Effects of Confinement in Chaperonin Assisted Protein Folding: Rate Enhancement by Decreasing the Roughness of the Folding Energy Landscape

Journal of Molecular Biology - Tập 332 Số 3 - Trang 701-713 - 2003
Andrij Baumketner1, Andrew I. Jewett1, Joan‐Emma Shea1
1Department of Chemistry & Biochemistry, University of California, Santa Barbara, CA 93106, USA.

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Hartl, 2002, Molecular chaperones in the cytosol: from nascent chain to folded protein, Science, 295, 1852, 10.1126/science.1068408

Saibil, H. R., Horwich, A. L. & Fenton, W. A. (2002). Allostery and protein substrate conformational change during GroEL/GroES-mediated protein folding. In Advances in Protein Chemistry, vol. 59, Academic Press, London.

Xu, 1997, The crystal structure of the asymmetric GroEL/GroES-(ADP)7 chaperonin comples, Nature, 388, 741, 10.1038/41944

Todd, 1994, Dynamics of the chaperonin ATPase cycle: implications for facilitated protein folding, Science, 265, 659, 10.1126/science.7913555

Todd, 1996, Chaperonin-facilitated protein folding: optimization of rate and yield by an iterative annealing mechanism, Proc. Natl Acad. Sci. USA, 93, 4030, 10.1073/pnas.93.9.4030

Lorimer, 1997, Folding with a two-stroke motor, Nature, 388, 720, 10.1038/41892

Shtilerman, 1999, Chaperonin function: folding by forced unfolding, Science, 284, 822, 10.1126/science.284.5415.822

Ellis, 1994, Opening and closing the Anfinsen cage, Curr. Biol., 4, 633, 10.1016/S0960-9822(00)00140-8

Ellis, 2001, Molecular chaperones: inside and outside the Anfinsen cage, Curr. Biol., 11, R1038, 10.1016/S0960-9822(01)00620-0

Brinker, 2001, Dual function of protein confinement in chaperonin-assisted protein folding, Cell, 107, 223, 10.1016/S0092-8674(01)00517-7

Weissman, 1994, GroEL-mediated protein folding proceeds by multiple rounds of binding and release of nonnative forms, Cell, 78, 693, 10.1016/0092-8674(94)90533-9

Gulukota, 1994, Statistical mechanics of kinetic proofreading in protein folding in vivo, Proc. Natl Acad. Sci. USA, 91, 9292, 10.1073/pnas.91.20.9292

Chan, 1996, A simple model of chaperonin-mediated protein folding, Proteins: Struct. Funct. Genet., 24, 345, 10.1002/(SICI)1097-0134(199603)24:3<345::AID-PROT7>3.0.CO;2-F

Sfatos, 1996, Simulations of chaperone-assisted folding, Biochemistry, 35, 334, 10.1021/bi952033a

Betancourt, 1999, Exploring the kinetic requirements for enhancement of protein folding rates in the GroEL cavity, J. Mol. Biol., 287, 627, 10.1006/jmbi.1999.2591

Gorse, 2001, Global minimization of an off-lattice potential energy function using a chaperone-based refolding method, Biopolymers, 59, 411, 10.1002/1097-0282(200111)59:6<411::AID-BIP1046>3.0.CO;2-J

Gorse, 2002, Application of a chaperone-based refolding method to two-and threedimensional off-lattice protein models, Biopolymers, 64, 146, 10.1002/bip.10148

Minton, 2001, The influence of macromolecular crowding and macromolecular confinement on biochemical reactions in physiological media, J. Biol. Chem., 276, 10577, 10.1074/jbc.R100005200

Goloubinoff, 1989, Reconstitution of active dimeric ribulose bisphosphate carboxylase from an unfolded state depends on two chaperonin proteins and Mg-ATP, Nature, 342, 884, 10.1038/342884a0

Nawrocki, 1999, Intermolecular aggregations are responsible for the slow kinetics observed in the folding of Cytochrome c at neutral pH, J. Mol. Biol., 293, 991, 10.1006/jmbi.1999.3226

Silow, 1997, Transient aggregates in protein folding are easily mistaken for folding intermediates, Proc. Natl Acad. Sci. USA, 94, 6084, 10.1073/pnas.94.12.6084

Stan, 2003, Annealing function of GroEL: structural and bioinformatic analysis, Biophys. Chem., 100, 453, 10.1016/S0301-4622(02)00298-3

Honeycutt, 1992, The nature of folded states of globular proteins, Biopolymers, 32, 695, 10.1002/bip.360320610

