Quantum simulations of the structure and binding of glycopeptide antibiotic aglycons to cell wall analogues

Article Abstract:

The rise of vancomycin-resistant enterococci (VRE) and vancomycin-resistant staphylococcus aureus (VRSA) has given new impetus to the study of the binding between glycopeptide antibiotics and bacterial cell wall termini. An extensive first principles investigation of the binding of vancomycin, avoparcin, teicoplanin, and ristocetin aglycons with dipetides, Ac-D-Ala-X, where X=D-Lac and D-Ser (characteristic of VREs) in liquid as well as gas phase was reported.

Glycoproteins, Protein binding, Plant cell walls, Cell walls, Chemical properties

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Molecular dynamics simulations of DNA with polarizable force fields: Convergence of an ideal B-DNA structure to the crystallographic structure

Article Abstract:

Multiple unrestrained molecular dynamics (MD) simulations of the DNA duplex were carried out to investigate the extent of MD simulations on DNA reproducing sequence specific features in different electrostatic descriptions and cell environments. Results showed that polarizable force fields perform better than simple point-charge force fields in reproducing the structural features of DNA.

Observations, Crystallography, Molecular dynamics

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Ab initio optical absorption spectra of size-expanded xDNA base assemblies

Article Abstract:

The article explains the ab initio optical absorption spectra of various size-expanded xDNA base assemblies. The optical response is found to get highly affected by the modifications of the frontier electron orbitals.

Analysis, Spectra, Density functionals, Density functional theory, Absorption spectra, Molecular orbitals

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