Dissecting and analyzing key residues in protein‐DNA complexes

Dissecting and analyzing key residues in protein‐DNA complexes Protein‐DNA interactions are involved in various fundamental biological processes such as replication, transcription, DNA repair, and gene regulation. To understand the interaction in protein‐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, function, 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 structural 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. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Journal of Molecular Recognition Wiley

Dissecting and analyzing key residues in protein‐DNA complexes

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Publisher
Wiley Subscription Services, Inc., A Wiley Company
Copyright
Copyright © 2018 John Wiley & Sons, Ltd.
ISSN
0952-3499
eISSN
1099-1352
D.O.I.
10.1002/jmr.2692
Publisher site
See Article on Publisher Site

Abstract

Protein‐DNA interactions are involved in various fundamental biological processes such as replication, transcription, DNA repair, and gene regulation. To understand the interaction in protein‐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, function, 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 structural 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.

Journal

Journal of Molecular RecognitionWiley

Published: Jan 1, 2018

Keywords: ; ; ; ; ;

References

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