Dissecting and analyzing key residues in protein‐DNA
M. Michael Gromiha
Department of Biotechnology, Bhupat and
Jyoti Mehta School of BioSciences, Indian
Institute of Technology Madras, Chennai 600
M. Michael Gromiha, Department of
Biotechnology, Bhupat and Jyoti Mehta School
of BioSciences, Indian Institute of Technology
Madras, Chennai 600 036, Tamilnadu, India.
Council of Scientific and Industrial Research
(CSIR), Grant/Award Number:
Protein‐DNA interactions are involved in various fundamental biological processes such as
replication, transcription, DNA repair, and gene regulation. To understand the interaction in pro-
tein‐DNA complexes, the integrative study of binding and stabilizing residues is important. In the
present study, we have identified key residues that play a dual role in both binding and stability
from a nonredundant dataset of 319 protein‐DNA complexes. We observed that key residues
are identified in very less number of complexes (29%) and only about 4% of stabilizing/binding
residues are identified as key residues. Specifically, stabilizing residues have higher preference
to be key residues than binding residues. These key residues include polar, nonpolar, aliphatic,
aromatic, and charged amino acids. Moreover, we have analyzed and discussed the key residues
in different protein‐DNA complexes, which are classified based on protein structural class, func-
tion, DNA strand, and their conformations. Especially, Ser, Thr, Tyr, Arg, and Lys residues are
commonly found in most of the subclasses of protein‐DNA complexes. Further, we analyzed
atomic contacts, which show that polar‐nonpolar is more enriched than other types of contacts.
In addition, the charged contacts are highly preferred in protein‐DNA complexes compared with
protein‐protein and protein‐RNA complexes. Finally, we have discussed the sequence and struc-
tural features of key residues such as conservation score, surrounding hydrophobicity, solvent
accessibility, secondary structure, and long‐range order. This study will be helpful to understand
the recognition mechanism and structural and functional aspects of protein‐DNA complexes.
binding site residues, disorder‐to‐order regions, folding and stability, key residues, propensity,
Protein‐DNA interactions are important for performing cellular func-
tions including transcription, replication, DNA repair, and DNA packag-
Transcription factors, a class of DNA binding proteins (DBPs),
regulate the gene expression, and alteration in the specificity and affin-
ity of these proteins lead to abnormal cellular processes. Further,
mutations in these proteins change their binding affinity and cause
Hence, protein‐DNA interactions are widely stud-
ied experimentally and computationally.
DNA binding proteins generally contain specific structural motifs
that help in binding to a DNA molecule, eg, Helix‐turn‐helix, Leucine‐
zipper, and Zinc finger domains.
DNA binding proteins recognize
its DNA binding site by direct and indirect readout mechanisms. In
direct readout mechanism, the protein shows significant plasticity
and does not change its conformation upon binding. Whereas in indi-
rect readout mechanism, the structural changes occur upon binding.
The stabilization and specificity of protein‐DNA complexes have been
influenced mainly by the noncovalent interactions. The major forces
stabilizing DNA and protein interactions are hydrophobic, electrostatic,
and van der Waals interactions. Additionally, many features are being
studied, which play important roles in protein‐DNA interactions.
Protein‐DNA interactions can be detected by using chromatin
immunoprecipitation assay, DNA electrophoretic mobility shift assay,
DNA pull‐down assay, reporter assay, microplate capture and detec-
tion assay, and DNA footprinting.
On the other hand, cost‐
effective computational techniques have also been developed for
predicting the binding site and affinity of protein‐DNA interactions.
These methods are broadly classified into sequence and structure
based predictors. Sequence‐based tools use amino acid composition,
Received: 13 July 2017 Revised: 6 November 2017 Accepted: 6 November 2017
J Mol Recognit. 2018;31:e2692.
Copyright © 2017 John Wiley & Sons, Ltd.wileyonlinelibrary.com/journal/jmr 1of10