Relative stability of homochiral and heterochiral dialanine peptides. Effects of perturbation pathways and force-field parameters on free energy calculations

Zhou, Tony Yu; Oostenbrink, Chris; Gunsteren, Wilfred F. van; Hagen, Wilfred R.; Leeuw, Simon W. de; Jongejan, Jaap A.

doi:10.1080/00268970500096889

Cited by 16 publications

(15 citation statements)

References 22 publications

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“…These methods include classical and quantum numerical simulations. Classical molecular dynamic and Monte-Carlo Docking calculations, [52][53][54][55][56] based on standard force fields, have been used especially to investigate conformational issues. Quantum approaches have generally been employed to carry out ab initio calculations of more or less higher accuracy, depending on the size of the basis set.…”

Section: Computational Methodologiesmentioning

confidence: 99%

Molecular and supramolecular chirality: R2PI spectroscopy as a tool for the gas‐phase recognition of chiral systems of biological interest

et al. 2008

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Dedicated to Professor Domenico Misiti on the occasion of his 75th birthday. ABSTRACTIn life sciences, diastereomeric chiral molecule/chiral receptor complexes are held together by a different combination of intermolecular forces and are therefore endowed with different stability and reactivity. Determination of these forces, which are normally affected in the condensed phase by solvent and supramolecular interactions, can be accomplished through the generation of diastereomeric complexes in the isolated state and their spectroscopic investigation. This review presents a detailed discussion of the mass resolved Resonant Two Photon Ionization (R2PI-TOF) technique in supersonic beams and introduces an overview of various other technologies currently available for the spectroscopic study of gas phase chiral molecules and supramolecular systems. It reports case studies primarily from our recent work using R2PI-TOF methodology for chiral recognition in clusters containing molecules of biological interest. The measurement of absorption spectra, ionization and fragmentation thresholds of diastereomeric clusters by this technique allow the determination of the nature of the intrinsic interactions, which control their formation and which affect their stability and reactivity.

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Section: Computational Methodologiesmentioning

confidence: 99%

Molecular and supramolecular chirality: R2PI spectroscopy as a tool for the gas‐phase recognition of chiral systems of biological interest

et al. 2008

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“…Blout et al (1956) report that incorporation of enantiomers into a homochiral peptide destabilizes the α-helical configuration. Zhou et al (2005) found evidence by experiments and computations that homochiral dipeptides are thermodynamically more stable than are heterochiral dipeptides. All these observations indicate that homochirality is a favoured configuration even for short strings.…”

Section: Introductionmentioning

confidence: 90%

Evolution of Homochirality by Epimerization of Random Peptide Chains. A Stochastic Model

Schmidt¹

2006

Orig Life Evol Biosph

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A cyclic process is described which is constituted of polymerization, epimerization, and hydrolysis steps. During the first cycle peptides with random sequences are formed from racemic amino acids. A small portion of these peptides have substructures with a terminal residue linked to a homochiral sequence of optical antipodes. In such a substructure the terminal residue is assumed to invert into its mirror image so that a thermodynamically favourable epimeric stucture with continuous homochirality is formed. In the hydrolysis step the peptides are split back to monomeric units with retention of configuration. Due to stochastic differences between L- and D-substructures a net excess of one of the enantiomers results. This excess enhances the probability of the formation of substructures having the dominant configuration in the next cycle. It is shown by probabilistic considerations and computer simulations that this mechanism generates an autocatalytic growth of one of the enantiomers which finally results in homochiral populations of amino acids. The number of cycles necessary to attain homochirality depends on the number of residues of the substructure, on the chain length distribution of the polymers and on the total number of amino acid units.

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“…Theoretical models (Zhou et al 2005(Zhou et al , 2006 give a difference of energy of 0.2 ± 0.1 kJ/mol between the two diastereoisomers in their zwitterionic form, which corresponds to γ ≈ 1.25 ± 0.1 at 80 • C. Some experimental data on dialanine are also invoked (Saetia et al 1993), giving a ratio [LD]+[DL]…”

Section: Epimerizationmentioning

confidence: 98%

“…If several experiments have been performed for the determination of the kinetic parameters concerning the stereoselectivities of polymerization (Bartlett and Dittmer 1957;Idelson and Blout 1958), only few experiments (Saetia et al 1993) and theoretical calculations (Zhou et al 2005(Zhou et al , 2006, up to our knowledge, were developed concerning the stereoselectivities of peptide hydrolysis and the relative stability of peptide diastereoisomers. Some researches were also involved in the study of biotic homochiral peptides (Goolcharran and Borchardt 1998;Li and Brill 2003), namely focusing on the formation kinetic of cyclic dipeptides (diketopiperazines, or DKP).…”

Section: Introductionmentioning

confidence: 99%

Reactivity of Alanylalanine Diastereoisomers in Neutral and Acid Aqueous Solutions: a Versatile Stereoselectivity

Plasson

Tsuji

Asakura

2011

Orig Life Evol Biosph

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A good comprehension of the reactivity of peptides in aqueous solution is fundamental in prebiotic chemistry, namely for understanding their stability and behavior in primitive oceans. Relying on the stereoselectivity of the involved reactions, there is a huge interest in amino acid derivatives for explaining the spontaneous emergence of homochirality on primitive Earth. The corresponding kinetic and thermodynamic parameters are however still poorly known in the literature. We studied the reactivity of alanylalanine in acidic to neutral conditions as a model system. The hydrolysis into amino acids, the epimerization of the N-terminal residue, and the cyclization into diketopiperazine could be successfully identified and studied. This kinetic investigation highlighted interesting behaviors. Complex mechanisms were observed in very acidic conditions. The relative kinetic stability of the diastereoisomers of the dipeptide is highly dependent of the pH, with the possibility to dynamically destabilize the thermodynamically more stable diastereoisomers. The existence of the cyclization of dipeptides adds complexity to the system. On one hand it brings additional stereoselectivities; on the other hand fast racemization of heterochiral dipeptides is obtained.

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Relative stability of homochiral and heterochiral dialanine peptides. Effects of perturbation pathways and force-field parameters on free energy calculations

Cited by 16 publications

References 22 publications

Molecular and supramolecular chirality: R2PI spectroscopy as a tool for the gas‐phase recognition of chiral systems of biological interest

Molecular and supramolecular chirality: R2PI spectroscopy as a tool for the gas‐phase recognition of chiral systems of biological interest

Evolution of Homochirality by Epimerization of Random Peptide Chains. A Stochastic Model

Reactivity of Alanylalanine Diastereoisomers in Neutral and Acid Aqueous Solutions: a Versatile Stereoselectivity

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