Prof. Andrzej Kolinski, University of Warsaw (Chemistry Department)

event date: 10 May 2019

The Centre of New Technologies invites to a seminar by

Prof. Andrzej Koliński

University of Warsaw (Chemistry Department)

Multiscale modeling of proteins and protein complexes

Date: May, 10th(Friday), 2019 at 12 p.m.

Venue: Centre of New Technologies, Banacha 2C,
Lecture Hall 0142 (Ground floor)

Host: Prof. Dariusz Plewczyński



The traditional, based on atomistic Molecular Dynamics, computational modeling of protein structure and dynamics remains difficult for many protein systems. It is mostly due to the size of protein conformational spaces and required simulation timescales. Shrinking the protein representation from all-atom to coarse-grained [1] extends the range of tractable systems. Two levels of coarse-graining and their applicability in the multiscale modeling strategies are discussed. Moderate resolution CABS (C-Alpha, Beta and Side-chain) enables quite efficient modeling of protein structure [2], dynamics [3-4] and protein-peptide molecular docking [5]. The model uses up to four united atoms for representations of main chain units and side chains of amino acid residues. The model of interactions is based on knowledge based statistical potentials and the sampling schemes employ Monte Carlo dynamics. CABS approach significantly speeds-up the modeling process and generates structures of sufficient resolution for realistic all-atom reconstruction. Unfortunately, CABS and related middle-resolution models are still computationally too expensive for the simulations of large  (size and time) systems. For this reason we developed a lower resolution (SURPASS-Single United Residue per Pre-Averaged Secondary Structure fragment) model [6], that still maintains several protein-like structural features thanks to knowledge-based sequence specific multibody interaction. SURPASS enables very fast, although  of low resolution, simulations of large proteins and protein systems [6-7]. Multiscale modeling strategies based on combination of these coarse-grained models are briefly discussed.

[1] S. Kmiecik, D. Gront, M. Kolinski, L. Wieteska, A. Dawid & A. Kolinski, “Coarse-grained protein models and their applications”, Chemical Reviews 116(14) 7898–7936 (2016)

[2] M. Blaszczyk, M. Jamroz, S. Kmiecik & A. Kolinski, “CABS-fold: server for de novo and consensus-based prediction of protein structure” Nucleic Acids Research 41(W1):W406-W411 (2013)

[3] Aleksander Kuriata, Aleksandra Gierut, Tymoteusz Oleniecki, Maciej Ciemny, Andrzej Kolinski, Mateusz Kurcinski, Sebastian Kmiecik, “CABS-flex 2.0: a web server for fast simulations of flexibility of protein structures”, Nucleic Acids Research, 46(W1):W338-W343 (2018)

[4] M. Kurcinski, T. Oleniecki, M. P. Ciemny, A. Kuriata, A. Kolinski & S. Kmiecik, “CABS-flex standalone: a simulations environment  for fast modeling of protein flexibility” Bioinformatics, in press

[5] M. Kurcinski, M. Jamroz, M. Blaszczyk, A. Kolinski & S. Kmiecik, “CABS-dock: web server for flexible docking of peptides to proteins without prior knowledge of the binding site”, Nucleic Acids Research 43(W1): W419-W424 (2015)

[6] A. E. Dawid, D. Gront & A. Kolinski, “SURPASS low–resolution coarse–grained protein modeling”, J. Chem. Theory Comp. 13(11):5766–5779 (2017)

[7] A. E. Dawid, D. Gront & A. Kolinski,  “Coarse-grained modeling of the interplay between secondary structure propensities and protein fold assembly”, J. Chem. Theory Comp. 14(4):2277-2278 (2018)