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http://yadda.icm.edu.pl:80/baztech/element/bwmeta1.element.baztech-0eff2b7b-03b3-43df-bb12-02655e972e7e

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TASK Quarterly : scientific bulletin of Academic Computer Centre in Gdansk

Tytuł artykułu

Determining critical amino acid contacts for knotted protein folding

Autorzy Dąbrowski-Tumański, P.  Niewieczerzał, S.  Sułkowska, J. I. 
Treść / Zawartość http://task.gda.pl/quart/index.html
Warianty tytułu
Języki publikacji EN
Abstrakty
EN Proteins with a non-trivial topological structure are currently well recognized, while a knotted protein chain represents a new motif in protein three dimensional folds. Recent comprehensive analysis of the Protein Data Base shows that knotted proteins represent 1.5% of known protein structures. Determination of a free energy landscape of knotted proteins, and its understanding provides a serious challenge for both experimentalists and theoreticians. Moreover the role of a knot for biological activity of protein still remains elusive. In this work we study the smallest knotted proteins ( PDB code 2efv) to understand/investigate their free energy landscape, by means of extensive molecular dynamics simulations. We explore the dependence of the thermodynamics, kinetics and protein folding pathways on the native-likes contact maps and on the length of the chain. We analyze two sets of native-like contacts , which differ by a number of long range interactions, and we consider the 2efv protein with two different lengths of its C-terminus end. We identify the subset of native contacts sufficient to explore the entire free energy landscape. Then, we analyze the influence of the remaining set of native contacts – we show that the set of additional contacts may enhance folding kinetics, and that it has an influence on folding pathways.
Słowa kluczowe
PL wiązanie białek   slipknot   2efv   mapa kontaktowa  
EN knotted protein   slipknot   2efv folding   contact map   native   non-native  
Wydawca Centrum Informatyczne Trójmiejskiej Akademickiej Sieci Komputerowej
Czasopismo TASK Quarterly : scientific bulletin of Academic Computer Centre in Gdansk
Rocznik 2014
Tom Vol. 18, No 3
Strony 265--279
Opis fizyczny Bibliogr. 38 poz., rys., tab., wykr.
Twórcy
autor Dąbrowski-Tumański, P.
  • Departament of Chemistry, University of Warsaw Pasteura 1, 02-093 Warsaw, Poland
  • Centre of New Technologies, University of Warsaw Banacha 2c, 02-097 Warsaw, Poland
autor Niewieczerzał, S.
  • Departament of Chemistry, University of Warsaw Pasteura 1, 02-093 Warsaw, Poland
autor Sułkowska, J. I.
  • Departament of Chemistry, University of Warsaw Pasteura 1, 02-093 Warsaw, Poland
Bibliografia
[1] Taylor W R 2000 Nature 406 (6798) 916
[2] Takusagawa F and Kamitori S 1996 Journal of the American Chemical Society 118 (37) 8945
[3] B ̈olinger D, Sułkowska J I, Hsu H-P, Mirny L A, Kardar M, Onuchic J N and Virnau P 2010 PLoS computational biology 6 (4) , e1000731
[4] Sułkowska J I, Rawdon E J, Millett K C, Onuchic J N and Stasiak A 2012 Proceedings of the National Academy of Sciences 109 (26) , E1715
[5] Jamroz M, Niemyska W, Rawdon E J, Stasiak A, Millett K C, Sułkowski P and Sułkowska J I 2014 Nucleic Acids Research , gku1059
