In this study,circular dichroism(CD)and molecular dynamics(MD)simulation were used to investigate the thermal unfolding pathway of staphylococcal enterotoxin B(SEB)at temperatures of 298–371 and 298–500 K,and the re...In this study,circular dichroism(CD)and molecular dynamics(MD)simulation were used to investigate the thermal unfolding pathway of staphylococcal enterotoxin B(SEB)at temperatures of 298–371 and 298–500 K,and the relationship between the experimental and simulation results were explored.Our computational findings on the secondary structure of SEB showed that at room temperature,the CD spectroscopic results were highly consistent with the MD results.Moreover,under heating conditions,the changing trends of helix,sheet and random coil obtained by CD spectral fitting were highly consistent with those obtained by MD.In order to gain a deeper understanding of the thermal stability mechanism of SEB,the MD trajectories were analyzed in terms of root mean square deviation(RMSD),secondary structure assignment(SSA),radius of gyration(R_(g)),free energy surfaces(FES),solvent-accessible surface area(SASA),hydrogen bonds and salt bridges.The results showed that at low heating temperature,domain Ⅰ without loops(omitting the mobile loop region)mainly relied on hydrophobic interaction to maintain its thermal stability,whereas the thermal stability of domain Ⅱ was mainly controlled by salt bridges and hydrogen bonds.Under high heating temperature conditions,the hydrophobic interactions in domain Ⅰ without loops were destroyed and the secondary structure was almost completely lost,while domain Ⅱ could still rely on salt bridges as molecular staples to barely maintain the stability of the secondary structure.These results help us to understand the thermodynamic and kinetic mechanisms that maintain the thermal stability of SEB at the molecular level,and provide a direction for establishing safer and more effective food sterilization processes.展开更多
The incorporation of mechanophores,motifs that transform mechanical stimulus into chemical reaction or optical variation,allows creating materials with stressresponsive properties.The most widely used mechanophore gen...The incorporation of mechanophores,motifs that transform mechanical stimulus into chemical reaction or optical variation,allows creating materials with stressresponsive properties.The most widely used mechanophore generally features a weak bond,but its cleavage is typical an irreversible process.Here,we showed that this problem can be solved by folding–unfolding of a molecular tweezer.We systematically studied the mechanochromic properties of polyurethanes with cyano-substituted oligo(p-phenylene)vinylene(COP)tweezer(DPU).As a control experiment,a class of polyurethanes containing only a single COP moiety(MPU)was also prepared.The DPU showed prominent mechanochromic properties,due to the intramolecular folding–unfolding of COP tweezer under mechanical stimulus.The process was efficient,reversible and optical detectable.However,due to the disability to form either intramolecular folding or intermolecular aggregation,the MPU sample was mechanical inert.展开更多
Aggregation of alpha-synuclein leads to the formation of Lewy bodies in the brains of patients affected by Parkinson's disease (PD). Native human alpha-synuclein is unfolded in solution but assumes a partial alpha...Aggregation of alpha-synuclein leads to the formation of Lewy bodies in the brains of patients affected by Parkinson's disease (PD). Native human alpha-synuclein is unfolded in solution but assumes a partial alpha-helical conformation upon transient binding to lipid membranes. Annealing Molecular Dynamics (AMD) was used to generate a diverse set of unfolded conformers of free monomeric wild-type alpha-synuclein and PD-associated mutants A30P and A53T. The AMD conformers were compared in terms of secondary structure, hydrogen bond network, solvent-accessible surface per residue, and molecular volume. The objective of these simulations was to identify structural properties near mutation sites and the non-amyloid component (NAC) region that differ between wild- type and disease-associated variants and may be associated to aggregation of alpha- synuclein. Based on experimental evidence, a hypothesis exists that aggregation involves the formation of intermolecular beta sheets. According to our results, disease-associated mutants of alpha-synuclein are no more propense to contain extended beta regions than wild-type alpha-synuclein. Moreover, extended beta structures (necessary for beta sheet formation) were not found at or around positions 30 and 53, or the NAC region in any unfolded conformer of wild-type, A30P or A53T alpha-synuclein, under the conditions of the simulations. These results do not support the hypothesis that the mutant's higher propensity to aggregation results solely from changes in amino acid sequence leading to changes in secondary structure folding propensity.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
