CENTER FOR BIOCRYSTALLOGRAPHIC RESEARCH
Head:
Mariusz Jaskólski
Research Staff:
Grzegorz Bujacz, Krzysztof Brzezinski
Research Support:
Marian Gawron, Mirosław Gilski, Mieczysława Kluge
Ph.D. Students:
Jakub Barciszewski, Magda Bejger, Humberto Fernandes, Agnieszka Wojtkowiak
Undergraduate Students:
Bartosz Siemiński
Keywords:
3D domain swapping, amyloidogenic proteins, hydrolytic enzymes, protease
inhibitors, antileukemic bacterial asparaginases, isoaspartyl aminopeptidases,
Ntn hydrolases, retroviral proteins, plant pathogenesis-related proteins,
RNA duplexes, high-resolution protein crystallography
X-Ray crystallography has been and continues to be the major source of information
about the three-dimensional structure of macromolecules. Typically, crystallographic
stud-ies of the structure of a macromolecule are divided into several steps.
First, the biomolecule under study has to be obtained in crystalline form,
often a success-limiting step. Next, the crystals are exposed to X-rays and
the diffraction pattern is recorded. The diffraction pattern is then the basis
for the structure determination process.
The Center is equipped and prepared to carry out all the steps necessary for
macromo-lecular structure determination, from protein purification and crystallization
through low-temperature diffraction experiments, to the structure evaluation
and analysis. The bio-molecules studied in the Center include both proteins
and nucleic acids.
The Center was created in 1994 with financial support from the Foundation
for Polish Science as a joint initiative of the Department of Crystallography,
A. Mickiewicz University and the Institute of Bioorganic Chemistry.
Current research activities:
3D Domain swapping;
Cysteine proteases and their inhibitors;
Retroviral enzymes;
Antileukemic bacterial asparaginases;
Plant-type asparaginases;
Plant pathogenesis-related proteins;
Protein structure at ultrahigh resolution;
High-resolution structure of RNA duplexes;
Crystallographic methodology;
Crystal engineering.
PROTEIN BIOCHEMISTRY GROUP
Head: Michał M. Sikorski
Research Support:
Alina Kasperska
Ph.D. Students:
Oliwia Pasternak
Undergraduate students:
Wiesława Włoszczak, Agnieszka Molińska, Katarzyna Konieczna
Keywords:
plant pathogenesis-related proteins, allergens, cytokinin-specific binding
proteins, gene expression, recombinant proteins
Current research activities:
- structure determination and expression analysis of plant genes encoding
pathogenesis-related proteins of class 10;
- preparation of recombinant proteins for functional and structural studies
(biological activity, crystal structure determination,
FTIR and NMR spectroscopy);
- involvement of cytokinin-specific binding proteins (CSBP) in plant signal
transduction pathways.
STRUCTURE-FUNCTION RELATIONSHIP IN BIOLOGICAL MOLECULES GROUP
Head: Wojciech R. Rypniewski
PhD. students:
Katarzyna Banaszak, Joanna Raczyńska, Agnieszka Kiliszek
Keywords:
key enzymes in fungi, non-canonical RNA duplexes, RNA hairpin-duplex transition
SELECTED PUBLICATIONS
H. Czapińska, J. Otlewski, Sz. Krzywda, G. M. Sheldrick, M. Jaskólski
High resolution structure of bovine pancreatic trypsin inhibitor with altered binding loop sequence.
J. Mol. Biol. 295, 1237-1249 (2000).
D. Borek, M. Jaskólski
Crystallization and preliminary crystallographic studies of a new L-asparaginase encoded
by the Escherichia coli genome.
Acta Cryst. D56, 1505-1507 (2000).
M. M. Sikorski, L. Handschuh, J. Biesiadka, A. B. Legocki
Two subclasses of yellow lupine PR10 proteins and their possible function during
the symbiosis development.
Current Plant Science and Biotechnology in Agriculture 38, 319-322 (2000).
D. A. Adamiak, W. R. Rypniewski, J. Milecki, R. W. Adamiak
The 1. 19 A X-ray structure of 2'-O-Me(CGCGCG)2 duplex shows dehydrated RNA with
2-methyl-2,4-pentanediol in the minor groove.
Nucleic Acids Res. 29, 4144-4153 (2001).