Guo, 1997, Thermodynamics of protein folding: a statistical mechanical study of a small all-β protein, Biopolymers, 42, 745, 10.1002/(SICI)1097-0282(199712)42:7<745::AID-BIP1>3.0.CO;2-T

Zhou, 2001, Stabilization of proteins in confined spaces, Biochemistry, 40, 11289, 10.1021/bi0155504

Socci, 1994, Folding kinetics of proteinlike heteropolymers, J. Chem. Phys., 101, 1519, 10.1063/1.467775

Lee, 2003, First-passage time distribution and non-Markovian diffusion dynamics of protein folding, J. Chem. Phys., 118, 959, 10.1063/1.1527672

Cieplak, 1999, Scaling of folding properties in simple models of proteins, Phys. Rev. Letters, 83, 1684, 10.1103/PhysRevLett.83.1684

Thirumalai, 2001, Chaperonin-mediated protein folding, Annu. Rev. Biophys. Biomol. Struct., 30, 245, 10.1146/annurev.biophys.30.1.245

Bryngelson, 1989, Intermediates and barrier crossing in a random energy model (with applications to protein folding), J. Phys. Chem, 93, 6902, 10.1021/j100356a007

Onuchic, 1997, Theory of protein folding: the energy landscape perspective, Annu. Rev. Phys. Chem, 48, 545, 10.1146/annurev.physchem.48.1.545

Kilmov, 1996, Criterion that determines the foldability of proteins, Phys. Rev. Letters, 76, 4070, 10.1103/PhysRevLett.76.4070

Veitshans, 1996, Protein folding kinetics: timescales, pathways and energy landscapes in terms of sequence-dependent properties, Fold. Des., 2, 1, 10.1016/S1359-0278(97)00002-3

Klimov, 1998, Linking rates of folding in lattice models of proteins with underlying thermodynamic characteristics, J. Chem. Phys., 109, 4119, 10.1063/1.477012

Camacho, 1993, Kinetics and thermodynamics of folding in model protein, Proc. Natl Acad. Sci. USA, 90, 6369, 10.1073/pnas.90.13.6369

Shea, 1998, Exploring the space of protein folding Hamiltonians: the balance of forces in a minimalist β-barrel model, J. Chem. Phys., 109, 2895, 10.1063/1.476842

Nymeyer, 1998, Folding funnels and frustration in off-lattice minimalist protein landscapes, Proc. Natl Acad. Sci. USA, 95, 5921, 10.1073/pnas.95.11.5921

Shea, 2000, Energetic frustration and the nature of the transition state in protein folding, J. Chem. Phys, 113, 7663, 10.1063/1.1313792

Cheung, 2002, Protein folding mediated by solvation: water expulsion and formation of the hydrophobic core occur after the structural collapse, Proc. Natl Acad. Sci. USA, 99, 685, 10.1073/pnas.022387699

Shea, 1999, Exploring the origins of topological frustration: design of a minimally frustrated model of fragment b of protein a, Proc. Natl Acad. Sci. USA, 96, 12512, 10.1073/pnas.96.22.12512

Klimov, 2002, Simulations of β-hairpin folding confined to spherical pores using distributed computing, Proc. Natl Acad. Sci. USA, 99, 8019, 10.1073/pnas.072220699

Chan, 1993, Energy landscapes and the collapse dynamics of homopolymers, J. Chem. Phys., 99, 2116, 10.1063/1.465277

Chan, H. S. (1997). Modelling protein folding by Monte Carlo dynamics: chevron plots, chevron rollover and non-Arrhenius kinetics. In Monte Carlo Approach to Biopolymers and Protein Folding, World Scientific, Singapore.

Thirumalai, 1999, Deciphering the timescales and mechanisms of protein folding using minimal off-lattice models, Curr. Opin. Struct. Biol., 9, 197, 10.1016/S0959-440X(99)80028-1

Creighton, 1992

Friedel, 2003, Effects of confinement and crowding on the thermodynamics and kinetics of folding of an off-lattice beta barrel model, J. Chem. Phys., 118, 8106, 10.1063/1.1564048

Allen, 1986

Klimov, 1997, Viscosity dependence of the folding rates of proteins, Phys. Rev. Letters, 79, 317, 10.1103/PhysRevLett.79.317

Baumketner, 2002, Diffusive dynamics of protein folding studied by molecular dynamics simulations of an off-lattice model, Phys. Rev. ser. E, 66, 011905/1, 10.1103/PhysRevE.66.011905

Ferrenberg, 1989, Optimized Monte Carlo data analysis, Phys. Rev. Letters, 63, 1195, 10.1103/PhysRevLett.63.1195