PROTEIN-SURF SIM

Program Development for the Molecular Simulation of Protein-Surface Interactions

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 Obiettivo del progetto (Objective)

'The ability to understand and predict the interactions between proteins and material surfaces represents a critical need for many applications in bionanotechnology and biomedical engineering. Empirical force field molecular simulation methods have the potential to provide this capability, with the European community currently leading the world in this area of research. However, methods have not yet been developed to adequately support these types of simulations. For these simulations, an ideal program will provide the capability of using a Class I protein force field (FF) to model the behavior of the protein in the solution phase, a Class II FF to model the behavior of the solid material phase, and an interfacial FF to control interactions at the liquid-solid interface. In addition, the program must be highly scalable to enable simulations to be efficiently run on today’s large computer clusters via parallel simulation. While no simulation code currently provides these capabilities, the LAMMPS program comes closest by providing the ability to run both Class I and II force fields in the same simulation with massively parallel processing capability, but without the capability to fully utilize an interfacial force field (IFF) to independently control interphase behavior. The objectives of the proposed research are to (1) modify the LAMMPS molecular simulation program to develop the capability to independently implement an interfacial force field (IFF) to control interfacial behavior (LAMMPS/IFF), (2) benchmark the performance of LAMMPS/IFF for large-scale parallel processing, and (3) apply LAMMP/IFF to demonstrate the ability to accurate simulate protein-surface interactions. The development of this molecular simulation program has the potential to revolutionize current capabilities to accurately predict protein-surface interactions and to serve as a valuable tool for the design of the surfaces to control the bioactive state of surface-bound proteins.'

Introduzione (Teaser)

An EU funded project has developed modules to simulate the behaviour of biomolecules when they come into contact with an artificial surface.

Descrizione progetto (Article)

Interactions of biomolecules such as proteins and DNA with synthetic surfaces are critical in many areas of bionanotechnology and biomedical engineering. For example, an implant like a hip-stem replacement necessitates integration with the host tissues, and protein adsorption facilitates this integration.

It is essential that researchers understand the behaviour of a protein when it comes into contact with a range of synthetic material surfaces. Researchers with the 'Program development for the molecular simulation of protein-surface interactions' (PROTEIN-SURF SIM) project developed a molecular dynamics simulator to predict how various proteins behave with a large variety of materials. This simulator is called Large Atomic/Molecular Massively Parallel Simulator (LAMMPS).

In each application, the protein bioactivity varies with the solvent accessibility and the structure of its bioactive domains. It is now possible to obtain data that enables the control of conformation and orientation of biomolecules.

The team also completed the development of the new set of modules necessary for simulating protein behaviour on surfaces in solution. The scientists also benchmarked the simulation methods. Module validation in specific biomolecule-surface systems was very successful and over 70-fold increase in computational efficiency was seen compared to the previously used simulation program.

After complete testing of each module, these have been made freely available for downloading from the (http://lammps.sandia.gov/ (LAMMPS)) website. Interested users will be primarily in healthcare but the technology could easily be modified to extend to other areas.