Z. Dauter, D. A. Adamiak
Anomalous signal of phosphorus used for phasing DNA oligomer: importance of data
redundancy.
Acta Cryst. D57, 990-995 (2001).
M. Jaskólski, M. Kozak, J. Lubkowski, G. Palm, A. Wlodawer
Structures of two highly homologous bacterial L-asparaginases: a case of enantiomorphic
space groups.
Acta Cryst. D57, 369-377 (2001).
A. Addlagatta, H. Czapińska, Sz. Krzywda, J. Otlewski, M. Jaskólski
Ultrahigh-resolution structure of a BPTI mutant.
Acta Cryst. D57, 649-663 (2001).
R. Janowski, M. Kozak, E. Jankowska, Z. Grzonka, A. Grubb, M. Abrahamson, M. Jaskólski
Human cystatin C, an amyloidogenic protein, dimerizes through 3D domain swapping.
Nature Struct. Biol. 8, 316-320 (2001).
M. Jaskólski
3D Domain swapping, protein oligomerization, and amyloid formation.
Acta Biochim. Polon. 48, 807-827 (2001).
K. Brzeziński, R. Janowski, J. Podkowiński, M. Jaskólski
Sequence determination and analysis of S-adenosyl-L-homocysteine hydrolase from yellow
lupine (Lupinus luteus).
Acta Biochim. Polon. 48, 477-483 (2001).
A. Hilgeroth, E. Tykarska, M. Jaskólski
Crystal structure of a novel synthetic inhibitor of HIV-1 protease.
J. Mol. Struct. 605, 63-70 (2002).
M. Kozak, D. Borek, R. Janowski, M. Jaskólski
Crystallization of D90E mutant of Escherichia coli L-asparaginase II in five crystal forms.
Acta Cryst. D58, 130-132 (2002).
R. Janowski, G. Bujacz, D. Gerlach, M. Jaskólski
Crystallization and preliminary crystallographic studies of Streptococcus pyogenes cysteine
protease precursor.
Acta Cryst. D58, 723-726 (2002).
P. Vishweshwar, R. Thaimattam, M. Jaskólski, G. R. Desiraju
Supramolecular synthons based on N-H...N and C-H...O hydrogen bonds. Crystal engineering
of a helical structure with 5,5-diethylbarbituric acid.
Chem. Commun. 2002, 1830-1831 (2002).
J. Biesiadka, G. Bujacz, M. M. Sikorski, M. Jaskólski
Crystal structures of two homologous pathogenesis-related proteins from yellow lupine.
J. Mol. Biol. 319, 1223-1234 (2002).
R. Thaimattam, E. Tykarska, A. Bierzyński, G.M. Sheldrick, M. Jaskólski
Atomic resolution structure of squash trypsin inhibitor: unexpected metal coordination.
Acta Cryst. D58, 1448-1461 (2002).
D. Piękna, M. M. Sikorski, H. Augustyniak
The gene encoding the PSST subunit of respiratory chain complex I is present in more than one copy in yellow lupine.
Biochim. Biophys. Acta 1577, 144-148 (2002).
R. Kołodziejczyk, M. Kochman, G. Bujacz, P. Dobryszycki, A. Ożyhar, M. Jaskólski
Crystallization and preliminary crystallographic studies of Juvenile Hormone Binding Protein from Galleria mellonella hemolymph.
Acta Cryst. D59, 519-521 (2003).
M. Cyrański, M. Gilski, M. Jaskólski, T. M. Krygowski
On the Aromatic Character of the Heterocyclic Bases of DNA and RNA.
J. Org. Chem. 68, 8607-8613 (2003).
G. D. Bujacz, O. Pasternak, Y. Fujimoto, Y. Hashimoto, M. M. Sikorski, M. Jaskólski
Crystallization and preliminary crystallographic studies of cytokinin-specific binding protein from mung bean.
Acta Cryst. D59, 522-525 (2003).
M. Perbandt, E. W. Guthöhrlein, W. R. Rypniewski, K. Idakieva, S. Stoeva, W. Voelter, N. Genov, Ch. Betzel
The structure of a functional unit from the wall of a gastropod hemocyanin offers a possible mechanism for cooperativity.
Biochemistry 42, 6341-6346 (2003).