Enthalpy-entropy compensation was found to be a universal law in protein unfolding based on over 3 000 experimental data. Water molecular reorganization accompanying the protein unfolding was suggested as the origin-o...Enthalpy-entropy compensation was found to be a universal law in protein unfolding based on over 3 000 experimental data. Water molecular reorganization accompanying the protein unfolding was suggested as the origin-of the enthalpy-entropy compensation in protein unfolding. It is indicated that the enthalpy-entropy compensation constitutes the physical foundation that satisfies the biological need of the small free energy changes in protein unfolding, without the sacrifice of the bio-diversity of proteins. The enthalpy-entropy compensation theory proposed herein also provides valuable insights into the Privalov’s puzzle of enthalpy and entropy convergence in protein unfolding.展开更多
Many biological functions of RNA molecules are re- lated to their pseudoknot structures. It is significant for predicting the structure and function of RNA that learning about the stability and the process of RNA pseu...Many biological functions of RNA molecules are re- lated to their pseudoknot structures. It is significant for predicting the structure and function of RNA that learning about the stability and the process of RNA pseudoknot folding and unfolding. The structural features of mouse mammary tumor virus （MMTV） RNA pseudoknot in different ion concentration, the unfolding process of the RNA pseudoknot, and the two hairpin helices that constitute the RNA pseudoknot were studied with all atom molecule dynam- ics simulation method in this paper. We found that the higher cation concentration can cause structure of the RNA molecules more stable, and ions played an indispensable role in keeping the structure of RNA molecules stable; the unfolding process of hair- pin structure was corresponding to the antiprocess of its folding process. The main pathway of pseudoknot unfolding was that the inner base pair opened first, and then, the two helices, which formed the RNA pseudoknot opened decussately, while the folding pathway of the RNA pseudoknot was a helix folding after forma- tion of the other helix. Therefore, the unfolding process of RNA pseudoknot is different from the antiprocess of its folding process, and the unfolding process of each helix in the RNA pseudoknot is similar to the hairpin structure＇s unfolding process, which means that both are the unzipping process.展开更多
An understanding of protein folding/unfolding processes has important implications for all biological processes, in- eluding protein degradation, protein translocation, aging, and diseases. All-atom molecular dynamics...An understanding of protein folding/unfolding processes has important implications for all biological processes, in- eluding protein degradation, protein translocation, aging, and diseases. All-atom molecular dynamics （MD） simulations are uniquely suitable for it because of their atomic level resolution and accuracy. However, limited by computational ca- pabilities, nowadays even for small and fast-folding proteins, all-atom MD simulations of protein folding still presents a great challenge. An alternative way is to study unfolding process using MD simulations at high temperature. High temper- ature provides more energy to overcome energetic barriers to unfolding, and information obtained from studying unfolding can shed light on the mechanism of folding. In the present study, a 1000-ns MD simulation at high temperature （500 K） was performed to investigate the unfolding process of a small protein, chicken villin headpiece （HP-35）. To infer the folding mechanism, a Markov state model was also built from our simulation, which maps out six macrostates during the folding/unfolding process as well as critical transitions between them, revealing the folding mechanism unambiguously.展开更多
a-Crystallin is the major structural protein of eye lens of vertebrates. In human lens, the ratio of aA-crystallin to aB-crystallin was found to be 3:1. aA-Crystallin contains two cysteine residues at positions 131 an...a-Crystallin is the major structural protein of eye lens of vertebrates. In human lens, the ratio of aA-crystallin to aB-crystallin was found to be 3:1. aA-Crystallin contains two cysteine residues at positions 131 and 142, which are at the junction between the a-crystallin domain and the C-terminal tail. We used the accessibility of the thiol groups by Ellman’s reagent (DTNB) as a tool to gain information about the various structural perturbations of hinge region of a-crystallin and during the binding with substrates. In the native condition, the cys-142 though reacted quite fast was not fully exposed. Several reagents were used to see the accessibility of cys-131. Rate constant for cys-131 was increased gradually with increase in the concentration of reagents. The bindings of substrates are affected by the accessibility of thiol indicating that the substrates bind to the hinge region of a-crystallin. By blocking of cys-142, it was observed that the accessibility of one thiol depends on the other thiol, and they are not independent. The hinge region of a-crystallin is very important as substrate binding site and from this study we have got various structural information about that region.展开更多
