Objective
Biological processes are inherently multi-scalar: exchanging a single amino acid of a protein can affect the macroscopic behavior of a cell. A computational model that can cover these scales and simulate the time evolution of locations, interactions, and atomistic structures of biomolecules in a cell would be transformative for the understanding of biology and the optimization of biotechnological processes. This ERC project will lay the methodological groundwork for such a model.
Recent breakthroughs in the long-standing problem of sampling rare transition events in molecular dynamics (MD) simulation have enabled us to simulate biomolecular processes such as folding and binding with atomistic models. The PI has co-pioneered the widely-used Markov State Models (MSMs) that combine extensive distributed MD simulations towards models of the molecular kinetics. Using these methods, we have demonstrated that protein-protein association can be simulated and timescales of seconds can be reached in all-atom models of small protein systems.
However, these methods have fundamental limitations to scale to the large biomolecules and the long length-scales involved in cellular signaling. To address these limitations, we will develop the following key technologies and disseminate them in open software:
1. A model that describes protein kinetics as a network of local switches which will overcome scaling limitations of MSMs that suffer from an exponential increase of parameters for large systems.
2. An “effective force field for cells” that predicts structure and kinetics of multi-body protein interactions based on simulations of relatively few protein interactions.
3. A multi-scale method to embed atomistic kinetic models in whole-cell reaction-diffusion simulations.
We will employ these methods and, in collaboration with leading experimentalists, investigate how the mechanochemical protein dynamin couples atomic-detail structure changes to membrane constriction in endocytosis.
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: https://op.europa.eu/en/web/eu-vocabularies/euroscivoc.
CORDIS classifies projects with EuroSciVoc, a multilingual taxonomy of fields of science, through a semi-automatic process based on NLP techniques. See: https://op.europa.eu/en/web/eu-vocabularies/euroscivoc.
- natural sciences biological sciences biochemistry biomolecules proteins
- natural sciences computer and information sciences artificial intelligence machine learning deep learning
- natural sciences biological sciences biophysics
- natural sciences computer and information sciences computational science multiphysics
- natural sciences chemical sciences organic chemistry amines
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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.
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H2020-EU.1.1. - EXCELLENT SCIENCE - European Research Council (ERC)
MAIN PROGRAMME
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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.
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.
ERC-COG - Consolidator Grant
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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.
(opens in new window) ERC-2017-COG
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Net EU financial contribution. The sum of money that the participant receives, deducted by the EU contribution to its linked third party. It considers the distribution of the EU financial contribution between direct beneficiaries of the project and other types of participants, like third-party participants.
14195 Berlin
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.