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Content archived on 2024-05-29

A computational study of protein folding and fluorescence


The understanding of protein folding represents one of the major challenges in molecular biology. Several techniques have been developed to study protein folding, among which the most powerful are single-molecule fluorescence-based methods that allow observing fluctuations in fluorescence properties of individual molecules over time.

Such experiments, although very promising, are still in early stages of development because requirements for high temporal and spatial resolution have to be met simultaneously. Moreover, the possible effects that the extrinsic fluorophores used to label the proteins might have on the folding dynamics are unknown.

In the present project the study of different dye-labelled peptides forming loops and helices by means of computational methods, in particular molecular dynamics (MD) simulation and quantum calculations, is proposed. The MD simulations will be used to aid in interpretation of the experimental results by providing an atomic picture of the events that are responsible for the experimental signal.

Particular attention will be given to the possible interference of the extrinsic dye on the real conformational dynamics of the peptides. This will be achieved by comparing the results from simulations with and without the extrinsic dye.

Moreover, a mixed quantum/classical strategy will be developed in order to reproduce the experimentally derived conformation-dependent fluorescence spectra. Such a synergistic collaboration between experiment and simulation can deliver exciting new insight into protein folding and can improve the interpretation and understanding of experimental data.

The project is intrinsically multidisciplinary as it combines MD simulation of the dye-labelled peptides, statistical mechanics analysis of their folding process and theoretical characterization of the associated fluorescence-signal.

Results from this work can be expected to find applications across a range of fields, e.g. bionanotechnology.

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