Honoring our Mathematical Methods Developers: Jorge Navaza craftsman of the FRF

The end result of the efforts of the crystallographic community is a set of Cartesian coordinates (x,y,z,  for each atom) that represent the arrangement of the atoms in the molecules inside the crystal.  These results have been stored since the beginnings of crystallography in databases. From the beginning, the Cambridge  Crystallographic Database, now Cambridge Crystallographic Data Centre (CCDC), contains the structures of all small molecules determined by X-ray Diffraction. Later, as the number of proteins structures began to grow in the early seventies, a devoted database was created (Protein Data Bank, PDB) storing the larger, more complex macromolecular structures involved in biological processes. This database (PDB) now contains more than 80,000 entries ranging from the early proteins such as hemoglobin and lysozyme to the structure of complex viruses and other important biological aggregates like ribosomes.  The most recent updates from the PDB indicate that approximately two-thirds of the structures deposited currently have been solved by molecular replacement methods using a related, pre-existing structure in the database. This is a tribute to the success of the discipline and definitively to the power of the Molecular Replacement method proposed and championed by Michael G. Rossmann and David Blow in the early sixties in parallel to the more experimentally demanding Multiple Isomorphous Replacement (MIR) method.

For the younger generations of structural biologists ‘Molecular Replacement’ refers to programs available in the CCP4 package that are used essentially as a ‘magic black box’ that either succeeds or fails in finding the structure of the known or ‘related’ fold inside the unknown crystal structure.  This state of affairs was not always so and many insightful crystallographers and computer scientists have developed the original idea to an extraordinary degree of effectiveness in the field.  In fact, some of the ‘crystallographers’ that improved dramatically the performance of the mathematical tools originally proposed were not bona fide crystallographers but rather mathematicians such as Gerard Bricogne or physicists like R.A. Crowther, who originally proposed the Fast Rotation Function expansion in terms of spherical harmonics in 1971. In this note, I would like to highlight one of them, Jorge Navaza, for several reasons. First and foremost are the impact that his contributions to crystallography and its younger sister (i.e., electron microscopy) have had in the two fields separately, and the resulting synergy that has ensued in the last decade. Second, the professional respect and personal friendship that Jorge has always inspired in the narrator. Finally, the momentous occasion of a modest homage that friends and colleagues of Jorge offered him on the occasion of his retirement from this latest research position at the laboratory of Structural Biology (IBS) in Grenoble, France.

The meeting was a unique gathering of early students, colleagues, collaborators and friends of Jorge and his spouse (Alda) and his son Rafael, in the Basque town of Getxo in the outskirts of Bilbao, Spain, on October 3-4, 2013. The meeting was entitled On the Frontier between Cryo-EM and Protein Crystallography and was organized by Diego Guerin, Ignacio Fita, Pedro Alzari,  Pepe Cascón and Jean Lepault with the support of several research institutions of France, Spain and the Basque Government: Consejo Superior de Investigaciones Cientificas (CSIC, Spain), Centre National de la Recherche Scientifique (CNRS, France), Gobierno Vasco/Eusko Jaurlaritza, Institut Pasteur (France), Universidad del País Vasco (UPV/EHU) and Fundacion Biofisica Bizkaia (FBB).

The meeting was brief but intense. The scientific talks centered around the collaborations that Jorge Navaza has had in the last few years related to difficult structures that were solved by the use of the AMoRE suite of programs , and also  on the successful applications of his software URO, for the combination of Cryo-EM data with crystallographic data.  Only the highlights are summarized; details of the different structures presented can be found in the published scientific papers. In the first session, Felix Rey from the Institut Pasteur (Paris) described the details of the structures of regular enveloped viruses and the implications for evolution. Later, Fasselli Coulibaly (Monash University, Australia) presented the protein-induced membrane remodeling by D13, the scaffolding protein of vaccinia virus.These lectures were followed by the impressive work of Jose (Pepe) R. Castón and collaborators (Group of Electron Microscopy of University Autonomous in Madrid, Spain) on the near atomic resolution (~ 4 Å) structure of the virus attacking the fungus Penicillium chrysogenum (PcV), a fungal dsRNA virus.  The mechanical and dynamical properties of the vault ribonucleoprotein particle were presented by Nuria Verdaguer (IBMB-CSIC, Barcelona, Spain). This aggregate is a massive  ‘vault-like’ structure composed of two identical subunits of 39 copies each of the component protein vault protein (MVP).

Eleanor Dobson eloquently presented the importance and impact that the first release of AMoRE had as a part of CCP4 release in 1994. The vastly improved mathematical procedures and the distinct introduction of automation within the suite of programs facilitated enormously the program performance and effectiveness to solve difficult structures by Molecular Replacement methods. This presentation was followed by spirited and often hilarious presentations by two of Jorge’s most brilliant students Leandro F. Strozi (Grenoble, France) and Stefano Trapani (Montpellier, France) who played an important role in the early publications related to the mathematical improvements of AMoRe. Xavier Gomis-Rüth presented the spectacular results of applying these methods to the intricate structure of the a2-macroglobulins later in the meeting.

Group photo of colleagues and friends of Jorge Navaza at the meeting in his honor in Getxo, Bizkaia, Spain.

