Hamiltonian replica exchange simulations of glucose oxidase adsorption on charged surfaces

Physical Chemistry Chemical Physics : PCCP
Yun XieJian Zhou

Abstract

The Hamiltonian replica exchange Monte Carlo (H-REMC) algorithm was applied to study protein adsorption and its performance was compared with that of the temperature replica exchange Monte Carlo (T-REMC). Comparisons indicate that the simulation results are consistent but the computational efficiency is improved for H-REMC. H-REMC could accurately and efficiently identify the preferred orientations of glucose oxidase (GOx) on charged surfaces; different preferential GOx orientations on different surfaces and solution conditions could be spotted with a much fewer number of simulation runs. On positively charged surfaces, when electrostatic interactions dominate, the negatively charged GOx can be easily adsorbed with the "standing" orientation for which the substrate-binding domain is accessible to substrates. As the surface charge densities decrease and ionic strengths increase, there is an increasing contribution from the van der Waals (vdW) interactions, and thus more possible orientations appear. When the vdW interactions dominate, the unfavorable "front-lying" becomes the preferred orientation for which the substrate-binding domain is blocked by the surface. On negatively charged surfaces, though GOx has a net charge of -30 ...Continue Reading

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Citations

Nov 15, 2019·Journal of Physics. Condensed Matter : an Institute of Physics Journal·Yusei KobayashiNoriyoshi Arai
May 1, 2021·Nanomaterials·Wiktoria LipińskaKatarzyna Siuzdak
Jul 26, 2018·Langmuir : the ACS Journal of Surfaces and Colloids·Shengjiang YangJian Zhou

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Methods Mentioned

BETA
biosensors
biosensor

Software Mentioned

REMC

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