scholarly journals Enzyme Architecture: Amino Acid Side-Chains That Function To Optimize the Basicity of the Active Site Glutamate of Triosephosphate Isomerase

2018 ◽  
Vol 140 (26) ◽  
pp. 8277-8286 ◽  
Author(s):  
Xiang Zhai ◽  
Christopher J. Reinhardt ◽  
M. Merced Malabanan ◽  
Tina L. Amyes ◽  
John P. Richard
Keyword(s):  
Amino Acid ◽  
Active Site ◽  
Triosephosphate Isomerase ◽  
Side Chains ◽  
Amino Acid Side Chains

Controlling the reactivity of radical intermediates by coenzyme B12-dependent methylmalonyl-CoA mutase

2002 ◽  
Vol 30 (4) ◽  
pp. 621-624 ◽  
Author(s):  
R. Banerjee ◽  
M. Vlasie
Keyword(s):  
Amino Acid ◽  
Small Group ◽  
Active Site ◽  
Side Chains ◽  
Coenzyme B12 ◽  
Structural Studies ◽  
Radical Chemistry ◽  
Radical Intermediates ◽  
Amino Acid Side Chains ◽  
Rearrangement Reactions

Adenosylcobalamin or coenzyme B12-dependent enzymes are members of the still relatively small group of radical enzymes and catalyse 1,2-rearrangement reactions. A member of this family is methylmalonyl-CoA mutase, which catalyses the isomerization of methylmalonyl-CoA to succinyl-CoA and, unlike the others, is present in both bacteria and animals. Enzymes that catalyse some of the most chemically challenging reactions are the ones that tend to deploy radical chemistry. The use of radical intermediates in an active site lined with amino acid side chains that threaten to extinguish the reaction by presenting alternative groups for abstraction poses the conundrum of how the enzymes control their reactivity. In this review, insights into this issue that have emerged from kinetic, mutagenesis and structural studies are described for methylmalonyl-CoA mutase.

THE CHEMICAL MODIFICATION OF CHYMOTRYPSIN

1964 ◽  
Vol 42 (6) ◽  
pp. 695-714 ◽  
Author(s):  
G. H. Dixon ◽  
H. Schachter
Keyword(s):  
Enzyme Activity ◽  
Amino Acid ◽  
Chemical Modification ◽  
Active Site ◽  
Specific Binding ◽  
Bond Breaking ◽  
Kinetic Properties ◽  
Side Chains ◽  
Amino Acid Side Chains

Chemical modification of chymotrypsin has led to the identification of several amino acid side-chains which are probably constituents of the active site of the enzyme. A single seryl and a single histidyl residue appear to cooperate in catalyzing the bond-breaking process while one or more tryptophanyl residues may be involved in the specific binding of substrate. Neither of the two methionyl residues is essential for enzyme activity although changes in kinetic properties occur when they are modified by oxidation or alkylation.

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>

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
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