[6] Mallam A L, Rogers J M and Jackson S E 2010 Proceedings of the National Academy of Sciences 107 (18) 8189
[7] Mallam A L and Jackson S E 2012 Nature chemical biology 8 (2) 147
[8] Andrews B T, Capraro D T, Sułkowska J I, Onuchic J N and Jennings P A 2012 The journal of physical chemistry letters 4 (1) 180
[9] Chavez L L, Onuchic J N and Clementi C 2004 Journal of the American Chemical Society 126 (27) 8426
[10] Ferguson N, Capaldi A P, James R, Kleanthous C and Radford S E 1999 Journal of molecular biology 286 (5) 1597
[11] Wensley B G, Batey S, Bone F A, Chan Z M, Tumelty N R, Steward A, Kwa L G, Borgia A and Clarke J 2010 Nature 463 (7281) 685
[12] Wallin S, Zeldovich K B and Shakhnovich E I 2007 Journal of molecular biology 368 (3) 884
[13] Sułkowska J I, Sułkowski P and Onuchic J N 2009 Proceedings of the National Academy of Sciences 106 (9) 3119
[14] Sułkowska J I, Noel J K and Onuchic J N 2012 Proceedings of the National Academy of Sciences 109 (44) 17783
[15] Li W, Terakawa T, Wang W and Takada S 2012 Proceedings of the National Academy of Sciences 109 (44) 17789
[16] Noel J K, Sułkowska J I and Onuchic J N 2010 Proceedings of the National Academy of Sciences 107 (35) 15403
[17] Noel J K, Onuchic J N and Sulkowska J I 2013 The Journal of Physical Chemistry Letters 4 (21) 3570
[18] Beccara S a, Skrbi ́c T, Covino R, Micheletti C and Faccioli P 2013PLoS computational biology 9(3) , e1003002
[19] Skrbi ́c T, Micheletti C and Faccioli P 2012 PLoS computational biology 8 (6) , e1002504
[20] Covino R, Skrbi ́c T, Faccioli P, Micheletti C, et al.2013 Biomolecules 4 (1) 1
[21] Godzik A, Skolnick J and Kolinski A 1993 Bein Engineering 6 ( 8 ) 801
[22] Noel J K, Whitford P C and Onuchic J N 2012 The Journal of Physical Chemistry B 116 ( 29 ) 8692
[23] Tsai J, Taylor R, Chothia C and Gerstein M 1999 Journal of molecular biology 290 (1) 253
[24] Clementi C, Nymeyer H and Onuchic J N 2000 Journal of molecular biology 298 (5) 937
[25] Lammert H, Schug A and Onuchic J N 2009 Proteins: Structure, Function, and Bioinformatics 77 (4) 881
[26] Noel J K, Whitford P C, Sanbonmatsu K Y and Onuchic J N 2010 Nucleic acids research 38 (2) , W657
[27] Cieplak M and Hoang T X 2002 International Journal of Modern Physics C 13( 09 ) 1231
[28] Whitford P C, Noel J K, Gosavi S, Schug A, Sanbonmatsu K Y and Onuchic J N 2009 Proteins: Structure, Function and Bioinformatics 75 (2) 430
[29] Kumar S, Rosenberg J M, Bouzida D, Swendsen R H and Kollman P A 1992 Journal of computational chemistry 13 (8) 1011
[30] Humphrey W, Dalke A and Schulten K 1996 Journal of molecular graphics 14 (1) 33
[31] Koniaris K and Muthukumar M 1991 The Journal of chemical physics 95 (4) 2873
[32] Sułkowska J I, Sułkowski P, Szymczak P and Cieplak M 2008 Physical review letters 100 (5) , 058106
[33] Freyd P, Yetter D, Hoste J, Lickorish W R, Millett K and Ocneanu A 1985 Bulletin of the American Mathematical Society 12 (2) 239
[34] Przytycki J H and Traczyk P 1988 Kobe Journal of Mathematics 4(2) 115
[35] Ewing B and Millett K C 1997 Progress in knot theory and related topics 5651
[36] Tuszynska I and Bujnicki J M 2010 Journal of Biomolecular Structure and Dynamics 27 (4) 511
[37] Rawdon E, Dobay A, Kern J C, Millett K C, Piatek M, Plunkett P and Stasiak A 2008 Macromolecules 41 ( 12 ) 4444
[38] Baker D 2000 Nature 405 (6782) 39
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