57,504 research outputs found
APBSmem: A Graphical Interface for Electrostatic Calculations at the Membrane
Electrostatic forces are one of the primary determinants of molecular interactions. They help guide the folding of proteins, increase the binding of one protein to another and facilitate protein-DNA and protein-ligand binding. A popular method for computing the electrostatic properties of biological systems is to numerically solve the Poisson-Boltzmann (PB) equation, and there are several easy-to-use software packages available that solve the PB equation for soluble proteins. Here we present a freely available program, called APBSmem, for carrying out these calculations in the presence of a membrane. The Adaptive Poisson-Boltzmann Solver (APBS) is used as a back-end for solving the PB equation, and a Java-based graphical user interface (GUI) coordinates a set of routines that introduce the influence of the membrane, determine its placement relative to the protein, and set the membrane potential. The software Jmol is embedded in the GUI to visualize the protein inserted in the membrane before the calculation and the electrostatic potential after completing the computation. We expect that the ease with which the GUI allows one to carry out these calculations will make this software a useful resource for experimenters and computational researchers alike. Three examples of membrane protein electrostatic calculations are carried out to illustrate how to use APBSmem and to highlight the different quantities of interest that can be calculated
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Carbohydrate-derived amphiphilic macromolecules: a biophysical structural characterization and analysis of binding behaviors to model membranes.
The design and synthesis of enhanced membrane-intercalating biomaterials for drug delivery or vascular membrane targeting is currently challenged by the lack of screening and prediction tools. The present work demonstrates the generation of a Quantitative Structural Activity Relationship model (QSAR) to make a priori predictions. Amphiphilic macromolecules (AMs) "stealth lipids" built on aldaric and uronic acids frameworks attached to poly(ethylene glycol) (PEG) polymer tails were developed to form self-assembling micelles. In the present study, a defined set of novel AM structures were investigated in terms of their binding to lipid membrane bilayers using Quartz Crystal Microbalance with Dissipation (QCM-D) experiments coupled with computational coarse-grained molecular dynamics (CG MD) and all-atom MD (AA MD) simulations. The CG MD simulations capture the insertion dynamics of the AM lipophilic backbones into the lipid bilayer with the PEGylated tail directed into bulk water. QCM-D measurements with Voigt viscoelastic model analysis enabled the quantitation of the mass gain and rate of interaction between the AM and the lipid bilayer surface. Thus, this study yielded insights about variations in the functional activity of AM materials with minute compositional or stereochemical differences based on membrane binding, which has translational potential for transplanting these materials in vivo. More broadly, it demonstrates an integrated computational-experimental approach, which can offer a promising strategy for the in silico design and screening of therapeutic candidate materials
(Tissue) P Systems with Anti-Membranes
The concept of a matter object being annihilated when meeting its corresponding
anti-matter object is taken over for membranes as objects and anti-membranes
as the corresponding annihilation counterpart in P systems. Natural numbers can be
represented by the corresponding number of membranes with a speci c label. Computational
completeness in this setting then can be obtained with using only elementary
membrane division rules, without using objects. A similar result can be obtained for tissue
P systems with cell division rules and cell / anti-cell annihilation rules. In both cases,
as derivation modes we may take the standard maximally parallel derivation modes as
well as any of the maximally parallel set derivation modes (non-extendable (multi)sets of
rules, (multi)sets with maximal number of rules, (multi)sets of rules a ecting the maximal
number of objects)
Membrane Systems and Petri Net Synthesis
Automated synthesis from behavioural specifications is an attractive and
powerful way of constructing concurrent systems. Here we focus on the problem
of synthesising a membrane system from a behavioural specification given in the
form of a transition system which specifies the desired state space of the
system to be constructed. We demonstrate how a Petri net solution to this
problem, based on the notion of region of a transition system, yields a method
of automated synthesis of membrane systems from state spaces.Comment: In Proceedings MeCBIC 2012, arXiv:1211.347
Configurational Temperature in Membrane Simulations Using Dissipative Particle Dynamics
The use of excessively long timesteps in dissipative particle dynamics
simulations may produce simulation artifacts due to the generation of
configurations which are not representative of the desired canonical ensemble.
The configurational temperature, amongst other quantities, may be used to
assess the extent of the deviation from equilibrium. This paper presents
results for simulations of models of water, and lipid bilayer membranes, to
illustrate the nature of the problems.Comment: 13 pages, 7 figures, RevTex
Modeling reaction-diffusion of molecules on surface and in volume spaces with the E-Cell System
The-Cell System is an advanced open-source simulation platform to model and analyze biochemical reaction networks. The present algorithm modules of the system assume that the reacting molecules are all homogeneously distributed in the reaction compartments, which is not the case in some cellular processes. The MinCDE system in Escherichia coli, for example, relies on intricately controlled reaction, diffusion and localization of Min proteins on the membrane and in the cytoplasm compartments to inhibit cell division at the poles of the rod-shaped cell. To model such processes, we have extended the E-Cell System to support reaction-diffusion and dynamic localization of molecules in volume and surface compartments. We evaluated our method by modeling the in vivo dynamics of MinD and MinE and comparing their simulated localization patterns to the observations in experiments and previous computational work. In both cases, our simulation results are in good agreement
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