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Simulation of Protein–Surface Interactions by a Coarse-Grained Method

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Abstract

The interaction between proteins and inorganic surfaces or nanoparticles is important for several aspects of bionanoscience, ranging from the interaction of nanoparticles with living biosystems to the use of surface-immobilized proteins as elements of sensing devices. Atomistic simulations of the interaction between proteins and inorganic surfaces can provide a microscopic picture behind such interactions. At present, classical molecular dynamics simulations, explicitly including all atoms of the systems and the water solvent, represent the best compromise between computational cost and accuracy in the description of the systems. Nevertheless, the time scale that can be routinely investigated with these methods is still limited to tens of nanoseconds. Coarse-grained models, where many protein atoms are condensed in a single effective particle, can extend this time scale by orders of magnitude. Here, we demonstrate how a recently proposed coarse-graining scheme can be used to simulate ubiquitin (a small model protein ubiquitous in eukaryotic cells) on gold surfaces in water. In particular, we verify that the coarse-grained model gives results coherent with those obtained with the fully atomistic simulations, at a much smaller computational cost.

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Acknowledgments

OCP thanks Prof. Modesto Orozco for useful discussions. We gratefully acknowledge IIT Platform Computational for funding through the IIT Seed project MOPROSURF, and the MIUR through the FIRB project Italnanonet.

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  1. CNR Istituto Nanoscienze, Centro S3, Modena, Italy

    O. Carrillo-Parramon, G. Brancolini & S. Corni

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  1. O. Carrillo-Parramon
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  2. G. Brancolini
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  3. S. Corni
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Correspondence to S. Corni.

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Carrillo-Parramon, O., Brancolini, G. & Corni, S. Simulation of Protein–Surface Interactions by a Coarse-Grained Method. BioNanoSci. 3, 12–20 (2013). https://doi.org/10.1007/s12668-012-0073-2

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  • DOI: https://doi.org/10.1007/s12668-012-0073-2

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