Characterization of Dimeric Interactions within Protrusion-Domain Interfaces of Parallel and X-Shaped Conformations of Macrobrachium rosenbergii Nodavirus: A Theoretical Study Using the DFT Method along with QTAIM and NBO Analyses

Elahe K Astani; Nai-Chi Chen; Yen-Chieh Huang; Sara Ersali; Pei-Ju Lin; Hong-Hsiang Guan; Chien-Chih Lin; Phimonphan Chuankhayan; Chun-Jung Chen

doi:10.1021/acsomega.9b03697

Characterization of Dimeric Interactions within Protrusion-Domain Interfaces of Parallel and X-Shaped Conformations of Macrobrachium rosenbergii Nodavirus: A Theoretical Study Using the DFT Method along with QTAIM and NBO Analyses

ACS Omega. 2020 Feb 13;5(7):3428-3443. doi: 10.1021/acsomega.9b03697. eCollection 2020 Feb 25.

Authors

Elahe K Astani^{1

2}, Nai-Chi Chen¹, Yen-Chieh Huang¹, Sara Ersali³, Pei-Ju Lin^{1

4}, Hong-Hsiang Guan¹, Chien-Chih Lin¹, Phimonphan Chuankhayan¹, Chun-Jung Chen^{1

5

6}

Affiliations

¹ Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, Hsinchu 30076, Taiwan.
² Department of Chemistry, Faculty of Science, Tarbiat Modares University, Tehran 14115-175, Iran.
³ Faculty of Chemistry and Chemical Engineering, Babeş-Bolyai University, Cluj-Napoca 400028, Romania.
⁴ Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu 30043, Taiwan.
⁵ Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan City 701, Taiwan.
⁶ Department of Physics, National Tsing Hua University, Hsinchu 30043, Taiwan.

Abstract

The protrusion domain (P-domain; MrNVPd) of Macrobrachium rosenbergii nodavirus (MrNV) exists in two conformations, parallel and X-shaped. We have performed a theoretical study to gain insight into the nature of the dimeric interactions involving the dimeric interfaces within parallel and X-shaped conformations of MrNVPd by applying 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 results reveal that the dimer-dimer interfaces of MrNVPd have hydrogen bonds of common types. Leu255-Lys287, Tyr257-Lys287, Lys287-Ser253, Met294-Cys328, Asp295-Lys327, Ser298-Ser324, Ile326-Asp295, and Cys328-Met294 are the key residue pairs of the dimer-dimer interfaces to maintain the dimer-dimer structures of MrNVPd through charge-charge, charge-dipole, dipole-dipole, hydrophobic, and hydrogen bonding interactions. The strengths of these intermolecular dimer-dimer interactions in the parallel conformation are much greater than those in the X-shaped conformation. The parallel trimeric interface is held basically by electrostatic and hydrophobic interactions. The electrostatic interactions accompanying a strong hydrogen bond of Oγ1-Hγ1···Oγ1 in the Thr276 A-Thr276 D pair maintain the intermolecular interface of two X-shaped MrNVPd dimers.