A Highly Tilted Membrane Configuration for the Prefusion State of Synaptobrevin

Abstract

The SNARE complex plays a vital role in vesicle fusion arising during neuronal exocytosis. Key components in the regulation of SNARE complex formation, and ultimately fusion, are the transmembrane and linker regions of the vesicle-associated protein, synaptobrevin. However, the membrane-embedded structure of synaptobrevin in its prefusion state, which determines its interaction with other SNARE proteins during fusion, is largely unknown. This study reports all-atom molecular-dynamics simulations of the prefusion configuration of synaptobrevin in a lipid bilayer, aimed at characterizing the insertion depth and the orientation of the protein in the membrane, as well as the nature of the amino acids involved in determining these properties. By characterizing the structural properties of both wild-type and mutant synaptobrevin, the effects of C-terminal additions on tilt and insertion depth of membrane-embedded synaptobrevin are determined. The simulations suggest a robust, highly tilted state for membrane-embedded synaptobrevin with a helical connection between the transmembrane and linker regions, leading to an apparently new characterization of structural elements in prefusion synaptobrevin and providing a framework for interpreting past mutation experiments.

A Structural Role for the Synaptobrevin 2 Transmembrane Domain in Dense-Core Vesicle Fusion Pores

“…Theoretical studies of SNARE-mediated fusion suggest tilting Risselada et al, 2011) or outward translocation (Lindau et al, 2012) of the TMDs during fusion. Molecular dynamics simulations suggest that the linker and TMD N terminus tilt in the lipid bilayer and that the C terminus is flexible with a pivot at residue G100 (Blanchard et al, 2014). Our results suggest that the fusion pore contains a constriction from residues 99 -105, which contains the putative G100 kink (Fig.…”

Efficient Exploration of Membrane-Associated Phenomena at Atomic Resolution

“…3). This result, combined with the favorable enhanced lipid lateral diffusion and headgroup atomic distributions (Ohkubo et al, 2012), began a push in the field to apply this methodology to proteins which are known or are thought to have substantial membrane interaction (Baylon et al, 2013; Wu and Schulten, 2014; Arcario and Tajkhorshid, 2014; Blanchard et al, 2014; Vermaas and Tajkhorshid, 2014a; Rhéault et al, 2015). …”

“…The HMMM model has been successfully applied to simulation studies of several membrane-associated protein systems(Ohkubo et al, 2012; Baylon et al, 2013; Vermaas and Tajkhorshid, 2014a; Blanchard et al, 2014; Arcario and Tajkhorshid, 2014; Wu and Schulten, 2014; Rhéault et al, 2015). We begin this review by describing the development trajectory of the HMMM model, followed by a set of its recent applications to a wide variety of membrane-associated phenomena including: phospholipid insertion into membrane (Vermaas and Tajkhorshid, 2014b), binding and insertion of peripheral proteins such as cytochrome P450 (Baylon et al, 2013), hemoglobin N (Rhéault et al, 2015), talin (Arcario and Tajkhorshid, 2014), synaptotagmin I (Wu and Schulten, 2014), and α -synuclein (Vermaas and Tajkhorshid, 2014a), and studies of pre-fusion configuration of synaptobrevin transmembrane helix in a lipid bilayer (Blanchard et al, 2014).…”

“…We begin this review by describing the development trajectory of the HMMM model, followed by a set of its recent applications to a wide variety of membrane-associated phenomena including: phospholipid insertion into membrane (Vermaas and Tajkhorshid, 2014b), binding and insertion of peripheral proteins such as cytochrome P450 (Baylon et al, 2013), hemoglobin N (Rhéault et al, 2015), talin (Arcario and Tajkhorshid, 2014), synaptotagmin I (Wu and Schulten, 2014), and α -synuclein (Vermaas and Tajkhorshid, 2014a), and studies of pre-fusion configuration of synaptobrevin transmembrane helix in a lipid bilayer (Blanchard et al, 2014). We conclude with outlining the best practices for utilizing the HMMM model and an outlook on its future developments.…”

Computational ‘microscopy’ of cellular membranes

“…State-of-the-art examples are studies of membrane binding and the formation of pores by antimicrobial and cell-penetrating peptides (Berglund et al, 2015;Huang and García, 2013;Moiset et al, 2013;Ulmschneider et al, 2012), of the specific binding of lipids to membrane proteins (Aponte-Santamaria et al, 2012;Contreras et al, 2012;Lee and Lyman, 2012;Pöyry et al, 2013), of the cyclodextrin-mediated extraction of cholesterol from membranes (López et al, 2013a), of the dynamic organization of multi-component membranes (Martinez-Seara et al, 2010;Sodt et al, 2014;Wu et al, 2014b), of lipid-peptide interplay in membrane fusion (Blanchard et al, 2014;Larsson and Kasson, 2013) and of the functioning of membrane proteins (Dror et al, 2011;Kopfer et al, 2014;Maffeo et al, 2012;Marinelli et al, 2014;Moradi et al, 2015;Ostmeyer et al, 2013;Romo et al, 2010).…”