Laboratory of Biopolymer Structure

Submitted by Stan on Mon, 05/31/2021 - 12:13
University
University of Gdańsk
Faculty/school/department
Intercollegiate Faculty of Biotechnology
Size of the team
number of researchers number of supporting staff number of PhD students
3
0
3
PI
PI name
Stanislaw Oldziej
PI email
stanislaw.oldziej@ug.edu.pl
PI bio

Received his PhD in Chemistry at the University of Gdańsk (1995). He carried out his postdoctoral training at the University of Montreal, Canada (1996-1998) working with prof. F. Major on modeling structure of small RNA molecules. In the years 2001-2004 he carried out his second post-doctoral training at the Cornell University, USA working with prof H.A. Scheraga on predicting three-dimensional structure of proteins. He became a habilitation doctor at 2005. Author of more than one hundred per-reviewed publications.

http://orcid.org/0000-0002-4583-3941

Contact person and e-mail
Contact person
Stanisław OŁDZIEJ
Contact person e-mail
stanislaw.oldziej@ug.edu.pl
Short description of research profile

Understanding mechanisms of action of small proteins and peptides in biological systems. As a part of a large international (Poland, South Korea, USA, Argentina, France, Sweden) informal research group we participate in a project to develop what is called a coarse-grained (simplified) model of polypeptide chain called UNRES (UNited RESidues). (www.unres.pl)

Search and study of short peptide sequences having a defined spatial structure and showing the ability to catalyze chemical reactions.

Searching for protein and peptide markers of diseases and pathological conditions using mass spectrometry and bioinformatic techniques

Research area
NATURAL SCIENCES » Biological sciences
MEDICAL AND HEALTH SCIENCES » Basic medical research
Scientific Themes (keywords)
NMR structural studies
proteomics
prebiotic chemistry
Bioinformatics
Publications

Representative publications

Urban Aleksandra, Volokhina Elena, Felberg Anna, Stasiłojć Grzegorz, Blom Anna M., Jongerius Ilse, van den Heuvel Lambertus, Thiel Marcel, Ołdziej Stanisław, Arjona Emilia, Rodriguez de Córdoba Santiago, Okrój Marcin. Gain-of-function mutation in complement C2 protein identified in patient with Ahus. Journal of Allergy and Clinical Immunology 2020, 146(4): 916-919 (doi: 10.1016/j.jaci.2020.02.014)    
Lewandowska Aleksandra Ewa, Macur Katarzyna, Czaplewska Paulina, Liss Joanna, Łukaszuk Krzysztof, Ołdziej Stanisław. Human follicular fluid proteomic and peptidomic composition quantitative studies by SWATH-MS methodology. Applicability of high pH RP-HPLC fractionation. Journal of Proteomics 2019, 191: 131-142 (doi: 10.1016/j.jprot.2018.03.010)
Keasar Chen, McGuffin Liam J, Wallner Bjorn, Chopra Gaurav, Adhikari Badri, Bhattacharya Debswapna, Blake Lauren, Bortot Leandro Oliveira, Cao Renzhi Dhanasekaran, Dimas, Itzhel, Faccioli Rodrigo Antonio, Faraggi Eshel, Ganzynkowicz Robert, Ghosh Sambit, Ghosh Soma, Gieldon Artur, Golon Lukasz, He Yi, Heo Lim, Hou Jie, Khan Main, Khatib Firas, Khoury George A, Kieslich Chris, Kim David E, Krupa Pawel, Lee Gyu Rie, Li Hongbo, Li Jilong, Lipska Agnieszka, Liwo Adam, Maghrabi Ali Hassan A., Mirdita Milot, Mirzaei Shokoufeh, Mozolewska Magdalena A., Onel Melis, Ovchinnikov Sergey, Shah Anand, Shah Utkarsh, Sidi Tomer, Sieradzan Adam K., Slusarz Magdalena, Slusarz Rafał, Smadbeck James, Tamamis Phanourios, Trieber Nicholas, Wirecki Tomasz, Yin Yanping, Zhang Yang, Bacardit Jaume, Baranowski Maciej, Chapman Nicholas, Cooper Seth, Defelicibus Alexandre, Flatten Jeff, Koepnick Brian, Popovic Zoran, Zaborowski Bartlomiej, Baker David, Cheng Jianlin, Czaplewski Cezary, Botazzo Delbem Alexandre Claudio, Floudas Christodoulos, Kloczkowski Andrzej, Ołdziej Stanislaw, Levitt Michael, Scheraga Harold, Seok Chaok, Soeding Johannes, Vishveshwara Saraswathi, Xu Dong, Crivelli Silvia N. An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12. Scientific Reports 2018, 8: 9939 (doi: 10.1038/s41598-018-26812-8)
Łebkowski Tomasz, Wolański Marcin, Ołdziej Stanisław, Flärdh Klas, Zakrzewska-Czerwińska Jolanta. AfsK-mediated site-specific phosphorylation regulates DnaA initiator protein activity in Streptomyces coelicolor. Journal of Bacteriology 2020, 202: e00597-19 (doi: 10.1128/JB.00597-19)
Liwo Adam, Sierdzan Adam K., Lipska Agnieszka G., Czaplewski Cezary, Joung InSuk, Żmudzińska Wioletta, Hałabis Anna, Ołdziej Stanisław. A general method for the derivation of the functional forms of the effective energy terms in coarse-grained energy functions of polymers. III. Determination of scale-consistent backbone-local and correlation potentials in the UNRES force field and force-field calibration and validation. The Journal of Chemical Physics 2019, 150: 155104 (doi: 10.1063/1.5093015)
Technology Expertise

NMR spectrosopy (compund identification and 3D structure determination)

Mass spectrometry (proteomics, peptidomics)

 

Partnerships and Cooperation
None