MPŠ
MPŠ MP&Scaron MP&Scaron MP&Scaron Avtorji

Mednarodna
podiplomska šola
Jožefa Stefana

Jamova 39
SI-1000 Ljubljana
Slovenija

Tel: (01) 477 31 00
Faks: (01) 477 31 10
E-pošta: info@mps.si

Išči

Opis predmeta

Od kristalov do 3D strukture makromolekul

Programi:

Nanoznanosti in nanotehnologije, 3. stopnja

Sodelavci:

prof. dr. Dušan Turk

Cilji:

Seznaniti študenta s celotnim postopkom določevanja 3-dimenzionalnih struktur na osnovi difrakcije žarkov na kristalih makromolekul. Študent mora praktično določiti vsaj eno takšno strukturo.

Vsebina:

Preverjanje čistosti in stabilnosti makromolekul
Kristalizacija makromolekul
Snemanje in procesiranje podatkov
Faziranje kristalografskih
- podatkov metoda molekularne zamenjave
- multi valovna anomalna disperzija (MAD,SAD)
- multipla in enojna izomorfna zamenjava (MIR,SIR)
Modifikacija elektronske gostote:
-identifikacija proteinske regije in topila
- postopki modifikacije regije proteina in topila
- uporaba ne kristalografske simetrije
- povprečenje elektronske gostote
Interpretacija elektronske gostote
- avtomatsko in
- manualno grajenje molekularnih modelov
Fitanje in predelovanje modelov
- tarčne funkcije (metoda najmanjših kvadratov in maksimalne podobnosti)
- počasno in hitro ohlajanje pregretih modelov
Analiza in preverjanje struktur
Biološka interpretacija modelov:
- pisanje članka
- zastavitev nadalnjih raziskav

Temeljna literatura in viri:

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

Tekoča relevantna literatura iz problematike (Biological Crystallography, Applied Crystallography, Structure, Journal of Molecular Biology, Nature, Science, Current Opinion of Structural Biology, ...)

Izbrane reference nosilca:

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.

Načini preverjanja znanja:

• seminar in ustni izpit (50%)
• pisanje znanstvenega članka (50%)

Obveznosti študentov:

• seminar in ustni izpit
• laboratorijsko delo

Zunanje povezave: