Free Energy Landscape and Proton Transfer Pathways of the Transimination Reaction at the Active site of the Serine Hydroxymethyltransferase Enzyme in Aqueous Medium

2021 ◽  
Author(s):  
Kumari Soniya ◽  
Amalendu Chandra
Keyword(s):  
Free Energy ◽  
Proton Transfer ◽  
Aqueous Medium ◽  
Active Site ◽  
Energy Landscape ◽  
Serine Hydroxymethyltransferase ◽  
Free Energy Landscape

Free-Energy Landscape and Proton Transfer Pathways in Oxidative Deamination by Methylamine Dehydrogenase

ChemPhysChem ◽  
2016 ◽  
Vol 18 (2) ◽  
pp. 208-222 ◽  
Author(s):  
Theodros Zelleke ◽  
Dominik Marx
Keyword(s):  
Free Energy ◽  
Proton Transfer ◽  
Energy Landscape ◽  
Free Energy Landscape ◽  
Methylamine Dehydrogenase ◽  
Oxidative Deamination

scholarly journals Reaction mechanism of nucleoside 2′-deoxyribosyltransferases: free-energy landscape supports an oxocarbenium ion as the reaction intermediate

2019 ◽  
Vol 17 (34) ◽  
pp. 7891-7899 ◽  
Author(s):  
Jon del Arco ◽  
Almudena Perona ◽  
Leticia González ◽  
Jesús Fernández-Lucas ◽  
Federico Gago ◽  
...  
Keyword(s):  
Free Energy ◽  
Reaction Mechanism ◽  
Active Site ◽  
Catalytic Mechanism ◽  
Energy Landscape ◽  
Free Energy Landscape ◽  
Reaction Intermediate ◽  
Oxocarbenium Ion

The all-atom catalytic mechanism of a nucleoside 2′-deoxyribosyltransferase within its active site using QM/MM methods supports an oxocarbenium species as the reaction intermediate.

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
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