Name: Gerard Kleywegt
Position: Network Coordinator/Researcher
Projects: Structural Neurobiology / Protein Crystallography / Structural Bioinformatics
Gender: M
Actual starting date: 1 June, 1997
Administrative starting date: 1 June, 1997
In 1997, I have begun independent research in the areas of protein crystallography and structural bioinformatics. In the former area, I continue to do methodological work (e.g., interpretation of electron-density maps [1], model refinement and rebuilding practice [3], and density modification [6]), and I am still involved in wrapping up previous crystallographic projects [2]. I have also initiated two new projects, both in the area of neurobiology and both of medical relevance, that are described below. Both projects have been started up from scratch; therefore, in both cases, we are still working hard on trying to obtain material of sufficient purity and quantity for crystallisation purposes. In the protein crystallographic projects, I employ one post-doctoral fellow (Dr. Kristina Bäckbro; funded through a Junior Individual Grant awarded to me by the Foundation for Strategic Research), and I have a position available for a PhD student (MAO project; position funded through SBNet).
In the structural bioinformatics area, I work on protein model validation [5] and analysis [4]. I have written a set of programs for detecting small structural motifs in protein models (SPASM), and have begun work on profile analysis methods (SBIN). These provide a mechanism through which structural information can be used to discover structural and/or functional relationships with proteins for which the sequence is known, but not the structure. I hope to finish this work in 1998 and submit it for publication.
The first crystallographic project involves the structure determination of the enzyme monoamine oxidase (MAO). MAO is involved in the biodegradation of aromatic monoamines, including classical neurotransmitters such as serotonin, adrenalin, histamine, and dopamine, and appears to play a central role in several psychiatric and neurological disorders (including clinical depression). This project is carried out in collaboration with Prof. Creed W. Abell (University of Texas at Austin) and Dr. Johan Wouters (Faculté Universitaire Notre-Dame de la Paix, Namur, Belgium). We have been working on the purification of MAO-B from bovine liver mitochondria, and expect to have pure material in March, 1998, so that crystallisation trials can commence. (At that stage, the student position will also be advertised.) In addition, Dr. Bäckbro has worked on the expression of MAO in E. coli, and this work will continue (both in Uppsala and in Austin) in 1998, in collaboration with Petra Franzén at the expression facility in Uppsala. In particular, we would like to obtain a C-terminal truncated mutant of MAO, which should be a soluble protein (wild-type MAO is anchored to the membrane through a C-terminal helix). We also consider to extend the project to include putrescine oxidase, a related enzyme that is expected to have the same fold as MAO, but that is soluble and can be expressed in bacteria.
The second crystallographic project involves structural and functional studies of so-called IAP proteins (Inhibitor of Apoptosis Proteins). Apoptosis, or programmed cell death, is a strictly regulated and evolutionary conserved mechanism through which multicellular organisms dispose of unwanted cells. It plays an important role in many physiological processes, such as the development of the retina and the removal of inter-digit webbing in human embryos. In addition, apoptosis occurs in certain pathological states, such as virus infection and cellular injury. Some IAP proteins have been demonstrated to block apoptosis; for instance, X-linked IAP (XIAP) interferes with a signalling cascade that emanates from TNF receptors. This project is a collaboration with the group of Prof. Dan Lindholm (Developmental Neurobiology, Uppsala University). During 1997, all efforts have been directed at trying to express (as GST-fusion proteins) and purify (from inclusion bodies) two IAP proteins, namely intact XIAP and a 400-residue fragment of NAIP (neuronal apoptosis inhibitor protein; implicated in Spinal Muscular Atrophy), unfortunately without much success to date. These efforts will be continued vigorously under 1998. Prof. Lindholm is coordinator for a proposal to the European Union for an international collaborative project on IAP proteins. If the proposal is funded, we would be responsible for the structural studies within the project.
Additional highlights during 1997:
* January-December: coordination of the Structural Biology Network (maintaining mailing list; designing and maintaining web site; etc.).
* April: trip to New Zealand (3 invited lectures, including "keynote speaker" at the "Crystal XX" conference in Queenstown).
* May/June: organisation of the First Annual Conference of the Structural Biology Network; chair of the session on "X-ray Techniques and Applications".
* June-December: consultant to the structural chemistry group at Pharmacia & Upjohn in Stockholm.
At present, I maintain three WWW sites with information, software and services relevant to the structural biology community:
* USF, the "Uppsala Software Factory", at http://xray.bmc.uu.se/usf/
* SBNet, at http://xray.bmc.uu.se/sbnet/
* HIC-Up, the "Hetero-compound Information Centre - Uppsala", at http://xray.bmc.uu.se/hicup/
Publications 1997.
(Note: only paper [6] was written during the period in which my position was funded by SBNet.)
[1] GJ Kleywegt & TA Jones (1997). Template convolution to enhance or detect structural features in macromolecular electron-density maps. Acta Cryst. D53, 179-185.
[2] GJ Kleywegt, JY Zou, C Divne, GJ Davies, I Sinning, J Ståhlberg, T Reinikainen, M Srisodsuk, TT Teeri & TA Jones (1997). The crystal structure of the catalytic core domain of endoglucanase I from Trichoderma reesei at 3.6 Å resolution, and a comparison with related enzymes. J. Mol. Biol. 272, 383-397.
[3] GJ Kleywegt & TA Jones (1997). Model-building and refinement practice. Methods Enzymol. 277, 208-230.
[4] GJ Kleywegt & TA Jones (1997). Detecting folding motifs and similarities in protein structures. Methods Enzymol. 277, 525-545.
[5] GJ Kleywegt (1997). Validation of protein models from C[[alpha]] coordinates alone. J. Mol. Biol. 273, 371-376.
[6] GJ Kleywegt & RJ Read (1997). Not your average density. Structure 5, 1557-1569.
Invited lectures 1997.
* "Structural basis of the interaction of a snake toxin with its target, acetyl cholinesterase", invited lecture, Department of Chemistry, University of Leiden (NL), January 1997.
* "Low-resolution refinement: the twilight zone of protein crystallography", keynote speaker at "Crystal XX", the 20th Meeting of the Society of Crystallographers in Australia, Queenstown (New Zealand), April 1997.
* "Averaging", invited seminar, Department of Biochemistry, Massey University, Palmerston North (New Zealand), April 1997.
* "Why you want to stay friends with your pet green mamba ... Structural basis of the interaction of a snake toxin with its target, acetylcholinesterase", invited lecture, New Zealand Institute of Chemistry, Manawatu branch, Palmerston North (New Zealand), April 1997.
* "Averaging and Map Interpretation", technical seminar, Pharmacia & Upjohn Structural Chemistry, Stockholm (S), June 1997.
* "Validation I", technical seminar, Pharmacia & Upjohn Structural Chemistry, Stockholm (S), August 1997.
* "Validation II", technical seminar, Pharmacia & Upjohn Structural Chemistry, Stockholm (S), October 1997.
* "Molecular Replacement", technical seminar, Pharmacia & Upjohn Structural Chemistry, Stockholm (S), November 1997.
Latest update at 9 March, 1998.