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1

Topological knots and links in proteins

Dabrowski-Tumanski, Pawel, Sulkowska, Joanna I.

Journal:

Proceedings of the National Academy of Sciences

Year:

2017

Language:

english

File:

PDF, 6.11 MB

english, 2017

2

KnotProt 2.0: a database of proteins with knots and other entangled structures

Dabrowski-Tumanski, Pawel, Rubach, Pawel, Goundaroulis, Dimos, Dorier, Julien, Sułkowski, Piotr, Millett, Kenneth C, Rawdon, Eric J, Stasiak, Andrzej, Sulkowska, Joanna I

Journal:

Nucleic Acids Research

Year:

2018

Language:

english

File:

PDF, 2.54 MB

english, 2018

3

Topoly: Python package to analyze topology of polymers

Dabrowski-Tumanski, Pawel, Rubach, Pawel, Niemyska, Wanda, Gren, Bartosz Ambrozy, Sulkowska, Joanna Ida

Journal:

Briefings in Bioinformatics

Year:

2020

File:

PDF, 1.04 MB

2020

4

Knotting pathways in proteins

Sułkowska, Joanna I., Noel, Jeffrey K., Ramírez‑Sarmiento, César A., Rawdon, Eric J., Millett, Kenneth C., Onuchic, José N.

Journal:

Biochemical Society Transactions

Year:

2013

Language:

english

File:

PDF, 354 KB

english, 2013

5

Tightening of Knots in Proteins

Sułkowska, Joanna I., Sułkowski, Piotr, Szymczak, P., Cieplak, Marek

Journal:

Physical Review Letters

Year:

2008

Language:

english

File:

PDF, 414 KB

english, 2008

6

The exclusive effects of chaperonin on the behavior of proteins with 52 knot

Zhao, Yani, Dabrowski-Tumanski, Pawel, Niewieczerzal, Szymon, Sulkowska, Joanna I., Keskin, Ozlem

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 7.38 MB

english, 2018

7

Protein Knotting by Active Threading of Nascent Polypeptide Chain Exiting From the Ribosome Exit Channel

Dabrowski-Tumanski, Pawel, Piejko, Maciej, Niewieczerzal, Szymon, Stasiak, Andrzej, Sulkowska, Joanna Ida

Journal:

Journal of Physical Chemistry B

Year:

2018

Language:

english

File:

PDF, 5.54 MB

english, 2018

8

Mg 2+ -Dependent Methyl Transfer by a Knotted Protein: A Molecular Dynamics Simulation and Quantum Mechanics Study

Perlinska, Agata, Kalek, Marcin, Christian, Thomas, Hou, Ya-Ming, Sulkowska, Joanna Ida

Journal:

Year:

2020

File:

PDF, 21.13 MB

2020

9

Slipknotting upon native-like loop formation in a trefoil knot protein

Jeffrey K. Noel, Joanna I. Sułkowska and José N. Onuchic

Journal:

Proceedings of the National Academy of Sciences

Year:

2010

Language:

english

File:

PDF, 1.81 MB

english, 2010

10

Connecting Thermal and Mechanical Protein (Un)folding Landscapes

Sun, Li, Noel, Jeffrey K., Sulkowska, Joanna I., Levine, Herbert, Onuchic, José N.

Journal:

Biophysical Journal

Year:

2014

Language:

english

File:

PDF, 1.42 MB

english, 2014

11

Methyl transfer by substrate signaling from a knotted protein fold

Christian, Thomas, Sakaguchi, Reiko, Perlinska, Agata P, Lahoud, Georges, Ito, Takuhiro, Taylor, Erika A, Yokoyama, Shigeyuki, Sulkowska, Joanna I, Hou, Ya-Ming

Journal:

Nature Structural and Molecular Biology

Year:

2016

Language:

english

File:

PDF, 3.40 MB

english, 2016

12

The Exclusive Effects of Chaperonin on the Free Energy Landscape of Proteins with Complex Knots

Sulkowska, Joanna I., Zhao, Yani, Dabrowski-Tumanski, Paweł, Niewieczerzal, Szymon

Journal:

Biophysical Journal

Year:

2018

Language:

english

File:

PDF, 64 KB

english, 2018

13

To Tie or Not to Tie? That Is the Question

Dabrowski-Tumanski, Pawel, Sulkowska, Joanna

Journal:

Year:

2017

Language:

english

File:

PDF, 16.30 MB

english, 2017

14

The APS-bracket – A topological tool to classify lasso proteins, RNAs and other tadpole-like structures

Dabrowski-Tumanski, Pawel, Sulkowska, Joanna I.

