scholarly journals All-atom molecular dynamics simulations of synaptic vesicle fusion I: a glimpse at the primed state

2021 ◽  
Author(s):  
Josep Rizo ◽  
Levent Sari ◽  
Yife Qi ◽  
Wonpil Im ◽  
Milo M Lin
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Neurotransmitter Release ◽  
Synaptic Vesicles ◽  
Plasma Membranes ◽  
Synaptotagmin 1 ◽  
Primed State ◽  
Dynamics Simulations ◽  
Synaptic Vesicle Fusion ◽  
Shed Light

Synaptic vesicles are primed into a state that is ready for fast neurotransmitter release upon Ca2+-binding to synaptotagmin-1. This state likely includes trans-SNARE complexes between the vesicle and plasma membranes that are bound to synaptotagmin-1 and complexins. However, the nature of this state and the steps leading to membrane fusion are unclear, in part because of the difficulty of studying this dynamic process experimentally. To shed light into these questions, we performed all-atom molecular dynamics simulations of systems containing trans-SNARE complexes between two flat bilayers or a vesicle and a flat bilayer with or without fragments of synaptotagmin-1 and/or complexin-1. Our results help visualize potential states of the release machinery en route to fusion, and suggest mechanistic features that may control the speed of release. In particular, the simulations suggest that the primed state contains almost fully assembled trans-SNARE complexes bound to the synaptotagmin-1 C2B domain and complexin-1 in a spring-loaded configuration where interactions of the C2B domain with the plasma membrane orient complexin-1 toward the vesicle, avoiding premature membrane merger but keeping the system ready for fast fusion upon Ca2+ influx.

Mechanistic analysis of light-driven overcrowded alkene-based molecular motors by multiscale molecular simulations

2021 ◽  
Vol 23 (14) ◽  
pp. 8525-8540
Author(s):  
Mudong Feng ◽  
Michael K. Gilson
Keyword(s):  
Molecular Dynamics ◽  
Excited State ◽  
Molecular Dynamics Simulations ◽  
Ground State ◽  
Molecular Motors ◽  
Motor Performance ◽  
Molecular Simulations ◽  
Mechanistic Analysis ◽  
Dynamics Simulations ◽  
Shed Light

Ground-state and excited-state molecular dynamics simulations shed light on the rotation mechanism of small, light-driven molecular motors and predict motor performance. How fast can they rotate; how much torque and power can they generate?

scholarly journals Self-assembly and adsorption of cetyltrimethylammonium bromide and didodecyldimethylammonium bromide surfactants at the mica–water interface

Soft Matter ◽  
2019 ◽  
Vol 15 (41) ◽  
pp. 8402-8411 ◽  
Author(s):  
Georgia Tsagkaropoulou ◽  
Finian J. Allen ◽  
Stuart M. Clarke ◽  
Philip J. Camp
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Self Assembly ◽  
Cetyltrimethylammonium Bromide ◽  
Ionic Surfactants ◽  
Water Interface ◽  
Didodecyldimethylammonium Bromide ◽  
Dynamics Simulations ◽  
Shed Light

Molecular-dynamics simulations are used to explore bilayers formed by simple ionic surfactants at the mica–water interface, and to shed light on experimental observations.

scholarly journals Functional synergy between the Munc13 C-terminal C1 and C2 domains

eLife ◽  
2016 ◽  
Vol 5 ◽  
Author(s):  
Xiaoxia Liu ◽  
Alpay Burak Seven ◽  
Marcial Camacho ◽  
Victoria Esser ◽  
Junjie Xu ◽  
...  
Keyword(s):  
Neurotransmitter Release ◽  
Plasma Membranes ◽  
Snare Complex ◽  
Complex Assembly ◽  
C2 Domains ◽  
Vesicle Docking ◽  
Synaptotagmin 1 ◽  
Primed State ◽  
Multiple Domains ◽  
Stimulation Of

Neurotransmitter release requires SNARE complexes to bring membranes together, NSF-SNAPs to recycle the SNAREs, Munc18-1 and Munc13s to orchestrate SNARE complex assembly, and Synaptotagmin-1 to trigger fast Ca2+-dependent membrane fusion. However, it is unclear whether Munc13s function upstream and/or downstream of SNARE complex assembly, and how the actions of their multiple domains are integrated. Reconstitution, liposome-clustering and electrophysiological experiments now reveal a functional synergy between the C1, C2B and C2C domains of Munc13-1, indicating that these domains help bridging the vesicle and plasma membranes to facilitate stimulation of SNARE complex assembly by the Munc13-1 MUN domain. Our reconstitution data also suggest that Munc18-1, Munc13-1, NSF, αSNAP and the SNAREs are critical to form a ‘primed’ state that does not fuse but is ready for fast fusion upon Ca2+ influx. Overall, our results support a model whereby the multiple domains of Munc13s cooperate to coordinate synaptic vesicle docking, priming and fusion.

Impact of Ionic Liquids in Aqueous Solution on Bacterial Plasma Membranes Studied with Molecular Dynamics Simulations

2014 ◽  
Vol 118 (35) ◽  
pp. 10444-10459 ◽  
Author(s):  
Geraldine S. Lim ◽  
Jernej Zidar ◽  
Daniel W. Cheong ◽  
Stephan Jaenicke ◽  
Marco Klähn
Keyword(s):  
Molecular Dynamics ◽  
Aqueous Solution ◽  
Ionic Liquids ◽  
Molecular Dynamics Simulations ◽  
Plasma Membranes ◽  
Dynamics Simulations

scholarly journals Structure and sum-frequency generation spectra of water on uncharged Q4 silica surfaces: a molecular dynamics study

2020 ◽  
Vol 22 (4) ◽  
pp. 2033-2045 ◽  
Author(s):  
Konstantin S. Smirnov
Keyword(s):  
Molecular Dynamics ◽  
Vibrational Spectrum ◽  
Molecular Dynamics Simulations ◽  
Sum Frequency Generation ◽  
Sum Frequency ◽  
Silica Surfaces ◽  
Frequency Generation ◽  
Dynamics Simulations ◽  
The Relationship ◽  
Shed Light

Molecular dynamics simulations shed light on the relationship between the structure and sum-frequency generation vibrational spectrum of water on uncharged Q4 surfaces of different affinity for water.

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