Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
Review
. 2023 Mar 6;13(3):307.
doi: 10.3390/membranes13030307.

Molecular Dynamics Simulations of the Proteins Regulating Synaptic Vesicle Fusion

Maria Bykhovskaia  1
Affiliations
Review

Molecular Dynamics Simulations of the Proteins Regulating Synaptic Vesicle Fusion

Maria Bykhovskaia. Membranes (Basel). .

Abstract

Neuronal transmitters are packaged in synaptic vesicles (SVs) and released by the fusion of SVs with the presynaptic membrane (PM). An inflow of Ca2+ into the nerve terminal triggers fusion, and the SV-associated protein Synaptotagmin 1 (Syt1) serves as a Ca2+ sensor. In preparation for fusion, SVs become attached to the PM by the SNARE protein complex, a coiled-coil bundle that exerts the force overcoming SV-PM repulsion. A cytosolic protein Complexin (Cpx) attaches to the SNARE complex and differentially regulates the evoked and spontaneous release components. It is still debated how the dynamic interactions of Syt1, SNARE proteins and Cpx lead to fusion. This problem is confounded by heterogeneity in the conformational states of the prefusion protein-lipid complex and by the lack of tools to experimentally monitor the rapid conformational transitions of the complex, which occur at a sub-millisecond scale. However, these complications can be overcome employing molecular dynamics (MDs), a computational approach that enables simulating interactions and conformational transitions of proteins and lipids. This review discusses the use of molecular dynamics for the investigation of the pre-fusion protein-lipid complex. We discuss the dynamics of the SNARE complex between lipid bilayers, as well as the interactions of Syt1 with lipids and SNARE proteins, and Cpx regulating the assembly of the SNARE complex.

Keywords: SNARE complex; complexin; exocytosis; lipid bilayers; neuronal transmitters; synaptotagmin.

PubMed Disclaimer

Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 2
Figure 2
The model of Cpx clamping function driven by AAMD simulations. (A) Two representations of the SNARE-Cpx complex. The structure was obtained by crystallography and equilibrated by AAMD. Reproduced from [72]. Blue: Sx; red: Sb; green: SN1; cyan SN2; magenta: Cpx. AH: Accessory helix. (B) Cpx stabilizes a partially unraveled state of Sb (Layers 6–8). Reproduced from [75] with permission (license 5472810090395). (C) The partially unraveled SNARE complex between lipid bilayers mimicking an SV and the PM. Note that Cpx (orange) creates a barrier between the SNARE bundle and the SV via its accessory helix, in addition to stabilizing the partially unraveled state of Sb.
Figure 1
Figure 1
SNARE zippering. (A) The structure of the SNARE bundle with the denoted layers [47]. (B) The initial (left) and the final (right) states of the molecular system mimicking the SV and PM bilayers attached to each other by four SNARE bundles. Red: Sx, blue: Sb, green: SNAP25. Blue spheres denote water molecules diffusing through the open pore in the final state. Reproduced with permission from [57]. (C) The separation of an SV and the PM at equilibrium plotted against the number of the SNARE complexes mediating the SV-PM attachment [60]. Note a steep drop as the number of the SNARE complexes increases from one to two, and a further reduction in the SV-PM separation as the number of the SNARE complexes increases to three. Note also the plateau, as the number of the complexes increases further. (D) The assembly time of the SNARE complex depends exponentially on the initial separation of the Sb and Sx C-terminals [59]. The inset shows the results obtained using three different models of the helix assembly, which largely converge.
Figure 3
Figure 3
Lipid binding of the isolated domains, as well as the C2AB tandem of Syt1. (A) The C2B domain binds the bilayer mimicking the PM via its Ca2+ binding loops (CBL), polybasic stretch (PB), and the RR (Arg398-Arg399) motif opposing the CBL. Green spheres denote Ca2+ ions. Red: PIP2. (B) CBL of the C2A domain attach to either the SV or PM bilayer; however, the interaction with the PM bilayer is more extensive and the penetration into the PM is deeper. (C) Both C2 domains within Ca2+C2AB tandem attach to the PM via their CBL and PB motifs. (D) The penetration into the PM bilayer is deeper for the isolated Ca2+-bound C2 domains compared to the Ca2+C2AB tandem. Reproduced from [83].
Figure 4
Figure 4
The prefusion Syt1-SNARE-Cpx complex. (A) Three conformational states of the Syt1-SNARE-Cpx complex obtained by AAMD simulations. Note that States 1 and 2 have Syt1 directly interacting with Cpx. (B) Two views of the prefusion Ca2+Syt1-SNARE-Cpx complex attached to the PM. Note the Ca2+-bound tips of C2 domains immersed into the PM. (C) The attachment of the C2B domain to the SNARE bundle decouples C2 domains and enables their deeper penetration into the PM. The graphs show the distributions of the penetration depths over respective 5 μs trajectories. (D) The prefusion Ca2+Syt1-SNARE-Cpx complex drives the merging of the SV (top) and the PM (bottom) bilayers. (E) The number of SV-PM Van der Waals contacts for the Ca2+-bound and Ca2+-free prefusion Syt1-SNARE-Cpx complexes along respective trajectories. Note continuous stretches of the SV-PM attachment for the Ca2+-bound complex (green lines). In contrast, for the Ca2+-free complex, the PM and SV bilayers are not in contact for most of the trajectory. Reproduced from [83].
Figure 5
Figure 5
SV-PM fusion mediated by four Syt1-SNARE-Cpx complexes. (A) The system at the initial (0 ns) and final (336 ns) points of the trajectory. (B) Each of the four complexes between the bilayers of the SV and PM in the end of the trajectory. Note that all the complexes have the C2B domains (navy) attached to the SNARE bundles. In contrast, the positions of the C2A domains (cyan) vary: two complexes (PC1 and PC4) have the C2A domain attached to the the PM, while the other two complexes (PC2 and PC3) have the C2A domains interacting with Cpx (yellow) and bridging to the SV. Reproduced from [92].
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

References

    1. Sudhof T.C., Rothman J.E. Membrane fusion: Grappling with SNARE and SM proteins. Science. 2009;323:474–477. doi: 10.1126/science.1161748. - DOI - PMC - PubMed
    1. Sudhof T.C. Neurotransmitter release: The last millisecond in the life of a synaptic vesicle. Neuron. 2013;80:675–690. doi: 10.1016/j.neuron.2013.10.022. - DOI - PMC - PubMed
    1. Kaeser P.S., Regehr W.G. Molecular mechanisms for synchronous, asynchronous, and spontaneous neurotransmitter release. Annu. Rev. Physiol. 2014;76:333–363. doi: 10.1146/annurev-physiol-021113-170338. - DOI - PMC - PubMed
    1. Rizo J., Xu J. The Synaptic Vesicle Release Machinery. Annu. Rev. Biophys. 2015;44:339–367. doi: 10.1146/annurev-biophys-060414-034057. - DOI - PubMed
    1. Chapman E.R. How does synaptotagmin trigger neurotransmitter release? Annu. Rev. Biochem. 2008;77:615–641. doi: 10.1146/annurev.biochem.77.062005.101135. - DOI - PubMed

Grants and funding

This research received no external funding.