scholarly journals The role of domain: Domain interactions versus domain: Water interactions in the coarse-grained simulations of the E1P to E2P transitions in Ca-ATPase (SERCA)

2012 ◽  
Vol 80 (8) ◽  
pp. 1929-1947 ◽  
Author(s):  
Anu Nagarajan ◽  
Jens Peter Andersen ◽  
Thomas B. Woolf
Keyword(s):  
Coarse Grained ◽  
Versus Domain ◽  
Domain Interactions ◽  
Coarse Grained Simulations

scholarly journals Investigating the Role of Bilayer Size and Composition on Membrane Fluctuations using Large Coarse-Grained Simulations

2015 ◽  
Vol 108 (2) ◽  
pp. 240a
Author(s):  
Philip W. Fowler ◽  
Heidi Koldsø ◽  
Anna Duncan ◽  
Mark S.P. Sansom
Keyword(s):  
Coarse Grained ◽  
Membrane Fluctuations ◽  
Coarse Grained Simulations

scholarly journals Mechanism of Mycolactone Toxin Membrane Permeation: Atomistic vs Coarse-Grained MARTINI Simulations

2018 ◽  
Author(s):  
F. Aydin ◽  
R. Sun ◽  
J. M. J. Swanson
Keyword(s):  
Buruli Ulcer ◽  
Mycobacterium Ulcerans ◽  
Coarse Grained ◽  
Membrane Permeation ◽  
Lipid Trafficking ◽  
Ulcer Disease ◽  
Cellular Processes ◽  
Coarse Grained Simulations ◽  
Dynamics Simulations

ABSTRACTMycolactone, a cytotoxic and immunosuppressive macrolide produced by Mycobacterium ulcerans, is the central virulent factor in the skin disease Buruli ulcer. This multifunctional cytotoxin affects fundamental cellular processes such as cell adhesion, immune response and cell death by targeting various cellular structures. Developing effective diagnostics that target mycolactone has been challenging, potentially due to suspected interactions with lipophilic architectures, including membranes. To better understand the pathogenesis of Buruli ulcer disease, aid in the development of diagnostics, and learn how amphiphiles in general use lipid trafficking to navigate the host environment, we seek to understand the nature of mycolactone-membrane interactions. Herein we characterize how the two dominant isomers of mycolactone (A and B) interact with and permeate DPPC membranes with all-atom molecular dynamics simulations employing transition tempered metadynamics, and compare these results with those obtained by MARTINI coarse-grained simulations. Our all-atom simulations reveal that both isomers have a strong preference to associate with the membrane, although their mechanisms and energetics of membrane permeation differ slightly. Water molecules are found to play an important role in the permeation process. Although the MARTINI coarse-grained simulations give the correct free energy of membrane association, they fail to capture the mechanism of permeation and role of water during permeation as seen in all-atom simulations.

Grand-Reaction Method for Simulations of Ionization Equilibria and Ion Partitioning in a Broad Range of pH and Ionic Strength

2019 ◽  
Author(s):  
Jonas Landsgesell ◽  
Oleg Rud ◽  
Pascal Hebbeker ◽  
Raju Lunkad ◽  
Peter Košovan ◽  
...  
Keyword(s):  
Mean Field ◽  
Coarse Grained ◽  
Reactive System ◽  
Acid Base ◽  
Buffer Solution ◽  
Reaction Method ◽  
Ionization Equilibria ◽  
Coarse Grained Simulations ◽  
Ph Range ◽  
Weak Polyelectrolytes

We introduce the grand-reaction method for coarse-grained simulations of acid-base equilibria in a system coupled to a reservoir at a given pH and concentration of added salt. It can be viewed as an extension of the constant-pH method and the reaction ensemble, combining explicit simulations of reactions within the system, and grand-canonical exchange of particles with the reservoir. Unlike the previously introduced methods, the grand-reaction method is applicable to acid-base equilibria in the whole pH range because it avoids known artifacts. However, the method is more general, and can be used for simulations of any reactive system coupled to a reservoir of a known composition. To demonstrate the advantages of the grand-reaction method, we simulated a model system: A solution of weak polyelectrolytes in equilibrium with a buffer solution. By carefully accounting for the exchange of all constituents, the method ensures that all chemical potentials are equal in the system and in the multi-component reservoir. Thus, the grand-reaction method is able to predict non-monotonic swelling of weak polyelectrolytes as a function of pH, that has been known from mean-field predictions and from experiments but has never been observed in coarse-grained simulations. Finally, we outline possible extensions and further generalizations of the method, and provide a set of guidelines to enable safe usage of the method by a broad community of users.<br><br>

Sign in / Sign up

Export Citation Format

Share Document