http://www.cnr.it/ontology/cnr/individuo/prodotto/ID267393

Minimalist Model of Protein Diffusion and Interactions: The Green Fluorescent Protein within the Cytoplasm (Articolo in rivista)

Type

Label

Minimalist Model of Protein Diffusion and Interactions: The Green Fluorescent Protein within the Cytoplasm (Articolo in rivista) (literal)

Anno

Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#doi

Alternative label

F. Trovato [1,3], R. Nifosì [2,3], A. Di Fenza [3], and V. Tozzini [2,3] (2013)
Minimalist Model of Protein Diffusion and Interactions: The Green Fluorescent Protein within the Cytoplasm
in Macromolecules (Online); American Chemical Society, Washington, DC (Stati Uniti d'America)
(literal)

Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#autori

F. Trovato [1,3], R. Nifosì [2,3], A. Di Fenza [3], and V. Tozzini [2,3] (literal)

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Rivista

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1 Center for Nanotechnology and Innovation @ NEST-Istituto Italiano di Tecnologia, 56127 Pisa, Italy 2 NEST- Istituto Nanoscienze, CNR, 56127 Pisa, Italy 3 Scuola Normale Superiore, Piazza San Silvestro 12, 56127 Pisa, Italy 4 MGU, MRC Harwell, Harwell Science and Innovation Campus, Oxfordshire OX11 0RD, U.K. (literal)

Titolo

Minimalist Model of Protein Diffusion and Interactions: The Green Fluorescent Protein within the Cytoplasm (literal)

Abstract

In this work, we present a minimalist model (one-bead-per-amino acid resolution) of a tracer protein (the green fluorescent protein) embedded in a meso scale cytoplasm (one-bead-per-crowder) for molecular dynamics simulations. The extremely low computational cost of the model allows a statistically relevant exploration of the tracer diffusive dynamics. The accurate description of diffusion and interactions is maintained by means of a careful choice of the functional forms and parameters of the force field terms, optimized by means of a semiheuristic strategy involving the use of a genetic algorithm. Consequently, the model is capable of implicitly reincluding some effects lost in the coarse graining, such as the shape effects (for crowders), hydrodynamics and correlations, hydration/dehydration and interaction specificity (for the tracer). The result is an accurate representation of the multiscale dynamics of the tracer, involving its internal flexibility, specific protein-protein interactions and diffusion. (literal)

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