Nearest-neighbor effects and structural preferences in dipeptides are a function of the electronic properties of amino acid side-chains

2006 ◽  
Vol 63 (4) ◽  
pp. 939-948 ◽  
Author(s):  
Donard S. Dwyer
Keyword(s):  
Amino Acid ◽  
Electronic Properties ◽  
Nearest Neighbor ◽  
Side Chains ◽  
Neighbor Effects ◽  
Structural Preferences ◽  
Amino Acid Side Chains

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

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>

ChemInform Abstract: Dimerization Energetics of Benzene and Aromatic Amino Acid Side Chains.

ChemInform ◽  
1987 ◽  
Vol 18 (17) ◽  
Author(s):  
S. K. BURLEY ◽  
G. A. PETSKO
Keyword(s):  
Amino Acid ◽  
Aromatic Amino Acid ◽  
Side Chains ◽  
Amino Acid Side Chains

scholarly journals Mobile unnatural amino acid side chains in the core of staphylococcal nuclease

1996 ◽  
Vol 5 (6) ◽  
pp. 1026-1031 ◽  
Author(s):  
Richard Wynn ◽  
Paul C. Harkins ◽  
Frederic M. Richards ◽  
Robert O. Fox
Keyword(s):  
Amino Acid ◽  
Staphylococcal Nuclease ◽  
Unnatural Amino Acid ◽  
Side Chains ◽  
The Core ◽  
Amino Acid Side Chains

scholarly journals Intrinsic Energy Landscapes of Amino Acid Side-Chains

2012 ◽  
Vol 52 (6) ◽  
pp. 1559-1572 ◽  
Author(s):  
Xiao Zhu ◽  
Pedro E.M. Lopes ◽  
Jihyun Shim ◽  
Alexander D. MacKerell
Keyword(s):  
Amino Acid ◽  
Side Chains ◽  
Energy Landscapes ◽  
Amino Acid Side Chains ◽  
Intrinsic Energy

The Influence of Amino Acid Side Chains on the Free Energy of Helix-Coil Transitions1

1966 ◽  
Vol 70 (4) ◽  
pp. 998-1004 ◽  
Author(s):  
George Némethy ◽  
S. J. Leach ◽  
Harold A. Scheraga
Keyword(s):  
Free Energy ◽  
Amino Acid ◽  
Side Chains ◽  
Amino Acid Side Chains
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