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Computational toolbox for protein surface docking

Objective

Recent combinatorial biotechnologies have shown that the molecular recognition capability of proteins can be specifically oriented toward inorganic surfaces. The use of technologies based on such specificity would give European industry a competitive edge in several emerging fields (from nanoelectronics over biomaterials science to drug design), spanning different thematic areas of FP6.

However, at present the principles regulating protein-surface interactions are poorly understood, thus hindering such technologies from taking off.

What features of the surface and of the proteins (electronic, structural, morphological) determine which protein is able to bind to a given surface and how?

PROSURF will answer this question and provide the European scientific/technological community with computational tools to enable rational design of protein-surface associations.

As automated in silico docking revolutionized the process of drug discovery, so the outcomes of PROSURF will open genuinely new routes to solve several urgent technological problems, such as self-assembly of nanoelectronic devices or design of highly biocompatible materials. PROSURF is risky because it addresses a largely unexplored subject; however, the risk is compensated by the potential of enormous impact.

Our strategy to probe the determinants of protein-surface specificity, and to implement the envisaged computational tools, integrates state-of-the-art computational techniques and experiments. It consists of a series of computational steps, including quantum-mechanics based parameterisation of protein-surface interactions, molecular dynamics simulation of proteins on surfaces, and the implementation of protein-surface docking software, corroborated by tailored experiments.

Although the project focus is on theory, feedback from experiments will be important both to validate the computational tools, and to gain new insight into the basis of protein-surface interactions.

Call for proposal

FP6-2004-NEST-C-1
See other projects for this call

Funding Scheme

STREP - Specific Targeted Research Project

Coordinator

UNIVERSITA' DEGLI STUDI DI MODENA E REGGIO EMILIA
Address
Via Universita' 4
Modena
Italy

Participants (4)

CONSIGLIO NAZIONALE DELLE RICERCHE
Italy
Address
Piazzale Aldo Moro 7
Roma
EML RESEARCH GGMBH
Germany
Address
Schloss-wolfsbrunnenweg 33
Heidelberg
LUDWIG MAXIMILIANS UNIVERSITY MUENCHEN
Germany
Address
Geschwister-scholl-platz 1
Munich
WEIZMANN INSTITUTE OF SCIENCE
Israel
Address
Herzl Street
Rehovot