Coarse‐Grain Simulations of the R‐SNARE Fusion Protein in its Membrane Environment Detect Long‐Lived Conformational Sub‐States

Abstract

Coarse-grain molecular dynamics are used to look at conformational and dynamic aspects of an R-SNARE peptide inserted in a lipid bilayer. This approach allows carrying out microsecond-scale simulations which bring to light long-lived conformational sub-states potentially interesting in the context of the membrane fusion mechanism mediated by the SNARE proteins. We show that these coarse-grain models are in agreement with most experimental data on the SNARE system, but differ in some details that may have a functional interest, most notably in the orientation of the soluble part of R-SNARE that does not appear to be spontaneously accessible for SNARE complex formation. We also compare rat and yeast sequences of R-SNARE and find some minor differences in their behavior.

Caught in the Act: Visualization of SNARE‐Mediated Fusion Events in Molecular Detail

“…Thus the insertion depth of the SNARE complex, which is an important and sensitive indicator of the underlying protein-bilayer interactions, is well reproduced by the CG model. [21] SNARE complex is driven towards the perimeter of the fusion region Figure 2 A and C reveal that the coarse-grained model of the SNARE complex is mechanical functional and that progression of the zipping pulls the vesicles toward each other. Over the course of microseconds, the single SNARE complex diffuses towards and along the perimeter of the fusion site (vertex ring), maintaining an orientation normal to the perimeter (Figure 2 A, C).…”

A Highly Tilted Membrane Configuration for the Prefusion State of Synaptobrevin

“…Prefusion synaptobrevin has a well-defined structure in the membrane Prior results from experiments and simulations have yielded two conflicting models for membrane-embedded synaptobrevin (12,15,16). One model proposes that the TM (residues 95-116) and linker (residues 85-94) regions are connected by a disordered segment, with little or no tilt in the TM domain, but a large tilt with regard to the membrane in the linker region (12,16); the second model proposes that the TM and linker regions form a continuous helix with a large tilt on the basis of CD and infrared spectroscopic measurements (15).…”

“…One model proposes that the TM (residues 95-116) and linker (residues 85-94) regions are connected by a disordered segment, with little or no tilt in the TM domain, but a large tilt with regard to the membrane in the linker region (12,16); the second model proposes that the TM and linker regions form a continuous helix with a large tilt on the basis of CD and infrared spectroscopic measurements (15). To distinguish between the two models, we employed MD simulations with a wide range of initial orientations to establish a well-defined structure for the TM and linker regions of synaptobrevin in the presence of a membrane.…”

“…Measurements (12,(15)(16)(17) for the insertion depth and tilt angle of the linker region relative to the membrane have yielded relatively consistent results but with vastly different structural interpretations. Experiments have shown that the tryptophan residues of the linker region are inserted well below the phosphate layer of the membrane (12) and that the linker region has a large tilt with respect to the membrane normal (15,17).…”

“…The results can be interpreted through either a continuous helix or a disordered connection between the TM and linker regions (12,15). Circular dichroism (CD) experiments suggest the existence of a continuous helix (15), whereas coarse-grained simulations have demonstrated a disordered connection (16). A helical connection between the TM and linker regions would invalidate the currently proposed structural segments of synaptobrevin (11).…”