The F_(1)-ATPase and V_(1)-ATPase are rotary biomotors.Alignment of their amino acid sequences,which originate from bovine heart mitochondria(1BMF)and Enterococcus hirae(3VR6),respectively,demonstrates that the segmen...The F_(1)-ATPase and V_(1)-ATPase are rotary biomotors.Alignment of their amino acid sequences,which originate from bovine heart mitochondria(1BMF)and Enterococcus hirae(3VR6),respectively,demonstrates that the segment forming the ATP catalytic pocket is highly conserved.Single-molecule experiments,however,have revealed subtle differences in efficiency between the F_(1) and V_(1) motors.Here,we perform both atomistic and coarse-grained molecular dynamics simulations to investigate the mechanochemical coupling and coordination in F_(1) and V_(1) ATPase.Our results show that the correlation between conformational changes in F_(1) is stronger than that in V_(1),indicating that the mechanochemical coupling in F_(1) is tighter than in V_(1).Moreover,the unidirectional rotation of F_(1) is more processive than that of V_(1),which accounts for the higher efficiency observed in F_(1) and explains the occasional backward steps detected in single-molecule experiments on V_(1).展开更多
RNA binding proteins(RBPs) are a crucial class of proteins that interact with RNA and play a key role in various biological process.Deficiencies or abnormalities of RBPs are closely linked to the occurrence and progre...RNA binding proteins(RBPs) are a crucial class of proteins that interact with RNA and play a key role in various biological process.Deficiencies or abnormalities of RBPs are closely linked to the occurrence and progression of numerous diseases,making RBPs potential therapeutic targets.However,the limited tissue penetration of 254 nm UV irradiation makes it difficult to efficiently crosslink weak and dynamic RNA-protein interactions in mammal tissues.Additionally,RNA degradation in metal catalyzed click reaction further hinders the enrichment of RNA-protein complexes(RPCs).Due to these inherent limitations,globally profiling the RNA binding proteome in mammal organs has long been a challenge.Herein,we proposed a novel method,which utilized a dual crosslinking with formaldehyde and 254 nm UV irradiation,metabolic labeling and metal-free thiol-yne click reaction to enable large-scale enrichment and identification of RBPs in mouse liver,called FTYc_UV.In this method,formaldehyde is first used to crosslink the crude RNA-protein complexes(cRPCs) in situ to address the problem of poor tissue penetration of 254 nm UV irradiation.Furthermore,this method integrates metabolic labeling with a metal-free thiol-yne click reaction to achieve non-destructive RNA tagging.After specifically RNA-RBPs crosslinking by 254 nm UV irradiation in tissue lysates,formaldehyde decrosslinking is employed to remove non-specific proteins,leading to effective enrichment of RPCs from mouse liver and thereby overcoming the poor specificity of formaldehyde crosslinking.Application of FTYc_UV in mouse liver successfully identified over 1600 RBPs covering approximately 75 % of previously reported RBPs.Furthermore,420 candidate RBPs,including 151metabolic enzymes,were also obtained,demonstrating the sensitivity of FTYc_UV and the potential of this method for in-depth exploration of RNA-protein interactions in biological and clinical research.展开更多
基金supported by the National Natural Science Foundation of China(Grant Nos.22193032 and 32401033)the Research Fund of Wenzhou Institute,Chinese Academy of Sciences(Grant Nos.WIUCASQD2020009,WIUCASQD2023005,XSZD2024004,2021HZSY0061,and WIUCASICTP2022)。
文摘The F_(1)-ATPase and V_(1)-ATPase are rotary biomotors.Alignment of their amino acid sequences,which originate from bovine heart mitochondria(1BMF)and Enterococcus hirae(3VR6),respectively,demonstrates that the segment forming the ATP catalytic pocket is highly conserved.Single-molecule experiments,however,have revealed subtle differences in efficiency between the F_(1) and V_(1) motors.Here,we perform both atomistic and coarse-grained molecular dynamics simulations to investigate the mechanochemical coupling and coordination in F_(1) and V_(1) ATPase.Our results show that the correlation between conformational changes in F_(1) is stronger than that in V_(1),indicating that the mechanochemical coupling in F_(1) is tighter than in V_(1).Moreover,the unidirectional rotation of F_(1) is more processive than that of V_(1),which accounts for the higher efficiency observed in F_(1) and explains the occasional backward steps detected in single-molecule experiments on V_(1).
基金financial support from the National Key R&D Program of China (No.2021YFA1302604)Scientific and technological innovation project of China Academy of Chinese Medical Sciences (No.CI2021B017)China Postdoctoral Science Foundation (No.2023T160727)。
文摘RNA binding proteins(RBPs) are a crucial class of proteins that interact with RNA and play a key role in various biological process.Deficiencies or abnormalities of RBPs are closely linked to the occurrence and progression of numerous diseases,making RBPs potential therapeutic targets.However,the limited tissue penetration of 254 nm UV irradiation makes it difficult to efficiently crosslink weak and dynamic RNA-protein interactions in mammal tissues.Additionally,RNA degradation in metal catalyzed click reaction further hinders the enrichment of RNA-protein complexes(RPCs).Due to these inherent limitations,globally profiling the RNA binding proteome in mammal organs has long been a challenge.Herein,we proposed a novel method,which utilized a dual crosslinking with formaldehyde and 254 nm UV irradiation,metabolic labeling and metal-free thiol-yne click reaction to enable large-scale enrichment and identification of RBPs in mouse liver,called FTYc_UV.In this method,formaldehyde is first used to crosslink the crude RNA-protein complexes(cRPCs) in situ to address the problem of poor tissue penetration of 254 nm UV irradiation.Furthermore,this method integrates metabolic labeling with a metal-free thiol-yne click reaction to achieve non-destructive RNA tagging.After specifically RNA-RBPs crosslinking by 254 nm UV irradiation in tissue lysates,formaldehyde decrosslinking is employed to remove non-specific proteins,leading to effective enrichment of RPCs from mouse liver and thereby overcoming the poor specificity of formaldehyde crosslinking.Application of FTYc_UV in mouse liver successfully identified over 1600 RBPs covering approximately 75 % of previously reported RBPs.Furthermore,420 candidate RBPs,including 151metabolic enzymes,were also obtained,demonstrating the sensitivity of FTYc_UV and the potential of this method for in-depth exploration of RNA-protein interactions in biological and clinical research.
