Profiling Transition-State Configurations on the Trypanosoma cruzi trans-Sialidase Free-Energy Reaction Surfaces

2014 ◽  
Vol 119 (3) ◽  
pp. 1192-1201 ◽  
Author(s):  
Ian L. Rogers ◽  
Kevin J. Naidoo
Keyword(s):  
Free Energy ◽  
Trypanosoma Cruzi ◽  
Transition State ◽  
Energy Reaction ◽  
Reaction Surfaces

A Minimum Free Energy Reaction Path for the E2 Reaction between Fluoro Ethane and a Fluoride Ion

2004 ◽  
Vol 126 (31) ◽  
pp. 9492-9493 ◽  
Author(s):  
Bernd Ensing ◽  
Alessandro Laio ◽  
Francesco L. Gervasio ◽  
Michele Parrinello ◽  
Michael L. Klein
Keyword(s):  
Free Energy ◽  
Reaction Path ◽  
Minimum Free Energy ◽  
Fluoride Ion ◽  
Energy Reaction

Elucidating the role of solvents in acid catalyzed dehydration of biorenewable hydroxy-lactones

2020 ◽  
Vol 5 (4) ◽  
pp. 651-662 ◽  
Author(s):  
Gourav Shrivastav ◽  
Tuhin S. Khan ◽  
Manish Agarwal ◽  
M. Ali Haider
Keyword(s):  
Free Energy ◽  
Transition State ◽  
Energy Barrier ◽  
Free Energy Barrier ◽  
Activation Free Energy ◽  
Acid Catalyzed

Utilizing the differential stabilization of reactant and transition state in the polar and apolar solvents to lower the activation free energy barrier for acid-catalyzed dehydration of hydroxy lactones.

scholarly journals Catalysis: transition-state molecular recognition?

2010 ◽  
Vol 6 ◽  
pp. 1026-1034 ◽  
Author(s):  
Ian H Williams
Keyword(s):  
Free Energy ◽  
Molecular Recognition ◽  
Transition State ◽  
Computational Modelling ◽  
Catalytic Antibodies ◽  
Single Atom ◽  
Boat Conformation ◽  
Methyl Transferase ◽  
Modelling Studies ◽  
Dynamics Simulations

The key to understanding the fundamental processes of catalysis is the transition state (TS): indeed, catalysis is a transition-state molecular recognition event. Practical objectives, such as the design of TS analogues as potential drugs, or the design of synthetic catalysts (including catalytic antibodies), require prior knowledge of the TS structure to be mimicked. Examples, both old and new, of computational modelling studies are discussed, which illustrate this fundamental concept. It is shown that reactant binding is intrinsically inhibitory, and that attempts to design catalysts that focus simply upon attractive interactions in a binding site may fail. Free-energy changes along the reaction coordinate for SN2 methyl transfer catalysed by the enzyme catechol-O-methyl transferase are described and compared with those for a model reaction in water, as computed by hybrid quantum-mechanical/molecular-mechanical molecular dynamics simulations. The case is discussed of molecular recognition in a xylanase enzyme that stabilises its sugar substrate in a (normally unfavourable) boat conformation and in which a single-atom mutation affects the free-energy of activation dramatically.

scholarly journals Application of rate-equilibrium free energy relationship analysis to nonequilibrium ion channel gating mechanisms

2009 ◽  
Vol 134 (2) ◽  
pp. 129-136 ◽  
Author(s):  
László Csanády
Keyword(s):  
Free Energy ◽  
Ion Channels ◽  
Transition State ◽  
Ion Channel ◽  
Conformational Transition ◽  
Limited Information ◽  
Relationship Analysis ◽  
Gating Mechanisms ◽  
Gating Mechanism ◽  
Transition State Structures

Rate-equilibrium free energy relationship (REFER) analysis provides information on transition-state structures and has been applied to reveal the temporal sequence in which the different regions of an ion channel protein move during a closed–open conformational transition. To date, the theory used to interpret REFER relationships has been developed only for equilibrium mechanisms. Gating of most ion channels is an equilibrium process, but recently several ion channels have been identified to have retained nonequilibrium traits in their gating cycles, inherited from transporter-like ancestors. So far it has not been examined to what extent REFER analysis is applicable to such systems. By deriving the REFER relationships for a simple nonequilibrium mechanism, this paper addresses whether an equilibrium mechanism can be distinguished from a nonequilibrium one by the characteristics of their REFER plots, and whether information on the transition-state structures can be obtained from REFER plots for gating mechanisms that are known to be nonequilibrium cycles. The results show that REFER plots do not carry information on the equilibrium nature of the underlying gating mechanism. Both equilibrium and nonequilibrium mechanisms can result in linear or nonlinear REFER plots, and complementarity of REFER slopes for opening and closing transitions is a trivial feature true for any mechanism. Additionally, REFER analysis provides limited information about the transition-state structures for gating schemes that are known to be nonequilibrium cycles.

scholarly journals Sampling the Folding Transition State Ensemble in a Tube-Like Model of Protein

10.29007/ml3c ◽  
2020 ◽  
Author(s):  
Ba Hung Nguyen ◽  
Hoang Trinh Xuan
Keyword(s):  
Free Energy ◽  
Transition State ◽  
Energy Surface ◽  
Sampling Technique ◽  
Small Region ◽  
Umbrella Sampling ◽  
Free Energy Surface ◽  
State Ensemble ◽  
State Region ◽  
Transition State Ensemble

We used the tube model with Go-like potential for native contacts to study the folding transition of a designed three-helix bundle and a designed protein G-like structure. It is shown that both proteins in this model are two-state folders with a cooperative folding transition coincided with the collapse transition. We defined the transition states as protein conformations in a small region around the saddle point on a free energy surface with the energy and the conformational root-mean-square deviation (RMSD) from the native state as the coordinates. The transition state region on the free energy surface then was sampled by using the umbrella sampling technique. We show that the transition state ensemble is broad consisting of different conformations that have different folded and unfolded elements.

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