Modeling DMPC lipid membranes with SIRAH force-field
| Autor: | Rodolfo D. Porasso, Exequiel Barrera, Sergio Pantano, Ezequiel N. Frigini |
|---|---|
| Jazyk: | angličtina |
| Rok vydání: | 2017 |
| Předmět: |
Física Atómica
Molecular y Química 0301 basic medicine Speedup Coarse-Grained Models Lipid Membranes Ciencias Físicas Lipid Bilayers Nanotechnology Molecular Dynamics Simulation Molecular Dynamics 01 natural sciences Catalysis Force field (chemistry) Inorganic Chemistry purl.org/becyt/ford/1 [https] 03 medical and health sciences Molecular dynamics 0103 physical sciences Dmpc Physical and Theoretical Chemistry Quantitative Biology::Biomolecules 010304 chemical physics Chemistry Organic Chemistry Proteins DNA purl.org/becyt/ford/1.3 [https] Computer Science Applications 030104 developmental biology Membrane Computational Theory and Mathematics Biological system Dimyristoylphosphatidylcholine CIENCIAS NATURALES Y EXACTAS |
| Zdroj: | CONICET Digital (CONICET) Consejo Nacional de Investigaciones Científicas y Técnicas instacron:CONICET |
| Popis: | Coarse-grained simulation schemes are increasingly gaining popularity in the scientific community because of the significant speed up granted, allowing a considerable expansion of the accessible time and size scales accessible to molecular simulations. However, the number of compatible force fields capable of representing ensembles containing different molecular species (i.e., Protein, DNA, etc) is still limited. Here, we present a set of parameters and simplified representation for lipids compatible with the SIRAH force field for coarse-grained simulations (http://www.sirahff.com). We show that the present model not only achieves a correct reproduction of structural parameters as area per lipid and thickness, but also dynamic descriptors such as diffusion coefficient, order parameters, and proper temperature driven variations. Adding phospholipid membranes to the existing aqueous solution, protein and DNA representations of the SIRAH force field permit considering the most common problems tackled by the biomolecular simulation community. Fil: Barrera Guisasola, Exequiel Ernesto. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Instituto Pasteur de Montevideo; Uruguay Fil: Frigini, Ezequiel Nazareno. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - San Luis. Instituto de Matemática Aplicada de San Luis "Prof. Ezio Marchi". Universidad Nacional de San Luis. Facultad de Ciencias Físico, Matemáticas y Naturales. Instituto de Matemática Aplicada de San Luis "Prof. Ezio Marchi"; Argentina Fil: Porasso, Rodolfo Daniel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - San Luis. Instituto de Matemática Aplicada de San Luis "Prof. Ezio Marchi". Universidad Nacional de San Luis. Facultad de Ciencias Físico, Matemáticas y Naturales. Instituto de Matemática Aplicada de San Luis "Prof. Ezio Marchi"; Argentina Fil: Pantano, Sergio. Instituto Pasteur de Montevideo; Uruguay |
| Databáze: | OpenAIRE |
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