VU-FALW: D. De Vos

Dirk De Vos

Postdoctoral Researcher - Kluyver Centre

Department of Molecular Cell Physiology
Faculty of Earth and Life Sciences
Vrije Universiteit Amsterdam

De Boelelaan 1085
NL-1081 HV Amsterdam
The Netherlands

E-mail: contact
Phone: +31 20 5987195

Education

Licenciate in Biochemistry, Ghent University, Belgium

PhD in Biochemistry, Ghent University, Belgium

Research Interests

As a PhD student in Biochemistry my primary interest was the structure-function relationship of enzymes. One of the main topics was to investigate how intermolecular interactions lead to the disctinct properties (catalytic, allosteric,...) of enzymes from extremophylic micro-organisms. Since then my interest has broadened towards the physiological level, and more specifically to understand how complex intermolecular interactions lead to emergent behaviour of the living cell. Indeed, a central goal of biology in the post-genomic era is to understand how thousands of encoded proteins serve to bring about the highly coordinated behavior of cells and tissues. This is studied in the novel field of Systems Biology. My work is currently focussed on modeling the molecular regulatory mechanisms of translation in S. cerevisiae.

List of publications

1) Academic dissertations:

De Vos, D. (2006) Structural insights into extremozymes. Subtitle: A study of Sulfolobus acidocaldarius and Moritella profunda aspartate carbamoyltransferase, and of Pseudoalteromonas haloplanktis xylanase pXyl. PhD thesis, Ghent University. [pdf file]
De Vos, D. (2000) Structure-function relationship of human ATP-citrate lyase as a potential target for drug-design in metabolic diseases like obesity. Licentiate thesis, Ghent University.

2) Articles:

Bevilacqua, A., Wilkinson, S.J., Dimelow, R., Murabito, E., Rehman, S., Nardelli, M., van Eunen, K., Rossell, S., Bruggeman, F.J., Blüthgen, N., De Vos, D., Bouwman, J., Bakker, B.M. and Westerhoff HV. (2008) Vertical systems biology: from DNA to flux and back. SEB Exp. Biol. Ser. 61, 65-91.
De Vos, D., Xu, Y., Aerts, T., Van Petegem, F. and Van Beeumen JJ. (2008) Crystal structure of Sulfolobus acidocaldarius aspartate carbamoyltransferase in complex with its allosteric activator CTP. Biochem. Biophys. Res. Commun. 372, 40-44.
Remmerie, B., Vandenbroucke, K., De Smet, L., Carpentier, W., De Vos, D., Stout, J., Van Beeumen, J. and Savvides, SN. (2008) Expression, purification, crystallization and structure determination of two glutathione S-transferase-like proteins from Shewanella oneidensis. Acta Cryst. F64, 548-553.
Van Petegem, F., De Vos, D., Savvides, S., Vergauwen, B. and Van Beeumen, J. (2007) Understanding nicotinamide dinucleotide cofactor and substrate specificity in class I flavoprotein disulfide oxidoreductases: crystallographic analysis of a glutathione amide reductase. J. Mol. Biol. 374, 883-889.
De Vos, D.*, Xu, Y.*, Hulpiau, P., Vergauwen, B. and Van Beeumen, J. (2007) Structural investigation of cold activity and regulation of aspartate carbamoyltransferase from the extreme psychrophilic bacterium Moritella profunda. J. Mol. Biol. 365, 379-395.
De Vos, D.*, Collins, T.*, Nerinckx, W., Savvides, S.N., Claeyssens, M., Gerday, C., Feller, G. and Van Beeumen, J. (2006) Oligosaccharide binding in family 8 glycosidases: crystal structures of active site mutants of the beta-1,4-xylanase pXyl from Pseudoalteromonas haloplanktis in complex with substrate and product. Biochemistry 45, 4797-4807.
Vergauwen, B., De Vos, D. and Van Beeumen, J. (2006) Characterization of the bifunctional gamma-glutamate cysteine ligase-glutathione synthetase enzyme (GshF) of Pasteurella multocida. J. Biol. Chem. 281, 4380-4394.
Collins T., Hoyoux A., Van Petegem, F., De Vos, D., Van Beeumen, J., Stals, I., Claeyssens, M., Georis J., Dauvrin T., Arnaut F., Gerday C. and Feller G. (2005) A novel family 8 psychrophilic xylanase: fundamentals and applications. The proceedings of the International Symposium on Extremophiles and Their Applications, Japan.
Collins, T.*, De Vos, D.*, Hoyoux, A., Savvides, S.N., Gerday, C., Van Beeumen, J. and Feller, G. (2005) Study of the active site residues of a glycoside hydrolase family 8 xylanase. J. Mol. Biol. 354, 425-435.
De Vos, D., Hulpiau, P., Vergauwen, B., Savvides, S.N. and Van Beeumen, J. (2005) Expression, purification, crystallization and preliminary crystallographic studies of a cold-adapted aspartate carbamoyltransferase from Moritella profunda. Acta Cryst. F61, 279-281.
De Vos, D., Van Petegem, F., Remaut, H., Legrain, C., Glansdorff, N. and Van Beeumen, J. (2004) Crystal Structure of T state aspartate carbamoyltransferase of the hyperthermophilic archaeon Sulfolobus acidocaldarius. J. Mol. Biol. 339, 887-900.

*joint first authorship

3) Book Chapter:

Bevilacqua, A., Wilkinson, S.J., Dimelow, R., Murabito, E., Rehman, S., Nardelli, M., van Eunen, K., Rossell, S., Bruggeman, F.J., Blüthgen, N., De Vos, D., Bouwman, J., Bakker, B.M. and Westerhoff HV. Vertical systems biology: from DNA to flux and back. In: Grierson, C., Hetherington, A. Practical Systems Biology, vol. 61 (2008) Taylor & Francis Ltd, New York, 218 pp.

/ VU - FALW: D. De Vos / Revised :