Objective
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.
Fields of science (EuroSciVoc)
CORDIS classifies projects with EuroSciVoc, a multilingual taxonomy of fields of science, through a semi-automatic process based on NLP techniques. See: The European Science Vocabulary.
CORDIS classifies projects with EuroSciVoc, a multilingual taxonomy of fields of science, through a semi-automatic process based on NLP techniques. See: The European Science Vocabulary.
- natural sciences computer and information sciences computational science
- natural sciences biological sciences biochemistry biomolecules proteins protein folding
- natural sciences physical sciences classical mechanics statistical mechanics
- natural sciences biological sciences molecular biology
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Keywords
Project’s keywords as indicated by the project coordinator. Not to be confused with the EuroSciVoc taxonomy (Fields of science)
Project’s keywords as indicated by the project coordinator. Not to be confused with the EuroSciVoc taxonomy (Fields of science)
Programme(s)
Multi-annual funding programmes that define the EU’s priorities for research and innovation.
Multi-annual funding programmes that define the EU’s priorities for research and innovation.
Topic(s)
Calls for proposals are divided into topics. A topic defines a specific subject or area for which applicants can submit proposals. The description of a topic comprises its specific scope and the expected impact of the funded project.
Calls for proposals are divided into topics. A topic defines a specific subject or area for which applicants can submit proposals. The description of a topic comprises its specific scope and the expected impact of the funded project.
Call for proposal
Procedure for inviting applicants to submit project proposals, with the aim of receiving EU funding.
Procedure for inviting applicants to submit project proposals, with the aim of receiving EU funding.
FP6-2005-MOBILITY-5
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Funding Scheme
Funding scheme (or “Type of Action”) inside a programme with common features. It specifies: the scope of what is funded; the reimbursement rate; specific evaluation criteria to qualify for funding; and the use of simplified forms of costs like lump sums.
Funding scheme (or “Type of Action”) inside a programme with common features. It specifies: the scope of what is funded; the reimbursement rate; specific evaluation criteria to qualify for funding; and the use of simplified forms of costs like lump sums.
Coordinator
HEIDELBERG
Germany
The total costs incurred by this organisation to participate in the project, including direct and indirect costs. This amount is a subset of the overall project budget.