A thermodynamic distance criterion of optimality for the calculation of free energy changes from computer simulations

1996 ◽  
Vol 105 (22) ◽  
pp. 10072-10083 ◽  
Author(s):  
J. C. Schön
Keyword(s):  
Free Energy ◽  
Computer Simulations

scholarly journals Standardizing a Protocol for Studying pH-dependent Transient Conformations using Computer Simulations

2020 ◽  
Author(s):  
Ruhar Singh ◽  
Andrew M Lynn
Keyword(s):  
Free Energy ◽  
High Temperature ◽  
Protein Stability ◽  
Computer Simulations ◽  
Energy Landscape ◽  
Alpha Helix ◽  
Free Energy Landscape ◽  
Pka Values ◽  
Constant Ph ◽  
Ph Dependent

1.ABSTRACTUnderstanding pH-dependent protein stability is important in biological - transport, storage, and delivery, in vivo conditions such as aggregation potential in neurodegenerative disease, and in studying the folding/unfolding of proteins. Using computer simulations, we can replace complex experimental determination and provide an atomistic-level interpretation of the cause and effect of pH on protein stability. Here, we standardize a method that provides a framework through which we examined pH-dependent transient conformations during unfolding simulations of proteins. Constant pH simulations utilized in the prediction of pKa values of charged groups of the peptide. The calculated pKa values employed to fix the appropriate protonation state of the amino acid to simulate the effect of pH on the system. Trajectories from multiple high-temperature MD simulations of the protein sample the conformational space during unfolding for a given pH state. The ensemble of conformations is analyzed from its free energy landscape to identify transient and stable conformations both at a given pH and between different pH. As a test system RN80, a protein fragment analog of the C-peptide from bovine pancreatic ribonuclease-A used to measure the accuracy of the predictions from simulations. Experimental measures of the helix content determined as a function of pH display a bell-shaped curve, i.e. RN80 alpha-helix formation is maximum at pH5 with a subsequent loss in helicity at higher and lower pH. The main forces stabilizing the alpha-helix are a salt-bridge formed between Glu-2 and Arg-10 and cation-pi-interaction between Tyr-8 and His-12. Our protocol includes constant pH calculations, optimal high-temperature simulations, and Free Energy landscape analysis exhibited the agreement with the experimental observations.

Density profiles of fluids in some special symmetries

1995 ◽  
Vol 73 (7-8) ◽  
pp. 432-439 ◽  
Author(s):  
Seong-Chan Lee ◽  
Zi-Hong Yoon ◽  
Soon-Chul Kim
Keyword(s):  
Free Energy ◽  
Computer Simulations ◽  
Hard Sphere ◽  
Density Functional ◽  
Energy Functional ◽  
Empirical Method ◽  
Density Profiles ◽  
Functional Approximation ◽  
Free Energy Functional ◽  
Lennard Jones

A free-energy-functional approximation based on a semi-empirical method is proposed. The main advantage of the free-energy-functional approximation is its accuracy compared with other models and its relative simplicity compared with other well-known weighted-density approximations. The free-energy-functional approximation is applied to predict the density profiles of the hard-sphere fluids and the Lennard–Jones fluids in some special symmetries. For the density profiles near a hard flat wall, the results reproduced the hard-sphere oscillatory structures qualitatively and quantitatively. For the density profiles of hard-sphere fluids confined in a spherical cage, the results are also in a fair agreement with the computer simulations. For Lennard–Jones fluids, two kinds of density-functional perturbation theories, the density-functional mean-field theory (DFMFT) and the density-functional perturbation theory (DFPT), examined. The results show that at higher temperature the DFPT compares well with computer simulations. However, the agreement deteriorates slightly as the temperature of the Lennard–Jones fluids is reduced. These results demonstrate that both the free-energy-functional approximation and the DFPT succesfully describe the inhomogeneous properties of classical fluids.

Calculation of free energy differences for water from computer simulations

1985 ◽  
Vol 113 (4) ◽  
pp. 372-379 ◽  
Author(s):  
F. Sussman ◽  
J.M. Goodfellow ◽  
P. Barnes ◽  
J.L. Finney
Keyword(s):  
Free Energy ◽  
Computer Simulations

scholarly journals Computation of drug solvation free energy in supercritical CO2: alternatives to all-atom computer simulations

2021 ◽  
pp. 113096
Author(s):  
N.N. Kalikin ◽  
Y.A. Budkov ◽  
A.L. Kolesnikov ◽  
D.V. Ivlev ◽  
M.A. Krestyaninov ◽  
...  
Keyword(s):  
Free Energy ◽  
Computer Simulations ◽  
Supercritical Co2 ◽  
Solvation Free Energy

scholarly journals Free energy and entropy of a dipolar liquid by computer simulations

2018 ◽  
Vol 148 (8) ◽  
pp. 084504
Author(s):  
Ricardo Palomar ◽  
Gemma Sesé
Keyword(s):  
Free Energy ◽  
Computer Simulations
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