Solvent induced conformational fluctuation of alanine dipeptide studied by using vibrational probes

Cai, Kezhou; Du, Fenfen; Liu, Jia; Su, Tingting

doi:10.1016/j.saa.2014.08.126

Cited by 11 publications

(6 citation statements)

References 87 publications

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“…Alanine dipeptide (ADP) is chosen as a model molecular system since it is a well studied model system for solvent models as well as enhanced sampling methods. , ADP has been mostly studied in aqueous environments, but there have been studies of how solvent, including chloroform, affects the observed configurations. − As in these previous studies, we are concerned with the monomer configurations observed in a solvent of chloroform as quantified by the ϕ and ψ backbone dihedrals.…”

Section: Resultsmentioning

confidence: 99%

Implicit Solvation Using the Superposition Approximation (IS-SPA): Extension to Peptides in a Polar Solvent

Lake

Mattson

McCullagh

2021

J. Chem. Theory Comput.

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Efficient, accurate, and adaptable implicit solvent models remain a significant challenge in the field of molecular simulation. A recent implicit solvent model, IS-SPA, based on approximating the mean solvent force using the superposition approximation, provides a platform to achieve these goals. IS-SPA was originally developed to handle nonpolar solutes in a polar solvent and did not accurately capture polar solvation. Here, we demonstrate that IS-SPA can accurately capture polar solvation by incorporating solvent orientation and accounting for the contributions from long ranged electrostatics. Solvent orientation is approximated as that of an ideal dipole aligned in a mean electrostatic field and an analytic form of the long ranged electrostatics is derived. Parameters for the model are calculated from explicit solvent simulations of an isolated atom or molecule and include atom-based solvent densities, mean electric field functions, radially symmetric averaged Lennard-Jones forces, and multipoles of the explicit solvent model. Using these parameters, IS-SPA accounts for asymmetry of charge solvation and reproduces the explicit solvent potential of mean force of dimerization of two oppositely charged Lennard-Jones spheres in chloroform with high fidelity. Additionally, the model more accurately captures the effect of explicit solvent on the monomer and dimer configurations of alanine dipeptide in chloroform than a generalized Born or constant density dielectric model. The current version of the algorithm is expected to outperform explicit solvent simulations for aggregation of small peptides at concentrations below 150 mM, well above the typical experimental concentrations for these materials.

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Section: Resultsmentioning

confidence: 99%

Implicit Solvation Using the Superposition Approximation (IS-SPA): Extension to Peptides in a Polar Solvent

Lake

Mattson

McCullagh

2021

J. Chem. Theory Comput.

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“…Analyses of short model compounds is a common approach in evaluation of the conformational properties of the selected amino acid residue. , The model compounds Ac-( Z )-ΔAla(βCl)-NHMe ( 1 ) and Ac-( E )-ΔAla(βCl)-NHMe ( 2 ) were calculated by the DFT method using the Gaussian 16 package . The initial structures were prepared with GaussView5 .…”

Section: Methodsmentioning

confidence: 99%

Insight into the Structure of Victorin, the Host-Selective Toxin from the Oat PathogenCochliobolus victoriae. Studies of the Unique Dehydroamino Acid β-Chlorodehydroalanine

Banaś

Lenartowicz

Staś

et al. 2023

J. Agric. Food Chem.

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Victorins, a family of peptide toxins, produced by the fungal pathogen Cochliobolus victoriae and responsible for disease of some oat varieties, contain a β-chlorodehydroalanine residue, ΔAla(βCl). To determine the conformational properties of this unique dehydroamino acid, a series of model compounds was studied using X-ray, NMR, and FT-IR methods, supported by theoretical calculations. The ΔAla(βCl) geometrical isomers differ in conformational profile. The isomer Z prefers the helical conformation α (φ, ψ = −61°, −24°), PPII type conformation β (φ, ψ = −47°, 136°), and semiextended conformation β2 (φ, ψ = −116°, 9°) in weakly and more polar solutions. The isomer E prefers mainly the extended conformation C5 (φ, ψ = −177°, 160°), but with an increase of the environment polarity also conformations β (φ, ψ = −44°, 132°) and α (φ, ψ = −53°, −39°). In the most stable conformations the N-H•••Cl hydrogen bond (5 γ ) occurs, created between the chlorine atom of the side chain and the N-H donor of the flanking amide group. The method of synthesis of the β-chlorodehydroalanine residue is proposed, by chlorination of dehydroalanine and then the photoisomerization from the isomer Z to E. The presented results indicate that the assignment of the geometrical isomer of the ΔAla(βCl) residue in naturally occurring victorins still remains an open question, despite being crucial for biological activity.

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“…ADP has been mostly studied in aqueous environment but there have been studies of how solvent, including chloroform, affects the observed configurations. [31][32][33] As in these previous studies, we are concerned with the monomer configurations observed in a solvent of chloroform as quantified by the φ and ψ backbone dihedrals.…”

Section: B Alanine Dipeptide In Chloroformmentioning

confidence: 99%

Implicit Solvation Using the Superposition Approximation (IS-SPA): Extension to Polar Solutes in Chloroform

Lake,

Mattson,

McCullagh

2020

Preprint

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Efficient, accurate, and adaptable implicit solvent models remain a significant challenge in the field of molecular simulation. A recent implicit solvent model, IS-SPA, based on approximating the mean solvent force using the superposition approximation, provides a platform to achieve these goals. IS-SPA was originally developed to handle non-polar solutes in the TIP3P water model but can be extended to accurately treat polar solutes in other polar solvents. In this manuscript, we demonstrate how to adapt IS-SPA to include the treatment of solvent orientation and long ranged electrostatics in a solvent of chloroform. The orientation of chloroform is approximated as that of an ideal dipole aligned in a mean electrostatic field. The solvent-solute force is then considered as an averaged radially symmetric Lennard-Jones component and a multipole expansion of the electrostatic component through the octupole term. Parameters for the model include atom-based solvent density and mean electric field functions that are fit from explicit solvent simulations of independent atoms or molecules. Using these parameters, IS-SPA accounts for asymmetry of charge solvation and reproduces the explicit solvent potential of mean force of dimerization of two oppositely charged Lennard-Jones spheres with high fidelity. Additionally, the model more accurately captures the effect of explicit solvent on the monomer and dimer configurations of alanine dipeptide in chloroform than a generalized Born or constant density dielectric model. The current version of the algorithm is expected to outperform explicit solvent simulations for aggregation of small peptides at concentrations below 150 mM, well above the typical experimental concentrations for these materials.

show abstract

Solvent induced conformational fluctuation of alanine dipeptide studied by using vibrational probes

Cited by 11 publications

References 87 publications

Implicit Solvation Using the Superposition Approximation (IS-SPA): Extension to Peptides in a Polar Solvent

Implicit Solvation Using the Superposition Approximation (IS-SPA): Extension to Peptides in a Polar Solvent

Insight into the Structure of Victorin, the Host-Selective Toxin from the Oat PathogenCochliobolus victoriae. Studies of the Unique Dehydroamino Acid β-Chlorodehydroalanine

Implicit Solvation Using the Superposition Approximation (IS-SPA): Extension to Polar Solutes in Chloroform

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