Protein folding is regarded as a quantum transition between the torsion states of a polypeptide chain.According to the quantum theory of conformational dynamics,we propose the dynamical contact order(DCO) defined as a...Protein folding is regarded as a quantum transition between the torsion states of a polypeptide chain.According to the quantum theory of conformational dynamics,we propose the dynamical contact order(DCO) defined as a characteristic of the contact described by the moment of inertia and the torsion potential energy of the polypeptide chain between contact residues.Conse-quently,the protein folding rate can be quantitatively studied from the point of view of dynamics.By comparing theoretical calculations and experimental data on the folding rate of 80 proteins,we successfully validate the view that protein folding is a quantum conformational transition.We conclude that(i) a correlation between the protein folding rate and the contact inertial moment exists;(ii) multi-state protein folding can be regarded as a quantum conformational transition similar to that of two-state proteins but with an intermediate delay.We have estimated the order of magnitude of the time delay;(iii) folding can be classified into two types,exergonic and endergonic.Most of the two-state proteins with higher folding rate are exergonic and most of the multi-state proteins with low folding rate are endergonic.The folding speed limit is determined by exergonic folding.展开更多
It is a challenging task to investigate the different in- fluence of long-range and short-range interactions on two-state and three-state folding kinetics of protein. The networks of the 30 two-state proteins and 15 t...It is a challenging task to investigate the different in- fluence of long-range and short-range interactions on two-state and three-state folding kinetics of protein. The networks of the 30 two-state proteins and 15 three-state proteins were constructed by complex networks analysis at three length scales: Protein Contact Networks, Long-range Interaction Networks and Short-range Interaction Networks. To uncover the relationship between structural properties and folding kinetics of the proteins, the correlations of protein network parameters with protein folding rate and topology parameters contact order were analyzed. The results show that Protein Contact Networks and Short-range Interaction Networks (for both two-state and three-state proteins) exhibit the “small-world” property and Long-range Interaction networks indicate “scale-free” behavior. Our results further indicate that all Protein Contact Networks and Short- range Interaction networks are assortative type. While some of Long-range Interaction Networks are of assortative type, the others are of disassortative type. For two-state proteins, the clustering coefficients of Short-range Interaction Networks show prominent correlation with folding rate and contact order. The assortativity coefficients of Short-range Interaction Networks also show remarkable correlation with folding rate and contact order. Similar correlations exist in Protein Contact Networks of three-state proteins. For two-state proteins, the correlation between contact order and folding rate is determined by the numbers of local contacts. Short- range interactions play a key role in determining the connecting trend among amino acids and they impact the folding rate of two-state proteins directly. For three-state proteins, the folding rate is determined by short-range and long-range interactions among residues together.展开更多
Understanding protein folding rate is the primary key to unlock the fundamental physics underlying protein structure and its folding mechanism.Especially,the temperature dependence of the folding rate remains unsolved...Understanding protein folding rate is the primary key to unlock the fundamental physics underlying protein structure and its folding mechanism.Especially,the temperature dependence of the folding rate remains unsolved in the literature.Starting from the assumption that protein folding is an event of quantum transition between molecular conformations,we calculated the folding rate for all two-state proteins in a database and studied their temperature dependencies.The non-Arrhenius temperature relation for 16 proteins,whose experimental data had previously been available,was successfully interpreted by comparing the Arrhenius plot with the first-principle calculation.A statistical formula for the prediction of two-state protein folding rate was proposed based on quantum folding theory.The statistical comparisons of the folding rates for 65 two-state proteins were carried out,and the theoretical vs.experimental correlation coefficient was 0.73.Moreover,the maximum and the minimum folding rates given by the theory were consistent with the experimental results.展开更多
The Late Cenozoic fold\|and\|thrust zone along the northwestern margin of the Tarim Basin and the adjacent Tian Shan of Central Asia is an actively deforming part of the India\|Asia collision system. This deformation ...The Late Cenozoic fold\|and\|thrust zone along the northwestern margin of the Tarim Basin and the adjacent Tian Shan of Central Asia is an actively deforming part of the India\|Asia collision system. This deformation zone has two remarkable oppositely vergence arcuate fold\|and\|thrust systems (Kepingtage and Kashi\|Atushi fold\|and\|thrust belts) reaching from east of Keping to west of Kashi. This shape is manifested by structure, topography and seismicity. From north to south, this deformation zone is characterized by four main kinematic elements: (1) a hanging\|wall block (Maidan fault and Tuotegongbaizi\|Muziduke thrust system) that represents the Cenozoic reactivation of a late Paleozoic thrust system; (2) an imbricated thrust stack (Kepingtage\|Tashipeshake thrust system) where slices of Tarim platform sediments are thrust south toward the basin; (3) the Kashi\|Atushi fold\|and\|thrust system where thrusting and folding verge toward the Tian Shan; (4) a foot\|wall block (Tarim craton) that dips gently northwest below the sediment\|filled southern Tian Shan basin and generally has little internal deformation.展开更多
基金supported by the Distinguished Scientist Award of Inner Mongolia Autonomous Region(2008)a Major Project Fund of Inner Mongolia University of Technology(Grant No.ZD200917)a Project Fund of Inner Mongolia Natural Science(Grant No.2010BS0104)
文摘Protein folding is regarded as a quantum transition between the torsion states of a polypeptide chain.According to the quantum theory of conformational dynamics,we propose the dynamical contact order(DCO) defined as a characteristic of the contact described by the moment of inertia and the torsion potential energy of the polypeptide chain between contact residues.Conse-quently,the protein folding rate can be quantitatively studied from the point of view of dynamics.By comparing theoretical calculations and experimental data on the folding rate of 80 proteins,we successfully validate the view that protein folding is a quantum conformational transition.We conclude that(i) a correlation between the protein folding rate and the contact inertial moment exists;(ii) multi-state protein folding can be regarded as a quantum conformational transition similar to that of two-state proteins but with an intermediate delay.We have estimated the order of magnitude of the time delay;(iii) folding can be classified into two types,exergonic and endergonic.Most of the two-state proteins with higher folding rate are exergonic and most of the multi-state proteins with low folding rate are endergonic.The folding speed limit is determined by exergonic folding.
