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Why is the Omicron main protease of SARS-CoV-2 less stable than its wild-type counterpart?A crystallographic,biophysical,and theoretical study

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hLife 2024年第8期2卷 419-433页

作者： Mohamed Ibrahim Xinyuanyuan Sun Vinicius Martins de Oliveira Ruibin Liu Joseph Clayton Haifa El Kilani jana shen Rolf Hilgenfeld Institute of Molecular Medicine University of Lübeck23562 LübeckGermany Department of Pharmaceutical Sciences University of Maryland School of PharmacyBaltimoreMD 21201USA Division of Applied Regulatory Science Office of Clinical PharmacologyOffice of Translational SciencesCenter for Drug Evaluation and ResearchUnited States Food and Drug AdministrationSilver SpringMD 20993USA German Center for Infection Research(DZIF) Hamburg-Lübeck-Borstel-Riems SiteUniversity of Lübeck23562 LübeckGermany

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 *** with its sublineages,it has maintained a prominent role ever *** Nsp5 main protease(Mpro)of the Omicron virus is characterized by a single dominant mutation,*** 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 *** 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 *** 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 ***-atom continuous constant-pH molecular dynamics(MD)simulations reveal that His132 and Glu240 display coupled *** pH 7,His132 is predominantly neutral and in a stacked configuration with respect to Glu240 which is *** 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 ***,we found little evidence of a correlation between the two mutation sites.

关键词： severe acute respiratory syndrome coronavirus 2(SARS-CoV-2) main protease Omicron molecular dynamics Pro>His mutant double mutant

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Identification of two glycerophosphodiester phosphodiesterase genes in maize leaf phosphorus remobilization

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The Crop Journal 2021年第1期9卷 95-108页

作者： Jingxin Wang Wenbo Pan Alexiy Nikiforov William King Wanting Hong Weiwei Li Yang Han jana Patton-Vogt Jianbo shen Lingyun Cheng Key Laboratory of Plant-Soil Interactions Ministry of Education/Key Laboratory of Plant NutritionMinistry of AgricultureDepartment of Plant NutritionChina Agricultural UniversityBeijing 100193China State Key Laboratory of Plant Genomics Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijing 100101China Department of Biological Sciences Duquesne UniversityPittsburghPA 15282USA

Phosphate deficiency is one of the leading causes of crop productivity *** degradation liberates phosphate to cope with phosphate *** phosphodiesterases(GPX-PDEs)hydrolyse the intermediate products of phospholipid catabolism glycerophosphodiesters into glycerol-3-phosphate,a precursor of ***,the function of GPX-PDEs in phosphate remobilization in maize remains *** the present study,we characterized two phosphate deficiency-inducible GPX-PDE genes,ZmGPX-PDE1 and ZmGPX-PDE5,in maize ***-PDE1 and ZmGPX-PDE5 were transcriptionally regulated by ZmPHR1,a well-described phosphate starvation-responsive transcription factor of the MYB *** of the yeast GPX-PDE mutant gde1Δindicated that ZmGPX-PDE1 and ZmGPX-PDE5 functioned as GPX-PDEs,suggesting their roles in phosphate recycling from *** vitro enzyme assays showed that ZmGPX-PDE1 and ZmGPX-PDE5 catalysed glycerophosphodiester degradation with different substrate preferences for glycerophosphoinositol and glycerophosphocholine,***-PDE1 was upregulated during leaf senescence,and more remarkably,loss of ZmGPXPDE1 inmaize compromised the remobilization of phosphorus fromsenescing leaves to young leaves,resulting in a stay-green phenotype under phosphate *** results suggest that ZmGPX-PDE1 catalyses the degradation of glycerophosphodiesters in maize,promoting phosphate recycling from senescing leaves to new *** mechanism is crucial for improving phosphorus utilization efficiency in crops.

关键词： Glycerophosphodiester phosphodiesterases Maize Phosphate deficiency Phosphorus remobilization Phospholipid

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On the helium bubble swelling in nano-oxide dispersion-strengthened steels

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Journal of Materials Science & Technology 2022年第10期105卷 172-181页

作者： Vladimir Krsjak Tielong shen Jarmila Degmova Stanislav Sojak Erik Korpas Pavol Noga Werner Egger Bingsheng Li Vladimir Slugen Frank A.Garner Slovak University of Technology Faculty of Electrical Engineering and Information TechnologyInstitute of Nuclear and Physical EngineeringIlkovicova 3Bratislava 81219Slovakia Chinese Academy of Sciences Institute of Modern PhysicsLanzhou 730000China Slovak University of Technology Faculty of Materials Science and TechnologyAdvanced Technologies Research InstituteJana Bottu 2781/25Trnava 91724Slovakia Universität der Bundeswehr München Institut für Angewandte Physik und Messtechnik LRT2Werner-Heisenberg-Weg 39Neubiberg85577Germany Southwest University of Science and Technology State Key Laboratory for Environment-friendly Energy MaterialsMianyangSichuan 621010China Texas A&M University Nuclear Engineering DepartmentCollege StationTX 77843USA Radiation Effects Consulting LLC Richland WA 99354USA

The development of structural materials resistant to harsh radiation environments requires an in-depth understanding of the early stage of the aging *** radiation environments with high transmutation helium production rates such as in fusion and spallation applications,even materials with otherwise acceptable radiation stability may suffer from radiation embrittlement related to helium bubble *** theoretical modeling of helium-assisted cavity nucleation in pure metals and simple alloys provides some useful guidelines at the atomic scale level,these,however,do not overlap with the size resolution of available experimental *** this study,we employed slow positron beam spectroscopy to characterize the nucleation and growth of nano-scale helium bubbles in martensitic steels strengthened by thermodynamically stable nano-oxide *** combination with transmission electron microscopy,we experimentally characterized the evolution of helium bubbles from small clusters of radiation-induced vacancies to large cavities well resolvable by *** radiation resistance of oxide-dispersion strengthened steels dominates only in the early stages of bubble evolution,where positron lifetime measurements provide a missing piece of the microstructural puzzle conventionally constructed by TEM.

关键词： Ion irradiation Bubble swelling Helium Positron annihilation spectroscopy Oxide dispersion strengthened steels

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