title: Reduced native state stability in crowded cellular environment due to protein-protein interactions.
abstract: The effect of cellular crowding environments on protein structure and stability is a key issue in molecular and cellular biology. The classical view of crowding emphasizes the volume exclusion effect that generally favors compact, native states. Here, results from molecular dynamics simulations and NMR experiments show that protein crowders may destabilize native states via protein-protein interactions. In the model system considered here, mixtures of villin head piece and protein G at high concentrations, villin structures become increasingly destabilized upon increasing crowder concentrations. The denatured states observed in the simulation involve partial unfolding as well as more subtle conformational shifts. The unfolded states remain overall compact and only partially overlap with unfolded ensembles at high temperature and in the presence of urea. NMR measurements on the same systems confirm structural changes upon crowding based on changes of chemical shifts relative to dilute conditions. An analysis of protein-protein interactions and energetic aspects suggests the importance of enthalpic and solvation contributions to the crowding free energies that challenge an entropic-centered view of crowding effects.
authors: RIKEN Advanced Institute for Computational Science, 7-1-26 minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047 Japan.
authors: Ryuhei
authors: R
authors: Harada
authors: Naoya
authors: N
authors: Tochio
authors: Takanori
authors: T
authors: Kigawa
authors: Yuji
authors: Y
authors: Sugita
authors: Michael
authors: M
authors: Feig
mesh_terms: D000818:Animals; D001426:Bacterial Proteins / Q000737:chemistry*; D002645:Chickens; D008840:Microfilament Proteins / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D019906:Nuclear Magnetic Resonance, Biomolecular; D010084:Oxidation-Reduction; D011485:Protein Binding
chemical_list: D001426:Bacterial Proteins; C034284:IgG Fc-binding protein, Streptococcus; D008840:Microfilament Proteins; C026615:villin
references: Biophys J. 2000 Jan;78(1):101-9
references: 10620277
references: J Biomol NMR. 2007 Mar;37(3):225-9
references: 17237976
references: J Cell Sci. 2006 Jul 15;119(Pt 14):2863-9
references: 16825427
references: J Chem Theory Comput. 2012 Jan 10;8(1):290-9
references: 26592890
references: Proc Natl Acad Sci U S A. 2005 May 24;102(21):7517-22
references: 15894611
references: J Am Chem Soc. 2012 Oct 10;134(40):16614-8
references: 22954326
references: Biophys J. 2010 Sep 8;99(5):1637-44
references: 20816077
references: J Am Chem Soc. 2012 Mar 14;134(10):4842-9
references: 22352398
references: Nature. 2009 Mar 5;458(7234):106-9
references: 19262675
references: Annu Rev Biophys. 2008;37:247-63
references: 18573081
references: Trends Biochem Sci. 1991 Jun;16(6):203-6
references: 1891800
references: J Mol Recognit. 2004 Sep-Oct;17(5):368-75
references: 15362094
references: J Am Chem Soc. 2010 Aug 4;132(30):10445-52
references: 20662522
references: J Am Chem Soc. 2011 Jun 1;133(21):8082-5
references: 21534566
references: Biochemistry. 1992 Apr 14;31(14):3597-603
references: 1567818
references: Annu Rev Biophys. 2008;37:375-97
references: 18573087
references: FEBS Lett. 2005 Mar 21;579(8):1783-8
references: 15763552
references: Proc Natl Acad Sci U S A. 2005 Nov 15;102(46):16662-7
references: 16269546
references: J Am Chem Soc. 2003 May 21;125(20):6032-3
references: 12785814
references: J Mol Graph. 1996 Feb;14(1):33-8, 27-8
references: 8744570
references: J Comput Chem. 2004 Aug;25(11):1400-15
references: 15185334
references: Biophys J. 2009 Jul 8;97(1):12-9
references: 19580740
references: Science. 1991 Aug 9;253(5020):657-61
references: 1871600
references: J Phys Chem B. 2012 Jan 12;116(1):599-605
references: 22117862
references: J Struct Funct Genomics. 2007 Dec;8(4):173-91
references: 18167031
references: J Am Chem Soc. 2011 May 11;133(18):7116-20
references: 21506571
references: J Phys Chem B. 2005 Aug 11;109(31):15080-6
references: 16852908
references: Curr Opin Struct Biol. 2010 Apr;20(2):196-206
references: 20167475
references: Arch Biochem Biophys. 2008 Jan 1;469(1):76-82
references: 17719556
references: J Phys Chem B. 1998 Apr 30;102(18):3586-616
references: 24889800
references: Nature. 2003 Sep 4;425(6953):27-8
references: 12955122
references: J Mol Graph Model. 2004 May;22(5):377-95
references: 15099834
references: Annu Rev Biophys Biomol Struct. 1993;22:27-65
references: 7688609
references: Biophys J. 2008 May 15;94(10):3748-59
references: 18234819
references: Biochemistry. 1995 Nov 21;34(46):15291-300
references: 7578145