Coarse-grained modeling of protein structure, dynamics and protein-protein interactions

• Autorzy: Koliński A. , Kmiecik S. , Jamróz M. , Błaszczyk M. , Kouza M. , Kurciński M.
• Języki publikacji: EN

Abstrakty

EN

Theoretical prediction of protein structures and dynamics is essent ial for understanding the molecular basis of drug action, metabolic and signaling pathway s in living cells, designing new technologies in the life science and material sciences . We developed and validated a novel multiscale methodology for the study of protein folding proces ses including flexible docking of proteins and peptides. The new modeling technique starts fr om coarse-grained large-scale simulations, followed by selection of the most plausible final structu res and intermediates and, finally, by an all-atom rectification of the obtained structures. Except f or the most basic bioinformatics tools, the entire computational methodology is based on the models an d algorithms developed in our lab. The coarse-grained simulations are based on a high-resol ution lattice representation of protein structures, a knowledge based statistical for ce field and efficient Monte Carlo dynamics schemes, including Replica Exchange algorithms. This p aper focuses on the description of the coarse-grained CABS model and its selected applications.

Słowa kluczowe

EN

coarse-grained modeling; protein folding; protein dynamics; molecular docking; protein docking

PL

gruboziarniste modelowanie; dynamika białka; dokowanie molekularne; dokowanie białka

• Wydawca: Politechnika Gdańska
• Czasopismo: TASK Quarterly : scientific bulletin of Academic Computer Centre in Gdansk
• Rocznik: 2014
• Tom: Vol. 18, No 3
• Strony: 219--229
• Opis fizyczny: Bibliogr. 37 poz., rys.

Twórcy

autor

Koliński A.

• Laboratory of Theory of Biopolymers, Faculty of Chemistry University of Warsaw Pasteura 1, 02-093 Warsaw, Poland

autor

Kmiecik S.

• Laboratory of Theory of Biopolymers, Faculty of Chemistry University of Warsaw Pasteura 1, 02-093 Warsaw, Poland

autor

Jamróz M.

• Laboratory of Theory of Biopolymers, Faculty of Chemistry University of Warsaw Pasteura 1, 02-093 Warsaw, Poland

autor

Błaszczyk M.

• Laboratory of Theory of Biopolymers, Faculty of Chemistry University of Warsaw Pasteura 1, 02-093 Warsaw, Poland

autor

Kouza M.

• Laboratory of Theory of Biopolymers, Faculty of Chemistry University of Warsaw Pasteura 1, 02-093 Warsaw, Poland

autor

Kurciński M.

• Laboratory of Theory of Biopolymers, Faculty of Chemistry University of Warsaw Pasteura 1, 02-093 Warsaw, Poland

Bibliografia

• [1] Laskowski R A and Thornton J M 2008 Nat. Rev. Genet. 9 (2) 141
• [2] Wolfson H J et al. 2005 Curr. Protein Pept. Sci. 6 (2) 171
• [3] Latek D, Ekonomiuk D and Kolinski A 2007 J. Comput. Chem. 28 (10) 1668
• [4] Kolinski A and Bujnicki J M 2005 Proteins 61 84
• [5] Bradley P, Misura K M and Baker D 2005 Science 309 (5742) 1868
• [6] Kmiecik S, Gront D and Kolinski A 2007 BMC Struct. Biol. 7 43
• [7] Schueler-Furman O. et al. 2005 Science 310 (5748) 638
• [8] Liwo A, Khalili M and Scheraga H A 2005 Proc. Natl. Acad. Sci. USA 102 (7) 2362
• [9] Oldziej S et al. 2005 Proc. Natl. Acad. Sci. USA 102 (21) 7547
• [10] Sieradzan A K, Liwo A and Hansmann U H 2012 Journal of Chemical Theory and Computation 8 (9) 3416
• [11] Kmiecik S and Kolinski A 2007 Proc. Natl. Acad. Sci. USA 104 (30) 12330
• [12] Kmiecik S and Kolinski A 2008 Biophys. J. 94 (3)726
• [13] Kurcinski M, Kolinski A and Kmiecik S 2014 J. Chem. Theory Comput. 10 (6) 2224
• [14] Lindorff-Larsen K. et al. 2011 Science 334 (6055) 517
• [15] Klepeis J L et al. 2009 Curr. Opin. Struct. Biol. 19 (2) 120
• [16] Kolinski A 2004 Acta Biochim Pol. 51(2) 349
• [17] Kurcinski M and Kolinski A 2007 J. Mol. Model 13 ((6–7)) 691
• [18] Kurcinski M and Kolinski A 2007 J. Steroid Biochem. Mol. Biol. 103 ((3–5)) 357
• [19] Kolinski A, Skolnick J and Yaris R 1986 Proc. Natl. Acad. Sci. USA 83 (19) 7267
• [20] Skolnick J and Kolinski A 1990 Science 250 (4984) 1121
• [21] Skolnick J, Kolinski A and Ortiz A R 1997 J. Mol. Biol. 265 (2) 217
• [22] Kolinski A et al. 2001 Proteins 44 (2)133
• [23] Gront D, Kmiecik S and Kolinski A 2007 J. Comput. Chem. 28 (9) 1593
• [24] Canutescu A A, Shelenkov A A and Dunbrack R L Jr. 2003 Protein Sci. 12 (9) 2001
• [25] Horwacik I et al. 2011 Int. J. Mol. Med. 28 (1) 47
• [26] Steczkiewicz K et al. 2011 Proc. Natl. Acad. Sci. USA 108 (23) 9443
• [27] Ritchie D W 2008 Curr. Protein Pept. Sci. 9 (1) 1
• [28] Bonvin A M 2006 Curr. Opin. Struct. Biol. 16 (2) 194
• [29] Wang C, Bradley P and Baker D 2007 J. Mol. Biol. 373 (2) 503
• [30] Lensink M F and Mendez R 2008 Curr. Pharm. Biotechnol. 9 (2) 77
• [31] Blaszczyk M, et al. 2013 Nucleic Acids Res. 41 , W406 (Web Server issue)
• [32] Jamroz M, Kolinski A and Kmiecik S 2014 Bioinformatics 30 (15) 2150
• [33] Jamroz M, Kolinski A and Kmiecik S 2013 Nucleic Acids Res. 41, W427 (Web Server issue)
• [34] Jamroz M, Kolinski A and Kmiecik S 2014 Methods Mol. Biol. 1137 235
• [35] Gront D and Kolinski A 2008 Bioinformatics 24 (4) 584
• [36] Gront D and Kolinski A 2006 Bioinformatics 22 (5) 621
• [37] Jamroz M and Kolinski A 2013 Bmc Bioinformatics 14 62