Protein folding in the cell: challenges and progress

Current Opinion in Structural Biology - Tập 21 Số 1 - Trang 32-41 - 2011
Anne Gershenson1, Lila M. Gierasch1,2
1Department of Biochemistry & Molecular Biology, University of Massachusetts, Amherst, MA, 01003, USA
2Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003, USA

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Zhou, 2008, Macromolecular crowding and confinement: biochemical, biophysical, and potential physiological consequences, Annu Rev Biophys, 37, 375, 10.1146/annurev.biophys.37.032807.125817

Elcock, 2010, Models of macromolecular crowding effects and the need for quantitative comparisons with experiment, Curr Opin Struct Biol, 20, 196, 10.1016/j.sbi.2010.01.008

Tsao, 2010, Macromolecular crowding induces polypeptide compaction and decreases folding cooperativity, Phys Chem Chem Phys, 12, 3491, 10.1039/b924236h

Hong, 2010, Macromolecular crowding remodels the energy landscape of a protein by favoring a more compact unfolded state, J Am Chem Soc, 132, 10445, 10.1021/ja103166y

Wang, 2010, Effect of Ficoll 70 on thermal stability and structure of creatine kinase, Biochemistry, 75, 648

Qin, 2009, Atomistic modeling of macromolecular crowding predicts modest increases in protein folding and binding stability, Biophys J, 97, 12, 10.1016/j.bpj.2009.03.066

Christiansen, 2010, Factors defining effects of macromolecular crowding on protein stability: an in vitro/in silico case study using cytochrome c, Biochemistry, 49, 6519, 10.1021/bi100578x

McGuffee, 2010, Diffusion, crowding & protein stability in a dynamic molecular model of the bacterial cytoplasm, PLoS Comput Biol, 6, e1000694, 10.1371/journal.pcbi.1000694

Hagen, 2010, Solvent viscosity and friction in protein folding dynamics, Curr Protein Pept Sci, 11, 385, 10.2174/138920310791330596

Dhar, 2010, Structure, function, and folding of phosphoglycerate kinase are strongly perturbed by macromolecular crowding, Proc Natl Acad Sci U S A, 107, 17586, 10.1073/pnas.1006760107

Nenninger, 2010, Size dependence of protein diffusion in the cytoplasm of Escherichia coli, J Bacteriol, 192, 4535, 10.1128/JB.00284-10

Kumar, 2010, Mobility of cytoplasmic, membrane, and DNA-binding proteins in Escherichia coli, Biophys J, 98, 552, 10.1016/j.bpj.2009.11.002

Li, 2009, Translational and rotational diffusion of a small globular protein under crowded conditions, J Phys Chem B, 113, 13390, 10.1021/jp907744m

Wang, 2010, Effects of proteins on protein diffusion, J Am Chem Soc, 132, 9392, 10.1021/ja102296k

Ando, 2010, Crowding and hydrodynamic interactions likely dominate in vivo macromolecular motion, Proc Natl Acad Sci U S A, 107, 18457, 10.1073/pnas.1011354107

Kramer, 2009, The ribosome as a platform for co-translational processing, folding and targeting of newly synthesized proteins, Nat Struct Mol Biol, 16, 589, 10.1038/nsmb.1614

Cabrita, 2010, Protein folding on the ribosome, Curr Opin Struct Biol, 20, 33, 10.1016/j.sbi.2010.01.005

Weinreis, 2010, Dynamic fluorescence depolarization: a powerful tool to explore protein folding on the ribosome, Methods, 52, 57, 10.1016/j.ymeth.2010.06.001

Zhang, 2011, Folding at the birth of the nascent chain: coordinating translation with co-translational folding, Curr Opin Struct Biol, 21, 25, 10.1016/j.sbi.2010.10.008

Eichmann, 2010, Cotranslational structure acquisition of nascent polypeptides monitored by NMR spectroscopy, Proc Natl Acad Sci U S A, 107, 9111, 10.1073/pnas.0914300107

Ugrinov, 2010, Cotranslational folding increases GFP folding yield, Biophys J, 98, 1312, 10.1016/j.bpj.2009.12.4291

Czech, 2010, Silent mutations in sight: co-variations in tRNA abundance as a key to unravel consequences of silent mutations, Mol BioSyst, 6, 1767, 10.1039/c004796c

Fredrick, 2010, How the sequence of a gene can tune its translation, Cell, 141, 227, 10.1016/j.cell.2010.03.033

Komar, 2009, A pause for thought along the co-translational folding pathway, Trends Biochem Sci, 34, 16, 10.1016/j.tibs.2008.10.002

Wilke, 2010, Signatures of protein biophysics in coding sequence evolution, Curr Opin Struct Biol, 20, 385, 10.1016/j.sbi.2010.03.004

Siller, 2010, Slowing bacterial translation speed enhances eukaryotic protein folding efficiency, J Mol Biol, 396, 1310, 10.1016/j.jmb.2009.12.042

