The Role of Cation−π Interactions in Biomolecular Association. Design of Peptides Favoring Interactions between Cationic and Aromatic Amino Acid Side Chains

2001 ◽  
Vol 123 (26) ◽  
pp. 6232-6245 ◽  
Author(s):  
Ekaterina V. Pletneva ◽  
Alain T. Laederach ◽  
D. Bruce Fulton ◽  
Nenad M. Kostić
Keyword(s):  
Amino Acid ◽  
Aromatic Amino Acid ◽  
Side Chains ◽  
Π Interactions ◽  
Amino Acid Side Chains ◽  
Association Design

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>

The Influence of the Aromatic Amino Acid Side-Chains on the Sign of the Soret Cotton Effect in Chironomus Hemoglobin (CTT III)

1972 ◽  
Vol 27 (5) ◽  
pp. 530-532 ◽  
Author(s):  
Jörg Fleischhauer ◽  
Axel Wollmer
Keyword(s):  
Amino Acid ◽  
Aromatic Amino Acid ◽  
Cotton Effect ◽  
Side Chain ◽  
Side Chains ◽  
Aromatic Side Chain ◽  
Rotational Strength ◽  
Amino Acid Side Chains ◽  
Atomic Coordinates

The origin of the positive Soret Cotton effect of myoglobin was calculated by Hsu and WOODY on the basis of a mechanism taking into account the coupling of the Soret and aromatic side-chain π—π* transitions. HUBER and coworkers have worked out the atomic coordinates of a monomeric insect hemoglobin which exhibits a negative Soret Cotton effect.It seemed of some importance to examine the capability of this mechanism to explain the observed inversion of sign. The calculations resulted indeed in a negative total rotational strength (—0,2 DBM), the main contributions arising from phenylalanine residues.

Role of charged amino acid side chains in the stability and lipid binding ofManduca sexta apolipophorin III

1995 ◽  
Vol 30 (2-3) ◽  
pp. 211-223 ◽  
Author(s):  
Minal Upadhyaya ◽  
Kim Oikawa ◽  
Cyril M. Kay ◽  
Douglas G. Scraba ◽  
Roger Bradley ◽  
...  
Keyword(s):  
Amino Acid ◽  
Lipid Binding ◽  
Side Chains ◽  
Apolipophorin Iii ◽  
Amino Acid Side Chains ◽  
The Stability

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>

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 ◽  
Predictive Model ◽  
Conceptual Model ◽  
Aromatic Amino Acid ◽  
Side Chains ◽  
Stacking Interactions ◽  
Amino Acid Side Chains

Development of both a quantitative predictive model of stacking interactions of heterocycles with Phe, Tyr, and Trp side chains and a conceptual model to understand and maximize these interactions in the context of design.

The role of amino acid side chains in stabilizing dipeptides: the laser ablation Fourier transform microwave spectrum of Ac-Val-NH2

2017 ◽  
Vol 19 (36) ◽  
pp. 24985-24990 ◽  
Author(s):  
I. León ◽  
E. R. Alonso ◽  
S. Mata ◽  
C. Cabezas ◽  
M. A. Rodríguez ◽  
...  
Keyword(s):  
Fourier Transform ◽  
Amino Acid ◽  
Laser Ablation ◽  
Molecular Beam ◽  
Microwave Spectrum ◽  
Steric Effects ◽  
Side Chains ◽  
Isopropyl Group ◽  
Amino Acid Side Chains

The steric effects imposed by the isopropyl group of valine in the conformational stabilization of the capped dipeptide N-acetyl-l-valinamide (Ac-Val-NH2) have been studied by laser ablation molecular beam Fourier transform microwave (LA-MB-FTMW) spectroscopy.

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