Dataset Information

Biomolecular Simulations under Realistic Macroscopic Salt Conditions.

ABSTRACT: Biomolecular simulations are typically performed in an aqueous environment where the number of ions remains fixed for the duration of the simulation, generally with either a minimally neutralizing ion environment or a number of salt pairs intended to match the macroscopic salt concentration. In contrast, real biomolecules experience local ion environments where the salt concentration is dynamic and may differ from bulk. The degree of salt concentration variability and average deviation from the macroscopic concentration remains, as yet, unknown. Here, we describe the theory and implementation of a Monte Carlo osmostat that can be added to explicit solvent molecular dynamics or Monte Carlo simulations to sample from a semigrand canonical ensemble in which the number of salt pairs fluctuates dynamically during the simulation. The osmostat reproduces the correct equilibrium statistics for a simulation volume that can exchange ions with a large reservoir at a defined macroscopic salt concentration. To achieve useful Monte Carlo acceptance rates, the method makes use of nonequilibrium candidate Monte Carlo (NCMC) moves in which monovalent ions and water molecules are alchemically transmuted using short nonequilibrium trajectories, with a modified Metropolis-Hastings criterion ensuring correct equilibrium statistics for an ( ??, N, p, T) ensemble to achieve a ?1046× boost in acceptance rates. We demonstrate how typical protein (DHFR and the tyrosine kinase Src) and nucleic acid (Drew-Dickerson B-DNA dodecamer) systems exhibit salt concentration distributions that significantly differ from fixed-salt bulk simulations and display fluctuations that are on the same order of magnitude as the average.

SUBMITTER: Ross GA

PROVIDER: S-EPMC6078207 | biostudies-literature | 2018 May

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Biomolecular Simulations under Realistic Macroscopic Salt Conditions.

Ross Gregory A GA Rustenburg Ariën S AS Grinaway Patrick B PB Fass Josh J Chodera John D JD

The journal of physical chemistry. B 20180501 21

Biomolecular simulations are typically performed in an aqueous environment where the number of ions remains fixed for the duration of the simulation, generally with either a minimally neutralizing ion environment or a number of salt pairs intended to match the macroscopic salt concentration. In contrast, real biomolecules experience local ion environments where the salt concentration is dynamic and may differ from bulk. The degree of salt concentration variability and average deviation from the ...[more]

PMID: 29649876

Similar Datasets

Project description:BackgroundAntimicrobial materials or surfaces are advertised as part of infection prevention bundles. However, the efficacy of such antimicrobial surfaces has not been sufficiently investigated in hospitals. In this study, the antimicrobial activity of examination gloves with light-activated antimicrobial properties against Gram-positive microorganisms was investigated modelling real live conditions.MethodIn a standardized experimental set-up with dry and realistic contamination, the antimicrobial properties of gloves claiming light dependent antimicrobial activity against Gram-positive organisms were tested in comparison with conventional examination gloves. All gloves were contaminated through a standardized activity of the test persons for construction with contaminated building blocks. For contamination suspensions of Enterococcus faecium ATCC 6057, Acinetobacter baumannii (outbreak strain), methicillin resistant Staphylococcus aureus ATCC 43300 or E. faecium (VRE) patient isolate were dried on the surfaces. After the standardized activity, the gloves were held for 10 min in the light present in the room (bright conditions) and the grade of contamination was determined subsequently by quantitative culture. In one experimental series gloves were held in a dark box after contamination as a control (dark conditions).ResultsThe light intensity in all experiments under bright conditions was significantly above the limit value specified by the manufacturer for the activation of antimicrobial properties (> 500 lx). The mean values for experiments with antimicrobial active and non-active gloves were 955 and 935 lx, respectively. As claimed by the manufacture, the gloves showed no sufficient efficacy against A. baumannii under bright conditions. Against Gram-positive microorganisms such as E. faecium, E. faecium (VRE) and methicillin resistant S. aureus the gloves showed only very low antimicrobial activity with a reduction factor < 1 log10 even after 10 min in bright conditions. Interestingly, comparable results for experiments with A. baumannii and E. faecium were shown under dark conditions.ConclusionThe lack of activity of the active principle against Gram-negative microorganisms could be confirmed. The reduction factors of > 4 log10 within 5 min for Gram-positive microorganisms claimed for the product using a standard test procedure (ASTM D7907) could not be confirmed in a realistic experimental test set-up even after 10 min of light exposure. The effectiveness against Gram-positive microorganisms should be further investigated under realistic (dry) conditions, including patient care. At this stage, the use of supposedly antimicrobial gloves should not be recommended, as the belief in their efficacy may encourage the misuse of gloves.

Dataset Information

Biomolecular Simulations under Realistic Macroscopic Salt Conditions.

Publications

Biomolecular Simulations under Realistic Macroscopic Salt Conditions.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets