachusetts Institute of Technology

Country

United States

ORCID For Submitting Author

0000-0001-9342-0191

Declaration of Conflict of Interest

The authors declare no competing financial interest.

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