Xiao-Dong Su
Position: "Forskare" (LU)
Project: Protein Crystallography at MAX II and Lund University
Funding ended: 31 December, 2001
Part of my job (about 20%) is user support for the beam line BL711 at MAX lab. Besides the user support, I have also taken part in the teaching activities of the department in 2001:
(1) Lecturer of the course 'Protein structure and function' (KEM043);
(2) Organiser and lecturer of the course 'Medicinal chemistry and drug design' (Läkemedelskemi) (KEM711).
My own research projects:
(1) Structural studies of cell adhesion molecule L1 and its interaction with integrins
Since cell adhesion molecules (CAMs) play important roles in many biological functions including cancer progression and metastasis, the three-dimensional structures of CAMs will help to understand the mechanisms of these events and to develop new drugs to inhibit the metastatic processes. L1 CAM is homologous to the insect immune protein hemolin which crystal structure was determined by me during my post-doc work at CalTech, USA (see Su XD et al. 1998. Crystal structure of hemolin: a horseshoe shape with implications for homophilic adhesion. Science 281:991-995). The objectives of this project are:
A) To determine the crystal structures of the extracellular domains of L1 family of CAMs, in order to understand L1s homophilic adhesion mechanism. These CAM proteins include human and mouse L1, Drosophila neuroglian. So far, small crystals are obtained on the first 4 domains of neuroglian (Nrg4D) and a two-domain fragment (Ig5-Ig6) of neuroglian. Human and mouse L1 domains are under preparation. It still requires lots of effort to improve these crystals for structure determination.
B) To study the structures of integrin domains, and later to try to co-crystallise the integrin domain(s) with its binding partner, the RGD domain(s) of L1 CAMs, in order to understand the heterophilic adhesion interactions.
This project has been funded by Cancerfonden in Sweden. Three manuscripts are in preparation related to this project, see below the publication list.
(2) Deciphering the form and function of LMW PTP homologues in the genomic era
Low-molecular-weight protein tyrosine phosphatase (LMW PTP) is a subfamily of protein tyrosine phosphatase (PTP) superfamily that in concert with protein tyrosine kinases (PTKs) determine the level of tyrosine phosphorylation in eukaryotic cells. This phosphorylation signal regulates cellular differentiation, division and development. It was thus believed that the PTPs exclusively exist in higher eukaryotes or host-cell related pathogens. However, the recent genomic sequencing efforts demonstrated that the LMW PTP homologues are widespread in most organisms including many bacteria, fungi, plants, worms and flies. Most of the homologues are with unknown functions; one family of the homologues belong to the bacterial arsenate reductase, participating in removal of the toxic arsenate and arsenic compounds in vivo.
Since tyrosine phosphorylation is rare in prokaryotes and the corresponding PTK gene is lacking, either the LMW PTP homologues have new functions or the role of tyrosine phosphorylation should be reevaluated in the prokaryotes. This project is focused on solving this dilemma by using a combination of molecular biology (genetics), enzymology and structural determination techniques.
We have chosen a Gram-positive bacterium B. subtilis to start this project, and it's planned to extend to other organisms in the future. So far, in subtilis we have knocked out the three genes of LMW PTP homologues, yfkJ, ywlE, and arsC, the phenotype characterisation are underway. We have also cloned, expressed, purified and set up crystallisation trials for two of the gene products, arsC (the arsenate reductase) and yfkJ, the closest LMW PTP in bacteria known so far (37% identity to bovine LMW PTP). The crystals that diffracted beyond 1.6 Å have been obtained for arsC protein, and the kinetics parameters of both enzymes have been measure on standard PTP substrates, the results are quite exciting, two papers have been published, more are in preparation.
On-going collaborative projects include:
1) The structure determination of human cystatin D, an inhibitor of papain-like cysteine proteinases is a collaboration of my group and Dr. Magnus Abrahamson's group at Department of Clinical Chemistry, Institute of Laboratory Medicine, Lund University Hospital, Sweden. We have solved the crystal structure of cystatin D to 1.8 Å at cryo temperature and 2.5 Å at room temperature separately since about one year ago. This is the first human cystatins solved so far, we are planning to go on along this direction to study more cystatins particularly their interactions with different cysteine proteinases in the future. A manuscript is under preparation entitled: "The crystal structure of cystatin D, an inhibitor of papain-like cysteine proteinases" (in preparation), by Marcia Alvarez-Fernandez, Magnus Abrahamson & Xiao-Dong Su
2) The structural studies of a beta-glucosidase, Zm-p60.1 from maize is a collaborative project between my group and the Laboratory of Plant Molecular Physiology, Faculty of Science, Masaryk University, Kotláfiská 2, CZ 611 37 Brno, Czech Republic. We have solved the crystal structure of this protein. Two papers were published in 2001.
3) Recently, I have solved the crystal structures of an extended spectrum beta-lactamase from K. oxytoca in collaboration with Dr. Shangwei Wu in the dept. of microbiology at Rockefeller University, the structure is still under refinement at the moment.
Financial situation and research group:
My salary and some running costs have been supported by SSF via SBNet. I have obtained grant support from:
1) 200, 000 SEK each year for two years (1999 and 2000) from Cancerfonden;
2) 400, 000 SEK each year for two years (2001 and 2002) from Cancerfonden;
My group is composed of the following persons excluding myself in 2000:
M.Sc. Jitka Vévodová: a joint Ph.D. student;
Dr. Zhi Guan: post-doc;
Dr. Matthew Bennett: post-doc
Publications:
1. Vévodová, J.; Marek, J.; Zouhar, J.; Brzobohaty, B.; and Su, X-D. "Purification, crystallisation and preliminary X-ray analysis of a maize cytokinin glucoside specific -glucosidase" (2001) Acta Crystallogr. D57, 140-142
2. Zouhar, J.; Vévodová, J.; Marek, J.; Damborsk[[breve]], J.; Su, X-D and Brzobohat[[breve]], J. "Insights into the Functional Architecture of the Catalytic Center of a Maize b-Glucosidase Zm-p60.1 " (2001) Plant Physiol. 127 973-985.
3. Guan, Z.; Hederstedt, L.; Li, J-P.; and Su, X-D. "Protein preparation and crystallisation of an arsenate reductase from bacillus subtilis" (2001) Acta Crystallogr. D57, 1718-21
4. Bennett, M.; Guan, Z.; Laurberg M. and Su, X-D. "Bacillus subtilis arsenate reductase is structurally and functionally similar to low molecular-weight protein tyrosine phosphatases " (2001) Proc. Natl. Acad. Sci. USA, 98:13577-13582
Latest update at 29 March, 2001.