Hydrogen bonds in Zif268 proteins – a theoretical perspective

Abstract

The aim of the work was to elucidate the presence of different hydrogen bond (H-bond) in five Zif268 proteins (1A1F, 1A1G, 1A1H, 1A1I and 1A1K). For this purpose, we have performed the QM/MM and molecular dynamics (MD) studies, the results of which reveal that H-bonds depend on the amino acid sequence and orientation of the H-bond donor atoms. Further, high specificity of Arg and Asn is observed for guanine and adenine, respectively. Furthermore, both conventional and non-conventional hydrogen bond also exists in the proteins, among them N–H⋯O H-bonds are the strongest. Besides, the non-conventional bonds play a role in the protein folding and DNA stacking. From the QSAR properties, amino acids such as asparagine and aspartic acids are the major reactive sites in the Zif268 protein. The electron affinities of Zif268 proteins are high, so the charge transfer occurs from the DNA to the protein molecules. NBO analysis indicates the majority of charge transfer occurs from DNA to the corresponding anti-bonding orbital of the peptides. Root mean square deviation and R_g (radius of gyration) show that 1A1F is more compact and in native state during MD simulation. The minimum R_g leads to the large number of hydrogen bonds formation in 1A1F. Higher solvent accessible surface area in 1A1I indicates that the cavity inside the protein is large.

Keywords:

• Zif268 proteins
• QM/MM
• MD
• hydrogen bond
• NBO

Acknowledgement

Authors Dr L. Senthilkumar and Miss P. Umadevi gratefully acknowledge the DST-SERB, New Delhi, India, for granting the project and fellowship under the Fast-Track scheme (SR/FTP/PS-115/2010).

Disclosure statement

No potential conflict of interest was reported by the authors.

Additional information

Funding

This work was supported by the Science and Engineering Research Board [grant number SR/FTP/PS-115/2010].