scholarly journals Determination of intrinsic hydrophilicity/hydrophobicity of amino acid side chains in peptides in the absence of nearest-neighbor or conformational effects

Biopolymers ◽  
2006 ◽  
Vol 84 (3) ◽  
pp. 283-297 ◽  
Author(s):  
James M. Kovacs ◽  
Colin T. Mant ◽  
Robert S. Hodges
Keyword(s):  
Amino Acid ◽  
Nearest Neighbor ◽  
Side Chains ◽  
Conformational Effects ◽  
Amino Acid Side Chains

Modeling amino acid side chains. 1. Determination of net atomic charges from ab initio self-consistent-field molecular electrostatic properties

1992 ◽  
Vol 96 (25) ◽  
pp. 10276-10284 ◽  
Author(s):  
Christophe Chipot ◽  
Bernard Maigret ◽  
Jean Louis Rivail ◽  
Harold A. Scheraga
Keyword(s):  
Amino Acid ◽  
Ab Initio ◽  
Atomic Charges ◽  
Side Chains ◽  
Electrostatic Properties ◽  
Consistent Field ◽  
Self Consistent ◽  
Amino Acid Side Chains ◽  
Self Consistent Field

Determination of stereochemistry stability coefficients of amino acid side-chains in an amphipathic alpha-helix

2002 ◽  
Vol 59 (1) ◽  
pp. 18-33 ◽  
Author(s):  
Y. Chen ◽  
C. T. Mant ◽  
R. S. Hodges
Keyword(s):  
Amino Acid ◽  
Alpha Helix ◽  
Side Chains ◽  
Amino Acid Side Chains ◽  
Amphipathic Alpha Helix

Modeling amino acid side chains. 2. Determination of point charges from electrostatic properties: toward transferable point charge models

1993 ◽  
Vol 97 (38) ◽  
pp. 9788-9796 ◽  
Author(s):  
Christophe Chipot ◽  
Janos G. Angyan ◽  
Bernard Maigret ◽  
Harold A. Scheraga
Keyword(s):  
Amino Acid ◽  
Point Charge ◽  
Side Chains ◽  
Point Charge Models ◽  
Electrostatic Properties ◽  
Amino Acid Side Chains

Predicting the Strength of Stacking Interactions Between Heterocycles and Aromatic Amino Acid Side Chains

2019 ◽  
Author(s):  
Andrea N. Bootsma ◽  
Analise C. Doney ◽  
Steven Wheeler
Keyword(s):  
Amino Acid ◽  
Binding Sites ◽  
Aromatic Amino Acid ◽  
Aromatic Amino Acids ◽  
Biologically Active ◽  
Side Chains ◽  
Stacking Interactions ◽  
Inhibitor Binding ◽  
Protein Binding Sites ◽  
Amino Acid Side Chains

<p>Despite the ubiquity of stacking interactions between heterocycles and aromatic amino acids in biological systems, our ability to predict their strength, even qualitatively, is limited. Based on rigorous <i>ab initio</i> data, we have devised a simple predictive model of the strength of stacking interactions between heterocycles commonly found in biologically active molecules and the amino acid side chains Phe, Tyr, and Trp. This model provides rapid predictions of the stacking ability of a given heterocycle based on readily-computed heterocycle descriptors. We show that the values of these descriptors, and therefore the strength of stacking interactions with aromatic amino acid side chains, follow simple predictable trends and can be modulated by changing the number and distribution of heteroatoms within the heterocycle. This provides a simple conceptual model for understanding stacking interactions in protein binding sites and optimizing inhibitor binding in drug design.</p>

A Strategy for Thioamide Incorporation During Fmoc Solid-Phase Peptide Synthesis with Robust Stereochemical Integrity

2019 ◽  
Author(s):  
luis camacho III ◽  
Bryan J. Lampkin ◽  
Brett VanVeller
Keyword(s):  
Amino Acid ◽  
Functional Groups ◽  
Peptide Synthesis ◽  
Solid Phase ◽  
Solid Phase Peptide Synthesis ◽  
Side Chains ◽  
Amino Acid Side Chains ◽  
Peptide Elongation

We describe a method to protect the sensitive stereochemistry of the thioamide—in analogy to the protection of the functional groups of amino acid side chains—in order to preserve the thioamide moiety during peptide elongation.<br>

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