Greenbug(Schizaphis graminum, Rondani) is a serious insect pest in many wheat growing regions and has been infesting cereal crops in the USA for over a century. Continuous occurrence of new greenbug biotypes makes it ...Greenbug(Schizaphis graminum, Rondani) is a serious insect pest in many wheat growing regions and has been infesting cereal crops in the USA for over a century. Continuous occurrence of new greenbug biotypes makes it essential to explore all greenbug resistant sources available to manage this pest. Gb1, a recessive greenbug resistance gene in DS28A, confers resistance to several economically important greenbug biotypes and is the only gene found to be resistant to greenbug biotype F. A set of 174 F_(2:3)lines from the cross DS28A × Custer was evaluated for resistance to greenbug biotype F in 2020 and 2022. Selective genotyping of the corresponding F_(2) population using single nucleotide polymorphism(SNP) markers generated by genotyping-by-sequencing(GBS) led to the identification of a candidate genomic region for Gb1. Thus, SSR markers previously mapped in this region were used to genotype the entire F2population,and kompetitive allele specific PCR(KASP) markers were also developed from SNPs in the target region.Gb1 was placed in the terminal region of the short arm of chromosome 1A, and its location was confirmed in a second population derived from the cross DS28A × PI 697274. The combined data analysis from the two mapping populations delimited Gb1 to a < 1 Mb interval between 13,328,200 and 14,241,426 bp on1AS.展开更多
The folding of many small proteins is kinetically a two-state process with one major free-energy barrier to overcome,which can be roughly regarded as the inverse process of unfolding.In this work,we first use a Gaussi...The folding of many small proteins is kinetically a two-state process with one major free-energy barrier to overcome,which can be roughly regarded as the inverse process of unfolding.In this work,we first use a Gaussian network model to predict the folding nucleus corresponding to the major free-energy barrier of protein 2 GB1,and find that the folding nucleus is located in theβ-sheet domain.High-temperature molecular dynamics simulations are then used to investigate the unfolding process of 2 GB1.We draw free-energy surface from unfolding simulations,taking RMSD and contact number as reaction coordinates,which confirms that the folding of 2 GB1 is kinetically a two-state process.The comparison of the contact maps before and after the free energy barrier indicates that the transition from native to non-native structure of the protein is kinetically caused by the destruction of theβ-sheet domain,which manifests that the folding nucleus is indeed located in theβ-sheet domain.Moreover,the constrained MD simulation further confirms that the destruction of the secondary structures does not alter the topology of the protein retained by the folding nucleus.These results provide vital information for upcoming researchers to further understand protein folding in similar systems.展开更多
Although the parallel incorporation of fluorinated aromatic amino acids(FAAAs)into proteins has been explored since 2010,the corresponding ^(19)F NMR investigation has been lacking to date.To assess the potential of t...Although the parallel incorporation of fluorinated aromatic amino acids(FAAAs)into proteins has been explored since 2010,the corresponding ^(19)F NMR investigation has been lacking to date.To assess the potential of the parallel incorporation of FAAAs in studies of protein structure,dynamics and interactions,we examine the protein yields,fluorine incorporation efficiencies,and ^(19)F NMR spectra upon simultaneously incorporating FAAAs including 3-fluorotyrosine(3FY),4-fluorophenylalanine(4FF)and 5-fluorotryptophan(5FW)into two model proteins:the structured protein GB1 domain(GB1)and the intrinsically disordered protein a-synuclein(a-syn).We found that the simultaneous incorporation of 3FY and 5FW achieved higher efficiency than combinations of 4FF and 5FW,4FF and 3FY,or 3FY,4FF and 5FW.Moreover,incorporating more types of FAAAs leads to a reduction in overall yield.The ^(19)F spectra of 3FY,4FF and 5FW residues in α-syn and GB1 exhibited good dispersion of chemical shifts.However,the GB1 spectrum showed complexity due to incomplete fluorination and interactions within aromatic cluster.This complexity could be significantly reduced by supplementing the medium with natural aromatic amino acids.To validate the advantage of ^(19)F NMR spectrum,we use 3FY-4FF-5FW-F94W-α-syn to investigate the interaction between α-syn and sodium dodecyl sulphate(SDS)micelle.Our study demonstrates that ^(19)F NMR spectroscopy of proteins with parallel incorporation of FAAAs provides a valuable tool for investigating protein conformation,dynamics and interactions.展开更多
In this work, multiple molecular dynamics simulations of protein G and protein L unfolding trajectories provide a direct demonstration of the diversity of unfolding pathway and give
基金supported by the USDA ARS CRIS Project (3072– 21000–009–00D)。
文摘Greenbug(Schizaphis graminum, Rondani) is a serious insect pest in many wheat growing regions and has been infesting cereal crops in the USA for over a century. Continuous occurrence of new greenbug biotypes makes it essential to explore all greenbug resistant sources available to manage this pest. Gb1, a recessive greenbug resistance gene in DS28A, confers resistance to several economically important greenbug biotypes and is the only gene found to be resistant to greenbug biotype F. A set of 174 F_(2:3)lines from the cross DS28A × Custer was evaluated for resistance to greenbug biotype F in 2020 and 2022. Selective genotyping of the corresponding F_(2) population using single nucleotide polymorphism(SNP) markers generated by genotyping-by-sequencing(GBS) led to the identification of a candidate genomic region for Gb1. Thus, SSR markers previously mapped in this region were used to genotype the entire F2population,and kompetitive allele specific PCR(KASP) markers were also developed from SNPs in the target region.Gb1 was placed in the terminal region of the short arm of chromosome 1A, and its location was confirmed in a second population derived from the cross DS28A × PI 697274. The combined data analysis from the two mapping populations delimited Gb1 to a < 1 Mb interval between 13,328,200 and 14,241,426 bp on1AS.
