During the continuing evolution of severe acute respiratory syndrome coronavirus 2(SARS-CoV-2),the Omicron variant of concern emerged in the second half of 2021 and has been dominant since November of that year.Along ...During the continuing evolution of severe acute respiratory syndrome coronavirus 2(SARS-CoV-2),the Omicron variant of concern emerged in the second half of 2021 and has been dominant since November of that year.Along with its sublineages,it has maintained a prominent role ever since.The Nsp5 main protease(Mpro)of the Omicron virus is characterized by a single dominant mutation,P132H.Here we determined the X-ray crystal structures of the P132H mutant(or O-Mpro)as a free enzyme and in complex with the Mpro inhibitor,the alpha-ketoamide 13b-K,and we conducted enzymological,biophysical,as well as theoretical studies to characterize the O-Mpro.We found that O-Mpro has a similar overall structure and binding with 13b-K;however,it displays lower enzymatic activity and lower thermal stability compared to the WT-Mpro(with“WT”referring to the prototype strain).Intriguingly,the imidazole ring of His132 and the carboxylate plane of Glu240 are in a stacked configuration in the X-ray structures determined here.Empirical folding free energy calculations suggest that the O-Mpro dimer is destabilized relative to the WT-Mpro due to less favorable van der Waals interactions and backbone conformations in the individual protomers.All-atom continuous constant-pH molecular dynamics(MD)simulations reveal that His132 and Glu240 display coupled titration.At pH 7,His132 is predominantly neutral and in a stacked configuration with respect to Glu240 which is charged.In order to examine whether the Omicron mutation eases the emergence of further Mpro mutations,we also analyzed the P132H+T169S double mutant,which is characteristic of the BA.1.1.2 lineage.However,we found little evidence of a correlation between the two mutation sites.展开更多
基金Financial support from the German Center for Infection Research(DZIFproject FF 01.905,to R.H.)+1 种基金the National Institutes of Health(R35GM148261 to J.S.)is gratefully acknowledged.R.H.is also supported by the Government of Schleswig-Holstein through its StructureExcellence Fund as well as by a close partnership between the Possehl Foundation(Lübeck)and the University of Lübeck.
文摘During the continuing evolution of severe acute respiratory syndrome coronavirus 2(SARS-CoV-2),the Omicron variant of concern emerged in the second half of 2021 and has been dominant since November of that year.Along with its sublineages,it has maintained a prominent role ever since.The Nsp5 main protease(Mpro)of the Omicron virus is characterized by a single dominant mutation,P132H.Here we determined the X-ray crystal structures of the P132H mutant(or O-Mpro)as a free enzyme and in complex with the Mpro inhibitor,the alpha-ketoamide 13b-K,and we conducted enzymological,biophysical,as well as theoretical studies to characterize the O-Mpro.We found that O-Mpro has a similar overall structure and binding with 13b-K;however,it displays lower enzymatic activity and lower thermal stability compared to the WT-Mpro(with“WT”referring to the prototype strain).Intriguingly,the imidazole ring of His132 and the carboxylate plane of Glu240 are in a stacked configuration in the X-ray structures determined here.Empirical folding free energy calculations suggest that the O-Mpro dimer is destabilized relative to the WT-Mpro due to less favorable van der Waals interactions and backbone conformations in the individual protomers.All-atom continuous constant-pH molecular dynamics(MD)simulations reveal that His132 and Glu240 display coupled titration.At pH 7,His132 is predominantly neutral and in a stacked configuration with respect to Glu240 which is charged.In order to examine whether the Omicron mutation eases the emergence of further Mpro mutations,we also analyzed the P132H+T169S double mutant,which is characteristic of the BA.1.1.2 lineage.However,we found little evidence of a correlation between the two mutation sites.
