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Unzipping of neuronal snare protein with steered molecular dynamics occurs in three steps

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Abstract

Soluble NSF-attachment protein receptors (SNAREs) play a crucial role in membrane fusion. Neuronal SNAREs, a four-helix bundle, help synaptic vesicles fuse with plasma membranes. We applied constant velocity pulling forces in silico to C terminal of synaptobrevin, one of the helices in the bundle, to understand unzipping mechanism of neuronal SNAREs. We observed unzipping of snaptobrevin from the other helices in three steps: linker domain unzipping, C terminal unzipping and N terminal unzipping. Our results have good qualitative agreement with a recent optical tweezer experiment that observes this stepwise unzipping. Since we performed 14 different simulations for two large spring force constants, our results are robust and they reveal atomistic details of these distinct unzipping steps.

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Acknowledgments

The numerical calculations reported in this paper were performed at TUBITAK ULAKBIM, High Performance and Grid Computing Center (Turkiye Bilimsel ve Teknik Arastirmalar Kurumu (Scientific and Technical Research Council of Turkey) - Ulusal Akademik Ag ve Bilgi Merkezi (National Academic Network and Information Center) (TUBITAK - ULAKBIM); Turk Ulusal e-Bilim e-Altyapisi (Turkish National electronic-Science electronic-Infrastructure) (TRUBA) Resources). We thank them for providing us computational resources for this research.

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Authors and Affiliations

  1. Department of Physics, Faculty of Science, Yuzuncu Yil University, Van, Turkey

    Mustafa Tekpinar

  2. Department of Physics, University at Buffalo, Buffalo, NY, USA

    Wenjun Zheng

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  1. Mustafa Tekpinar
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  2. Wenjun Zheng
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Correspondence to Mustafa Tekpinar.

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Tekpinar, M., Zheng, W. Unzipping of neuronal snare protein with steered molecular dynamics occurs in three steps. J Mol Model 20, 2381 (2014). https://doi.org/10.1007/s00894-014-2381-7

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