Molecular Dynamics Simulations Shed Light on the Enthalpic and Entropic Driving Forces That Govern the Sequence Specific Recognition between Netropsin and DNA

2010 ◽  
Vol 114 (34) ◽  
pp. 11164-11172 ◽  
Author(s):  
Jožica Dolenc ◽  
Sarah Gerster ◽  
Wilfred F. van Gunsteren
2021 ◽  
Vol 23 (14) ◽  
pp. 8525-8540
Author(s):  
Mudong Feng ◽  
Michael K. Gilson

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?


Soft Matter ◽  
2019 ◽  
Vol 15 (41) ◽  
pp. 8402-8411 ◽  
Author(s):  
Georgia Tsagkaropoulou ◽  
Finian J. Allen ◽  
Stuart M. Clarke ◽  
Philip J. Camp

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.


2020 ◽  
Vol 22 (3) ◽  
pp. 1053-1060
Author(s):  
Kenji Mochizuki

Thermo-sensitive aqueous polymers undergo a coil-to-globule transition on heating, with drastic chemical and structural changes. We performed molecular dynamics simulations for PVCL in water to study the driving forces for the polymer's collapse.


2021 ◽  
Author(s):  
Josep Rizo ◽  
Levent Sari ◽  
Yife Qi ◽  
Wonpil Im ◽  
Milo M Lin

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.


2020 ◽  
Vol 22 (4) ◽  
pp. 2033-2045 ◽  
Author(s):  
Konstantin S. Smirnov

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.


Sign in / Sign up

Export Citation Format

Share Document