Role of tyrosine hot-spot residues at the interface of colicin E9 and immunity protein 9: A comparative free energy simulation study

2012 ◽  
Vol 81 (3) ◽  
pp. 461-468 ◽  
Author(s):  
Manuel P. Luitz ◽  
Martin Zacharias
Keyword(s):  
Free Energy ◽  
Simulation Study ◽  
Hot Spot ◽  
Energy Simulation ◽  
Immunity Protein ◽  
Colicin E9

Dual Recognition and the Role of Specificity-Determining Residues in Colicin E9 DNase−Immunity Protein Interactions†

Biochemistry ◽  
1998 ◽  
Vol 37 (34) ◽  
pp. 11771-11779 ◽  
Author(s):  
Wei Li ◽  
Stefan J. Hamill ◽  
Andrew M. Hemmings ◽  
Geoffrey R. Moore ◽  
Richard James ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Immunity Protein ◽  
Colicin E9

Determination of Base Flipping Free Energy Landscapes from Nonequilibrium Stratification

2019 ◽  
Author(s):  
Xiaohui Wang ◽  
Zhaoxi Sun
Keyword(s):  
Free Energy ◽  
Energy Landscape ◽  
Sampling Technique ◽  
Umbrella Sampling ◽  
Energy Simulation ◽  
Nonlinear Dependence ◽  
Free Energy Landscape ◽  
Convergence Criterion ◽  
Base Flipping ◽  
Convergence Behavior

<p>Correct calculation of the variation of free energy upon base flipping is crucial in understanding the dynamics of DNA systems. The free energy landscape along the flipping pathway gives the thermodynamic stability and the flexibility of base-paired states. Although numerous free energy simulations are performed in the base flipping cases, no theoretically rigorous nonequilibrium techniques are devised and employed to investigate the thermodynamics of base flipping. In the current work, we report a general nonequilibrium stratification scheme for efficient calculation of the free energy landscape of base flipping in DNA duplex. We carefully monitor the convergence behavior of the equilibrium sampling based free energy simulation and the nonequilibrium stratification and determine the empirical length of time blocks required for converged sampling. Comparison between the performances of equilibrium umbrella sampling and nonequilibrium stratification is given. The results show that nonequilibrium free energy simulation is able to give similar accuracy and efficiency compared with the equilibrium enhanced sampling technique in the base flipping cases. We further test a convergence criterion we previously proposed and it comes out that the convergence behavior determined by this criterion agrees with those given by the time-invariant behavior of PMF and the nonlinear dependence of standard deviation on the sample size. </p>

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