pH-dependent polymorphism of the structure of SARS-CoV-2 nsp7

Abstract

The solution structure of SARS-CoV-2 nonstructural protein 7 (nsp7) at pH 7.0 has been determined by NMR spectroscopy. nsp7 is conserved in the coronavirinae subfamily and is an essential co-factor of the viral RNA-dependent RNA polymerase for active and processive replication. Similar to the previously deposited structures of SARS-CoV-1 nsp7 at acidic and basic conditions, SARS-CoV-2 nsp7 has a helical bundle folding at neutral pH. Remarkably, the α4 helix shows gradual dislocation from the core α2-α3 structure as pH increases from 6.5 to 7.5. The protonation state of residue H36 contributes to the change of nsp7's intramolecular interactions, and thus, to the structural variation near-neutral pH. Spin-relaxation results revealed that all three loop regions in nsp7 possess dynamic properties associated with this structural variation.

Breaking boundaries: TINTO in POKY for computer vision-based NMR walking strategies

“…We tested TINTO 2D using 2D TOCSY and NOESY spectra (Fig. S1) and TINTO 3D using 2D 15 N-HSQC spectrum and 3D HNCACB and CBCA(CO)NH spectra (Fig. S2).…”

“…The simulated data set was generated using POKY's SIM-PROC module to simulate backbone 3D experiments of ubiquitin (two-letter-code "me"). The other data sets were obtained from our published works 14,15 .…”

“…To evaluate TINTO's performance on triple resonance experiments for backbone assignments, we used spectral data from Nsp7 and Ubiquitin as described in Table 1. Specifically, we used 2D 1 H, 15 N-HSQC, 3D HNCACB and 3D CBCA(CO)NH spectra as inputs. We employed TINTO in the strip plot tool (two-letter-code "sp") to find the strip from the following residue and evaluate its "sequence walking" performance.…”