A clear diagram for the unfolding of protein induced by denaturant is a classical but still unsolved challenge. To explore the unfolded conformations of ubiquitin under different urea concentrations, we performed hybr...A clear diagram for the unfolding of protein induced by denaturant is a classical but still unsolved challenge. To explore the unfolded conformations of ubiquitin under different urea concentrations, we performed hybrid Monte Carlo-molecular dynamics simulations (MC-MD) guided by small angle X-ray scattering (SAXS) structural information. Conformational ensembles sampled by the hybrid MC-MD algorithm exhibited typical 3D structures at different urea concentrations. These typical structures suggested that ubiquitin was subjected to a sequential unfolding, where the native contacts between adjacent β-sheets at first were disrupted together with the exposure of hydrophobic core, followed by the conversion of remaining β-strands and helices into random coils. Ubiquitin in 8 mol·L?1 urea is almost a random coil. With the disruption of native structure, urea molecules are enriched at protein hydrated layer to stabilize newly exposed residues. Compared with water, urea molecules prefer to form hydrogen bonds with the backbone of ubiquitin, thus occupying nodes of the hydrogen bonding network that construct the secondary structure of proteins. Meanwhile, we also found that the slow dynamics of urea molecules was almost unchanged while the dynamics of water was accelerated in the hydration shell when more residues were unfolded and exposed. The former was also responsible for the stabilization of unfolded structures.展开更多
Conformation and dynamical evolution of block copolymers in shear flow is an important topic in polymer physics that underscores the forming process of various materials.We explored deformation and dynamics of copolym...Conformation and dynamical evolution of block copolymers in shear flow is an important topic in polymer physics that underscores the forming process of various materials.We explored deformation and dynamics of copolymers composed of rigid or flexible blocks in simple shear flow by employing multiparticle collision dynamics integrated with molecular dynamics simulations.We found that compared with the proportion between rigid and flexible blocks,the type of the central blocks plays more important role in the conformational and dynamical evolution of copolymers.That is,if the central block is a coil,the copolymer chain takes end-over-end tumbling motion,while if the central block is a rod,the copolymer chain undergoes U-shape or S-shape deformation at mid shear rate.As the shear strength increases,all copolymers behave similar to flexible polymers at high shear rate.This can be attributed to the fact that shear flow is strong enough to overcome the buckling force of the rigid blocks.These results provide a deeper understanding of the roles played by rod and coil blocks in copolymers for phase interface during forming processing.展开更多
The tumbling dynamics of individual absorbed polymer chains in shear flow is studied by employing multi-particle collision dynamics simulation techniques combined with molecular dynamics simulations.We find that the d...The tumbling dynamics of individual absorbed polymer chains in shear flow is studied by employing multi-particle collision dynamics simulation techniques combined with molecular dynamics simulations.We find that the dependence of tumbling frequencies on shear rate is independent of both adsorption strength and surface corrugate.展开更多
基金financially supported by the National Natural Science Foundation of China (Nos. 21504092 and U1832177)One Hundred Person Project of the Chinese Academy of Sciences+1 种基金Computing Center of Jilin ProvinceHenan Province Supercomputer Center for essential support
文摘A clear diagram for the unfolding of protein induced by denaturant is a classical but still unsolved challenge. To explore the unfolded conformations of ubiquitin under different urea concentrations, we performed hybrid Monte Carlo-molecular dynamics simulations (MC-MD) guided by small angle X-ray scattering (SAXS) structural information. Conformational ensembles sampled by the hybrid MC-MD algorithm exhibited typical 3D structures at different urea concentrations. These typical structures suggested that ubiquitin was subjected to a sequential unfolding, where the native contacts between adjacent β-sheets at first were disrupted together with the exposure of hydrophobic core, followed by the conversion of remaining β-strands and helices into random coils. Ubiquitin in 8 mol·L?1 urea is almost a random coil. With the disruption of native structure, urea molecules are enriched at protein hydrated layer to stabilize newly exposed residues. Compared with water, urea molecules prefer to form hydrogen bonds with the backbone of ubiquitin, thus occupying nodes of the hydrogen bonding network that construct the secondary structure of proteins. Meanwhile, we also found that the slow dynamics of urea molecules was almost unchanged while the dynamics of water was accelerated in the hydration shell when more residues were unfolded and exposed. The former was also responsible for the stabilization of unfolded structures.
基金supported by the National Natural Science Foundation of China(Nos.21774128,U1832177)Key Research Program of Frontier Sciences(No.QYZDY-SSWSLH027)NSFC Resource and Ecology Based Synthetic Polymeric Materials(No.51988102)。
文摘Conformation and dynamical evolution of block copolymers in shear flow is an important topic in polymer physics that underscores the forming process of various materials.We explored deformation and dynamics of copolymers composed of rigid or flexible blocks in simple shear flow by employing multiparticle collision dynamics integrated with molecular dynamics simulations.We found that compared with the proportion between rigid and flexible blocks,the type of the central blocks plays more important role in the conformational and dynamical evolution of copolymers.That is,if the central block is a coil,the copolymer chain takes end-over-end tumbling motion,while if the central block is a rod,the copolymer chain undergoes U-shape or S-shape deformation at mid shear rate.As the shear strength increases,all copolymers behave similar to flexible polymers at high shear rate.This can be attributed to the fact that shear flow is strong enough to overcome the buckling force of the rigid blocks.These results provide a deeper understanding of the roles played by rod and coil blocks in copolymers for phase interface during forming processing.
基金supported by the National Natural Science Foundation of China (No. 21274153)
文摘The tumbling dynamics of individual absorbed polymer chains in shear flow is studied by employing multi-particle collision dynamics simulation techniques combined with molecular dynamics simulations.We find that the dependence of tumbling frequencies on shear rate is independent of both adsorption strength and surface corrugate.