文摘It is a challenging task to investigate the different in- fluence of long-range and short-range interactions on two-state and three-state folding kinetics of protein. The networks of the 30 two-state proteins and 15 three-state proteins were constructed by complex networks analysis at three length scales: Protein Contact Networks, Long-range Interaction Networks and Short-range Interaction Networks. To uncover the relationship between structural properties and folding kinetics of the proteins, the correlations of protein network parameters with protein folding rate and topology parameters contact order were analyzed. The results show that Protein Contact Networks and Short-range Interaction Networks (for both two-state and three-state proteins) exhibit the “small-world” property and Long-range Interaction networks indicate “scale-free” behavior. Our results further indicate that all Protein Contact Networks and Short- range Interaction networks are assortative type. While some of Long-range Interaction Networks are of assortative type, the others are of disassortative type. For two-state proteins, the clustering coefficients of Short-range Interaction Networks show prominent correlation with folding rate and contact order. The assortativity coefficients of Short-range Interaction Networks also show remarkable correlation with folding rate and contact order. Similar correlations exist in Protein Contact Networks of three-state proteins. For two-state proteins, the correlation between contact order and folding rate is determined by the numbers of local contacts. Short- range interactions play a key role in determining the connecting trend among amino acids and they impact the folding rate of two-state proteins directly. For three-state proteins, the folding rate is determined by short-range and long-range interactions among residues together.
基金supported by the Distinguished Scientist Award of Inner Mongolia Autonomous Region(2008)
文摘Understanding protein folding rate is the primary key to unlock the fundamental physics underlying protein structure and its folding mechanism.Especially,the temperature dependence of the folding rate remains unsolved in the literature.Starting from the assumption that protein folding is an event of quantum transition between molecular conformations,we calculated the folding rate for all two-state proteins in a database and studied their temperature dependencies.The non-Arrhenius temperature relation for 16 proteins,whose experimental data had previously been available,was successfully interpreted by comparing the Arrhenius plot with the first-principle calculation.A statistical formula for the prediction of two-state protein folding rate was proposed based on quantum folding theory.The statistical comparisons of the folding rates for 65 two-state proteins were carried out,and the theoretical vs.experimental correlation coefficient was 0.73.Moreover,the maximum and the minimum folding rates given by the theory were consistent with the experimental results.
文摘The Late Cenozoic fold\|and\|thrust zone along the northwestern margin of the Tarim Basin and the adjacent Tian Shan of Central Asia is an actively deforming part of the India\|Asia collision system. This deformation zone has two remarkable oppositely vergence arcuate fold\|and\|thrust systems (Kepingtage and Kashi\|Atushi fold\|and\|thrust belts) reaching from east of Keping to west of Kashi. This shape is manifested by structure, topography and seismicity. From north to south, this deformation zone is characterized by four main kinematic elements: (1) a hanging\|wall block (Maidan fault and Tuotegongbaizi\|Muziduke thrust system) that represents the Cenozoic reactivation of a late Paleozoic thrust system; (2) an imbricated thrust stack (Kepingtage\|Tashipeshake thrust system) where slices of Tarim platform sediments are thrust south toward the basin; (3) the Kashi\|Atushi fold\|and\|thrust system where thrusting and folding verge toward the Tian Shan; (4) a foot\|wall block (Tarim craton) that dips gently northwest below the sediment\|filled southern Tian Shan basin and generally has little internal deformation.
