Analysis of Thermodynamic Determinants in Helix Propensities of Nonpolar Amino Acids through a Novel Free Energy Calculation

1996 ◽  
Vol 118 (5) ◽  
pp. 995-1001 ◽  
Author(s):  
Jing Wang ◽  
Enrico O. Purisima
Keyword(s):  
Amino Acids ◽  
Free Energy ◽  
Free Energy Calculation ◽  
Energy Calculation

scholarly journals Topological Water Network Analysis Around Amino Acids

Molecules ◽  
2019 ◽  
Vol 24 (14) ◽  
pp. 2653 ◽  
Author(s):  
Kwang-Eun Choi ◽  
Eunkyoung Chae ◽  
Anand Balupuri ◽  
Hye Ree Yoon ◽  
Nam Sook Kang
Keyword(s):  
Amino Acids ◽  
Free Energy ◽  
Md Simulations ◽  
Data Bank ◽  
Free Energy Calculation ◽  
Protein Hydration ◽  
Water Molecules ◽  
Energy Calculation ◽  
Water Network ◽  
Energy Perturbation

Water molecules play a key role in protein stability, folding, function and ligand binding. Protein hydration has been studied using free energy perturbation algorithms. However, the study of protein hydration without free energy calculation is also an active field of research. Accordingly, topological water network (TWN) analysis has been carried out instead of free energy calculation in the present work to investigate hydration of proteins. Water networks around 20 amino acids in the aqueous solution were explored through molecular dynamics (MD) simulations. These simulation results were compared with experimental observations. Water molecules from the protein data bank structures showed TWN patterns similar to MD simulations. This work revealed that TWNs are effected by the surrounding environment. TWNs could provide valuable clues about the environment around amino acid residues in the proteins. The findings from this study could be exploited for TWN-based drug discovery and development.

Free Energy Calculation Methods of Biomolecules

2011 ◽  
Vol 27 (5) ◽  
pp. 395-402 ◽  
Author(s):  
Changjun CHEN ◽  
Yanzhao HUANG ◽  
Yi XIAO
Keyword(s):  
Free Energy ◽  
Free Energy Calculation ◽  
Energy Calculation ◽  
Calculation Methods

scholarly journals Predicting gas selectivity in organic ionic plastic crystals by free energy calculations

RSC Advances ◽  
2021 ◽  
Vol 11 (32) ◽  
pp. 19623-19629
Author(s):  
Vinay S. Kandagal ◽  
Jennifer M. Pringle ◽  
Maria Forsyth ◽  
Fangfang Chen
Keyword(s):  
Free Energy ◽  
Gas Separation ◽  
Free Energy Calculations ◽  
Free Energy Calculation ◽  
Energy Calculation ◽  
Plastic Crystal ◽  
Plastic Crystals ◽  
New Type ◽  
Gas Molecules ◽  
Gas Selectivity

The free energy calculation shows the different free energy changes of the adsorption and absorption of gas molecules into an organic ionic plastic crystal, successfully predicting the gas selectivity of this new type of gas separation material.

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