文摘In this study,circular dichroism(CD)and molecular dynamics(MD)simulation were used to investigate the thermal unfolding pathway of staphylococcal enterotoxin B(SEB)at temperatures of 298–371 and 298–500 K,and the relationship between the experimental and simulation results were explored.Our computational findings on the secondary structure of SEB showed that at room temperature,the CD spectroscopic results were highly consistent with the MD results.Moreover,under heating conditions,the changing trends of helix,sheet and random coil obtained by CD spectral fitting were highly consistent with those obtained by MD.In order to gain a deeper understanding of the thermal stability mechanism of SEB,the MD trajectories were analyzed in terms of root mean square deviation(RMSD),secondary structure assignment(SSA),radius of gyration(R_(g)),free energy surfaces(FES),solvent-accessible surface area(SASA),hydrogen bonds and salt bridges.The results showed that at low heating temperature,domain Ⅰ without loops(omitting the mobile loop region)mainly relied on hydrophobic interaction to maintain its thermal stability,whereas the thermal stability of domain Ⅱ was mainly controlled by salt bridges and hydrogen bonds.Under high heating temperature conditions,the hydrophobic interactions in domain Ⅰ without loops were destroyed and the secondary structure was almost completely lost,while domain Ⅱ could still rely on salt bridges as molecular staples to barely maintain the stability of the secondary structure.These results help us to understand the thermodynamic and kinetic mechanisms that maintain the thermal stability of SEB at the molecular level,and provide a direction for establishing safer and more effective food sterilization processes.
基金This work was financially supported by the National Natural Science Foundation of China(Grant Nos.52103141 and 51803090)the Natural Science Foundation of Jiangsu Province(Grant Nos.BK20181025 and BK20191022)for financial support.
文摘The incorporation of mechanophores,motifs that transform mechanical stimulus into chemical reaction or optical variation,allows creating materials with stressresponsive properties.The most widely used mechanophore generally features a weak bond,but its cleavage is typical an irreversible process.Here,we showed that this problem can be solved by folding–unfolding of a molecular tweezer.We systematically studied the mechanochromic properties of polyurethanes with cyano-substituted oligo(p-phenylene)vinylene(COP)tweezer(DPU).As a control experiment,a class of polyurethanes containing only a single COP moiety(MPU)was also prepared.The DPU showed prominent mechanochromic properties,due to the intramolecular folding–unfolding of COP tweezer under mechanical stimulus.The process was efficient,reversible and optical detectable.However,due to the disability to form either intramolecular folding or intermolecular aggregation,the MPU sample was mechanical inert.
文摘Aggregation of alpha-synuclein leads to the formation of Lewy bodies in the brains of patients affected by Parkinson's disease (PD). Native human alpha-synuclein is unfolded in solution but assumes a partial alpha-helical conformation upon transient binding to lipid membranes. Annealing Molecular Dynamics (AMD) was used to generate a diverse set of unfolded conformers of free monomeric wild-type alpha-synuclein and PD-associated mutants A30P and A53T. The AMD conformers were compared in terms of secondary structure, hydrogen bond network, solvent-accessible surface per residue, and molecular volume. The objective of these simulations was to identify structural properties near mutation sites and the non-amyloid component (NAC) region that differ between wild- type and disease-associated variants and may be associated to aggregation of alpha- synuclein. Based on experimental evidence, a hypothesis exists that aggregation involves the formation of intermolecular beta sheets. According to our results, disease-associated mutants of alpha-synuclein are no more propense to contain extended beta regions than wild-type alpha-synuclein. Moreover, extended beta structures (necessary for beta sheet formation) were not found at or around positions 30 and 53, or the NAC region in any unfolded conformer of wild-type, A30P or A53T alpha-synuclein, under the conditions of the simulations. These results do not support the hypothesis that the mutant's higher propensity to aggregation results solely from changes in amino acid sequence leading to changes in secondary structure folding propensity.
