| 06-12-2021 |
Development and use of the GRAPE computational engineering strategy in Antarctic PET hydrolases
In recent decades, numerous enzymes from bacteria that degrade PET plastics have been described, including enzymes described by our laboratory from Antarctic organisms that are catalytically active at room temperature. However, the stability of these enzymes is insufficient for their biotechnological use, thus experimental and computational enzyme engineering strategies have been developed to optimize these parameters. In this research, we seek to develop and use the GRAPE computational engineering strategy, which produces a library of mutations for preliminary experimental characterization and subsequent clustering in a final designed enzyme, to improve the stability of Antarctic PET hydrolases.
Prerequisites:
None.
Evaluation method: Nota 1-7, with 0/1 available vacants |
Mentor(s): Open in the plataform |
| 24-07-2020 |
Development of hybrid model for protein folding simulations
Protein folding is a biological phenomenon with a timescale in the order of milliseconds to seconds. Thus, it is challenging to explore these processes in molecular dynamics simulations. However, recent years have witnessed the development of models rigorously footed in the energy landscape theory of protein folding that enable simulating these phenomena with low computational costs. This is the case of the SMOG2 software, that generates both all-atom and single-bead coarse-grained modelos for simulations in GROMACS. However, it has been recently determined that hybrid double-bead (alpha + beta carbon) or pseudo-empiric models are useful to simulate protein folding processed that incorporate sequence-dependent information (electrostatics, hydrophobic). In this research, SMOG2-dependent hybrid models will be developed for protein folding simulations in GROMACS.
Prerequisites:
None.
Evaluation method: Nota 1-7, with 0/1 available vacants |
Mentor(s): Open in the plataform |