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developer of the AIDS-HIV Reference project
Abstract No.: ThP-222
Session: Protein Conformation and Structure Biology
Presentation date: Thu, Aug 31, 2006
Presentation time: 14:30 – 16:00

Mass Spectrometry Contribution to Structural Genomics: Defining Domains and Assessing New Protein Targets

Jean Armengaud1, Julie Augier1, Guillaume Gabant1, Jean-Charles Gaillard1, Jean-Luc Pellequer1, Alain Dedieu1

1 CEA Valrho - DSV/DIEP/SBTN, Bagnols sur Ceze, France

Correspondence address: Alain Dedieu, CEA, DSV/DIEP/SBTN, BP 17171, 30207 - Bagnols sur Ceze, 30207 France.

Keywords: Cross-linking; Genomics; Labeling; Structure Determination.

Novel aspect: In this poster we outline how mass spectrometry by gathering low resolution data, may help in protein structure determination, in ranking three-dimensional models and in prioritizing targets in structural genomics programs.


Structural genomics aims at covering the protein space so that every protein sequence comes within model building distance of a protein of known structure. Unfortunately, a significant number of proteins are not easily amenable to structure determination. In addition, the theoretical modelling of distantly related proteins is still a difficult challenge. First, we propose experimental strategies to define structured domain-boundaries of multi-domain proteins. Second, a novel complementary approach where evolutionary information, biophysical and topology data are combined allows to assess the de novo structure predictions of each domain. For this, we developed several mass spectrometry-based strategies to obtain a set of low resolution structural information. Kinetic data from limited proteolysis with various endoproteases are useful to point out accessible and flexible regions in proteins. Lysine labelling with chemical reagents can reveal solvent exposed residues. Cross-links between amino acids may indicate that these residues are spatially close and in adequate conformation to be cross-linked. If concordant, these mass-spectrometry experimental data can be used to rank multiple three-dimensional models generated by a de novo procedure. This strategy will be illustrated with experimental evidences obtained on three archaeal targets: PAB1283, SSO0551 and PAB0124. Such approach may help in prioritizing targets in current or future structural genomics programs.

J. Armengaud, A. Dedieu, O. Solques, J-L. Pellequer and E. Quemeneur, BMC Struct. Biol. 5, 3 (2005).
G. Gaband, S. Auxilien, I. Tuszynska, M. Locard, M. J. Gajda, G. Chaussinand, B. Fernandez, A. Dedieu, H. Grosjean, B. Golinelli-Pimpaneau, J. M. Bujnicki and J. Armengaud, Nucleic Acids Res. manuscript under revision (2006).