Fig. 1. Group photo of colleagues and friends of Jorge Navaza at the meeting in his honor in Getxo, Bizkaia, Spain. From left to right: Pedro Alzari, Jorge Navaza, Diego Guerin, Alda Navaza, Pepe Caston, Ignacio Fita (behind) and Cele Abad-Zapatero. Courtesy of A. Podjarny.

The emotional highlight of the meeting was in the late afternoon of October 3 after the first technical sessions.  Briefly introduced by the narrator describing Jorge’s flirtation with Structure-Based Drug Design, Jorge presented a retrospective of his work on crystallography starting from the core of physicists friends at the University of La Plata in Argentina: E. Castellano, Alberto Podjarny, Abelardo Silva and the younger Pedro Alzari.  Pedro followed with a series of emotional photos of the younger Navaza and the group and soon thereafter appeared the surprise of the evening.  A Basque dancer-player (‘Dantzari-Txistulari’) pair appeared in the room to perform a symbolic Basque dance named ‘Aurresku’ in homage to Jorge. This is a unique intricate dance based on the 5/8 meter. At the end, he was presented with a silver-decorated walking stick (or ‘makila’) as a sign of respect from his friends and peers (Fig. 1).

The next day the first presentations highlighted computation developments related to structure determination. Abelardo Silva (Advanced Molecular Sciences, USA) discussed his efforts to revisit and improve the issue of parameters describing the molecular geometry and Garib Murshudov (MRC, Cambridge, UK) discussed his efforts to improve the refinement of structures at medium to low resolution.

These lectures were followed by another series of structural results. Alberto Podjarny (IGBMC, Strasbourg, France) presented his results of neutron diffraction combined with subatomic X-ray diffraction (<1 Å resolution) in two systems: human Aldose Reductase (h-AR) and the antifreeze proteins (AFD) of artic fish.  Philippe Dumas (University of Strasbourg, France) presented an intriguing lecture on the use of the classical Clayperon-Clausius Equation  (CCE) and a generalized form (GCCE) to physical phenomena ranging from thermal regulation in biological systems to black holes.  Vicente Rubio (IBV-CSIC, Valencia, Spain) presented his twenty year journey studying enzymes of the urea cycle in humans in collaboration with Ignacio Fita (IBMC, Barcelona , Spain) . The meeting was closed with the presentation by Dino Moras of the work of his group on the structure of Nuclear Hormone Receptors and its regulation via DNA transcription, combining SAXS, SANS and FRET to establish the architecture of the heterodimers bound to DNA elements.  Dino’s concluding remarks impressed on the audience the impact that the work of Jorge Navaza’s has had on the structural biological community as judged by the number of citations (~5,000 for a single paper) present in the literature. An emotional applause concluded the sessions of the meeting honoring this ‘craftsman’ of the mathematics behind the implementation of the Molecular Replacement method and the calculation of the Fast Rotation Function.

Fig.2. View of the Gorrondatxe-Aizkorri beach in the proximity of Getxo, Bizkaia, Spain.

Fig.2. View of the Gorrondatxe-Aizkorri beach in the proximity of Getxo, Bizkaia, Spain, where a ‘golden spike’ marker (inset) by the International Union of Geological Scientists has placed the beginning of the ‘Lutetian’ Stage (dated 47.8 Million years ago). Copyright C.A-Z.

 

There were many touristic temptations to pique the curiosity of the attendees to the meeting. From the world-renowned Guggenheim Museum in downtown Bilbao to the magnificent vistas of the beaches and cliffs in the seashore (Fig.2). For the Geology enthusiasts, there was a special treat. The seashore of the Atlantic Coast of Spain where the Basque country is located, from Bizkaia to Bayonne in France, is a treasure trove of remarkable formations that serve as reference points for the stratigraphy of  various Epochs of the Earth history. Just a few kilometers away from the meeting venue, there is a recent (Feb. 2012) ‘golden spike’ placed by the International Union of Geology Scientists at the Aizkorri beach to mark the base of the ‘Lutetian ‘ stage (Fig.2, inset) of the Eocene Epoch dated near 48 millions years ago.

 

 

 

International Symposium On the frontier of Cryo-EM and Protein Crystallography, Hotel Igeretxe, Getxo, Spain, 3-4 October 2013. Image courtesy of Xabi Muniz

International Symposium ‘On the frontier between  Cryo-EM and Protein Crystallography’, Hotel Igeretxe, Getxo (Bizkaia), Spain, 3-4 October 2013. Image courtesy of Xabi Muniz

 

 

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About Cele Abad-Zapatero

Biophysicist, Protein Crystallographer, Drug Designer and Science Writer. Licenciado Degree, University of Valladolid, Spain, 1969. Physics, Mathematics. Graduate work, University of Salamanca, 1969-1972. Biological Sciences. Fullbright Scholarship for Graduate studies in the USA (1972). Ph. D. University of Texas at Austin, 1978. Biophysics Postdoc with M.G.Rossmann, Purdue University, 1979-1985. Group Leader-Associate Research Fellow, Abbott Laboratories-Retired 2008. Adjunct Professor to the Graduate Faculty, University of Illinois at Chicago. current
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