Funded by EU Framework 6


»Project & People  |  Partnership
Partnership  |  Publications


Partner 1 (Florence, Bertini): The Magnetic Resonance Center of the University of Florence (CERM), managed by the Consorzio Interuniversitario di Risonanze Magnetiche di Metalloproteine Paramagnetiche (CIRMMP), has a long experience, dating back to the mid Seventies, in the field of biological inorganic chemistry. The team has a unique expertise in NMR of paramagnetic systems. The group is leader in the exploitation of paramagnetism-based constraints for structural determination, and has developed several software tools to include this information in available solution structure calculation protocols. The first structure of a paramagnetic metalloprotein was solved in Florence in 1994. The group is now developing new methods and hardware equipments for the study of large molecules and protein/protein adducts, essentially based on heteronuclear direct detection NMR. The group comprises 10 senior research staff members, coordinating research groups with expertise spanning from browsing of genomic databank information to NMR of paramagnetic molecules and nuclear and electron relaxation theory. The equipment available comprises the following high field NMR spectrometers: 900, 800, 700x3, 600, 500, 400 MHz and lower fields. The 500, 800 and 900 MHz spectrometers are equipped with cryoprobes, and one of the three 700MHz spectrometers is equipped with a probe optimised for heteronuclear direct detection. Another 700 MHz, presently under installation, is dedicated to solid-state NMR. In addition, the following is available: bioinformatic tools for genome analysis; molecular biology labs fully equipped and automated for HTP protein cloning, expression and production with robotic equipment; mass spectrometry (MALDI-TOF and ESI instrumentation); atomic absorption (ICP), W- and X-band EPR, and isothermal titration calorimetry (ITC). The Florence partner has a strong experience in the coordination of collaborative projects at the European level. In particular, besides several RTD projects, the Florence partner has coordinated a Concerted Action on NMR in the Life sciences within the 4th Framework Programme, and an Infrastructure Cooperation Network on Post-genomic NMR within the 5th Framework Programme.

Partner 2 (GSF, prev. EMBL, Sattler): The group of Prof. Dr Michael Sattler is based at the GSF and the Technical University in Munich, where he is Director of the Bavarian NMR Centre (BNMRZ). The group uses solution state NMR to characterize the structure, dynamics and molecular interactions of proteins and protein complexes involved in RNA metabolism and signal transduction. Novel methods are implemented and developed to enhance these studies. These include isotope and deuterium labeling techniques, NMR methods and multidisciplinary approaches, for example combining NMR with small angle scattering. Staff contributing to the project by monitoring progress and exchange of expertise: Dr. Gerd Gemmecker, a senior staff member (and facility manager at the Bavarian NMR Centre, BNMRZ) with strong expertise in NMR theory and experimental methodology, Dipl. Biol. Alexander Frenzel and Dr. Peijian Zou, a senior technical officer, both with long expertise in molecular biology and protein biochemistry. Excellent wet lab infrastructure for molecular biology, and protein isotope labeling and purification are available. The group has access to 500, two 600, 750 and 900 MHz NMR spectrometers equipped with cryoprobes (600, 900) at the BNMRZ in Munich.

Partner 3 (Utrecht, Boelens): The Bijvoet Center for Biomolecular Research is a joint research institute of Utrecht University and the Chemical Sciences Research Council (NWO-CW) whose research focuses on mechanisms of molecular recognition and interactions. Research in the NMR group focuses on protein-DNA interactions, studies on ribosomal proteins, photosensory proteins, and modeling protein-protein interactions. Novel methods are developed for studying large proteins, complexes and modeling protein-protein complexes. The NMR infrastructure comprises a 900 MHz spectrometer, a 750 MHz and a 700 MHz instrument, a solids 500 MHz spectrometer, two 500 MHz and two 600 MHz spectrometers, and a 360 MHz instrument. The 900 MHz NMR spectrometer and one 600 MHz NMR spectrometer have triple-resonance cryoprobes. These instruments are used for NMR research by groups of the Bijvoet Center, for research by Dutch groups making use of the NMR facility at Utrecht University, and for NMR projects of various external groups using the facility in collaborative projects. The group relies on a state-of-the-art computational infrastructure consisting of 30 modern Linux PC workstations plus a 70 processor Beowulf computer cluster, and a state-of-the-art laboratory for protein expression and purification including an expression robot.

Partner 4 (Frankfurt, Schwalbe): The Frankfurt University Center for Biomolecular Magnetic Resonance (BMRZ) comprises institutes for Biophysical (Dötsch, Glaubitz), Physical and Theoretical (Prisner) and Organic Chemistry (Schwalbe). The MR center has expanded with funds from pharmaceutical companies in order to establish industrial collaborations. The center comprises 18 NMR spectrometers, ranging in proton operating frequencies from 250 to 900 MHz. Several spectrometers are equipped with cryoprobes, and some are equipped for solid-state NMR. The 700 MHz NMR spectrometer has a LASER operated kinetic device. Some 60 workstations connected to servers and to the university-computing center are available. The institutes operate facilities for chemical synthesis and for molecular biological and biochemical studies. Fermenters and state-of-the-art chromatographic equipment for recombinant techniques are available for producing isotope enriched proteins and nucleic acids. Selective or block labeling with stable isotopes are possible with a home-built cell-free device.

