Molecular dynamics simulation of the membrane binding and disruption mechanisms of antimicrobial peptides

Project Information

AMP-MEMBRANE MD

Grant agreement ID: 254559

Project closed

Start date 15 June 2010

End date 14 June 2012

Funded under

• Specific programme "People" implementing the Seventh Framework Programme of the European Community for research, technological development and demonstration activities (2007 to 2013)

Total cost € 162 248,80

EU contribution € 162 248,80

Coordinated by

RIJKSUNIVERSITEIT GRONINGEN
Netherlands

Objective

Antimicrobial peptides (AMPs) are a promising new class of antibiotics, the mechanism of which usually involves binding to membranes with subsequent disruption. The disruption process is, however, still poorly understood, mostly because it seems to be mediated by states - pore formation or in-depth AMP insertion - that are unordered and very short-lived. My PhD work focused on using and developing biophysical methodologies to study the conditions at which the AMP-mediated disruption is triggered. Models bridging these results with in vivo observations were developed, establishing important relationships between AMP concentration and activity. Molecular Dynamics (MD) simulations allow the visualization of molecular level interactions with spatial and time resolution unsurpassed by experimental techniques, having already provided important clues on AMP-mediated membrane pore formation. In this project the interactions of AMPs with phospholipid bilayers and vesicles will be followed by MD simulations. A comparative study will be performed on a family of peptides derived from two naturally occurring AMPs (cecropin and melittin; base template XKLFKKILKXL-NH2) to gather insight on the different activities and toxicities of each of the peptides, and, from there, better understand the molecular characteristics responsible for those features. Work will also focus on the optimization and application of Coarse Grained (CG) simulation models, which allow significant reductions of processing time without major loss of detail. The interaction models that arise from MD simulations will be experimentally validated, making use of the researcher's background complemented by the host group's strong network of collaborating laboratories. The shift to computer simulation techniques will definitely broaden the researcher’s range of skills, with the added value that these techniques are easily portable and straightforward to implement independently in the future.

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.

• natural sciences › biological sciences › biochemistry › biomolecules
• medical and health sciences › basic medicine › pharmacology and pharmacy › pharmaceutical drugs › antibiotics
• natural sciences › mathematics › applied mathematics › mathematical model

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Programme(s)

• FP7-PEOPLE - Specific programme "People" implementing the Seventh Framework Programme of the European Community for research, technological development and demonstration activities (2007 to 2013)

Topic(s)

• FP7-PEOPLE-2009-IEF - Marie Curie Action: "Intra-European Fellowships for Career Development"

Call for proposal

FP7-PEOPLE-2009-IEF
See other projects for this call

Funding Scheme

MC-IEF - Intra-European Fellowships (IEF)

Coordinator

RIJKSUNIVERSITEIT GRONINGEN

• EU contribution: € 162 248,80
• Address: Broerstraat 5 ; 9712CP Groningen ; Netherlands
• Activity type: Higher or Secondary Education Establishments
• Total cost: No data