title: Simulation of chaperonin effect on protein folding: a shift from nucleation-condensation to framework mechanism.
abstract: The iterative annealing mechanism (IAM) of chaperonin-assisted protein folding is explored in a framework of a well-established coarse-grained protein modeling tool, which enables the study of protein dynamics in a time-scale well beyond classical all-atom molecular mechanics. The chaperonin mechanism of action is simulated for two paradigm systems of protein folding, B domain of protein A (BdpA) and B1 domain of protein G (GB1), and compared to chaperonin-free simulations presented here for BdpA and recently published for GB1. The prediction of the BdpA transition state ensemble (TSE) is in perfect agreement with experimental findings. It is shown that periodic distortion of the polypeptide chains by hydrophobic chaperonin interactions can promote rapid folding and leads to a decrease in folding temperature. It is also demonstrated how chaperonin action prevents kinetically trapped conformations and modulates the observed folding mechanisms from nucleation-condensation to a more framework-like.
authors: Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland. sekmi@chem.uw.edu.pl
authors: Sebastian
authors: S
authors: Kmiecik
authors: Andrzej
authors: A
authors: Kolinski
references: Proc Natl Acad Sci U S A. 2003 Nov 11;100(23):13286-91
references: 14595026
references: Curr Opin Cell Biol. 2009 Feb;21(1):97-108
references: 19223165
references: Proc Natl Acad Sci U S A. 2004 May 4;101(18):6837-8
references: 15123824
references: J Am Chem Soc. 2010 Jul 14;132(27):9444-52
references: 20568747
references: Biophys J. 2008 Feb 1;94(3):726-36
references: 17890394
references: Proc Natl Acad Sci U S A. 2006 May 9;103(19):7298-303
references: 16648265
references: Proc Natl Acad Sci U S A. 2000 Jan 4;97(1):133-8
references: 10618383
references: Annu Rev Phys Chem. 2007;58:57-83
references: 17034338
references: Protein Sci. 1997 Jul;6(7):1449-57
references: 9232646
references: Proc Natl Acad Sci U S A. 2007 Jul 24;104(30):12330-5
references: 17636132
references: Nature. 2010 Jan 21;463(7279):379-83
references: 20090755
references: Proteins. 2006 Sep 1;64(4):960-7
references: 16786595
references: Proteins. 2002 May 1;47(2):99-105
references: 11933057
references: Mol Cell. 2007 May 11;26(3):415-26
references: 17499047
references: Proc Natl Acad Sci U S A. 1996 Apr 30;93(9):4030-5
references: 8633011
references: Proc Natl Acad Sci U S A. 2004 May 4;101(18):6952-6
references: 15069202
references: Proc Natl Acad Sci U S A. 2002 Apr 16;99(8):5343-8
references: 11943859
references: Proc Natl Acad Sci U S A. 2005 Sep 6;102(36):12748-53
references: 16116078
references: Proteins. 2009 May 1;75(2):430-41
references: 18837035
references: Proc Natl Acad Sci U S A. 2003 Nov 25;100(24):13898-903
references: 14623983
references: J Am Chem Soc. 2003 Dec 3;125(48):14841-6
references: 14640661
references: Proc Natl Acad Sci U S A. 1994 Sep 27;91(20):9292-6
references: 7937758
references: J Mol Biol. 2001 Jul 13;310(3):673-85
references: 11439031
references: Comput Appl Biosci. 1997 Jun;13(3):291-5
references: 9183534
references: Fold Des. 1997;2(2):123-33
references: 9135985
references: Phys Biol. 2009 Feb 10;6(1):015003
references: 19208937
references: Cell Mol Life Sci. 2010 Jan;67(2):255-76
references: 19851829
references: Bioinformatics. 2006 Mar 1;22(5):621-2
references: 16407320
references: Bioinformatics. 2008 Feb 15;24(4):584-5
references: 18227118
references: Science. 1995 Jul 21;269(5222):393-6
references: 7618103
references: Nat Struct Mol Biol. 2009 Jun;16(6):574-81
references: 19491934
references: J Mol Biol. 2005 Jul 22;350(4):757-75
references: 15967458
references: Acta Biochim Pol. 2004;51(2):349-71
references: 15218533
references: Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11367-72
references: 12947041
references: Proc Natl Acad Sci U S A. 2002 Aug 6;99(16):10394-8
references: 12140363
references: Cell. 2008 Apr 4;133(1):142-53
references: 18394994
references: J Chem Theory Comput. 2010 Feb 9;6(2):583-595
references: 23620713