ABSTRACT
The MArtini Database (MAD - https://mad.ibcp.fr) is a web server designed for the sharing of structures and topologies of molecules parametrized with the Martini coarse-grained (CG) force field. MAD can also convert atomistic structures into CG structures and prepare complex systems (including proteins, lipids, etc.) for molecular dynamics (MD) simulations at the CG level. It is dedicated to the generation of input files for Martini 3, the most recent version of this popular CG force field. Specifically, the MAD server currently includes tools to submit or retrieve CG models of a wide range of molecules (lipids, carbohydrates, nanoparticles, etc.), transform atomistic protein structures into CG structures and topologies, with fine control on the process and assemble biomolecules into large systems, and deliver all files necessary to start simulations in the GROMACS MD engine.
Subject(s)
Molecular Dynamics Simulation , Proteins , Thermodynamics , Proteins/chemistry , Computers , LipidsABSTRACT
The Martini 3 force field is a full reparametrization of the Martini coarse-grained model for biomolecular simulations. Due to the improved interaction balance, it allows for a more accurate description of condensed phase systems. In the present work, we develop a consistent strategy to parametrize carbohydrate molecules accurately within the framework of Martini 3. In particular, we develop a canonical mapping scheme which decomposes arbitrarily large carbohydrates into a limited number of fragments. Bead types for these fragments have been assigned by matching physicochemical properties of mono- and disaccharides. In addition, guidelines for assigning bonds, angles, and dihedrals were developed. These guidelines enable a more accurate description of carbohydrate conformations than in the Martini 2 force field. We show that models obtained with this approach are able to accurately reproduce osmotic pressures of carbohydrate water solutions. Furthermore, we provide evidence that the model differentiates correctly the solubility of the polyglucoses dextran (water-soluble) and cellulose (water insoluble but soluble in ionic liquids). Finally, we demonstrate that the new building blocks can be applied to glycolipids. We show they are able to reproduce membrane properties and induce binding of peripheral membrane proteins. These test cases demonstrate the validity and transferability of our approach.
Subject(s)
Cellulose , Water , Thermodynamics , Water/chemistry , Carbohydrate ConformationABSTRACT
Artificial rotary molecular motors convert energy into controlled motion and drive a system out of equilibrium with molecular precision. The molecular motion is harnessed to mediate the adsorbed protein layer and then ultimately to direct the fate of human bone marrow-derived mesenchymal stem cells (hBM-MSCs). When influenced by the rotary motion of light-driven molecular motors grafted on surfaces, the adsorbed protein layer primes hBM-MSCs to differentiate into osteoblasts, while without rotation, multipotency is better maintained. We have shown that the signaling effects of the molecular motion are mediated by the adsorbed cell-instructing protein layer, influencing the focal adhesion-cytoskeleton actin transduction pathway and regulating the protein and gene expression of hBM-MSCs. This unique molecular-based platform paves the way for implementation of dynamic interfaces for stem cell control and provides an opportunity for novel dynamic biomaterial engineering for clinical applications.
Subject(s)
Bone Marrow Cells/metabolism , Energy Metabolism/genetics , Mesenchymal Stem Cells/metabolism , Molecular Motor Proteins/chemistry , Bone Marrow Cells/cytology , Cell Differentiation/genetics , Humans , Mesenchymal Stem Cells/cytology , Molecular Motor Proteins/genetics , Molecular Motor Proteins/metabolism , Osteoblasts/metabolism , Signal Transduction/geneticsABSTRACT
Plant light-harvesting complex II (LHCII) is the key antenna complex for plant photosynthesis. We present coarse-grained molecular dynamics simulations of monomeric and trimeric LHCII in a realistic thylakoid membrane environment based on the Martini force field. The coarse-grained protein model has been optimized with respect to atomistic reference simulations. Our simulations provide detailed insights in the thylakoid lipid fingerprint of LHCII which compares well with experimental data from membrane protein purification. Comparing the monomer and trimeric LHCII reveals a stabilizing effect of trimerization on the chromophores as well as the protein. Moreover, the average chromophore distance shortens in the trimer leading to stronger excitonic couplings. When changing the native thylakoid environment to a model membrane the protein flexibility remains constant, whereas the chromophore flexibility is reduced. Overall, the presented LHCII model lays the foundation to investigate the µs dynamics of this key antenna protein of plants.
Subject(s)
Coenzymes/chemistry , Light-Harvesting Protein Complexes/chemistry , Phosphatidylcholines/chemistry , Plants/chemistry , Thylakoids/chemistry , Binding Sites , Biophysical Phenomena , Coenzymes/metabolism , Light-Harvesting Protein Complexes/metabolism , Lipid Bilayers , Molecular Dynamics Simulation , Phosphatidylcholines/metabolism , Photosynthesis , Plants/metabolism , Protein Binding , Protein Conformation , Protein Multimerization , Structure-Activity RelationshipABSTRACT
We demonstrate that using a pressure corrected three-dimensional reference interaction site model one can accurately predict salting-out (Setschenow's) constants for a wide range of organic compounds in aqueous solutions of NaCl. The approach, based on classical molecular force fields, offers an alternative to more heavily parametrized methods.
