Conformational analysis of small peptides of the type Ac–X–NHMe, where X=Gly, Ala, Aib and Cage

Bisetty, Krishna; Catalán, Jesús Gómez; Kruger, Hendrik G.; Pérez, Juan J.

doi:10.1016/j.theochem.2005.04.037

Cited by 28 publications

(22 citation statements)

References 27 publications

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“…Comprehensive analysis of the Ramachandran maps performed at the different levels of calculation revealed the tendency of AcTris-NHMe to prefer helical conformations viz, C 7ax , C 7eq , 3 10 , and L as indeed was the case with Ac-PCU-NHMe. 15,16 These results seem to confirm observations in the literature that any -substituted peptide will have a large helical propensity. This simply means that the peptide will stabilize itself through intramolecular hydrogen bonding, resulting in helical structures that in turn are considered to be stable minimum energy conformers.…”

Section: Resultssupporting

confidence: 89%

“….O bond length of 2.01 Å and N-H. . .O angle of 148.48) 16 closely resembles the C 7ax conformation obtained at a similar computational level for Ac-TrisNHMe.…”

Section: Figuresupporting

confidence: 76%

“…These results are similar to those computed for the naturally occurring amino acids. 16,[28][29][30][31] The similarities observed are the region of local minima obtained for both peptides (3b and 4b), corresponding to the C 7ax , C 7eq, 3 10 , and L conformers (see Supplementary Material). Closer inspection of the Ramachandran plots show that both peptides [Ac-Tris-NHMe (3b) and Ac-PCU-NHMe (4b)] have local minima appearing at similar coordinates.…”

Section: Figurementioning

confidence: 86%

“…therefore expected that both cage structures will induce the same conformational constraints when experimentally incorporated in nonnatural peptides. The conformational space of Ac-Tris-NHMe was compared with our previous results, 15,16 including Ac-PCU-NHMe, Ac-Ala-NHMe, Ac-Gly-NHMe, and Ac-Aib-NHMe (see Supplementary Material). Glycine tends to favor extended conformations and alanine exhibit some helical conformations, while the conformations of aminoisobutyric acid 16,[32][33][34] are very similar to that exhibited by Ac-Tris-NHMe.…”

Section: Figurementioning

confidence: 99%

“…This is a logical extension of our conformational studies on the PCU cage dipeptide (4b) as the model compound. [14][15][16] We have concluded that the PCU cage residue exhibits preferences for helical conformations as well as induces promising -turn [17][18][19] characteristics. A nonrelated experimental and computational investigation on peptide analogues containing a PCU scaffold was recently published.…”

Section: Introductionmentioning

confidence: 99%

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Analysis of the conformational profile of trishomocubane amino acid dipeptide

Bisetty¹,

Govender²,

Kruger³

2005

Biopolymers

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4-Amino-(D3)-trishomocubane-4-carboxylic acid is a constrained alpha-amino acid residue that exhibits promising conformational characteristics, i.e., helical and beta-turns. As part of the development of conformational guidelines for the design of peptides and protein surrogates, the conformational energy calculations on trishomocubane using molecular mechanics and ab initio methods are presented. The C(alpha) carbon of trishomocubane forms part of the cyclic structure, and consequently a peptidic environment was simulated with an acetyl group on its N-terminus and a methylamide group on its C-terminus. Ramachandran maps computed at the molecular mechanics level using the standard AMBER (parm94) force field libraries compared reasonably well with the corresponding maps computed at the Hartree Fock level, using the 6-31G* basis set. Trishomocubane peptide (Ac-Tris-NHMe) is characterized by four low energy conformers corresponding to the C7ax, C7eq, 3(10), and alpha(L) helical structures.

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Section: Resultssupporting

confidence: 89%

“….O bond length of 2.01 Å and N-H. . .O angle of 148.48) 16 closely resembles the C 7ax conformation obtained at a similar computational level for Ac-TrisNHMe.…”

Section: Figuresupporting

confidence: 76%

Section: Figurementioning

confidence: 86%

Section: Figurementioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Analysis of the conformational profile of trishomocubane amino acid dipeptide

Bisetty¹,

Govender²,

Kruger³

2005

Biopolymers

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The Stability of C_α Peptide Radicals: Why Glycyl Radical Enzymes?

Hioe

Savaşçı

Brand

et al. 2011

Chemistry A European J

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The conformational space of dipeptide models derived from glycine, alanine, phenylalanine, proline, tyrosine, and cysteine has been searched extensively and compared with the corresponding C(α) dipeptide radicals at the G3(MP2)-RAD level of theory. The results indicate that the (least-substituted) glycine dipeptide radical is the thermochemically most stable of these species. Analysis of the structural parameters indicates that this is due to repulsive interactions between the C(α) substituents and peptide units in the radical. A comparison of the conformational preferences of dipeptide radicals and their closed-shell parents also indicates that radical stability is a strongly conformation-dependent property.

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Conformational Preferences in Small Peptide Models: The Relevance of cis/trans‐Conformations

Jangra

Haindl

Achrainer

et al. 2016

Chemistry A European J

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The accurate description of cis/trans peptide structures is of fundamental relevance for the field of protein modeling and protein structure determination. A comprehensive conformational analysis of dipeptide model Ace-Gly-NMe (1) has been carried out by using a combination of theoretical calculations and experimental ((1) H and (13) C NMR and NOESY) spectroscopic measurements to assess the relevance of cis-peptide conformers. NMR measurements in dimethyl sulfoxide (DMSO) solution and calculations employing a continuum solvation model both point to the extended trans,trans conformer C5_tt as the global minimum. The cis-peptide structures C5_ct and C5_tc, with the N- or C-terminal amide group in cis-conformation, are observed separately and located 13.0±2 kJ mol(-1) higher in energy. This is in close agreement with the theoretical prediction of around 12 kJ mol(-1) in DMSO. The ability of common protein force fields to reproduce the energies of the cis-amide conformers C5_ct and C5_tc in 1 is limited, making these methods unsuitable for the description of cis-peptide structures in protein simulations.

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Conformational analysis of small peptides of the type Ac–X–NHMe, where X=Gly, Ala, Aib and Cage

Cited by 28 publications

References 27 publications

Analysis of the conformational profile of trishomocubane amino acid dipeptide

Analysis of the conformational profile of trishomocubane amino acid dipeptide

The Stability of C_α Peptide Radicals: Why Glycyl Radical Enzymes?

Conformational Preferences in Small Peptide Models: The Relevance of cis/trans‐Conformations

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Conformational analysis of small peptides of the type Ac–X–NHMe, where X=Gly, Ala, Aib and Cage

Cited by 28 publications

References 27 publications

Analysis of the conformational profile of trishomocubane amino acid dipeptide

Analysis of the conformational profile of trishomocubane amino acid dipeptide

The Stability of Cα Peptide Radicals: Why Glycyl Radical Enzymes?

Conformational Preferences in Small Peptide Models: The Relevance of cis/trans‐Conformations

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The Stability of C_α Peptide Radicals: Why Glycyl Radical Enzymes?