Conformational analysis and structural study by ab initio gradient geometry optimizations of the model tripeptide N-formyl L-alanyl L-alanine amide

Christian Van Alsenoy, Ming Cao, Susan Q. Newton, Brian Teppen, A. Perczel, I. Csizmadia, Frank A. Momany, Lothar Schäfer

Research output: Contribution to journalArticle

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Abstract

The geometries of 15 conformations of the model tripeptide N-formyl l-alanyl l-alanine amide (Ala-Ala) were determined by ab initio gradient geometry refinements at the HF/4-21G level. The results can be compared with previous HF/4-21G calculations on the single residue, N-formyl alanine amide (Ala), and the model hexapeptide, N-formyl pentaalanine amide (Penta-Ala). Cooperative energy effects are found in Ala-Ala that are subtle in some (φ1, ψ1 and φ2, ψ2) conformations, such as (C7eq C7ax), (β, C7eq) and (C7ax, C7ax), but more pronounced in bend forms, such as (C7eq, α'), (C7eq, αl), and (C7ax, 3 10). Optimization of α-helical structures leads to 3 10-type helices, both in empirical charmm and ab initio HF/4-21G calculations, away from αR. This property of the calculated vacuum structures is in agreement with experimental investigations of short alanine based peptides in aqueous solution. The conformationally dependent structural trends found here for Ala-Ala are in agreement with the trends previously derived for Ala and Penta-Ala. They are particularly significant for the N-C(α)-C' angle. This parameter shows variations of up to 8° in the selected conformers and, regardless of how the residues are combined, its extension follows the approximate sequence β <C7eq <C7ax ≈ 3 10-helix.

Original languageEnglish
Pages (from-to)149-163
Number of pages15
JournalJournal of Molecular Structure: THEOCHEM
Volume286
Issue numberC
DOIs
Publication statusPublished - Oct 29 1993

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alanine
Amides
Alanine
amides
gradients
optimization
Geometry
geometry
helices
Conformations
trends
Vacuum
Peptides
peptides
aqueous solutions
vacuum

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry
  • Computational Theory and Mathematics
  • Atomic and Molecular Physics, and Optics

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Conformational analysis and structural study by ab initio gradient geometry optimizations of the model tripeptide N-formyl L-alanyl L-alanine amide. / Van Alsenoy, Christian; Cao, Ming; Newton, Susan Q.; Teppen, Brian; Perczel, A.; Csizmadia, I.; Momany, Frank A.; Schäfer, Lothar.

In: Journal of Molecular Structure: THEOCHEM, Vol. 286, No. C, 29.10.1993, p. 149-163.

Research output: Contribution to journalArticle

Van Alsenoy, Christian ; Cao, Ming ; Newton, Susan Q. ; Teppen, Brian ; Perczel, A. ; Csizmadia, I. ; Momany, Frank A. ; Schäfer, Lothar. / Conformational analysis and structural study by ab initio gradient geometry optimizations of the model tripeptide N-formyl L-alanyl L-alanine amide. In: Journal of Molecular Structure: THEOCHEM. 1993 ; Vol. 286, No. C. pp. 149-163.
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AU - Newton, Susan Q.

AU - Teppen, Brian

AU - Perczel, A.

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