Calculation of the water-cyclohexane transfer free energies of neutral amino acid side-chain analogs using the OPLS all-atom force field

2003 ◽  
Vol 24 (15) ◽  
pp. 1930-1935 ◽  
Author(s):  
Justin L. MacCallum ◽  
D. Peter Tieleman
Keyword(s):  
Amino Acid ◽  
Force Field ◽  
Neutral Amino Acid ◽  
Side Chain ◽  
Amino Acid Side Chain ◽  
Free Energies

Amino acid side-chain populations in aqueous and saline solution: Bis-penicillamine enkephalin

Biopolymers ◽  
1992 ◽  
Vol 32 (12) ◽  
pp. 1623-1629 ◽  
Author(s):  
Paul E. Smith ◽  
B. Montgomery Pettitt
Keyword(s):  
Amino Acid ◽  
Saline Solution ◽  
Side Chain ◽  
Amino Acid Side Chain

scholarly journals Adsorption of Amino Acids on Graphene: Assessment of Current Force Fields

2019 ◽  
Author(s):  
Siva Dasetty ◽  
John K. Barrows ◽  
Sapna Sarupria
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Force Field ◽  
Force Fields ◽  
Principal Component ◽  
Free Energies ◽  
Adsorbed State ◽  
Free Energy Of Adsorption ◽  
Density Based Clustering ◽  
Structural Preferences

<div> <div> <div> <p>We compare the free energies of adsorption (∆Aads) and the structural preferences of amino acids obtained using the force fields — Amberff99SB-ILDN/TIP3P, CHARMM36/modified-TIP3P, OPLS-AA/M/TIP3P, and Amber03w/TIP4P/2005. The amino acid–graphene interactions are favorable irrespective of the force field. While the magnitudes of ∆Aads differ between the force fields, the trends in the free energy of adsorption with amino acids are similar across the studied force fields. ∆Aads positively correlates with amino acid–graphene and negatively correlates with graphene–water interaction energies. Using a combination of principal component analysis and density-based clustering technique, we grouped the structures observed in the graphene adsorbed state. The resulting population of clusters, and the conformation in each cluster indicate that the structures of the amino acid in the graphene adsorbed state vary across force fields. The differences in the conformations of amino acids are more severe in the graphene adsorbed state compared to the bulk state for all the force fields. Our findings suggest that while the thermodynamics of adsorption of proteins and peptides would be described consistently across different force fields, the structural preferences of peptides and proteins on graphene will be force field dependent. </p> </div> </div> </div>

Effect of charged amino acid side chain length on lateral cross-strand interactions between carboxylate- and guanidinium-containing residues in a β-hairpin

Amino Acids ◽  
2015 ◽  
Vol 47 (5) ◽  
pp. 885-898 ◽  
Author(s):  
Hsiou-Ting Kuo ◽  
Shing-Lung Liu ◽  
Wen-Chieh Chiu ◽  
Chun-Jen Fang ◽  
Hsien-Chen Chang ◽  
...  
Keyword(s):  
Amino Acid ◽  
Chain Length ◽  
Side Chain ◽  
Amino Acid Side Chain ◽  
Side Chain Length
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