Journal:

Reactive and Functional Polymers

Year:

2018

Language:

english

File:

PDF, 1.03 MB

english, 2018

15

Chemical composition and biological activity of extracts from fruiting bodies and mycelial cultures of Fomitopsis betulina

Sułkowska-Ziaja, Katarzyna, Szewczyk, Agnieszka, Galanty, Agnieszka, Gdula-Argasińska, Joanna, Muszyńska, Bożena

Journal:

Molecular Biology Reports

Year:

2018

Language:

english

File:

PDF, 1.06 MB

english, 2018

16

Restriction of S-adenosylmethionine conformational freedom by knotted protein binding sites

Perlinska, Agata P., Stasiulewicz, Adam, Nawrocka, Ewa K., Kazimierczuk, Krzysztof, Setny, Piotr, Sulkowska, Joanna I., Wade, Rebecca C.

Journal:

PLoS Computational Biology

Year:

2020

File:

PDF, 8.03 MB

2020

17

The Folding of Knotted Proteins: Distinguishing the Distinct behavior of Shallow and Deep Knots

Piejko, Maciej, Niewieczerzal, Szymon, Sulkowska, Joanna I.

Journal:

Israel Journal of Chemistry

Year:

2020

File:

PDF, 9.21 MB

2020

18

Competition of drugs to serum albumin in combination therapy

Anna Sułkowska, Barbara Bojko, Joanna Równicka, Wiesław Sułkowski

Journal:

Year:

2004

Language:

english

File:

PDF, 264 KB

english, 2004

19

Competition of cytarabine and aspirin in binding to serum albumin in multidrug therapy

Anna Sułkowska, Barbara Bojko, Joanna Równicka, Wiesław W. Sułkowski

Journal:

Year:

2006

Language:

english

File:

PDF, 301 KB

english, 2006

20

Stability of the complex BSA-6-propyl-2-thiouracil in the presence of Gu·HCl and urea

Joanna Równicka, Anna Sułkowska, Jadwiga Pożycka, Barbara Bojko, Wiesław W. Sułkowski

Journal:

Journal of Molecular Structure

Year:

2006

Language:

english

File:

PDF, 205 KB

english, 2006

21

Predicting the order in which contacts are broken during single molecule protein stretching experiments

Joanna I. Sułkowska, Andrzej Kloczkowski, Taner Z. Sen, Marek Cieplak, Robert L. Jernigan

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.07 MB

english, 2008

22

Determination of the binding site of chloro(triethylphosphine)gold(I) in serum albumin

Anna Sułkowska, Wiesław W. Sułkowski, Krzysztof Nowak, Danuta Pentak, Małgorzata Maciążek-Jurczyk, Joanna Równicka-Zubik

Journal:

Journal of Molecular Structure

Year:

2010

Language:

english

File:

PDF, 391 KB

english, 2010

23

Evaluation of Apoptosis Markers in Conjunctival and Eyelid Benign and Malignant Tumors

JOANNA RESZEC, MARIOLA SULKOWSKA, LUIZA KANCZUGA-KODA, JERZY JANICA, MALGORZATA SKAWRONSKA, WITOLD PEPINSKI, STANISLAW SULKOWSKI

Journal:

Annals of the New York Academy of Sciences

Year:

2003

File:

PDF, 97 KB

2003

24

Expression of Cell Proliferation and Apoptosis Markers in Papillomas and Cancers of Conjunctiva and Eyelid

JOANNA RESZEC, MARIOLA SULKOWSKA, MARIUSZ KODA, LUIZA KANCZUGA-KODA, STANISLAW SULKOWSKI

Journal:

Annals of the New York Academy of Sciences

Year:

