MPŠ
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Jožef Stefan
International
Postgraduate School

Jamova 39
SI-1000 Ljubljana
Slovenia

Phone: +386 1 477 31 00
Fax: +386 1 477 31 10
Email: info@mps.si

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Course Description

From Crystals to 3D Structure of Macromolecules

Program

Nanosciences and Nanotechnologies, third-level study programme

Lecturers:

prof. dr. Dušan Turk

Goals:

To inform student with all steps of determination of crystal structure of macromolecules. Student will solve at least one such structure.

Content:

Verifying purity and stability of macromolecules
Crystallization of macromolecules.
Data collection and processing.
Phasing of crystallographic data:
- molecular replacement (MR)
- multi-wavelength anomalous dispersion technique
(MAD, SAD)
- multiple and single isomorphous replacement (MIR and SIR)
Modifications of density maps:
- identification of protein and solvent regions
- separate procedures for solvent and protein regions
- exploiting non-crystallographic symmetry: electron density averaging
Interpretation of electron density maps:
- automated and
- manual model building
Refinement and model rebuilding
- target functions (least square and maximum-likelihood targets)
- " slow" (simulated annealing) and " fast" cooling minimization techniques
Analysis and validation of 3-D models
Model interpretation:
- manuscript preparation
- basis for further investigations

Course literature:

Crystallography of biological macromolecules: International Tables for Crystallography, Volume F, edited by Michael G. Rossmann and Eddy Arnold (2001). Kluwer Academic Publishers, ISBN 0-7923-6857-6.

Macromolecular crystallography. Part A. Methods in Enzymology, Vol. 276. Edited by CHARLES W. CARTER JR and ROBERT M. SWEET. New York: Academic Press, 1997. ISBN 0-12-182177-3

Relevant current articles from the field (Biological Crystallography, Applied Crystallography, Structure, Journal of Molecular Biology, Nature, Science, Current Opinion of Structural Biology, ...)

Significant publications and references:

Andrejašič, M,, Praznikar, J, Turk, D (2008) PURY: a database of geometric restraints of hetero compounds for refinement in complexes with macromolecular structures. Acta Cryst., D64, 1093-1109.

Mihelič, M, Doberšek, A, Guncar, G., Turk, D. (2008) Inhibitory fragment from the p41 form of invariant chain can regulate activity of cysteine cathepsins in antigen presentation. J. Biol. Chem., 283(21), 14453-60.

Turk, D. (2007) Density modification in MAIN. Evolving methods for macromolecular crystallography : proceedings of the NATO Advanced Study Institute on Evolving Methods for Macromolecular Crystallography, 19-28 May 2005, Erice, Italy, (Read, R., Sussman, j. eds.) NATO science series, series II., Mathematics, physics and chemistry, 254. Springer Verlag, 111-122.

Terwilliger, T.C. Grosse-Kunstleve, R., Afonine, P.V., Adams, P.D., Moriarty, N.W., Zwart, P. Read, R.J. Turk, D., Hung, Li-Wei (2007) Multiple iterative rebuilding of macromolecular models yields an estimate of precision and a lower limit of uncertainty. Biol. Cryst. (Acta Cryst.) D 63, 597-610.

Jenko Kokalj S, Guncar G, Stern I, Morgan G, Rabzelj S, Kenig M, Staniforth RA, Waltho JP, Zerovnik E, Turk D. (2007) Essential role of proline isomerization in stefin B tetramer formation. J Mol Biol. 366(5), 1569-79. Epub 2006 Dec 16.

STERN, Igor, SCHASCHKE, Norbert, MORODER, Luis, TURK, Dusan. Crystal structure of NS-134 in complex with bovine cathepsin B: a two-headed epoxysuccinyl inhibitor extends along the entire active-site cleft. Biochem. j., 2004, vol. 381, str. 511-517.

TURK, Dusan, JANJIC, Vojko, STERN, Igor, PODOBNIK, Marjetka, LAMBA, Doriano, DAHL, Soren Weis, LAURITZEN, Connie, PEDERSEN, John, TURK, Vito, TURK, Boris. (2001) Structure of human dipeptidyl peptidase I (cathepsin C): exclusion domain added to an endopeptidase framework creates the machine for activation of granular serine proteases. EMBO j. 20, 6570-6582.

Examination:

• seminar and oral exam (50%)
• manuscript writting (50%)

Students obligations:

• seminar and oral exam
• experimental work

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