Coarse-grained MD simulations reveal beta-amyloid fibrils of various sizes bind to interfacial liquid-ordered and liquid-disordered regions in phase separated lipid rafts with diverse membrane-bound conformational states - ScienceDirectThe membrane binding behaviors of beta-amyloid fibrils, dimers to penta...
For the CG models with implicit solvent, while they have proven invaluable in addressing biological problems, there are difficulties in their implementations that do not arise in atomistic MD simulations. When CG MD simulation with the implicit solvent approximation is parallelized on multiple processors...
Coarse-grained MD simulations give us a tool to study these complex macromolecular systems. By grouping heavy atoms into single interaction centers, we can reduce the total number of particles, and thus number of computations, by orders of magnitude. The grouping, or “mapping,” scheme chosen ...
Based on the CG potentials, the MD simulations reproduce all the local distributions of pure systems and the miscibility of mixed systems. Moreover, the global conformational properties are also closer to the target ones than those obtained using the previous CG potentials. The changes in density ...
(NP)s46, and the behavior of the NPs at different stages of the in-vitro gene delivery pathway45,53,54. To the best of our knowledge, MD simulations exploring pulmonary systems have not been studied for PEI-based NPs. However, pulmonary surfactants have been studied in other contexts. For...
The new CG model and CG potentials from OZPY1+IBI method was further tested through CGMD simulation of PEG with DP = 40 system. No significant changes are observed in the comparison of PCFs from CGMD simulations of PEG with DP = 20 and 40 systems indicating that the potential is ...
membraneactivitymoleculardynamicssimulationsmolecularrecognitionCoarse-grained molecular dynamics (CGMD) simulation technique (MARTINI force field) is applied to monitor the aggregation of helical peptides representing the transmembrane sequence and its extension of bone marrow stromal cell antigen 2 (BST-2)....
To help elucidate its mechanism of membrane-lytic activity, we performed a total of 8μs of coarse-grained molecular dynamics (CG-MD) simulations of M1.1 in the presence of zwitterionic phospholipid membranes. Several systems were simulated in which the peptide/lipid ratio was varied. At a low...
Cho. Gpu-optimized hybrid neighbor/cell list algorithm for coarse-grained md simulations of protein and rna folding and assembly. In Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics, BCB'13, pages 633:633-633:640, New York, NY, USA, ...
Membrane Protein Simulations Using AMBER Force Field and Berger Lipid Parameters. AMBER force fields are among the most commonly used in molecular dynamics (MD) simulations of proteins. Unfortunately, they lack a specific set of lipid pa... G Caltabiano,A Cordomí,L Pardo - 《Journal of Chemic...