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
文摘Enthalpy-entropy compensation was found to be a universal law in protein unfolding based on over 3 000 experimental data. Water molecular reorganization accompanying the protein unfolding was suggested as the origin-of the enthalpy-entropy compensation in protein unfolding. It is indicated that the enthalpy-entropy compensation constitutes the physical foundation that satisfies the biological need of the small free energy changes in protein unfolding, without the sacrifice of the bio-diversity of proteins. The enthalpy-entropy compensation theory proposed herein also provides valuable insights into the Privalov’s puzzle of enthalpy and entropy convergence in protein unfolding.
基金supported by the National Key Basic Research Program of China(973)(2009CB918500,2003CB514104)National Natural Science Foundation of China(20973016,11021463,31170682)~~
基金Supported by the National Natural Science Foundation of China(10774115)the Doctoral Fund of Ministry of Education of China(20110141110009)
文摘Many biological functions of RNA molecules are re- lated to their pseudoknot structures. It is significant for predicting the structure and function of RNA that learning about the stability and the process of RNA pseudoknot folding and unfolding. The structural features of mouse mammary tumor virus （MMTV） RNA pseudoknot in different ion concentration, the unfolding process of the RNA pseudoknot, and the two hairpin helices that constitute the RNA pseudoknot were studied with all atom molecule dynam- ics simulation method in this paper. We found that the higher cation concentration can cause structure of the RNA molecules more stable, and ions played an indispensable role in keeping the structure of RNA molecules stable; the unfolding process of hair- pin structure was corresponding to the antiprocess of its folding process. The main pathway of pseudoknot unfolding was that the inner base pair opened first, and then, the two helices, which formed the RNA pseudoknot opened decussately, while the folding pathway of the RNA pseudoknot was a helix folding after forma- tion of the other helix. Therefore, the unfolding process of RNA pseudoknot is different from the antiprocess of its folding process, and the unfolding process of each helix in the RNA pseudoknot is similar to the hairpin structure＇s unfolding process, which means that both are the unzipping process.
基金Project supported by the National Natural Science Foundation of China(Grant Nos.11175068 and 11474117)the Self-determined Research Funds of CCNU from the Colleges Basic Research and Operation of MOE,China(Grant No.230-20205170054)
文摘An understanding of protein folding/unfolding processes has important implications for all biological processes, in- eluding protein degradation, protein translocation, aging, and diseases. All-atom molecular dynamics （MD） simulations are uniquely suitable for it because of their atomic level resolution and accuracy. However, limited by computational ca- pabilities, nowadays even for small and fast-folding proteins, all-atom MD simulations of protein folding still presents a great challenge. An alternative way is to study unfolding process using MD simulations at high temperature. High temper- ature provides more energy to overcome energetic barriers to unfolding, and information obtained from studying unfolding can shed light on the mechanism of folding. In the present study, a 1000-ns MD simulation at high temperature （500 K） was performed to investigate the unfolding process of a small protein, chicken villin headpiece （HP-35）. To infer the folding mechanism, a Markov state model was also built from our simulation, which maps out six macrostates during the folding/unfolding process as well as critical transitions between them, revealing the folding mechanism unambiguously.
文摘a-Crystallin is the major structural protein of eye lens of vertebrates. In human lens, the ratio of aA-crystallin to aB-crystallin was found to be 3:1. aA-Crystallin contains two cysteine residues at positions 131 and 142, which are at the junction between the a-crystallin domain and the C-terminal tail. We used the accessibility of the thiol groups by Ellman’s reagent (DTNB) as a tool to gain information about the various structural perturbations of hinge region of a-crystallin and during the binding with substrates. In the native condition, the cys-142 though reacted quite fast was not fully exposed. Several reagents were used to see the accessibility of cys-131. Rate constant for cys-131 was increased gradually with increase in the concentration of reagents. The bindings of substrates are affected by the accessibility of thiol indicating that the substrates bind to the hinge region of a-crystallin. By blocking of cys-142, it was observed that the accessibility of one thiol depends on the other thiol, and they are not independent. The hinge region of a-crystallin is very important as substrate binding site and from this study we have got various structural information about that region.
