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Joanna Ida Sulkowska

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2015
KnotProt: a database of proteins with knots and slipknotsJamroz, M. et al.Nucleic Acids Research 43, D306-D314, 2015.
Prediction of the optimal set of contacts to fold the smallest knotted protein.Dabrowski-Tumanski, P., Jarmolinska, A.I. & Sulkowska, J.I.J Phys Condens Matter 27, 354109, 2015.
2014
Connecting thermal and mechanical protein (un)folding landscapesSun, L., Noel, J.K., Sulkowska, J.I., Levine, H. & Onuchic, J.N.Biophysical Journal 107(12), 2950-61, 2014.
Pierced Lasso Bundles are a New Class of Knot MotifsHaglund, E. et al.PLoS computational biology 10(6), , 2014.
2013
Hysteresis as a Marker for Complex, Overlapping Landscapes in Proteins.Andrews, B.T., Capraro, D.T., Sulkowska, J.I., Onuchic, J.N. & Jennings, P.A.Journal of Physicak Chemistry Letters 4, 180-188, 2013.
Identifying knots in proteins.Millett, K.C., Rawdon, E.J., Stasiak, A. & Sulkowska, J.I.Biochemical Society Transactions 41, 533-7, 2013.
Knot localization in proteins.Rawdon, E.J., Millett, K.C., Sulkowska, J.I. & Stasiak, A.Biochemical Society Transactions 41, 538-41, 2013.
Knotting a Protein in Explicit SolventNoel, J.K., Onuchic, J.N. & Sulkowska, J.I.The Journal of Physical Chemistry Letters 4, 3570-3573, 2013.
Knotting pathways in proteins.Sulkowska, J.I. et al.Biochemical Society Transactions 41, 523-7, 2013.
2012
Conservation of complex knotting and slipknotting patterns in proteins.Sulkowska, J.I., Rawdon, E.J., Millett, K.C., Onuchic, J.N. & Stasiak, A.Proceedings of the National Academy of Sciences of the United States of America 109, E1715-23, 2012.
Energy landscape of knotted protein folding.Sulkowska, J.I., Noel, J.K. & Onuchic, J.N.Proceedings of the National Academy of Sciences of the United States of America 109, 17783-8, 2012.
Genomics-aided structure prediction.Sulkowska, J.I., Morcos, F., Weigt, M., Hwa, T. & Onuchic, J.N.Proceedings of the National Academy of Sciences of the United States of America 109, 10340-5, 2012.
The unique cysteine knot regulates the pleotropic hormone leptin.Haglund, E. et al.PLoS One 7, e45654, 2012.
2011
BSDB: the biomolecule stretching database.Sikora, M., Sulkowska, J.I., Witkowski, B.S. & Cieplak, M.Nucleic Acids Research 39, D443-50, 2011.
2010
Slipknotting upon native-like loop formation in a trefoil knot protein.Noel, J.K., Sulkowska, J.I. & Onuchic, J.N.Proceedings of the National Academy of Sciences of the United States of America 107, 15403-8, 2010.
A Stevedore's protein knot.Bölinger, D. et al.PLoS Comput Biol 6, e1000731, 2010.
Untying knots in proteins.Sulkowska, J.I., Sułkowski, P., Szymczak, P. & Cieplak, M.Journal of the American Chemical Society 132, 13954-6, 2010.
2009
Dodging the crisis of folding proteins with knots.Sulkowska, J.I., Sułkowski, P. & Onuchic, J.Proceedings of the National Academy of Sciences of the United States of America 106, 3119-24, 2009.
Jamming proteins with slipknots and their free energy landscape.Sulkowska, J.I., Sułkowski, P. & Onuchic, J.N.Phys Rev Lett 103, 268103, 2009.
Mechanical strength of 17,134 model proteins and cysteine slipknots.Sikora, M., Sulkowska, J.I. & Cieplak, M.PLoS Comput Biol 5, e1000547, 2009.
On the remarkable mechanostability of scaffoldins and the mechanical clamp motif.Valbuena, A. et al.Proceedings of the National Academy of Sciences of the United States of America 106, 13791-6, 2009.
Tests of the Structure-Based Models of ProteinsCieplak, M. & Sulkowska, J.I.ACTA PHYSICA POLONICA A 115, , 2009.
2008
Predicting the order in which contacts are broken during single molecule protein stretching experiments.Sulkowska, J.I., Kloczkowski, A., Sen, T.Z., Cieplak, M. & Jernigan, R.L.Proteins 71, 45-60, 2008.
Selection of optimal variants of Gō-like models of proteins through studies of stretching.Sulkowska, J.I. & Cieplak, M.Biophys J 95, 3174-91, 2008.
Stabilizing effect of knots on proteins.Sulkowska, J.I., Sulkowski, P., Szymczak, P. & Cieplak, M.Proceedings of the National Academy of Sciences of the United States of America 105, 19714-9, 2008.

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