scholarly journals Tetrahydrofuranyl and tetrahydropyranyl protection of amino acid side-chains enables synthesis of a hydroxamate-containing aminoacylated tRNA

2015 ◽  
Vol 13 (8) ◽  
pp. 2341-2349
Author(s):  
Lester J. Lambert ◽  
Marvin J. Miller ◽  
Paul W. Huber
Keyword(s):  
Transcription Factor ◽  
Amino Acid ◽  
Unnatural Amino Acid ◽  
Side Chains ◽  
Site Specific ◽  
Suppressor Trna ◽  
Amino Acid Side Chains

O-protection using tetrahydrofuranyl or tetrahydropyranyl enabled addition of a hydroxamate-containing unnatural amino acid to a suppressor tRNA, allowing subsequent site-specific incorporation of the amino acid into the transcription factor, TFIIIA.

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 Is There a Dynamic DNA-Protein Interface in the Transcription Factor IIIA-5 S rRNA Gene Complex?

2005 ◽  
Vol 280 (16) ◽  
pp. 16115-16124 ◽  
Author(s):  
Kristina L. Brady ◽  
David R. Setzer
Keyword(s):  
Transcription Factor ◽  
Amino Acid ◽  
Direct Interaction ◽  
Rrna Gene ◽  
Side Chains ◽  
Gene Complex ◽  
Protein Interface ◽  
Transcription Factor Iiia ◽  
Dynamic Interface ◽  
Amino Acid Side Chains

Others (Foster, M. P., Wuttke, D. S., Radhakrishnan, I., Case, D. A., Gottesfeld, J. M., and Wright, P. E. (1997)Nat. Struct. Biol.4, 605–608; Wuttke, D. S., Foster, M. P., Case, D. A., Gottesfeld, J. M., and Wright, P. E. (1997)J. Mol. Biol.273, 183–206) have proposed that several amino acid side chains exhibit considerable conformational mobility at the DNA-protein interface in the transcription factor IIIA·5 S rRNA gene complex and that the rapid movements of these side chains permit them to make fluctuating contacts with adjacent bp in the DNA target site. This “dynamic interface” model makes biochemical predictions concerning the consequences of truncating specific amino acid side chains and the effects of these truncations on sequence selectivity in DNA binding. The model also makes predictions concerning the effects of DNA sequence context on the apparent energetic contributions to binding made by individual bp. We have tested these predictions, and our results are inconsistent with any significant energetic role being played by the contact of multiple bp by conformationally mobile amino acid side chains. They do, however, show that some individual amino acids affect the recognition of multiple bp through mechanisms other than direct interaction.

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 Site-Specific Dynamics of Aβ1-23 Amyloid Formation and Fibrillar Configuration using an Unnatural Amino Acid

2015 ◽  
Vol 108 (2) ◽  
pp. 64a ◽  
Author(s):  
Deguo Du ◽  
Haiyang Liu ◽  
Richard Lantz ◽  
Patrick Cosme ◽  
Andrew C. Terentis ◽  
...  
Keyword(s):  
Amino Acid ◽  
Unnatural Amino Acid ◽  
Amyloid Formation ◽  
Site Specific
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