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Coarse-Grained Molecular Dynamics Provides Insight into the Interactions of Lipids and Cholesterol with Rhodopsin

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G Protein-Coupled Receptors - Modeling and Simulation

Part of the book series: Advances in Experimental Medicine and Biology ((AEMB,volume 796))

Abstract

Protein function is a complicated interplay between structure and dynamics, which can be heavily influenced by environmental factors and conditions. This is particularly true in the case of membrane proteins, such as the visual receptor rhodopsin. It has been well documented that lipid headgroups, polyunsaturated tails, and the concentration of cholesterol in membranes all play a role in the function of rhodopsin. Recently, we used all-atom simulations to demonstrate that different lipid species have preferential interactions and possible binding sites on rhodopsin’s surface, consistent with experiment. However, the limited timescales of the simulations meant that the statistical uncertainty of these results was substantial. Accordingly, we present here 32 independent 1.6 μs coarse-grained simulations exploring lipids and cholesterols surrounding rhodopsin and opsin, in lipid bilayers mimicking those found naturally. Our results agree with those found experimentally and in previous simulations, but with far better statistical certainty. The results demonstrate the value of combining all-atom and coarse-grained models with experiment to provide a well-rounded view of lipid-protein interactions.

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Acknowledgements

We would like to thank Nick Leioatts, Dejun Lin and Tod Romo for critical reviews of this manuscript. We would also like to gratefully acknowledge financial support from the U.S. National Institutes of Health (1R01GM095496). We also thank the University of Rochester’s Center for Integrated Research Computing for the computing resources necessary to support this work.

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  1. Department of Biochemistry and Biophysics, University of Rochester Medical Center, 601 Elmwood Ave, 712, Rochester, NY, 14642, USA

    Joshua N. Horn, Ta-Chun Kao & Alan Grossfield

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  1. Joshua N. Horn
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  2. Ta-Chun Kao
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Correspondence to Alan Grossfield .

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  1. Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, New York,, New York, USA

    Marta Filizola

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Horn, J.N., Kao, TC., Grossfield, A. (2014). Coarse-Grained Molecular Dynamics Provides Insight into the Interactions of Lipids and Cholesterol with Rhodopsin. In: Filizola, M. (eds) G Protein-Coupled Receptors - Modeling and Simulation. Advances in Experimental Medicine and Biology, vol 796. Springer, Dordrecht. https://doi.org/10.1007/978-94-007-7423-0_5

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