Title:	Investigation of protein-protein and protein-metal surface interaction via molecular dynamics simulation
DNr:	NAISS 2025/22-860
Project Type:	NAISS Small Compute
Principal Investigator:	Johan Nilsson <johne@chalmers.se>
Affiliation:	Chalmers tekniska högskola
Duration:	2025-06-11 – 2026-04-01
Classification:	10407
Keywords:

Abstract

Fouling caused by protein adsorption onto solid surfaces remains a critical challenge in a wide range of applications, from biomedical device performance to membrane filtration in water treatment. To advance fundamental understanding of this phenomenon, we propose a computational study employing molecular dynamics (MD) simulations to investigate the interactions between proteins and metal oxide surfaces, with a specific focus on chromium(III) oxide (Cr₂O₃). This study will also extend to protein-protein interactions near surfaces to evaluate their role in aggregation and multilayer fouling behavior. The core objective of this project is to uncover the atomistic mechanisms driving protein adsorption, orientation, conformational changes, and possible denaturation upon contact with Cr₂O₃ surfaces. We aim to explore how surface properties, such as crystallographic orientation and charge distribution, influence protein binding energetics and kinetics. This information is crucial to designing anti-fouling materials and improving surface engineering strategies. To achieve this, we will perform all-atom MD simulations using established force fields (e.g., CHARMM, AMBER) and parameterizations suitable for metal oxides and biomolecules. Simulations will be conducted for a set of representative proteins (e.g., lysozyme, BSA) in explicit solvent, both in isolation and in proximity to Cr₂O₃ surfaces. Periodic boundary conditions, energy minimization, and long-timescale production runs will be employed to capture relevant dynamic behavior. Enhanced sampling techniques may also be used to access rare events or overcome energy barriers related to adsorption. This computationally intensive project requires high-performance computing resources to handle the large system sizes, long simulation timescales (hundreds of nanoseconds to microseconds), and extensive sampling necessary for statistically meaningful insights. The resulting data will be analyzed to quantify interaction energies, adsorption free energies, structural changes, and aggregation phenomena, contributing to a better understanding of biofouling at the molecular level. The findings from this project will provide valuable insights into the design of anti-fouling coatings and inform experimental studies aiming to control protein-material interactions. We anticipate that the results will be disseminated through high-impact publications and collaborative research with experimental partners.