T. Ruiz, I. Mechin, J. Bär, W. R. Rypniewski, G. Kopperschläger, M. Radermacher
The 10.8 Å structure of Saccharomyces cerevisiae phosphofructokinase determined by
cryo electron microscopy: localization of the putative fructose 6-phosphate binding sites.
J. Struct. Biol. 143, 124-134 (2003).
A. Schmidt, Ch. Jelsch, P. Oestergaard, W. R. Rypniewski, V. S. Lamzin
Trypsin revisited: Crystallography at (sub)atomic resolution and quantum chemistry revealing details of catalysis.
J. Biol. Chem. 278, 43357-43362 (2003).
K. Brzeziński, B. Rogoziński, T. Stępkowski, G. Bujacz, M. Jaskólski
Cloning, purification, crystallization and preliminary crystallographic studies of Bradyrhizobium fucosyltransferase NodZ.
Acta Cryst. D60, 344-346 (2004).
D. Borek, K. Michalska, K. Brzeziński, A. Kisiel, J. Podkowiński, D. T. Bonthron, D. Krowarsch,
J. Otlewski, M. Jaskólski
Expression, purification, and catalytic activity of Lupinus luteus asparagine b-amidohydrolase and its Escherichia coli homolog.
Eur. J. Biochem. 271, 3215-3226 (2004).
M. Nilsson, X. Wang, S. Rodziewicz-Motowidło, R. Janowski, V. Lindstrom, P. Onnerfjord,
G. Westermark, Z. Grzonka, M. Jaskólski, A. Grubb
Prevention of domain swapping inhibits dimerization and amyloid fibril formation
of cystatin C: use of engineered disulfide bridges, antibodies and carboxymethylpapain
to stabilize the monomeric form of cystatin C.
J. Biol. Chem. 279, 24236-24245 (2004).
R. Janowski, M. Abrahamson, A. Grubb, M. Jaskólski
3D Domain-Swapped Dimers of N-Truncated Human Cystatin C.
J. Mol. Biol. 341, 151-160 (2004).
M. Vallazza, M. Perbandt, S. Klussmann, W. Rypniewski, H. M. Einspahr, V. A. Erdmann, C. Betzel.
First look at RNA in L-configuration.
Acta Cryst. D60, 1-7 (2004).
D. N. Georgieva, M. Perbandt, W. Rypniewski, K. Hristov, N. Genov, Ch. Betzel
The X-ray structure of a snake venom Gln48 phospholipase A2 at 1.9 Å resolution reveals an ion-binding sites.
Biochem. Biophys. Res. Commun. 316, 33-38 (2004).
S. Benini, W. R. Rypniewski, K. S. Wilson, S. Mangani, S. Ciurli
Molecular details of urease inhibition by boric acid: Insights into the catalytic mechanism.
J. Am. Chem. Soc. 126, 3714-3715 (2004).
D. N. Georgieva, W. R. Rypniewski, A. Gabdoulkhakov, N. Genov, Ch. Betzel
Phospholipase A2-Elaidoylamide complex: a new mode of inhibition.
Biochem. Biophys. Res. Commun. 319, 1314-1321 (2004).
K. Banaszak, I. Mechin, G. Frost, W. R. Rypniewski
Structure of the reduced disulpfide-bond isomerase DsbC from Escherichia coli.
Acta Cryst. D60, 1747-1752 (2004).
D. N. Georgieva, W. R. Rypniewski, H. Echner, M. Perbandt, M. Koker, J. Clos, L. Redecke, R. Bredehorst, W. Voelter, N. Genov, Ch. Betzel
Synthetic human prion protein octapeptide repeat binds to the proteinase K active site.
Biochem. Biophys. Res. Commun. 325, 1406-1411 (2004).
O. Pasternak, J. Biesiadka, R. Dolot, G. Bujacz, M. M. Sikorski, M. Jaskólski
Crystal structure of a yellow lupine pathogenesis-related PR-10 protein belonging to a novel subclass.
Acta Cryst. D61, 99-107 (2005).
T. Stępkowski, K. Brzeziński, A. B. Legocki, M. Jaskólski, G. Bena
Bayesian phylogenetic analysis reveals two-domain topology of S-adenosylhomocysteine hy-drolase protein sequences.
Mol. Phylogenet. Evol. 34, 15-28 (2005).