Mechanical properties of protein molecules

In recent years, the development of experimental tools allowing the precise application and measurement of minute forces has opened new perspectives in material- and life sciences. In particular, it became possible to perform single-molecule mechanical experiments and measure the rupture forces of molecular bonds using optical tweezers or atomic force microscopy. This gives an exciting opportunity to study of the protein folding and unfolding mechanisms on a single molecule level. Those experimental developments inspired new theoretical and numerical studies of the mechanical properties of proteins.

We investigate mechanical properties of single protein molecules by considering topology-based coarse-grained models of the proteins. Coarse-grained models simplify the complex molecular details but aim to capture the fundamental physics of the folding process. In particular, stretching and folding of single proteins under the influence of a constant force was analyzed and it was shown that, although the experimentally observed rapid changes in the end-to-end distance of the protein mirror microscopic events during folding, the course of the folding itself is different than that for proteins in vivo.

We have also analyzed the behavior of single protein molecules in a flow field. As it turns out, the proteins in the flow show a surprisingly rich dynamical behavior, as a result of an interplay between the hydrodynamic forces and direct molecular forces. Unfolding of proteins induced by a flow usually involves a larger number of intermediate states than the force-induced unfolding (as in the AFM force clamp). Those features offer potentially wider diagnostic tools to investigate structure of proteins compared to experiments based on the atomic force microscopy.

Recently, the influence of non-trivial topology (i.e. knotted backbone) on protein properties was analyzed and it was shown that relatively small structural differences between the proteins which, however, alter the topology of the backbone, result in dramatic changes in their mechanical properties and stability.

Unfolding of ubiquitin by a constant flow (upper left) involves two intermediate conformations (right), whereas in a force clamp (lower left) it unfolds usually in a single kinetic step

In collaboration with

• Marek Cieplak (Polish Academy of Sciences)
• Joanna Sułkowska (University of California San Diego)
• Piotr Sułkowski (California Institute of Technology)
• Harald Janovjak (University of California Berkeley)

Relevant publications

• P. Szymczak, Periodic forces trigger knot untying during translocation of knotted proteins, Sci. Rep., 6, 21702, 2016 [pdf] [movie1] [movie2]
• P. Szymczak, Translocation of knotted proteins through a pore, Eur. Phys. J. Special Topics, 223, 1805-1812, 2014 [pdf]
• M. Wojciechowski, P. Szymczak, M. Carrion-Vazquez, M. Cieplak Protein unfolding by biological unfoldases: insights from modeling, Biophys. J.,107, 1661-1668, 2014 [pdf]
• P. Szymczak, Tight knots in proteins: can they block the mitochondrial pores?, Biochem. Soc. Trans., 41, 620-624, 2013 [pdf]
• P. Szymczak, M. Cieplak, Hydrodynamic effects in proteins (invited review), J. Phys. Cond. Matt., 23, 033102, 2011 [pdf]
• J. Sułkowska, P. Sułkowski, P. Szymczak, M. Cieplak, Untying knots in proteins, J. Am. Chem. Soc., 132, 13954-13956, 2010 [pdf] (press coverage)
• P. Szymczak, H. Janovjak, Periodic forces trigger a complex mechanical response in ubiquitin, J. Mol. Biol., 390, 443, 2009 [pdf] [frontcover]
• J. Sułkowska, P. Sułkowski, P. Szymczak, M. Cieplak, Stabilizing effect of knots on proteins, Proc. Natl. Acad. Sci. USA, 105, 19714, 2008 [pdf] (press coverage)
• J. Sułkowska, P. Sułkowski, P. Szymczak, M. Cieplak, Tightening of knots in proteins, Phys. Rev. Lett., 100, 058106, 2008 [pdf] [supplementary material]
• P. Szymczak, M. Cieplak, Proteins in a shear flow, J. Chem. Phys. 127, 155106, 2007 [pdf]
• P. Szymczak, M. Cieplak, Influence of hydrodynamic interactions on mechanical unfolding of proteins, J. Phys. Cond. Matt., 19, 285224, 2007 [pdf]
• P. Szymczak, M. Cieplak, Stretching of proteins in a uniform flow, J. Chem. Phys., 125, 164903, 2006 [pdf]
• M. Cieplak, P. Szymczak, Protein folding in a force clamp, J. Chem. Phys., 124 , 194901, 2006 [pdf]
• P. Szymczak, M. Cieplak, Stretching of proteins in a force-clamp, J. Phys. Cond. Matt., 18, L21, 2006 [pdf]