Application of advanced sampling and analysis methods to predict the structure of adsorbed protein on a material surface

Biointerphases
Tigran AbramyanRobert A Latour

Abstract

The use of standard molecular dynamics simulation methods to predict the interactions of a protein with a material surface have the inherent limitations of lacking the ability to determine the most likely conformations and orientations of the adsorbed protein on the surface and to determine the level of convergence attained by the simulation. In addition, standard mixing rules are typically applied to combine the nonbonded force field parameters of the solution and solid phases the system to represent interfacial behavior without validation. As a means to circumvent these problems, the authors demonstrate the application of an efficient advanced sampling method (TIGER2A) for the simulation of the adsorption of hen egg-white lysozyme on a crystalline (110) high-density polyethylene surface plane. Simulations are conducted to generate a Boltzmann-weighted ensemble of sampled states using force field parameters that were validated to represent interfacial behavior for this system. The resulting ensembles of sampled states were then analyzed using an in-house-developed cluster analysis method to predict the most probable orientations and conformations of the protein on the surface based on the amount of sampling performed, from whi...Continue Reading

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Citations

Jun 14, 2018·Journal of Biomedical Materials Research. Part a·Thomas A Horbett
Oct 16, 2019·Advanced Healthcare Materials·Steffen BrauneFriedrich Jung
Jul 1, 2017·Biointerphases·Tobias Weidner
Jun 28, 2019·Langmuir : the ACS Journal of Surfaces and Colloids·Pratiti Bhadra, Shirley W I Siu

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