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

We
investigate unexpectedly short non-covalent distances (<85%
of the sum of van der Waals radii) in X-ray crystal structures of
proteins. We curate over 11 000 high-quality protein crystal
structures and an ultra-high-resolution (1.2 Å or better) subset
containing >900 structures. Although our non-covalent distance
criterion
excludes standard hydrogen bonds known to be essential in protein
stability, we observe over 75 000 close contacts (CCs) 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 CC 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 >5000 CCs with symmetry-adapted perturbation theory
to enable decomposition of interactions. We observe the majority of
CCs 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.