Computational insights into the binding pattern of mitochondrial calcium uniporter inhibitor through homology modeling, molecular dynamics simulation, binding free energy prediction and density functional theory calculation

Molecular docking and molecular dynamics simulation study on the toxicity mechanism of bongkrekic acid

BKA belongs to gram-negative brevibacterium. It can cause poisoning in humans or animals and can be fatal in severe cases. There are few investigations on toxic mechanisms of BKA because of foodborne factors. MD simulations were used to study the stability and intermolecular interactions of BKA and ANT complexes to reveal the mechanism of BKA in this paper. BKA blocked ANT protein translocation mainly through Van der Waals force, hydrophobic and hydrogen bonding interactions by the MD simulations. The conformational flexibility of the complex system during different simulation times indicated that BKA affected the conformational changes of ANT through strong interactions of hydrogen bonds with active domain residues Gln-93, Tyr-196, Arg-287 and Arg-245. The results of binding free energy, principal component analysis, hydrophobic interactions and root-mean-square fluctuation showed that the prominent binding force of Tyr-196 with C₂₆ of BKA was significant to the toxicity. The active site interactions analysis indicated that the essential positively charged polar amino acids which play a crucial role within the active site of the ANT protein undergo conformational changes with BKA as the branch point.

Multiscale Simulation of Adsorption Based Microcantilever Biosensors for Radiation Exposure Effects

Background

This article is focused on biological measurements based on molecular interactions. The specific biomarker implemented for radiation biosensor is FLT3, which bears changes in the body regarding radiation exposure. Experimental results of sensing vancomycin verify the overall results of two steps of numerical methods for different scales.

Objectives

The aim is to provide adequate modeling procedures to predict sensory data. Multiscale modeling is implemented to simulate molecular interaction and its consequent micro mechanical effects. The method is implemented to calculate surface traction of microcantilever biosensor.

Materials and Methods

The method consists of molecular dynamics simulation of adsorption process by implementing classical mechanics theory to calculate the final response of the sensor as tip deflection. The sequential information transaction is assumed between the physical parameters of two governing scales. The numerical method consists of the location of particles providing for a nano-metric periodic boundary conditioned functionalized surface implemented, and the numerical thermodynamic formula is, in turn, use energy parameters to acquire macro-mechanical deflection of a specific microcantilever. Also, novel sensitivity analysis of the results as the adsorption process moves toward more saturated substrate provided.

Results

Verification of the simulation method for Vancomycin sensing results enjoys less than 20 percent of deviation regarding the experimental data. The standard deviation of 0.054 in the final expected response of the sensor is calculated as the accuracy of the radiation biosensor based on FLT3.

Conclusions

The method is still to reach a correlation between the concentration of target molecules in solution and the number of adsorbed molecules per area of the sensor. A scaled correlation between sensor's response and the amount of biomarker is found using tip deflection of a sample designed microcantilever. Around one micrometer deflection that can be read out using various conventional methods was observed at saturation of adsorption surface. The analyses provide adequate data to design a sensor capable of measuring the effect of cosmic radiation to the human body.