PROTEIN-SURF SIM · Program Development for the Molecular Simulation of Protein-Surface Interactions

Program Development for the Molecular Simulation of Protein-Surface Interactions

This Marie Curie International Incoming Fellowship (IIF) program sponsored Prof. Robert Latour (McQueen-Quattlebaum Professor of Bioengineering, Clemson University, Clemson, SC, USA) to serve as an international incoming fellow to work with host scientist, Dr. Chris Lorenz (Senior Lecturer, Department of Physics, King’s College, University of London, London, UK). The goal of this research collaboration was the development of new capabilities in the LAMMPS molecular simulation program (LAMMPS: Large Atomic/Molecular Massively Parallel Simulator) to enhance its capabilities to simulate the interactions of biomolecules, such as proteins and DNA, with synthetic material surfaces. The interaction of biomolecules (e.g., proteins, DNA) with synthetic material surfaces is of great interest for a very broad range of applications in biomedical engineering and biotechnology. In each application, the bioactivity of the adsorbed or tethered biomolecule is a function of the solvent accessibility and structure of its bioactive domains. It is therefore desirable to control the orientation and conformation of biomolecules when they are adsorbed or covalently linked to a material surface. These properties, however, are very difficult to quantitatively determine using experimental methods alone. Molecular simulation methods provide an approach to directly predict and visualize these properties at the atomistic level. However, before these capabilities can be achieved, molecular modeling methods must first be designed and developed to enable the interactions between biomolecules and surfaces to be accurately simulated. The overall objectives of this research program were to develop and construct new modules in the LAMMPS molecular simulation program to provide these capabilities. The specific objectives of this research program were: (1) to develop a set of new LAMMPS modules that were determined to be necessary to support the simulation of the interactions between biomolecules in solution and a material surface, (2) to benchmark the performance of the developed simulation methods, and (3) to apply the developed methods to specific biomolecule-surface systems for methods evaluation and validation. At this time, we have largely completed specific objectives (1) and (2), and have tested and validated some of the completed modules under objective (3). The new modules that have been finalized and tested have proven to be highly successful, with one of the evaluation tests with LAMMPS providing the capability of achieving more than a 70-fold increase in computational efficiency over our previously used molecular simulation program (CHARMM). This collaboration between Dr. Lorenz and Prof. Latour is ongoing, with expectations to complete the development and testing of all of the new LAMMPS modules over the next few months. Once completed, the complete set of new modules and supporting documentation will be submitted to the LAMMPS development group at the Sandia National Laboratories in the USA for incorporation into the LAMMPS suite of programs. Once accepted and incorporated into the new version of LAMMPS, these modules will be freely accessible for interested users via the LAMMPS website (<http://lammps.sandia.gov/>) for widespread use.

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