Partner 5 (Berlin, Oschkinat): The Berlin group is interested in Structural Genomics of mammalian proteins by NMR and has installed automated NMR data acquisition procedures, wet lab routines for the screening of a large number of clones, automated structure calculation procedures and small molecule screening by NMR and conventional methods within a formerly received grant, the Protein Structure Factory. These procedures are applied to investigate mammalian proteins, non-catalytic protein domains and their complexes with peptides and subunits of complex I. Furthermore, NMR concepts for rapid resonance assignment using amino acid type selective triple resonance experiments were worked out and software for automated assignment procedures based on those experiments is currently written. The core of the Structural Genomics unit in our department is a highly automated wet lab, with pipetting robots for cloning, high throughput protein purification units and procedures for the parallel expression testing of clones. One NMR spectrometer is equipped for automated screening of ligands; both spectrometers dedicated to Structural Genomics (600 and 750 MHz) are equipped with a cryoprobe. There have been a number of structures determined in the past two years, some with typical Structural Genomics implications. In one case the Berlin group was able to propose the activity of a protein from the structure, in another determined the first structure of a subunit of complex I. Furthermore, there were significant contributions to amino acid type selective pulse sequences and on the value of chemical shifts for structure determination. As a methodological component, a structure determination concept for MAS solid-state NMR was developed to enable Structural Genomics of membrane proteins.

Partner 6 (Paris, Bodenhausen): This partner is specializing on the development of new methods to determine the extent of internal mobility of proteins and nucleic acids, by measuring the correlations of conformational fluctuations by modern NMR methods. Such motions are greatly affected when a protein or nucleic acid forms a complex with a small ligand or with another macromolecule. Such variations of the internal mobility upon binding are indicative of entropic contributions to the binding affinity. A better understanding of such effects should provide insight into the deeper reasons why some ligands are recognized with a remarkably high specificity. Current efforts focus on Major Urinary Protein (MUP) which forms complexes with various pheromones. Associate to this partner are the Institut Pasteur (Paris), which has a long tradition in the development of innovative software tools, and the Ecole Normale Supérieure de Lyon, which is one of the best European centers for solid state NMR (equipped with a Bruker Avance 700 SB spectrometer).

Partner 7 (Copenaghen, Poulsen): Professor Flemming M. Poulsen is head of the "Structural Biology and NMR Laboratory" at the Institute of Molecular Biology, University of Copenhagen. He is the author of 112 papers, mainly on studies of proteins using NMR spectroscopy. The main interest of the research group is concerned with studies of protein folding and the determination of protein structures using NMR spectroscopy. The group has performed de novo structure determinations of 24 protein structures, and has been involved in many aspects of developments of methods for the applications of NMR spectroscopy for protein structure determination, developing NMR methods and software for NMR data analysis. The group is presently studying in depth the folding process of a four-helix protein model system using NMR spectroscopy. Associate to this partner are the Lund University and Goteborg University. Both centers have a strong tradition in the investigation of protein structure and dynamics, which are relevant for intermolecular interactions.

Partner 8 (Brno, Sklenar): The NMR group at Masaryk University in Brno functions partially within the National Centre for Biomolecular Research and also serves the needs of the chemical departments of the faculty of science. The permanent staff consists of seven scientists and is supplemented by five graduate and several undergraduate students. The main expertise of the group in the biomolecular field is in the development of new methods of NMR spectroscopy and their applications to the studies of structure and dynamics of proteins and nucleic acids. Recently, the group has developed triple resonance methods with increased sensitivity specifically designed for nucleic acid bases. A growing part of the work involves ab initio calculations of NMR parameters such as chemical shifts and scalar couplings and their dependence on the structural features of nucleic acids. The NMR laboratory is equipped with three NMR spectrometers Bruker Avance working at proton resonance frequencies 300, 500 and 600 MHz. The 600 MHz system is equipped with TCI cryoprobehead. For molecular dynamics and quantum mechanical calculations, the Center is equipped with a computer cluster consisting of 64 Pentium III processors working at 800 MHz, the cluster is currently being expanded by another 80 processors Xeon working at 2.4 GHz.

Partner 9 (Cambridge, Laue): Scientist in charge: Prof. Ernest Laue. Staff involved: Dr. Rasmus Fogh, Dr. Wayne Boucher and Dr. Tim Stevens. The Cambridge group has been developing new NMR methods for structural studies of macromolecules and applying these methods to particular biochemical problems since 1987. Together with others, they have pioneered the use of pulsed field gradients for recording multi-dimensional NMR spectra as well as alternative methods, in particular maximum entropy techniques, for NMR data processing (now part of the AZARA package). Both technologies are now regarded as essential for the recording and processing of multi-dimensional NMR spectra. In recent years they have also developed new strategies for structure determination of larger proteins using 3D/4D NMR in conjunction with fractional deuteration and the production of methyl-protonated proteins. The group is expert in the development of software for computer-aided analysis of such multi-dimensional NMR spectra (the ANSIG program) and is currently producing an updated version (CcpNmr Analysis). The group is also coordinating the Collaborative Computing Project in NMR (CCPN) to define a data model for NMR and develop a framework for software generation. This will allow easier exchange of data between software programs and provides the basis for the development of the integrated set of tools for structural studies of protein complexes. The approaches developed in the laboratory can then be applied directly to the proteins and protein complexes, which are being studied. Thus both "end-users" and software developers can be involved at every stage of the process.

Partner 10 (Oxford, Campbell): The expertise of Dr. Campbell's research group at Oxford University in the area of NMR is in the study of the structure and dynamics of modular proteins, in protein folding and real-time NMR methods. Another faculty member of Oxford University (A. Watts) is an expert in solid state NMR of membrane proteins. Other facilities include protein expression and purification, mass spectrometry, X-ray diffraction, electron microscopy, surface plasmon resonance, circular dichroism, fluorescence, FT IR, calorimetry and analytical ultra-centrifugation.