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“SEE-DRUG ” is a FP7 - RESEARH POTENTIAL project that aims to the upgrade the Structural Biology capacities of UPAT and to the Establishment of a Center of Excellence for Structure-Based Drug Target chracterization efforts in South-Eastern EU region.
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“SEE-STRUCT” is structure-oriented module of SEE-DRUG project and aims to the structural elucidation of proteins, enzymes and other interesting drug-targets. The tools offered for these efforts are a state-of-the-art high field NMR instrument of 700 MHz equipped with a highly sensitive probe and crystallization robot.
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“SEE-PROT” & “SEE-PHARM” are the protein production and the preclinical evaluation of molecules, modules of SEE-DRUG project. The tools offered for these efforts are protein production and characterization facilities an upgraded confocal microscope, an intravital microscope and myographs.
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NMR
700MHz
High sensetivity probe
Studies in solution
Conformation/Dynamics
3D Structure determination, mobility, protein-protein interaction, protein-drug interactions
Confocal
In-cell imaging
Leica Microscope
Tandem Scanner
Additional laser
Sub-cellular ablation in live cells, protein-complexes, protein drug interactions in vivo
Robot
Crystal growth
Automation
Crystalization trials
Fast & efficient
Crystal growth optimization, screen of protein targes in paraller with NRM Spectroscopy
Microscopes
Myographs
intravital Microscope
In vivo
Ex vivo
Drug screening for anti-inflammatory compounds, evaluation of vasoactive compounds

Stuctural Biology
NMR & Xray
2H/13C/15N labeling
Selective labeling
Crystallization
Conformation dynamics, Modeling Structure determination, 3D solutions & crystal models, Bioinformatics
Molecular Biology
Biochemistry
Drug-targets
Biochemical pathways
Protein production
High-yield protein expression, labeling & isolation for structural studies, protein biochemistry
Imaging
In-cell studies
Functional imaging
Light Microscopy
FRET measurements
Studies of biomolecular functions through Advanced Light Microscopy, Sub-cellular ablations
Pharmacology
Inflammation
Vascular Biology
Cell-based assays
Signaling pathways
Monitoring cell processes (migration. proliferation, apoptosis), in vivo & ex vivo assays

Expertise Exchange
Twinnings
Knowledge transfer
Best practices
New applications
Exchange of researchers between UPAT and partnering organizations - EU Centers of excellence
Events
Workshops
Structural Biology
Biochemistry
Imaging
Workshops and scientific meetings will be organized at UPAT, Advanced training course in NMR
Dissemination
Conferences
Biomolecular NMR
Life Sciences
Analysis
Invited talks, Meeting participation & Poster presentations by SEE-DRUG members
Brokerage Events
Info-days
Meet the expers
Links with industry
Regional Authorities
Colloquia with invited speakers from academia or industry and private sector stakeholders

NMR Applications

The anticipated 700 MHZ NMR instrumentation is an optimal compromise of cost-effective, high-field and high-resolution NMR equipment suitable for biomolecular studies.

The UPAT’s 700 MHz NMR (SEE-STRUCT Module) with a cryogenically cooled probe for enhanced sensitivity and four channels, in concert with uniformly or selectively enriched recombinant proteins (in 13C, 15N and 2H), allows the set up of various applications in the field of structural biology and drug design. Such an instrument will permit the:

  • High-resolution, comparable to X-ray, structure determination of protein drug-targets with molecular weight above 10 kDa, and atomic-level insight in protein and protein-protein/drug complexes dynamics, interaction and determination of binding affinity.
  • Novel NMR experiments for fast acquisition of 3D, 4D, 5D, nD, using automated spectra collection and analysis of projections of N-dimensional spectra (K. Wüthrich et. al. Proc Natl Acad Sci USA 2005, 102;10876-10881). This application measures the information content of high dimensional spectra in low dimensional projection spectra, which results in a drastic reduction in acquisition time (while the acquisition of a complete set of heteronuclear 2D/3D experiments requires up to 3 weeks for a protein sample of 80-100 residues, this technique requires less than a week).
  • Coupled fast acquisition and automated assignment techniques with unsupervised structure determination of proteins that reduces the time of the entire procedure from months to weeks.
  • Time-resolved kinetics and fast acquisition of 2D fingerprint, diagnostic, 1H-15N HSQC spectra (~1 sec), eventually crucial for monitoring protein-protein/peptide/small-molecules transient complexes, folding/unfolding processes and mechanistic studies, protein-drug screening applicable in drug-design process.
  • Use of reduced protein amounts and investigation of low concentration protein samples (since numerous proteins exhibit low expression yields, while others tend to homo- or hetero-oligomerize or aggregate in medium to high concentrations, i.e. >0.4-0.6 mM).

The UPAT’s existing 400 MHz NMR instrument, will still be exploited in the fine-tuning of the peptide/protein sample experimental conditions and the characterization of the small molecules. The 700 MHz NMR machine will be dedicated to high-resolution structural studies, high-throughput protein samples and screening of drug candidates and structure-based drug-design efforts.

Additionally, it will allow researchers from the entire Greek Academia or Industry and all the other Southern-East Europe countries (like Bulgaria, Turkey or others) to have access to this modern instrumentation. Access will be provided not only on a protein sample screening basis prior to NMR studies or X-ray crystallography, but also on a joint collaboration basis.

It will also allow the researchers working with small molecules to perform daily walk-in analysis of their samples. Finally, and even more importantly, cutting-edge structural biology projects will be eventually performed.

Upcoming Events

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  • 01 Jan 2012 Starting data of SEE-DRUG project

  • 23 Feb 2012 Kick-off meeting

  • 23 Apr2012 External Advisory Board meeting

  • 29 Apr 2013 700MHz NMR installed