DFT studies on helix formation in N-acetyl-(L-alanyl)n-N′-methylamide for n=1–20

Elstner, Marcus; Jalkanen, K. J.; Knapp-Mohammady, Michaela; Frauenheim, Thomas; Suhai, Sándor

doi:10.1016/s0301-0104(00)00100-2

Cited by 101 publications

(100 citation statements)

References 35 publications

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“…63 The SCC-DFTB method is chosen because it is computationally efficient and is rather accurate. [64][65][66][67] As seen in Table 1, it predicts the gas-phase proton dissociation energy of CH 3 CH 2 SH very close to density functional theory (B3LYP) calculations, although both SCC-DFTB and B3LYP gave too low proton affinities compared to CCSD/cc-pVTZ. 68 For the interaction between SCC-DFTB and TIP3P, both electrostatic and van der Waals interactions are considered.…”

Section: Test Calculations On Ch 3 Ch 2 Sh and Analysismentioning

confidence: 59%

pK_a Calculations with QM/MM Free Energy Perturbations

Cui

2003

J. Phys. Chem. B

129

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A new approach for predicting the pK a value for a specific residue in complex environments has been proposed. It is based on a combination of hybrid quantum mechanical/molecular mechanical (QM/MM) potential and the free energy perturbation (FEP) technique. With a specific thermodynamic cycle, the QM/MM-FEP protocol can be carried out for pK a predictions taking advantage of the dual-topology-single-coordinate scheme proposed earlier for performing FEP calculations with QM/MM potentials. The new method has been tested for ethanethiol (CH 3 CH 2 SH) in solution. It was shown that, although the dominant contribution is from electrostatic interactions between the solute and solvent, many other factors have to be carefully dealt with to obtain reliable pK a values. The contribution from van der Waals interactions associated with the dummy atom was found to be insignificant for the present case, because the solvent structure around the solute is essentially determined by the heavy atoms. With more systematic benchmark calculations, the QM/MM-FEP approach will become a useful tool for pK a predictions in systems such as metalloenzymes, where nontrivial electronic structural change and/or atomic structural rearrangements are expected as the protonation state of a specific residue varies.

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Section: Test Calculations On Ch 3 Ch 2 Sh and Analysismentioning

confidence: 59%

pK_a Calculations with QM/MM Free Energy Perturbations

Cui

2003

J. Phys. Chem. B

129

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“…The SCC-DFTB method has been previously described in detail. [51][52][53][54][55][56][57][58][60][61][62] The DFT calculations were performed with the Gaussian'98 suite of programs 100 …”

Section: Methodsmentioning

confidence: 99%

Computational Characterization of Sulfur−Oxygen Three-Electron-Bonded Radicals in Methionine and Methionine-Containing Peptides: Important Intermediates in One-Electron Oxidation Processes

2003

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Density functional theory and semiempirical methods were employed to characterize the structure and properties of sulfur-oxygen-bonded radical cations formed during the one-electron oxidation of various organic sulfides and methionine-containing peptides. In general, all of the examined sulfur-oxygen bonds can be described as two-center, three-electron-bonded systems. The usefulness of approximate computational approaches (SCC-DFTB, AM1 and PM3) for the reliable description of three-electron-bonded species was examined.

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“…Over the last years, numerous groups have thus studied unsolvated model peptide chains of increasing size using various levels of theory. [1][2][3][4][5][6][7][8][9][10][11][12][13][14][15] In a few cases, structures of small peptides protected on both their C and N termini, have been studied in order to investigate the competition between different protein secondary structures, such as ␤-turns, ␤-strands, and ␣ or 3 10 helices. 1,3,6,[12][13][14][15] Computational studies could not be easily compared to experimental investigations, which have been carried out so far in condensed phases.…”

Section: Introductionmentioning

confidence: 99%

Secondary structures of short peptide chains in the gas phase: Double resonance spectroscopy of protected dipeptides

Chin

Dognon

Canuel

et al. 2005

The Journal of Chemical Physics

162

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The conformational structure of short peptide chains in the gas phase is studied by laser spectroscopy of a series of protected dipeptides, Ac-Xxx-Phe-NH 2 , XxxϭGly, Ala, and Val. The combination of laser desorption with supersonic expansion enables us to vaporize the peptide molecules and cool them internally; IR/UV double resonance spectroscopy in comparison to density functional theory calculations on Ac-Gly-Phe-NH 2 permits us to identify and characterize the conformers populated in the supersonic expansion. Two main conformations, corresponding to secondary structures of proteins, are found to compete in the present experiments. One is composed of a doubly ␥-fold corresponding to the 2 7 ribbon structure. Topologically, this motif is very close to a ␤-strand backbone conformation. The second conformation observed is the ␤-turn, responsible for the chain reversal in proteins. It is characterized by a relatively weak hydrogen bond linking remote NH and CO groups of the molecule and leading to a ten-membered ring. The present gas phase experiment illustrates the intrinsic folding properties of the peptide chain and the robustness of the ␤-turn structure, even in the absence of a solvent. The ␤-turn population is found to vary significantly with the residues within the sequence; the Ac-Val-Phe-NH 2 peptide, with its two bulky side chains, exhibits the largest ␤-turn population. This suggests that the intrinsic stabilities of the 2 7 ribbon and the ␤-turn are very similar and that weakly polar interactions occurring between side chains can be a decisive factor capable of controlling the secondary structure.

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DFT studies on helix formation in N-acetyl-(L-alanyl)n-N′-methylamide for n=1–20

Cited by 101 publications

References 35 publications

pK_a Calculations with QM/MM Free Energy Perturbations

pK_a Calculations with QM/MM Free Energy Perturbations

Computational Characterization of Sulfur−Oxygen Three-Electron-Bonded Radicals in Methionine and Methionine-Containing Peptides: Important Intermediates in One-Electron Oxidation Processes

Secondary structures of short peptide chains in the gas phase: Double resonance spectroscopy of protected dipeptides

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DFT studies on helix formation in N-acetyl-(L-alanyl)n-N′-methylamide for n=1–20

Cited by 101 publications

References 35 publications

pKa Calculations with QM/MM Free Energy Perturbations

pKa Calculations with QM/MM Free Energy Perturbations

Computational Characterization of Sulfur−Oxygen Three-Electron-Bonded Radicals in Methionine and Methionine-Containing Peptides: Important Intermediates in One-Electron Oxidation Processes

Secondary structures of short peptide chains in the gas phase: Double resonance spectroscopy of protected dipeptides

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pK_a Calculations with QM/MM Free Energy Perturbations

pK_a Calculations with QM/MM Free Energy Perturbations