ABSTRACT Free energy perturbation calculations are carried out to estimate the effective pKa of an Arginine (Arg) sidechain as a function of its location in the Dipalmitoylphosphatidylcholine (DPPC)...
Allostery and cooperativity revisited (2008)
Although phenomenlogical models that account for cooperativity in allosteric systems date back to the early and mid-60's (e.g., the KNF and MWC models), there is resurgent interest in the topic due...
Haibo Yu, Liang Ma, Yang Yang, Qiang Cui
Although the major structural transitions in molecular motors are often argued to couple to the binding of Adenosine triphosphate (ATP), the recovery stroke in the conventional myosin has been shown...
Mechanochemical Coupling in the Myosin Motor Domain. II. Analysis of Critical Residues (2007)
Haibo Yu, Liang Ma, Yang Yang, Qiang Cui
An important challenge in the analysis of mechanochemical coupling in molecular motors is to identify residues that dictate the tight coupling between the chemical site and distant structural...
Haibo Yu, Liang Ma, Yang Yang, Qiang Cui
Understanding the structure-function relationship in molecular motors relies on a quantitative description of how the local structural changes associated with ATP hydrolysis are propagated over a...
Mechanochemical coupling in the myosin motor domain. II. Analysis of critical residues (2006)
Haibo Yu, Liang Ma, Yang Yang, Qiang Cui
Understanding the structure-function relationship in molecular motors relies on a quantitative description of how the local structural changes associated with ATP hydrolysis are propagated over a...
Protein structural variation in computational models and crystallographic data (2006)
Kondrashov, Dmitry A., Van Wynsberghe, Adam W., Bannen, Ryan M., Cui, Qiang, Phillips Jr, George N.
Normal mode analysis offers an efficient way of modeling the conformational flexibility of protein structures. Simple models defined by contact topology, known as elastic network models, have been...
Kondrashov, Dmitry A., Cui, Qiang, Phillips Jr, George N.
Simple coarse-grained models, such as the Gaussian Network Model, have been shown to capture some of the features of equilibrium protein dynamics. We extend this model by using atomic contacts to...
Ca -atpase, Guohui Li, Qiang Cui
ABSTRACT The structural flexibilities of two molecular machines, myosin and Ca 21-ATPase, have been analyzed with normal mode analysis and discussed in the context of their energy conversion...
The effect of dissolving salts or gases in water sprayed on a hot surface (2001)
grantor: University of Toronto
Guo, Hong, Cui, Qiang, Lipscomb, William N., Karplus, Martin
Chorismate mutase acts at the first branch-point of aromatic amino acid biosynthesis and catalyzes the conversion of chorismate to prephenate. The results of molecular dynamics simulations of the...
A block normal mode (BNM) algorithm, originally proposed by Tama et al., (Proteins Struct. Func. Genet. 41:1-7, 2000) was implemented into the simulation program CHARMM. The BNM approach projects the...
The structural flexibilities of two molecular machines, myosin and Ca2+-ATPase, have been analyzed with normal mode analysis and discussed in the context of their energy conversion functions. The...
Comparison of Mode Analyses at Different Resolutions Applied to Nucleic Acid Systems
Van Wynsberghe, Adam W., Cui, Qiang
More than two decades of different types of mode analyses has shown that these techniques can be useful in describing large-scale motions in protein systems. A number of mode analyses are available...
Guo, Hong, Cui, Qiang, Lipscomb, William N., Karplus, Martin
Chorismate mutase acts at the first branch-point of aromatic amino acid biosynthesis and catalyzes the conversion of chorismate to prephenate. The results of molecular dynamics simulations of the...
A block normal mode (BNM) algorithm, originally proposed by Tama et al., (Proteins Struct. Func. Genet. 41:1-7, 2000) was implemented into the simulation program CHARMM. The BNM approach projects the...
The structural flexibilities of two molecular machines, myosin and Ca2+-ATPase, have been analyzed with normal mode analysis and discussed in the context of their energy conversion functions. The...
Comparison of Mode Analyses at Different Resolutions Applied to Nucleic Acid Systems
Van Wynsberghe, Adam W., Cui, Qiang
More than two decades of different types of mode analyses has shown that these techniques can be useful in describing large-scale motions in protein systems. A number of mode analyses are available...
Yu, Haibo, Ma, Liang, Yang, Yang, Cui, Qiang
Although the major structural transitions in molecular motors are often argued to couple to the binding of Adenosine triphosphate (ATP), the recovery stroke in the conventional myosin has been shown...
Mechanochemical Coupling in the Myosin Motor Domain. II. Analysis of Critical Residues
Yu, Haibo, Ma, Liang, Yang, Yang, Cui, Qiang
An important challenge in the analysis of mechanochemical coupling in molecular motors is to identify residues that dictate the tight coupling between the chemical site and distant structural...
Tang, Yuye, Cao, Guoxin, Chen, Xi, Yoo, Jejoong, Yethiraj, Arun, Cui, Qiang
The gating pathways of mechanosensitive channels of large conductance (MscL) in two bacteria (Mycobacterium tuberculosis and Escherichia coli) are studied using the finite element method. The...
Optimization and Evaluation of a Coarse-Grained Model of Protein Motion Using X-Ray Crystal Data
Kondrashov, Dmitry A., Cui, Qiang, Phillips, George N.
Simple coarse-grained models, such as the Gaussian network model, have been shown to capture some of the features of equilibrium protein dynamics. We extend this model by using atomic contacts to...
Qiang Cui, Emanuele Baldacci, Benedict J. Clements, Sanjeev Gupta
Social policy , Human capital , Developing countries , Government expenditures , Economic growth , Millennium Development Goals ,
Social Spending, Human Capital, and Growth in Developing Countries
Baldacci, Emanuele, Clements, Benedict, Gupta, Sanjeev, Cui, Qiang
Summary Using panel data from 118 developing countries in 1971-2000, this paper explores the channels linking social spending, human capital, and growth and compares the effects of alternative...
Does Arginine Remain Protonated in the Lipid Membrane? Insights from Microscopic pKa Calculations
Free energy perturbation calculations are carried out to estimate the effective pKa of an arginine (Arg) sidechain as a function of its location in the dipalmitoylphosphatidylcholine bilayer. Similar...
Macro-fiscal policy challenges and public investment in new EU member states
Schwartz, Gerd, Corbacho, Ana, Cui, Qiang, Ganelli, Giovanni, Manasse, Paolo
Most new EU member states (NMS) need further fiscal adjustment to support economic growth and macroeconomic stability. In this context, achieving income convergence with other EU members rests more...
Amino acids with an intermolecular proton bond as proton storage site in bacteriorhodopsin
Phatak, Prasad, Ghosh, Nilanjan, Yu, Haibo, Cui, Qiang, Elstner, Marcus
The positions of protons are not available in most high-resolution structural data of biomolecules, thus the identity of proton storage sites in biomolecules that transport proton is generally...
Chen, Xi, Cui, Qiang, Tang, Yuye, Yoo, Jejoong, Yethiraj, Arun
A hierarchical simulation framework that integrates information from molecular dynamics (MD) simulations into a continuum model is established to study the mechanical response of mechanosensitive...
Tang, Yuye, Yoo, Jejoong, Yethiraj, Arun, Cui, Qiang, Chen, Xi
Part II of this study is based on the continuum mechanics-based molecular dynamics-decorated finite element method (MDeFEM) framework established in Part I. In Part II, the gating pathways of...
Allostery and cooperativity revisited
Although phenomenlogical models that account for cooperativity in allosteric systems date back to the early and mid-60's (e.g., the KNF and MWC models), there is resurgent interest in the topic due...