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bioRxiv · 10.1101/2020.02.20.957316

Characterization of the dimeric interactions of dimeric and tetrameric conformations of the PvNV protrusion-domain using a mixed DFT/QTAIM approach

Astani, E. K.·Chen, N.-C.·Huang, Y.-C.·Ersali, S.·Lin, P.-J.·Guan, H.-H.·Lin, C.-C.·Chuankhayan, P.·Chen, C.-J.
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Abstract

The protrusion-domain (P-domain) of Penaeus vannamei nodavirus (PvNV) exists as two dimer-dimer conformations: one is a protein dimer and the other is a protein tetramer. We undertook a theoretical study to gain a clear understanding of the nature of the stabilizing interactions at the dimeric interfaces of the dimeric and tetrameric conformations of the PvNV P-domain (PvNVPd) using the quantum theory of atoms in molecules (QTAIM) and natural-bond orbital (NBO) analyses in the framework of the density-functional theory (DFT) approach. The QTAIM analysis characterized the presence of multiple hydrogen bonds of common types with strength ranging from electrostatic to the covalent limit inside the PvNVPd dimer-dimer interfaces. Val257-Lys335, Phe294-Val330, Gln296-Thr328, Glu296-Thr329, Thr328-Gln297, Val330-Ala293, Lys335-Asp256 and Lys335-Val257 pairs are critical residue pairs of all three dimeric interfaces of PvNVPd. They preserve these dimeric interfaces through charge-charge, charge-dipole, dipole-dipole, hydrophobic and hydrogen bond interactions. The strongest intermolecular dimer-dimer interactions belong to the dimeric interface between subunits A and B of PvNVPd in the tetrameric conformation.

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Astani, E. K., Chen, N.-C., Huang, Y.-C., Ersali, S., Lin, P.-J., Guan, H.-H., Lin, C.-C., Chuankhayan, P., Chen, C.-J.. 2020-02-20. Characterization of the dimeric interactions of dimeric and tetrameric conformations of the PvNV protrusion-domain using a mixed DFT/QTAIM approach. https://doi.org/10.1101/2020.02.20.957316

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