Predicting the orientation of protein G B1 on hydrophobic surfaces using Monte Carlo simulations

Citation

Harrison, E. T.; Weidner, T.; Castner, D. G.; & Interlandi, G. (2017). Predicting the orientation of protein G B1 on hydrophobic surfaces using Monte Carlo simulations. Biointerphases, 12(2).

Abstract

A Monte Carlo algorithm was developed to predict the most likely orientations of protein G B1, an immunoglobulin G (IgG) antibody-binding domain of protein G, adsorbed onto a hydrophobic surface. At eachMonte Carlo step, the protein was rotated and translated as a rigid body. The assumption about rigidity was supported by quartz crystal microbalance with dissipation monitoring experiments, which indicated that protein G B1 adsorbed on a polystyrene surface with its native structure conserved and showed that its IgG antibody-binding activity was retained. The Monte Carlo simulations predicted that protein G B1 is likely adsorbed onto a hydrophobic surface in two different orientations, characterized as two mutually exclusive sets of amino acids contacting the surface. This was consistent with sum frequency generation (SFG) vibrational spectroscopy results. In fact, theoretical SFG spectra calculated from an equal combination of the two predicted orientations exhibited reasonable agreement with measured spectra of protein G B1 on polystyrene surfaces. Also, in explicit solvent molecular dynamics simulations, protein G B1 maintained its predicted orientation in three out of four runs. This work shows that using a Monte Carlo approach can provide an accurate estimate of a protein orientation on a hydrophobic surface, which complements experimental surface analysis techniques and provides an initial system to study the interaction between a protein and a surface in molecular dynamics simulations. (C) 2016 Author(s).

Keyword(s)

Adsorption
force-fields
in-situ
ion mass-spectrometry
molecular-dynamics simulations
peptide
self-assembled monolayers
solid-surfaces
sum-frequency generation
tof-sims

Notes

Es2vv
Times Cited:2
Cited References Count:64

Reference Type

Journal Article

Secondary Title

Biointerphases

Author(s)

Harrison, E. T.
Weidner, T.
Castner, D. G.
Interlandi, G.

Year Published

2017

Date Published

1496275200

Volume Number

Issue Number

ISSN/ISBN

1934-8630

DOI

Artn 02d401
10.1116/1.4971381