Assuming that the main variables in the life processes at the molecular level are the conforma- tion of biological macromolecules and their frontier electrons a formalism of quantum theory on conformation-electron sys...Assuming that the main variables in the life processes at the molecular level are the conforma- tion of biological macromolecules and their frontier electrons a formalism of quantum theory on conformation-electron system is proposed. Based on the quantum theory of conformation-electron system, the protein folding is regarded as a quantum transition between torsion states on polypep- tide chain, and the folding rate is calculated by nonadiabatic operator method. The rate calculation is generalized to the case of frequency variation in folding. An analytical form of protein folding rate formula is obtained, which can be served as a useful tool for further studying protein folding. The application of the rate theory to explain the protein folding experiments is briefly summarized. It includes the inertial moment dependence of folding rate, the unified description of two-state and multistate protein folding, the relationship of folding and unfolding rates versus denaturant concen- tration, the distinction between exergonic and endergonic foldings, the ultrafast and the downhill folding viewed from quantum folding theory, and, finally, the temperature dependence of folding rate and the interpretation of its non-Arrhenius behaviors. All these studies support the view that the protein folding is essentially a quantum transition between conformational states.展开更多
We have developed a web-server for predicting the folding rate of a protein based on its amino acid sequence information alone. The web- server is called Pred-PFR (Predicting Protein Folding Rate). Pred-PFR is feature...We have developed a web-server for predicting the folding rate of a protein based on its amino acid sequence information alone. The web- server is called Pred-PFR (Predicting Protein Folding Rate). Pred-PFR is featured by fusing multiple individual predictors, each of which is established based on one special feature derived from the protein sequence. The ensemble pre-dictor thus formed is superior to the individual ones, as demonstrated by achieving higher correlation coefficient and lower root mean square deviation between the predicted and observed results when examined by the jack-knife cross-validation on a benchmark dataset constructed recently. As a user-friendly web- server, Pred-PFR is freely accessible to the public at www.csbio.sjtu.edu.cn/bioinf/Folding Rate/.展开更多
寻找改进蛋白质折叠速率可预测性的经验参数,是理解蛋白质折叠机制的重要途径之一。假设蛋白质的折叠元件为天然态二级结构,对折叠元件的组织过程即为折叠。构造了表征折叠自由能垒高度的经验参数——二级结构数与非局域相互作用的耦合(...寻找改进蛋白质折叠速率可预测性的经验参数,是理解蛋白质折叠机制的重要途径之一。假设蛋白质的折叠元件为天然态二级结构,对折叠元件的组织过程即为折叠。构造了表征折叠自由能垒高度的经验参数——二级结构数与非局域相互作用的耦合(coupling of secondary structure number and nonlocal interaction,CSNI),进一步按照过渡态理论建立了折叠速率预测模型。在现有实验资料集上检验,CSNI模型对折叠速率的拟合优度达到R2=0.73,相关性优于现有的典型模型,并且由CSNI模型所呈现的折叠自由能景观,为深入理解蛋白质折叠机制提供了见解.展开更多
文摘Assuming that the main variables in the life processes at the molecular level are the conforma- tion of biological macromolecules and their frontier electrons a formalism of quantum theory on conformation-electron system is proposed. Based on the quantum theory of conformation-electron system, the protein folding is regarded as a quantum transition between torsion states on polypep- tide chain, and the folding rate is calculated by nonadiabatic operator method. The rate calculation is generalized to the case of frequency variation in folding. An analytical form of protein folding rate formula is obtained, which can be served as a useful tool for further studying protein folding. The application of the rate theory to explain the protein folding experiments is briefly summarized. It includes the inertial moment dependence of folding rate, the unified description of two-state and multistate protein folding, the relationship of folding and unfolding rates versus denaturant concen- tration, the distinction between exergonic and endergonic foldings, the ultrafast and the downhill folding viewed from quantum folding theory, and, finally, the temperature dependence of folding rate and the interpretation of its non-Arrhenius behaviors. All these studies support the view that the protein folding is essentially a quantum transition between conformational states.
文摘We have developed a web-server for predicting the folding rate of a protein based on its amino acid sequence information alone. The web- server is called Pred-PFR (Predicting Protein Folding Rate). Pred-PFR is featured by fusing multiple individual predictors, each of which is established based on one special feature derived from the protein sequence. The ensemble pre-dictor thus formed is superior to the individual ones, as demonstrated by achieving higher correlation coefficient and lower root mean square deviation between the predicted and observed results when examined by the jack-knife cross-validation on a benchmark dataset constructed recently. As a user-friendly web- server, Pred-PFR is freely accessible to the public at www.csbio.sjtu.edu.cn/bioinf/Folding Rate/.
文摘寻找改进蛋白质折叠速率可预测性的经验参数,是理解蛋白质折叠机制的重要途径之一。假设蛋白质的折叠元件为天然态二级结构,对折叠元件的组织过程即为折叠。构造了表征折叠自由能垒高度的经验参数——二级结构数与非局域相互作用的耦合(coupling of secondary structure number and nonlocal interaction,CSNI),进一步按照过渡态理论建立了折叠速率预测模型。在现有实验资料集上检验,CSNI模型对折叠速率的拟合优度达到R2=0.73,相关性优于现有的典型模型,并且由CSNI模型所呈现的折叠自由能景观,为深入理解蛋白质折叠机制提供了见解.
