Objective
Research objectives and content
The objective of the research plan is to bring deeper understanding in the protein folding using molecular dynamics simulations with a detailed atomic model. These simulations can be done only over few nanoseconds time scale, but the folding reaction, even in small fast-folding proteins, takes of the order of milliseconds. To overcome these difficulties new theoretical tools will be developed and applied to decipher the nature (kinetics and thermodynamics) of the folding reaction at a microscopic level: (1) to represent the unfolded state we will generate a set of relevant unfolded conformations with specifically developed methods and simulate the refolding starting from these conformations; (2) to speed up the folding process simulation and define the folding pathways we will introduce a time-dependent perturbation designed to prevent the exploration of conformations which are not relevant to the folding reaction while introducing minimum disturbance to the system; (3) the free energy profile along a reaction coordinate will be computed along the folding pathways by using standard techniques and will bring an extremely detailed picture of the folding reaction.
We propose to implement and apply this approach to several proteins which have already been studied experimentally, using a variety of kinetic and structural methods. The combined use of simulations and experiments should provide new insights into protein folding.
Training content (objective, benefit and expected impact)
During the development of the project I will learn advanced experimental techniques and I will interpret experimental results using theoretical and computational tools as a guidance. The objective is to export the experimental knowledge to theoretical research groups and improve the exchange between theoreticians and experimentalists in this particular field.
Links with industry / industrial relevance (22)
As a result of this project, we hope to get new insights into the inner workings of the folding mechanism. These insights can be relevant for designing proteins with desired properties. On the other hand, I plan to include the computational tools I will be developing into the CHARMM program, and thus make them available both to academic and industrial research.
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 physical sciences thermodynamics
- natural sciences biological sciences biochemistry biomolecules proteins protein folding
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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.
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Procedure for inviting applicants to submit project proposals, with the aim of receiving EU funding.
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
OX1 3QT OXFORD
United Kingdom
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.