Extension of CAVS coarse-grained model to phospholipid membranes: The importance of electrostatics
نویسندگان
چکیده
It is evident from experiment that electrostatic potential (or dipole potential) is positive inside PC or PE lipid bilayers in the absence of ions. MARTINI coarse-grained (CG) model, which has been widely used in simulating physical properties of lipid bilayers, fails to reproduce the positive value for the dipole potential in the membrane interior. Although the total dipole potential can be correctly described by the BMW/MARTINI model, the contribution from the ester dipoles, playing a nontrivial role in the electrostatic potential across lipid membranes, is neglected by this hybrid approach. In the ELBA CG model, the role of the ester dipoles is considered, but it is overweighed because various atomistic models have consistently shown that water is actually the leading contributor of dipole potential. Here, we present a CG approach by combining the BMW-like water model (namely CAVS model) with the ELBA-like lipid model proposed in this work. Our CG model was designed not only to correctly reproduce the positive values for the dipole potential inside PC and PE lipid bilayers but also to properly balance the individual contributions from the ester dipoles and water, surmounting the limitations of current CG models in the calculations of dipole potential. © 2017 Wiley Periodicals, Inc.
منابع مشابه
Molecular Dynamics Simulations of Freezing Behavior of Pure Water and 14% Water-NaCl Mixture Using the Coarse-Grained Model
We performed molecular dynamics simulations using the coarse-grained model to study the freezing behavior of pure water and 14% water-salt mixture in a wide range of temperatures for a very long time around 50 nanoseconds. For the salty water, an interface in nanoscale was used. For both systems, the f...
متن کاملAn experimental study on hydraulic behavior of free-surface radial flow in coarse-grained porous media
The equations of fluids in porous media are very useful in designing the rockfill and diversion dams, gabions, breakwaters and ground water reserves. Researches have been showed that the Forchheimer equation is not sufficient for the analysis of hydraulic behavior of free-surface radial flows; because, in these flows, in addition to the hydraulic gradient and velocity, the variable of radius is...
متن کاملImproved Coarse-Grained Modeling of Cholesterol-Containing Lipid Bilayers
Cholesterol trafficking, which is an essential function in mammalian cells, is intimately connected to molecular-scale interactions through cholesterol modulation of membrane structure and dynamics and interaction with membrane receptors. Since these effects of cholesterol occur on micro- to millisecond timescales, it is essential to develop accurate coarse-grained simulation models that can re...
متن کاملCoarse-grained model for phospholipid/cholesterol bilayer.
We construct a coarse-grained (CG) model for dipalmitoylphosphatidylcholine (DPPC)/cholesterol bilayers and apply it to large-scale simulation studies of lipid membranes. Our CG model is a two-dimensional representation of the membrane, where the individual lipid and sterol molecules are described by pointlike particles. The effective intermolecular interactions used in the model are systematic...
متن کاملAn improved joint model: POS tagging and dependency parsing
Dependency parsing is a way of syntactic parsing and a natural language that automatically analyzes the dependency structure of sentences, and the input for each sentence creates a dependency graph. Part-Of-Speech (POS) tagging is a prerequisite for dependency parsing. Generally, dependency parsers do the POS tagging task along with dependency parsing in a pipeline mode. Unfortunately, in pipel...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
برای دانلود متن کامل این مقاله و بیش از 32 میلیون مقاله دیگر ابتدا ثبت نام کنید
ثبت ناماگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید
ورودعنوان ژورنال:
- Journal of computational chemistry
دوره 38 13 شماره
صفحات -
تاریخ انتشار 2017