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SimViRNA

Financiado

Multiscale Simulations of HIV capsid assembly and RNA

In this project, I will perform computer simulations and develop new computational methods to elucidate viral functions and RNA. The first two years will take place in the group of Prof Voth in Chicago. Here, I will characterize a... ver más

30/06/2026

SISSA

265K€

Presupuesto del proyecto: 265K€

Líder del proyecto

SCUOLA INTERNAZIONALE SUPERIORE DI STUDI AVAN... No se ha especificado una descripción o un objeto social para esta compañía.

TRL 4-5

Ver 3 Participantes

Financiación concedida El organismo HORIZON EUROPE notifico la concesión del proyecto el día 2023-04-19

HORIZON-MSCA-2022-PF-01-01: MSCA Postdoctoral Fellowships 2022 ExpectedOutcome:

I+D

Cerrada hace 2 años

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3 Participantes

SISSA

265.10K€ | Lider

THE UNIVERSITY OF CHICAGO

University of Chicago

N.D. | Participante

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Duración del proyecto: 38 meses Fecha Inicio: 2023-04-19
Fecha Fin: 2026-06-30

Líder del proyecto

SCUOLA INTERNAZIONALE SUPERIORE DI STUDI AVAN... No se ha especificado una descripción o un objeto social para esta compañía.

TRL 4-5

Presupuesto del proyecto 265K€

Descripción del proyecto In this project, I will perform computer simulations and develop new computational methods to elucidate viral functions and RNA. The first two years will take place in the group of Prof Voth in Chicago. Here, I will characterize and quantitatively describe proteolytic cleavage of the CA/SP1 subdomain of the Gag-protein in HIV using quantum mechanical/molecular mechanical (QM/MM) Molecular Dynamics simulations (MD). Furthermore, I will employ free energy techniques to simulate binding and unbinding of the protease to CA/SP1 to determine the binding and configurational free energies. These processes are essential for HIV maturation and hence also targeted by drugs. Subsequently, I will parameterize Coarse-grained models for the Protease/CA/SP1 system and develop a Coarse-grained Green's Function Reaction Dynamics method. This method combines the Coarse-grained description with the mesoscopic scale, and hence allows me to simulate structural assembly of the virus capsid coupled to proteolytic cleavage at physiological conditions. This coherent computational approach targets biomolecular processes of outmost relevance, and will greatly advance our understanding, but likewise also push the boundaries of molecular simulations due to the methodological innovations. The third year will be spent in Trieste, in the group of Prof Bussi. In this period, I will develop a hybrid all-atom molecular mechanics / Coarse-grained (MM/CG) model for RNA. It facilitates the simulation of RNA fragments at atomistic resolution while capturing long-range allosteric interactions due to the Coarse-grained representation of the surrounding. This will set a new standard to simulate RNA macromolecules and offers a wide range of application.

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