Conformational effects of one glycine residue on the other glycine residues in the Ac-Gly-Gly-Gly-NHMe tripeptide motif: an ab initio exploratory study

Mehdizadeh, Azar; Chass, Gregory A.; Farkas, Ödön; Perczel, András; Torday, Ladislaus L.; Varró, András; Papp, Julius Gy.

doi:10.1016/s0166-1280(02)00172-0

Cited by 14 publications

(11 citation statements)

References 35 publications

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“…The preference of g D and g L structures over a-type conformers was also found for the Tyr-Gly and Tyr-Gly-Gly peptides. 7,8 However, this result is in disagreement with the results of two HF studies on capped glycine tripeptides, 55,56 which found that a fully extended b-b-b conformation had the lowest energy of the conformations considered. Both studies only considered the conformation of the central glycine residue, keeping the terminal residues at the b conformation.…”

Section: Selection Of the Most Stable Gly-gly-gly Conformersmentioning

confidence: 60%

“…2 shows that the N-and C-termini are involved in H-bonding interactions, and the capped peptides considered in ref. 55 and 56 cannot form the same stabilising interactions. Yakubovich et al 57 also considered only the twisting angles of the middle glycine in glycine tripeptide.…”

Section: Selection Of the Most Stable Gly-gly-gly Conformersmentioning

confidence: 98%

“…The conformation with (j,c) = (À1001, 1701) was suggested to be most likely for the extended helix assumed by polypeptides with ionised side chains. Mehdizadeh et al 55 studied the capped glycine tripeptide (Ac-Gly-Gly-Gly-NHMe) at the HF/3-21G level of theory. The j, c angles of each glycine residue were varied at 301 intervals while keeping the other two residues restrained in the b conformation.…”

Section: Introductionmentioning

confidence: 99%

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Structure of the gas-phase glycine tripeptide

Toroz

Mourik

2010

Phys. Chem. Chem. Phys.

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The structural preferences of the neutral gas-phase glycine tripeptide have been investigated using a variety of strategies including a hierarchy of electronic structure theory (encompassing HF/3-21G single-point energy calculation and geometry optimisation, B3LYP/6-31G(d) geometry optimisation and MP2/6-31+G(d) single-point energy calculation and/or geometry optimisation). The structures and relative stabilities of the 20 most stable conformers identified were verified by M05-2X and mPW2-PLYP-D calculations. The most stable conformer located has a folded gamma-turn structure, with an NH...N interaction between the N-terminal nitrogen and the amide hydrogen of glycine (2) and an NH...O interaction between the amide hydrogen of glycine (3) and the carboxyl oxygen of glycine (1). The results show a clear preference for folded over extended structures.

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Section: Selection Of the Most Stable Gly-gly-gly Conformersmentioning

confidence: 60%

Section: Selection Of the Most Stable Gly-gly-gly Conformersmentioning

confidence: 98%

Section: Introductionmentioning

confidence: 99%

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Structure of the gas-phase glycine tripeptide

Toroz

Mourik

2010

Phys. Chem. Chem. Phys.

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“…Eqs. (3) and (4) As to the gas-phase glycine molecule, thirteen stationary points were located on its potential energy surface (PES) (Császár, 1992;Mehdizadeh et al, 2002;Liao et al, 2003). However, only seven of them have populations larger than 1.0%, see Table 1 (Császár, 1992) were also given in parentheses Table 1 The dihedral values of seven most stable gas-phase glycine structures as well as their populations a,b Figure 5 it was found that the Θ 1 , Θ 2 and Θ 3 dihedrals of the gas-phase structures suit perfectly with Eqs.…”

Section: Relationships Among Different Glycine Con-mentioning

confidence: 99%

“…At MP2/6-311++G(d,p) level of theory, thirteen stationary points of the gas-phase glycine were located on the potential energy surface (PES) (Császár, 1992). This contribution is considered as the landmark in the computational aspects of amino acids (Mehdizadeh et al, 2002;Liao et al, 2003). On such basis, the conformations of many other amino acids have been clearly understood at the molecular level (Barone et al, 1995;Lesarri et al, 2006;Zhang et al, 2006;Schlund et al, 2008).…”

Section: Introductionmentioning

confidence: 99%

First-principle conformational analysis of glycine residues in the αβ-tubulin dimer

Yang

Cheng

Liu

et al. 2009

Interdiscip Sci Comput Life Sci

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Amino acids, especially glycine, have been extensively studied whereas their conformational behaviors in proteins are rather limited. In this work, all the polypeptides containing glycine residues are truncated from the alphabeta-tubulin dimer and refined with the partial optimization technique, where the backbone atoms of the previous and posterior residues to the glycine residues are fixed at the experimental Cartesian positions whereas the others fully relaxed. The combination of the polypeptide models and partial optimization technique is validated by twolayer ONIOM calculations, being effective to retain the local structures of proteins and meanwhile optimizing the concerned glycine residues towards energy minima. Owing to the lack of side chains, various types of hydrogen bonding interactions are detected in the glycine residues. The conformational analyses of proteins are mainly based on the dihedrals. Theta(1)( angleH(5)C(2)C(3)O(4)), Theta(2)( angleH(6)C(2)C(3)O(4)) and Theta(3)( angleN(1)C(2)C(3)O(4)) are the three key dihedrals to determine the glycine conformations, which were found to change synchronously and correlate with each other by four linear equations. It thus provided the first evidence of the correlation of intra-dihedrals for the amino acid residues in proteins. In addition, the three dihedrals of the gas-phase glycine conformations were also found to suit well with these linear equations, elucidating the rationality of using amino acids as the computational models of proteins.

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An exhaustive conformational analysis of N-formyl-l-tyrosinamide using a genetic algorithm for multimodal search

Guerdaoui¹,

Merbouh²,

Tijar³

et al. 2016

Comptes Rendus. Chimie

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This work reports a detailed conformational study on N-formyl-L-tyrosinamide diamide system through genetic algorithm based on multiniche crowding technique. We tried to evaluate the effect of the OH hydroxyl substitution of the benzene ring on the adopted folds by comparing them with those found previously for the N-formyl-L-phenylalaninamide. Among the 26 and 28 conformations detected for both systems N-formyl-Ltyrosinamide and N-formyl-L-phenylalaninamide successively, 19 conformations have similar geometrical structures (identical backbones and side-chain orientations). The comparison of 19 common conformation geometries of both systems revealed nearly perfect linear adjustments with R 2 values of 0.9997, 0.9996, 0.9998, and 0.9996 for the dihedral angles 4, j, c 1 , and c 2 successively. This work also includes a comparison between theoretical calculations and experimental results of X-ray crystallography and nuclear magnetic resonance spectroscopy extracted from protein data bank.

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Conformational effects of one glycine residue on the other glycine residues in the Ac-Gly-Gly-Gly-NHMe tripeptide motif: an ab initio exploratory study

Cited by 14 publications

References 35 publications

Structure of the gas-phase glycine tripeptide

Structure of the gas-phase glycine tripeptide

First-principle conformational analysis of glycine residues in the αβ-tubulin dimer

An exhaustive conformational analysis of N-formyl-l-tyrosinamide using a genetic algorithm for multimodal search

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