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

• DOI: 10.1101/2020.02.20.957316
• Publication Date: 2020-02-21T11:45:15Z
• Authors: Elahe K. Astani; Nai-Chi Chen; Yen-Chieh Huang; Sara Ersali; Pei-Ju Lin; Hong-Hsiang Guan; Chien-Chih Lin; Phimonphan Chuank...; Chun-Jung Chen
• Keywords: Tetramer; Atoms in molecules; Natural bond orbital; Trimer

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