Quantum Chemical Quantification of Weakly Polar Interaction Energies in the TC5b Miniprotein

Hatfield, Marcus P. D.; Palermo, Nicholas Y.; Csontos, József; Murphy, Richard F.; Lovas, Sándor

doi:10.1021/jp077674h

Cited by 22 publications

(32 citation statements)

References 50 publications

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“…The energy of the Ar-Ar interaction in CLN025 is between −0.43 and −8.11 kcal mol −1 . Energies of −1 to −2 kcal mol, −1 46 −2 to −4 kcal mol −1 12, 13, 26 and −3 to −7 kcal mol −1 47 were calculated previously for the Ar-Ar interaction. The energies of the CH-π interactions between Tyr2 and Pro4 were between 1.72 and −12.47 kcal mol −1 which is consistent with previously calculated energies for Ar-Pro interactions of −1.41 to −8.05 kcal mol −1 13 and individual CH-π interactions of −1.5 to −3 kcal mol.…”

Section: Resultsmentioning

confidence: 99%

Molecular Dynamics Analysis of the Conformations of a β-Hairpin Miniprotein

2010

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Molecular Dynamics simulations of a β-hairpin miniprotein, CLN025, were performed to examine the conformational stability of the peptide in H 2 O at 278 K, 300 K, 333 K and 363 K as well as in TFE, MeOH and DMSO at 300 K. CLN025 is a variant of the Chignolin miniprotein, in which the terminal Gly residues of Chignolin are replaced with Tyr residues, which leads to a 29.7 K increase in melting temperature. The energy of the intramolecular interactions were calculated using DFT quantum chemical calculations at the BH and HLYP/cc-pVTZ level of theory. CLN025 maintained a β-hairpin conformation in all environments. The β-hairpin is stabilized by hydrogen bonds, an electrostatic interaction between the charged termini of the peptide and weakly polar interactions. The interaction between the backbones of the N and C-terminal strands accounts for −97.32 to −120.87 kcal mol −1 of the stabilization energy. The energy of the CH-π interactions between Tyr2 and Pro4 were between −1.80 and −8.9 kcal mol −1 and the energy of the Tyr2-Trp9 Ar-Ar interaction was between −0.43 and −8.11 kcal mol −1 . Increasing temperature caused the Tyr2-Pro4 CH-π and the Tyr2-Trp9 and Tyr2-Tyr10 Ar-Ar interactions to become less favorable but the Tyr1-Trp9 interaction became more favorable and played an important role in stabilizing the β-hairpin of CLN025 that resulted in the increased melting temperature. The weakly polar interactions play an important role in the structure and stability of CLN025 and other proteins.

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Section: Resultsmentioning

confidence: 99%

Molecular Dynamics Analysis of the Conformations of a β-Hairpin Miniprotein

2010

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“…Weakly polar interactions can be as strong as hydrogen bonds. 5–12 They play an important role in the stabilization of secondary structure such as α-helices, 5 and the tertiary structure of peptides such as the TC5b 8 and APP 10, 12 miniproteins. Numerous β-hairpins have been designed to take advantage the aromatic-aromatic (Ar-Ar) interactions, 13–17 cation-π interactions, 16–18 and CH-π interactions.…”

Section: Introductionmentioning

confidence: 99%

VCD spectroscopic properties of the β‐hairpin forming miniprotein CLN025 in various solvents

2010

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Electronic and vibrational circular dichroism are often used to determine the secondary structure of proteins, because each secondary structure has a unique spectrum. In order to determine these spectral features, polypeptides that are known to adopt a particular conformation along their entire length are studied ideally. Little is known about the vibrational circular dichroic spectroscopic features of the β-hairpin. In this study, the VCD spectral features of a decapeptide, YYDPETGTWY (CLN025), which forms a stable β-hairpin that is stabilized by intramolecular weakly polar interactions and hydrogen bonds were determined. Molecular Dynamics simulations and ECD spectropolarimetry were used to confirm that CLN025 adopts a β-hairpin in water, TFE, MeOH and DMSO and to examine differences in the secondary structure, hydrogen bonds and weakly polar interactions. CLN025 was synthesized by microwave-assisted solid phase peptide synthesis with Nα-Fmoc protected amino acids. The VCD spectra displayed a (−,+,−) pattern with bands at 1640 to 1656 cm−1, 1667 to 1687 cm−1 and 1679 to 1686 cm−1 formed by the overlap of a lower frequency negative couplet and a higher frequency positive couplet. A maximum IR absorbance was observed at 1647 to 1663 cm−1 with component bands at 1630 cm−1, 1646 cm−1, 1658 cm−1 and 1675 to 1680 cm−1 that are indicative of the β-sheet, random meander, either random meander or loop and turn, respectively. These results are similar to the results of others, who examined the VCD spectra of β-hairpins formed by DPro-Xxx turns and indicate that observed pattern is typical of β-hairpins.

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“…Doing that, one goes from a CH…π hydrogen bond in the heterochiral complex of Figure 16(c), to the more repulsive situation of Figure 16(b). This leads to the calculated decrease of the binding energy by 8-9 kJ/mol, a value usually associated with CH…π interactions [164,165,248]. Chiral discrimination rests therefore on the existence, or not, of the CH…π interaction.…”

Section: Role Of Ancillary Hydrogen Bondsmentioning

confidence: 91%

Chirality effects in gas-phase spectroscopy and photophysics of molecular and ionic complexes: contribution of low and room temperature studies

Zehnacker‐Rentien

2014

International Reviews in Physical Chemistry

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This review focuses on chirality effects in spectroscopy and photophysics of chiral molecules or protonated ions, and their weakly bound complexes, isolated in the gas phase. Low-temperature studies in jet-cooled conditions allow disentangling the different interactions at play and shed light on the ancillary interactions responsible for chiral recognition, like OH…π or CH…π, which would be blurred at room temperature. The consequences of these interactions on chiral recognition in condensed phase are described, as well as the influence of higher energy conformers, which can be accessed in room-temperature experiments. The role of kinetic effects and solvation in jet-cooled experiments is discussed. Last, examples of dramatic chirality effects in photo-induced dissociation are given.

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Quantum Chemical Quantification of Weakly Polar Interaction Energies in the TC5b Miniprotein

Cited by 22 publications

References 50 publications

Molecular Dynamics Analysis of the Conformations of a β-Hairpin Miniprotein

Molecular Dynamics Analysis of the Conformations of a β-Hairpin Miniprotein

VCD spectroscopic properties of the β‐hairpin forming miniprotein CLN025 in various solvents

Chirality effects in gas-phase spectroscopy and photophysics of molecular and ionic complexes: contribution of low and room temperature studies

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