MPŠ MP&Scaron MP&Scaron MP&Scaron Avtorji

Jožef Stefan
Postgraduate School

Jamova 39
SI-1000 Ljubljana

Phone: +386 1 477 31 00
Fax: +386 1 477 31 10


Course Description

From Crystals to 3D Structure of Macromolecules


Nanosciences and Nanotechnologies, third-level study programme


prof. dr. Dušan Turk


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


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
- 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.


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

Students obligations:

• seminar and oral exam
• experimental work