Laboratorium Modelowania Biomolekularnego

Celem naszych badań jest zrozumienie mechanizmów fizycznych leżących u podstaw funkcjonowania układów biomolekularnych. Chcemy odpowiedzieć na pytanie w jaki sposób struktura makromolekuł determinuje ich właściwości dynamiczne i w jaki sposób dynamika przekłada się na zdolność do pełnienia określonej roli w żywej komórce. W naszej pracy posługujemy się symulacjami komputerowymi, metodami fizyki statystycznej, technikami bioinformatycznymi oraz narzędziami analizy danych.

W obecnej chwili skupiamy się na:
– badaniu roli zlokalizowanych cząsteczek wody w strukturach kinaz białkowych,
– badaniu oddziaływania peptydu fuzyjnego wirusa grypy z błoną lipidową,
– rozwijaniu metod opisu hydratacji makromolekuł.

Realizowane projekty
– Efekty hydratacyjne w kinazach białkowych (Sonata, NCN)
– Embo Installation Grant

dr hab. Piotr Setny
e-mail: p.setny@cent.uw.edu.pl
telefon: +48 22 55 43660
pokój: 4006
www: http://setnylab.cent.uw.edu.pl

Research interests
Piotr Setny is a theoretical and computational biophysicist. He develops and applies physical models to describe and simulate biological molecules in order to gain insight into principles governing their structure, dynamics and function. He is particularly interested in the interplay between the molecules themselves and aqueous environment they live in. To this end, he is studying conformation dependent protein hydration free energies, investigate the role buried water molecules, and develop new theoretical approaches to describe macromolecular hydration. One of his new recent research topics is behaviour of polypeptides and proteins at the interface between aqueous solution and lipid membranes

Education and degrees:
2008 PhD, with honours, Physics Department, University of Warsaw, Poland
2003 MSc, summa cum laude, Physics Department, University of Warsaw, Poland
2001 MD, Medical University of Warsaw, Poland

Positions:
2017 – group leader at CeNT
2013 – 2017 independent researcher, CeNT
2009 -2013 postdoctoral researcher, Physics Department, Technical University of Munich, Germany (the group of Prof. Martin Zacharias)
2009 visiting scholar, Department of Chemistry and Biochemistry and Center for Theoretical Biological Physics, University of California, San Diego, USA (the group of Prof. J. Andrew McCammon)

Selected publications:
• Piotr Setny, Marta D. Wiśniewska, Water-mediated conformational preselection mechanism in substrate binding cooperativity to protein kinase A, PNAS, 115:3852, 2018
• Piotr Setny, Anita Dudek, Explicit Solvent Hydration Benchmark for Proteins With Application to the PBSA Method, JCTC, 13:2762, 201
• Remigiusz Worch, Joanna Krupa, Alicja Filipek, Anna Szymaniec, Piotr Setny,
• Three conserved C-terminal residues of influenza fusion peptide alter its behavior at the membrane interface, BBA-GEN Subjects, 2:97, 2017
• Piotr Setny, Prediction of water binding to protein hydration sites with discrete, semi-explicit solvent model, JCTC, 11:5961, 2015
• Piotr Setny, Hydration in Discrete Water (II): From Neutral to Charged Solutes, J. Phys Chem. B, 119:5970, 2015
• Piotr Setny, and M. Zacharias, Elastic network models of nucleic acids flexibility, JCTC, 9:5460, 2013
• Piotr Setny, Peter Kekenes-Huskey, Riccardo Baron, J. Andrew McCammon, and Joachim Dzubiella, Solvent fluctuations in hydrophobic cavity-ligand binding kinetics, Proc. Natl. Acad. Sci. U.S.A., 110:1194, 2013
• Piotr Setny and Martin Zacharias, A coarse-grained force field for Protein-RNA docking, Nucleic Acids Res., 39: 9118, 2011
• Riccardo Baron, Piotr Setny, and J. Andrew McCammon, Water in Cavity-Ligand Recognition, J. Am. Chem. Soc., 132: 12091, 2010


Water-mediated conformational preselection mechanism in substrate binding cooperativity to protein kinase A
Setny, P., & Wiśniewska, M. D. (2018).
Proceedings of the National Academy of Sciences, 115(15), 3852-3857.
Charged N-terminus of Influenza Fusion Peptide Facilitates Membrane Fusion
Worch, R., Dudek, A., Krupa, J., Szymaniec, A., & Setny, P. (2018).
International journal of molecular sciences, 19(2), 578
Affinity, kinetics, and pathways of anisotropic ligands binding to hydrophobic model pockets
Weiß, R. G., Chudoba, R., Setny, P., & Dzubiella, J.
The Journal of Chemical Physics, 149(9)
Three conserved C-terminal residues of influenza fusion peptide alter its behavior at the membrane interface.
Worch, R., Krupa, J., Filipek, A., Szymaniec, A., & Setny, P. (2017).
Biochimica et Biophysica Acta (BBA)-General Subjects, 1861(2), 97-105.
Explicit Solvent Hydration Benchmark for Proteins with Application to the PBSA Method.
Setny, P., & Dudek, A. (2017).
Journal of chemical theory and computation, 13(6), 2762-2776.
Principles for Tuning Hydrophobic Ligand–Receptor Binding Kinetics.
Weiß, R. G., Setny, P., & Dzubiella, J. (2017).
Journal of chemical theory and computation, 13(6), 3012-3019.
Computational study on donor–acceptor optical markers for Alzheimer’s disease: a game of charge transfer and electron delocalization
Peccati, F., Wiśniewska, M., Solans-Monfort, X., & Sodupe, M. (2016).
Physical Chemistry Chemical Physics, 18(17), 11634-11643.
Structural and energetic comparison of the complexes of aminoglycosides with the model of the ribosomal A-site
Kulik, M., & Trylska, J. (2016).
RAIRO-Operations Research, 50(2), 375-386.
Solvent Fluctuations Induce Non-Markovian Kinetics in Hydrophobic Pocket-Ligand Binding
Weiß, R. G., Setny, P., & Dzubiella, J. (2016).
The Journal of Physical Chemistry B, 120(33), 8127-8136.
Hydration in Discrete Water (II): From Neutral to Charged Solutes.
Setny, P. (2015).
The Journal of Physical Chemistry B, 119(19), 5970-5978.
Hydratation in Discrete Water (II): From neutral to charged solutes
Setny, P. (2015)
The Journal of Physical Chemistry B, 119(19), 5970-5978.
Elastic network models of nucleic acids flexibility.
Setny, P., & Zacharias, M. (2013).
Journal of chemical theory and computation, 9(12), 5460-5470.
Tytuł Termin nadsyłania aplikacji
PhD Student in Biomolecular Modellig Group 15/05/2019