Department of Crystallography Center for Biocrystallographic Research


Head:
Prof. Mariusz Jaskólski


Staff:

Prof. Grzegorz Bujacz,

Dr. Mirosław Gilski,

Dr. Barbara Imiołczyk,

Dr. Marcin Kowiel,

Dr. Joanna Raczyńska,

Dr. Kamil Szpotkowski


PhD Students:

Tomasz Manszewski,

Barbara Stańska

 Wojciech Witek

 

 

 

 


 

 


 

 


 

 


 

 


Affiliated Laboratory:
Laboratory of Protein Engineering

 

Key words

3D domain swapping, amyloidogenic proteins, hydrolytic enzymes, protease inhibitors, antileukemic asparaginases, isoaspartyl amino­peptidases, Ntn-hydrolases, retroviral protease, metallo-b-lactamases, plant pathogenesis-related proteins, plant-bacterium symbiosis, atomic-resolution biocrystallography, crystallographic methodology

 

Research profile

The Center, created in 1994 as a joint initiative of the Department of Crystallography, A. Mickiewicz University and the Institute of Bioorganic Chemistry, was the first protein crystallography laboratory in Central Europe. Over the years, it has matured in the scope of the pursued projects and in its comprehensive approach to structural biological problems, continuing the original research on retroviral enzymes as well as establishing new vigorous lines of research, e.g. in structural enzymology and in plant structural biology. Experimentally, we are self-sufficient and can work from gene to atomic resolution structure as our labs are furnished with state-of-the art equipment and facilities. Even more importantly, our team includes experts in protein chemistry and overexpression, and two parallel crystallography groups.

 

Current research activity 

  • aggregation mechanisms of amyloidogenic proteins
  • hydrolase-inhibitor systems in pathogenesis
  • metallo-b-lactamases
  • fitohormone binding proteins
  • plant-bacterium symbiosis
  • macromolecular structure at ultimate resolution

 

Most important research achievements

 

  • At the inception of the Center, we were involved, in collaboration with the National Cancer Institute (USA), in the determination of the crystal structure of retroviral protease and the catalytic domain of retroviral integrase. Currently, this project has been extended to include new retroviruses and has resulted in crystal structure determination of a single subunit of retroviral protease (from M-PMV), which in its functional form is an obligate homodimer. This unprecedented result was achieved with massive involvement of ?citizen scientists? helping to solve scientific problems through a specially designed on-line game (Foldit).
  • Our discovery of 3D domain swapping in the amyloidogenic protein human cystatin C has established the involvement of this mechanism in amyloid fibril formation. Subsequent protein engineering experiments have shown that abrogation of 3D domain swapping can successfully prevent amyloid aggregation.
  • Our structural characterization of plant phytohormone binding proteins and pathogenesis-related PR-10 proteins revealed that they have the same structure, with a characteristic huge cavity enclosed by the elements of the protein fold. The cavity can bind different numbers of the cargo molecules, which can be of variable type, including such diversified phytohormones as cytokinins, gibberellins or melatonin, in various, but highly ordered ways. This discovery sheds new light on protein-ligand recognition, underlying the role of mutual structural adaptability.
  • We have discovered that, in addition to antileukemic asparaginases, bacteria (such as E. coli) also express L-asparaginases that are typically associated with the plant kingdom. These proteins have dual enzymatic activity and are most effective as isoaspartyl aminopeptidases. They belong to the family of Ntn hydrolases and are generated from immature precursors in autoproteolytic activation. Our studies have helped to dissect the catalytic apparatus of these enzymes and the mode of their activation. We have also elucidated the structural basis of the potassium dependence of some of these enzymes.
  • We have contributed to macromolecular crystallographic methodology, especially through very careful studies at ultimate resolution. There are several protein structures determined in our laboratory at the resolution of about 0.7 ?, and a structure of a Z-DNA duplex at a record-setting resolution of 0.55 ?.

