Comprehensive conformational analysis of N-acetyl-l-isoleucine-N-methylamide: an ab initio study

Calaza, Florencia; Rigo, Marı́a V.; Rinaldoni, Ana N.; Masman, Marcelo F.; Koo, Joseph C.P; Rodrı́guez, Ana; Enriz, Ricardo D.

doi:10.1016/s0166-1280(03)00344-0

Cited by 10 publications

(12 citation statements)

References 20 publications

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“…However, it is clear that an apolar side chain may also influence the topology of an E = E (ϕ, ψ, χ 1 , χ 2 )‐type potential energy hypersurface (PEHS) as well. Previous results reported for formyl‐ L ‐valinamide 9–14 and more recently for N ‐acetyl‐ L ‐isoleucine‐ N ‐methylamide ( I ) 15, 16 (Fig. 1) support this concept.…”

Section: Introductionsupporting

confidence: 56%

“…Valine (Val) has been studied exhaustively 9–14; however, compared with Val, Ile has received relatively little attention. As an extension of our preliminary survey of the potential energy surfaces (PES) at the RHF/3‐21G 15 and RHF/6‐31G( d ) 16 levels of theory, we go beyond the previous work reporting a comprehensive study of the conformations of I using density functional theory (DFT) calculations and Bader analysis. Only backbone/backbone interactions were taken into account for compound I at the levels of theory previously reported 15, 16.…”

Section: Introductionmentioning

confidence: 99%

“…As an extension of our preliminary survey of the potential energy surfaces (PES) at the RHF/3‐21G 15 and RHF/6‐31G( d ) 16 levels of theory, we go beyond the previous work reporting a comprehensive study of the conformations of I using density functional theory (DFT) calculations and Bader analysis. Only backbone/backbone interactions were taken into account for compound I at the levels of theory previously reported 15, 16. However, it is evident that to determine weak hydrogen bonding (CH…O) in this amino acid residue more precisely, a higher level of calculations, including electron‐correlation and Bader analysis, are needed.…”

Section: Introductionmentioning

confidence: 99%

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Conformational and electronic study ofN‐acetyl‐L‐isoleucine‐N‐methylamide using DFT and IPCM calculations

Rodrı́guez¹,

Koo²,

Rojas³

et al. 2006

Int J of Quantum Chemistry

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ABSTRACT:A conformational and electronic study on N-acetyl-l-isoleucine-Nmethylamide was carried out. All side-chain as well as backbone conformations were explored for this compound. Multidimensional conformational analysis predicts 81 structures in the case of N-acetyl-l-isoleucine-N-methylamide, 53 relaxed structures were determined at the DFT (B3LYP/6-31G(d)) level of theory. An exhaustive electronic study employing the atoms-in-molecules (AIM) method was carried out. In addition, the effects of three solvents (water, acetonitrile, and chloroform) were included in the calculations using the isodensity polarizable continuum model (IPCM) method.

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Section: Introductionsupporting

confidence: 56%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Conformational and electronic study ofN‐acetyl‐L‐isoleucine‐N‐methylamide using DFT and IPCM calculations

Rodrı́guez¹,

Koo²,

Rojas³

et al. 2006

Int J of Quantum Chemistry

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“…Furthermore the N-acetyl and N-methylamide derivatives of homocysteine [15,16] and selenocysteine [17] and of the normal amino acids tryptophane [18,19] histidine [20], methionine [16], isoleucine [21][22][23]23], aspartic acid [24][25][26][27] and glutamine [28] have been theoretically investigated. A further theoretical study combined with FT-IR and Raman measurements on KBr pellets has been performed on N-acetyl-L-alanine [29], N-acetyl-L-aspartic and glutamic acid [30].…”

Section: Introductionmentioning

confidence: 99%

A theoretical and matrix-isolation FT-IR investigation of the conformational landscape of N-acetylcysteine

Boeckx

Ramaekers

Maes

2010

Journal of Molecular Spectroscopy

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“…6). For N ‐acetyl‐ L ‐isoleucine‐ N ‐methylamide, the same backbone fold was found as the lowest energy structure by ab initio methods at both the 3‐21G and 6‐31G(d) basis sets, but with a fully g − side‐chain orientation 29. Previous computations of small, apolar amino acid model systems24, 30, 31 showed that their global minimum is always localized in γ L ‐type backbone fold.…”

Section: Resultsmentioning

confidence: 55%

Peptide models XLV: Conformational properties of N‐formyl‐L‐methioninamide and its relevance to methionine in proteins

2004

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The conformational space of the most biologically significant backbone folds of a suitable methionine peptide model was explored by density functional computational method. Using a medium [6-31G(d)] and a larger basis set [6-311++G(2d,2p)], the systematic exploration of low-energy backbone structures restricted for the "L-region" in the Ramachandran map of N-formyl-L-methioninamide results in conformers corresponding to the building units of an extended backbone structure (betaL), an inverse gamma-turn (gammaL), or a right-handed helical structure (alphaL). However, no poly-proline II type (epsilonL) fold was found, indicating that this conformer has no intrinsic stability, and highlighting the effect of molecular environment in stabilizing this backbone structure. This is in agreement with the abundance of the epsilonL-type backbone conformation of methionine found in proteins. Stability properties (DeltaE) and distinct backbone-side-chain interactions support the idea that specific intramolecular contacts are operative in the selection of the lowest energy conformers. Apart from the number of different folds, all stable conformers are within a 10 kcal x mol(-1) energy range, indicating the highly flexible behavior of methionine. This conformational feature can be important in supporting catalytic processes, facilitating protein folding and dimerization via metal ion binding. In both of the biological examples discussed (HIV-1 reverse transcriptase and PcoC copper-resistant protein), the conformational properties of Met residues were found to be of key importance. Spatial proximity to other types of residues or the same type of residue seems to be crucial for the structural integrity of a protein, whether Met is buried or exposed.

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Comprehensive conformational analysis of N-acetyl-l-isoleucine-N-methylamide: an ab initio study

Cited by 10 publications

References 20 publications

Conformational and electronic study ofN‐acetyl‐L‐isoleucine‐N‐methylamide using DFT and IPCM calculations

Conformational and electronic study ofN‐acetyl‐L‐isoleucine‐N‐methylamide using DFT and IPCM calculations

A theoretical and matrix-isolation FT-IR investigation of the conformational landscape of N-acetylcysteine

Peptide models XLV: Conformational properties of N‐formyl‐L‐methioninamide and its relevance to methionine in proteins

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