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

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 each Monte 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.