 

Research projects

  • Structural studies of amyloidogenic motifs (intramural funds)
  • Structural biology of plant-symbiont interactions (intramural funds)
  • Plant hormone binding proteins (intramural funds)
  • Structural enzymology (intramural funds)
  • Structure-guided design of inhibitors of metallo-b-lactamases (JPIAMR/NCBR)

 

Selected publications

H. Fernandes, K. Michalska, M. Sikorski, M. Jaskolski
Structural and functional aspects of PR-10 proteins.
FEBS J.280, 1169-1199 (2013).

P. Drozdzal, M. Gilski, R. Kierzek, L. Lomozik, M. Jaskolski
Ultrahigh-resolution crystal structures of Z-DNA in complex with Mn2+ and Zn2+ ions.
Acta Cryst. D69, 1180-1190 (2013).

M. Ruszkowski, K. Szpotkowski, M. Sikorski, M.Jaskolski
The landscape of cytokinin binding by a plant nodulin.
Acta Cryst. D69, 2365-2380 (2013).

A. Wlodawer, W. Minor, Z. Dauter, M. Jaskolski
Protein crystallography for aspiring crystallographers, or how to avoid pitfalls and traps in macromolecular structure determination.
FEBS J. 280, 5705-5736 (2013).

E. Kopera, W. Bal, M. Lenarčič Živkovič, A. Dvornyk, B. Kludkiewicz, K. Grzelak, I. Zhukov, W. Zagórski-Ostoja, M. Jaskolski, S. Krzywda
Atomic Resolution Structure of a Protein Prepared by Non-Enzymatic His-Tag Removal. Crystallographic and NMR Study of GmSPI-2 Inhibitor.
PLoSOne 9, e106936, 1-11 (2014).

J. Sliwiak, M. Jaskolski, Z. Dauter, A. McCoy, R.J. Read
Likelihood-based molecular replacement solution for a highly pathological crystal with tetartohedral twinning and seven-fold translational non-crystallographic symmetry.
Acta Cryst. D70, 471-480 (2014).

M. Bejger, B. Imiolczyk, D. Clavel, M. Gilski, A. Pajak, F. Marsolais, M. Jaskolski
Na+/K+ exchange switches the catalytic apparatus of K-dependent plant L-asparaginase.
Acta Cryst. D70, 1854-1872 (2014).

M. Kowiel, M. Jaskolski, Z. Dauter
ACHESYM: an algorithm and server for standardized placement of macromolecular models in the unit cell.
Acta Cryst. D70, 3290-3298 (2014).

M. Jaskolski, Z. Dauter, A. Wlodawer
A brief history of macromolecular crystallography, illustrated by a family tree and its Nobel fruits.
FEBS J. 281, 3985-4009 (2014).

M. Ruszkowski, J. Sliwiak, A. Ciesielska, J. Barciszewski, M. Sikorski, M. Jaskolski
Specific binding of gibberellic acid by Cytokinin-Specific Binding Proteins: a new aspect of plant hormone-binding proteins with PR-10 fold.
Acta Cryst. D70, 2032-2041 (2014).

D. Borek, M. Kozak, J. Pei, M. Jaskolski
Crystal structure of active-site mutant of antileukemic L-asparaginase reveals conserved zinc-binding site.
FEBS J. 281, 4097-4111 (2014).

J. Sliwiak, Z. Dauter, M. Kowiel, A. McCoy, R.J. Read, M. Jaskolski
ANS complex of St John?s wort PR-10 protein with 28 copies in the asymmetric unit: a fiendish combination of pseudosymmetry with tetartohedral twinning.
Acta Cryst. D71, 829-843 (2015).

I. Shabalin, Z. Dauter, M. Jaskolski, W. Minor, A. Wlodawer
Crystallography and chemistry should always go together: a cautionary tale of protein complexes with cisplatin and carboplatin.
Acta Cryst. D71, 1965-1979 (2015).