2004

Language:

english

File:

PDF, 246 KB

english, 2004

25

Expression of the Insulin-Like Growth Factor-I Receptor and Proapoptotic Bax and Bak Proteins in Human Colorectal Cancer

MARIUSZ KODA, JOANNA RESZEC, MARIOLA SULKOWSKA, LUIZA KANCZUGA-KODA, STANISLAW SULKOWSKI

Journal:

Annals of the New York Academy of Sciences

Year:

2004

Language:

english

File:

PDF, 291 KB

english, 2004

26

Dodging The Crisis Of Folding Proteins With Knots

Sulkowska, Joanna I., Sulkowski, Piotr, Onuchic, Jose

Journal:

Biophysical Journal

Year:

2009

Language:

english

File:

PDF, 36 KB

english, 2009

27

The Force-Induced Activation of Talin in a Structure-Based Model Simulation

Sun, Li, Sulkowska, Joanna, Noel, Jeff, Onuchic, José

Journal:

Biophysical Journal

Year:

2012

Language:

english

File:

PDF, 34 KB

english, 2012

28

Electromagnetic radiation in modern medicine: Physical and biophysical properties

Paweł Sowa, Joanna Rutkowska-Talipska, Urszula Sulkowska, Krzysztof Rutkowski, Ryszard Rutkowski

Journal:

Polish Annals of Medicine

Year:

2012

Language:

english

File:

PDF, 378 KB

english, 2012

29

Ionizing and non-ionizing electromagnetic radiation in modern medicine

Paweł Sowa, Joanna Rutkowska-Talipska, Urszula Sulkowska, Krzysztof Rutkowski, Ryszard Rutkowski

Journal:

Polish Annals of Medicine

Year:

2012

Language:

english

File:

PDF, 450 KB

english, 2012

30

Stretching to Understand Proteins—A Survey of the Protein Data Bank

Sułkowska, Joanna I., Cieplak, Marek

Journal:

Biophysical Journal

Year:

2008

Language:

english

File:

PDF, 405 KB

english, 2008

31

Selection of Optimal Variants of Gō-Like Models of Proteins through Studies of Stretching

Sułkowska, Joanna I., Cieplak, Marek

Journal:

Biophysical Journal

Year:

2008

Language:

english

File:

PDF, 280 KB

english, 2008

32

Mechanical stretching of proteins—a theoretical survey of the Protein Data Bank

Sułkowska, Joanna I, Cieplak, Marek

Journal:

Journal of Physics Condensed Matter

Year:

2007

Language:

english

File:

PDF, 6.16 MB

english, 2007

33

Knot localization in proteins

Rawdon, Eric J., Millett, Kenneth C., Sułkowska, Joanna I., Stasiak, Andrzej

Journal:

Biochemical Society Transactions

Year:

2013

Language:

english

File:

PDF, 300 KB

english, 2013

34

Identifying knots in proteins

Millett, Kenneth C., Rawdon, Eric J., Stasiak, Andrzej, Sułkowska, Joanna I.

Journal:

Biochemical Society Transactions

Year:

2013

Language:

english

File:

PDF, 269 KB

english, 2013

35

Knotting a Protein in Explicit Solvent

Noel, Jeffrey K., Onuchic, José N., Sulkowska, Joanna I.

Journal:

The Journal of Physical Chemistry Letters

Year:

2013

Language:

english

File:

PDF, 1.18 MB

english, 2013

36

Structure Based Protein Models and In Vitro Experiments to Investigate the Folding Landscape of the Human Obesity Protein Leptin

Haglund, Ellinor, Sulkowska, Joanna I., Jennings, Patricia A., Onuchic, José

Journal:

Biophysical Journal

Year:

2012

Language:

english

File:

PDF, 69 KB

english, 2012

37

Protein Knot Forming, Terminal-Through-Loop Threading Events can Occur on the Microsecond (

Noel, Jeffrey, Sulkowska, Joanna, Onuchic, Jose

Journal:

Biophysical Journal

Year:

2012

Language:

english

File:

PDF, 69 KB

english, 2012

38

Jamming Proteins with Slipknots and Their Free Energy Landscape

Sulkowska, Joanna I., Sulkowski, Piotr, Onuchic, Jose N.

