Objective
Transmembrane proteins interact which each other directly or mediated via their influence on the lipid membrane structure and fluctuations. The interactions govern the dynamics of integral protein insertion, (re-) folding and assembly in functional oligomeric structures such as the tetrameric potassium channel KcsA.
On the other hand, antimicrobial peptides as defensins and magainins aggregate supposedly either in the lipid head group region or in a transmembrane fashion leading to permeation and rupture of bacterial membranes. The mechanisms of these processes are very difficult to study experimentally.
The objective of our research proposal is to model protein-membrane interactions by multi-scale molecular dynamics simulation. Using a quantitative coarse g rain description, we can access the spatial and temporal scales of these processes, which are too large for direct simulation with atomistic molecular dynamics.
However, using a special interface between our coarse grain representation and the all atom rep resentation of the system, we can connect the mesoscale phenomena to the underlying atomistic details.
Using special techniques as path sampling and the novel metadynamics method, we will map out the free energy landscape of interacting transmembrane prote ins in terms of generic hydrophobic, hydrophilic and electrostatic interactions, specific protein residue interactions, and interactions induced by lipid ordering and friction.
If successful, the results are expected to gain insight in how peptides and proteins insert and interact in biomembranes which is of interest to a wide variety of applications, in particular for drug design and for the development of biomimetic antimicrobials.
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 biological sciences biochemistry biomolecules proteins
- natural sciences biological sciences cell biology cell metabolism
- 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.
FP6-2002-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
Switzerland
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.