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

Treść / Zawartość
Identyfikatory
Warianty tytułu
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.
Rocznik
Strony
219--229
Opis fizyczny
Bibliogr. 37 poz., rys.
Twórcy
autor
  • Laboratory of Theory of Biopolymers, Faculty of Chemistry University of Warsaw Pasteura 1, 02-093 Warsaw, Poland
autor
  • Laboratory of Theory of Biopolymers, Faculty of Chemistry University of Warsaw Pasteura 1, 02-093 Warsaw, Poland
autor
  • Laboratory of Theory of Biopolymers, Faculty of Chemistry University of Warsaw Pasteura 1, 02-093 Warsaw, Poland
  • Laboratory of Theory of Biopolymers, Faculty of Chemistry University of Warsaw Pasteura 1, 02-093 Warsaw, Poland
autor
  • Laboratory of Theory of Biopolymers, Faculty of Chemistry University of Warsaw Pasteura 1, 02-093 Warsaw, Poland
  • 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
Typ dokumentu
Bibliografia
Identyfikator YADDA
bwmeta1.element.baztech-e538c553-5e8d-4c3c-a4d2-f45fd6062e83
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