基金supported by the Strategic Priority Research Program of Chinese Academy of Sciences(Grant No.XDA17010504)the National Natural Science Foundation of China(Grant No.11947302)。
文摘The folding of many small proteins is kinetically a two-state process with one major free-energy barrier to overcome,which can be roughly regarded as the inverse process of unfolding.In this work,we first use a Gaussian network model to predict the folding nucleus corresponding to the major free-energy barrier of protein 2 GB1,and find that the folding nucleus is located in theβ-sheet domain.High-temperature molecular dynamics simulations are then used to investigate the unfolding process of 2 GB1.We draw free-energy surface from unfolding simulations,taking RMSD and contact number as reaction coordinates,which confirms that the folding of 2 GB1 is kinetically a two-state process.The comparison of the contact maps before and after the free energy barrier indicates that the transition from native to non-native structure of the protein is kinetically caused by the destruction of theβ-sheet domain,which manifests that the folding nucleus is indeed located in theβ-sheet domain.Moreover,the constrained MD simulation further confirms that the destruction of the secondary structures does not alter the topology of the protein retained by the folding nucleus.These results provide vital information for upcoming researchers to further understand protein folding in similar systems.
基金supported by the Ministry of Science and Technology of China[grants 2021YFA1302602]the National Natural Science Foundation of China[grants 21925406,21991082,21921004]the Strategic Priority Research Program of the Chinese Academy of Sciences(XDB0540000 and YSBR-068).
文摘Although the parallel incorporation of fluorinated aromatic amino acids(FAAAs)into proteins has been explored since 2010,the corresponding ^(19)F NMR investigation has been lacking to date.To assess the potential of the parallel incorporation of FAAAs in studies of protein structure,dynamics and interactions,we examine the protein yields,fluorine incorporation efficiencies,and ^(19)F NMR spectra upon simultaneously incorporating FAAAs including 3-fluorotyrosine(3FY),4-fluorophenylalanine(4FF)and 5-fluorotryptophan(5FW)into two model proteins:the structured protein GB1 domain(GB1)and the intrinsically disordered protein a-synuclein(a-syn).We found that the simultaneous incorporation of 3FY and 5FW achieved higher efficiency than combinations of 4FF and 5FW,4FF and 3FY,or 3FY,4FF and 5FW.Moreover,incorporating more types of FAAAs leads to a reduction in overall yield.The ^(19)F spectra of 3FY,4FF and 5FW residues in α-syn and GB1 exhibited good dispersion of chemical shifts.However,the GB1 spectrum showed complexity due to incomplete fluorination and interactions within aromatic cluster.This complexity could be significantly reduced by supplementing the medium with natural aromatic amino acids.To validate the advantage of ^(19)F NMR spectrum,we use 3FY-4FF-5FW-F94W-α-syn to investigate the interaction between α-syn and sodium dodecyl sulphate(SDS)micelle.Our study demonstrates that ^(19)F NMR spectroscopy of proteins with parallel incorporation of FAAAs provides a valuable tool for investigating protein conformation,dynamics and interactions.
文摘In this work, multiple molecular dynamics simulations of protein G and protein L unfolding trajectories provide a direct demonstration of the diversity of unfolding pathway and give