Journal:

Biophysical Journal

Year:

2010

Language:

english

File:

PDF, 30 KB

english, 2010

39

Knotting a Protein in Explicit Solvent

Sulkowska, Joanna I., Noel, Jeffrey K., Onuchic, José N.

Journal:

Biophysical Journal

Year:

2014

Language:

english

File:

PDF, 111 KB

english, 2014

40

Conservation of Complex Knotting and Slipknotting Patterns in Proteins

Sulkowska, Joanna I., Rawdon, Eric J., Millet, Kenneth C., Onuchic, Jose N., Stasiak, Andrzej

Journal:

Biophysical Journal

Year:

2012

Language:

english

File:

PDF, 39 KB

english, 2012

41

Energy Landscape of Knotted Protein Folding

Sulkowska, Joanna I., Noel, Jeff K., Onuchic, Jose N.

Journal:

Biophysical Journal

Year:

2013

Language:

english

File:

PDF, 33 KB

english, 2013

42

Hysteresis as a Marker for Complex, Overlapping Landscapes in Proteins

Andrews, Benjamin T., Capraro, Dominique T., Sulkowska, Joanna I., Onuchic, José N., Jennings, Patricia A.

Journal:

The Journal of Physical Chemistry Letters

Year:

2013

Language:

english

File:

PDF, 1.69 MB

english, 2013

43

Untying Knots in Proteins

Sułkowska, Joanna I., Sułkowski, Piotr, Szymczak, Piotr, Cieplak, Marek

Journal:

Journal of the American Chemical Society

Year:

2010

Language:

english

File:

PDF, 782 KB

english, 2010

44

Thermal unfolding of proteins

Cieplak, Marek, Sułkowska, Joanna I.

Journal:

The Journal of Chemical Physics

Year:

2005

Language:

english

File:

PDF, 252 KB

english, 2005

45

In Vitro Study of Ketoprofen and Indapamide Used in Multidrug Therapy: 1 H-NMR Analysis

Maciążek-Jurczyk, M., Sułkowska, A., Równicka-Zubik, Joanna, Szkudlarek-Haśnik, A., Sułkowski, W. W.

Journal:

Spectroscopy Letters

Year:

2012

Language:

english

File:

PDF, 448 KB

english, 2012

46

Thermotropic Phase Behavior of Liposome Entrapped 5-FU and LCV

Pentak, Danuta, Sułkowska, Anna, Czopek, Izabela, Bojko, Barbara, Równicka-Zubik, Joanna, Sułkowski, Wiesław W.

Journal:

Molecular Crystals and Liquid Crystals

Year:

2010

Language:

english

File:

PDF, 535 KB

english, 2010

47

Jamming Proteins with Slipknots and Their Free Energy Landscape

Sułkowska, Joanna I., Sułkowski, Piotr, Onuchic, José N.

Journal:

Physical Review Letters

Year:

2009

Language:

english

File:

PDF, 305 KB

english, 2009

48

A Stevedore's Protein Knot

Bölinger, Daniel, Sułkowska, Joanna I., Hsu, Hsiao-Ping, Mirny, Leonid A., Kardar, Mehran, Onuchic, José N., Virnau, Peter, Taylor, William

Journal:

PLoS Computational Biology

Year:

2010

Language:

english

File:

PDF, 548 KB

english, 2010

49

Mechanical Strength of 17 134 Model Proteins and Cysteine Slipknots

Sikora, Mateusz, Sułkowska, Joanna I., Cieplak, Marek, Garcia, Angel

Journal:

PLoS Computational Biology

Year:

2009

Language:

english

File:

PDF, 586 KB

english, 2009

50

The Influence of Polyurethane Component on the Properties of Polyurethane-Rubber Composites Obtained from Waste Materials

Bartecka, Gabriela, Równicka-Zubik, Joanna, Sułkowska, Anna, Moczyński, Marek, Famulska, Wioletta, Sułkowski, Wiesław W.

Journal:

Molecular Crystals and Liquid Crystals

Year:

2014

Language:

english

File:

PDF, 79 KB

english, 2014