Seminar Dirk Stratman January 24th, 2012.

Title: Sub-domain protein fragments

Abstract: Globular proteins can be decomposed into sub-domain structural fragments with
tight ends. These “tightened end fragments (TEF)”[1] (also named "closed loops"[2]) play an
important role for the fold of a protein. We propose here an alternative approach for the TEF
decomposition of a protein structure aiming at a better cover of the chain. For a biophysical
sound framework for the TEF decomposition of a protein structure, we search to predict the
conformational stability of a TEF taken alone to select the most stable TEFs for the
decomposition. We would like to apply 3D-Blast [3] for the structural classification of the
TEFs. At the beginning of the talk, I will also give a short summary of my former work
(automated NMR spectra assignment (NOEnet)[4], quantitative use of NMR chemical shifts
for protein-protein docking (CS-HADDOCK)[5]).
References:
[1] M. Lamarine, J. P. Mornon, N. Berezovsky and J. Chomilier, Distribution of tightened end
fragments of globular proteins statistically matches that of topohydrophobic positions:
towards an efficient punctuation of protein
folding? Cellular and Molecular Life Sciences: CMLS, 58:492-498, 2001
[2] I. N. Berezovsky, A. Y. Grosberg, and E. N. Trifonov, Closed loops of nearly standard
size: common basic element of protein structure. FEBS Letters, 466:283-286, 2000.
[3] Mavridis L, Ghoorah AW, Venkatraman V, Ritchie DW., "Representing and comparing
protein folds and fold families using three-dimensional shape-density representations.",
Proteins. 2011 Oct 12. [Epub ahead of print]
[4] D. Stratmann, E. Guittet, and C. van Heijenoort, « Robust structure-based resonance
assignment for functional protein studies by NMR », Journal of Biomolecular NMR, vol. 46,
no. 2, p. 157-173, Feb. 2010.
[5] D. Stratmann, R. Boelens, and A. M. J. J. Bonvin, « Quantitative use of chemical shifts for
the modeling of protein complexes », Proteins, vol. 79, no. 9, p. 2662-2670, sept. 2011.

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