scholarly journals A QM/MM study on the origin of retro-aldolase activity of a catalytic antibody

2021 ◽  
Author(s):  
Daria De Raffele ◽  
Sergio Martí ◽  
Vicent Moliner
Keyword(s):  
Free Energy ◽  
Energy Landscape ◽  
Free Energy Landscape ◽  
Catalytic Antibody ◽  
Aldolase Activity

The retro-aldolase mechanism of methodol catalysed by the catalytic antibody 33F12 is described based on the exploration of the free energy landscape obtained with QM/MM methods.

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>

The Perturbed Free Energy Landscape: Linking Ligand Binding to Biomolecular Folding

ChemBioChem ◽  
2020 ◽  
Author(s):  
fareed aboul-ela ◽  
Abdallah S Abdelsatter ◽  
Youssef Mansour
Keyword(s):  
Free Energy ◽  
Ligand Binding ◽  
Energy Landscape ◽  
Free Energy Landscape

Free-Energy Landscape of a pH-Modulated G·C Base Pair Transition from Watson–Crick to Hoogsteen State in Duplex DNA

2021 ◽  
Vol 17 (4) ◽  
pp. 2556-2565
Author(s):  
Hyeonjun Kim ◽  
Changwon Yang ◽  
Youngshang Pak
Keyword(s):  
Free Energy ◽  
Base Pair ◽  
Energy Landscape ◽  
Free Energy Landscape ◽  
Duplex Dna

Topography of the Free Energy Landscape on the Claisen-Schmidt Condensation: Solvent and Temperature Effect in the Rate-Controlling Step

2021 ◽  
Author(s):  
Nayara Dantas Coutinho ◽  
Hugo Gontijo Machado ◽  
Valter Henrique Carvalho-Silva ◽  
Wender A. Silva
Keyword(s):  
Free Energy ◽  
Temperature Effect ◽  
Strong Influence ◽  
Aldol Condensation ◽  
Energy Landscape ◽  
Bond Formation ◽  
Free Energy Landscape ◽  
Rate Controlling Step ◽  
Formation Step

Recent studies have assigned hydroxide elimination and C=C bond formation step in base-promoted aldol condensation the role of having a strong influence in the overall rate reaction, in contrast to...

scholarly journals Crystallization of hard spheres revisited. I. Extracting kinetics and free energy landscape from forward flux sampling

2018 ◽  
Vol 148 (12) ◽  
pp. 124110 ◽  
Author(s):  
David Richard ◽  
Thomas Speck
Keyword(s):  
Free Energy ◽  
Hard Spheres ◽  
Energy Landscape ◽  
Free Energy Landscape

scholarly journals Exploring the Free Energy Landscape of Nucleosomes

2016 ◽  
Vol 138 (26) ◽  
pp. 8126-8133 ◽  
Author(s):  
Bin Zhang ◽  
Weihua Zheng ◽  
Garegin A. Papoian ◽  
Peter G. Wolynes
Keyword(s):  
Free Energy ◽  
Energy Landscape ◽  
Free Energy Landscape
Sign in / Sign up

Export Citation Format

Share Document