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N–H···N Hydrogen Bonds Involving Histidine Imidazole Nitrogen Atoms: A New Structural Role for Histidine Residues in Proteins
journal contribution
posted on 2016-06-15, 00:00 authored by R. N.
V. Krishna Deepak, Ramasubbu SankararamakrishnanThe
amino acid histidine can play a significant role in the structure
and function of proteins. Its various functions include enzyme catalysis,
metal binding activity, and involvement in cation−π,
π–π, salt-bridge, and other types of noncovalent
interactions. Although histidine’s imidazole nitrogens (Nδ
and Nε) are known to participate in hydrogen bond (HB) interactions
as an acceptor or a donor, a systematic study of N–H···N
HBs with the Nδ/Nε atom as the acceptor has not been conducted.
In this study, we have examined two data sets of ultra-high-resolution
(data set I) and very high-resolution (data set II) protein structures
and identified 28 and 4017 examples of HBs of the N–H···Nδ/Nε
type from both data sets involving histidine imidazole nitrogen as
the acceptor. In nearly 70% of them, the main-chain N–H bond
is the HB donor, and a majority of the examples are from the N–H
group separated by two residues (Ni+2–Hi+2) from histidine. Quantum chemical calculations
using model compounds were performed with imidazole and N-methylacetamide, and they assumed conformations from 19 examples
from data set I with N–H···Nδ/Nε
HBs. Basis set superposition error-corrected interaction energies
varied from −5.0 to −6.78 kcal/mol. We also found that
the imidazole nitrogen of 9% of histidine residues forming N–H···Nδ/Nε
interactions in data set II participate in bifurcated HBs. Natural
bond orbital analyses of model compounds indicate that the strength
of each HB is mutually influenced by the other. Histidine residues
involved in Ni+2–Hi+2···Nδi/Nεi HBs are frequently observed
in a specific N-terminal capping position giving rise to a novel helix-capping
motif. Along with their predominant occurrence in loop segments, we
propose a new structural role for histidines in protein structures.