Clarke, 2010, Increased incidence of rare codon clusters at 5′ and 3′ gene termini: implications for function, BMC Genomics, 11, 118, 10.1186/1471-2164-11-118

Tuller, 2010, An evolutionarily conserved mechanism for controlling the efficiency of protein translation, Cell, 141, 344, 10.1016/j.cell.2010.03.031

Tuller, 2010, Translation efficiency is determined by both codon bias and folding energy, Proc Natl Acad Sci U S A, 107, 3645, 10.1073/pnas.0909910107

Kudla, 2009, Coding-sequence determinants of gene expression in Escherichia coli, Science, 324, 255, 10.1126/science.1170160

Zhang, 2009, Transient ribosomal attenuation coordinates protein synthesis and co-translational folding, Nat Struct Mol Biol, 16, 274, 10.1038/nsmb.1554

Bartoszewski, 2010, A synonymous single nucleotide polymorphism in ΔF508 CFTR alters the secondary structure of the mRNA and the expression of the mutant protein, J Biol Chem, 285, 28741, 10.1074/jbc.M110.154575

Hunt, 2009, Silent (synonymous) SNPs: should we care about them?, Methods Mol Biol, 578, 23, 10.1007/978-1-60327-411-1_2

Skach, 2009, Cellular mechanisms of membrane protein folding, Nat Struct Mol Biol, 16, 606, 10.1038/nsmb.1600

Nakatogawa, 2002, The ribosomal exit tunnel functions as a discriminating gate, Cell, 108, 629, 10.1016/S0092-8674(02)00649-9

Bhushan, 2010, Structural basis for translational stalling by human cytomegalovirus and fungal arginine attenuator peptide, Mol Cell, 40, 138, 10.1016/j.molcel.2010.09.009

Seidelt, 2009, Structural insight into nascent polypeptide chain-mediated translational stalling, Science, 326, 1412, 10.1126/science.1177662

Peterson, 2010, The conformation of a nascent polypeptide inside the ribosome tunnel affects protein targeting and protein folding, Mol Microbiol, 78, 203, 10.1111/j.1365-2958.2010.07325.x

Kosolapov, 2009, Tertiary interactions within the ribosomal exit tunnel, Nat Struct Mol Biol, 16, 405, 10.1038/nsmb.1571

Tu, 2010, A folding zone in the ribosomal exit tunnel for Kv1.3 helix formation, J Mol Biol, 396, 1346, 10.1016/j.jmb.2009.12.059

Daniel, 2008, Control of translocation through the Sec61 translocon by nascent polypeptide structure within the ribosome, J Biol Chem, 283, 20864, 10.1074/jbc.M803517200

Fujiwara, 2010, A systematic survey of in vivo obligate chaperonin-dependent substrates, EMBO J, 29, 1552, 10.1038/emboj.2010.52

McClellan, 2007, Diverse cellular functions of the Hsp90 molecular chaperone uncovered using systems approaches, Cell, 131, 121, 10.1016/j.cell.2007.07.036

Apetri, 2008, Chaperonin chamber accelerates protein folding through passive action of preventing aggregation, Proc Natl Acad Sci U S A, 105, 17351, 10.1073/pnas.0809794105

Horwich, 2009, Chaperonin-mediated protein folding: using a central cavity to kinetically assist polypeptide chain folding, Q Rev Biophys, 42, 83, 10.1017/S0033583509004764

Lin, 2008, GroEL stimulates protein folding through forced unfolding, Nat Struct Mol Biol, 15, 303, 10.1038/nsmb.1394

Sharma, 2008, Monitoring protein conformation along the pathway of chaperonin-assisted folding, Cell, 133, 142, 10.1016/j.cell.2008.01.048

Elad, 2007, Topologies of a substrate protein bound to the chaperonin GroEL, Mol Cell, 26, 415, 10.1016/j.molcel.2007.04.004

Clare, 2009, Chaperonin complex with a newly folded protein encapsulated in the folding chamber, Nature, 457, 107, 10.1038/nature07479

Chakraborty, 2010, Chaperonin-catalyzed rescue of kinetically trapped states in protein folding, Cell, 142, 112, 10.1016/j.cell.2010.05.027

Hofmann, 2010, Single-molecule spectroscopy of protein folding in a chaperonin cage, Proc Natl Acad Sci U S A, 107, 11793, 10.1073/pnas.1002356107

Natale, 2008, Sec- and Tat-mediated protein secretion across the bacterial cytoplasmic membrane—distinct translocases and mechanisms, Biochim Biophys Acta, 1778, 1735, 10.1016/j.bbamem.2007.07.015

Junker, 2009, Vectorial transport and folding of an autotransporter virulence protein during outer membrane secretion, Mol Microbiol, 71, 1323, 10.1111/j.1365-2958.2009.06607.x

Peterson, 2010, Secretion of a bacterial virulence factor is driven by the folding of a C-terminal segment, Proc Natl Acad Sci U S A, 107, 17739, 10.1073/pnas.1009491107

Hebert, 2007, In and out of the ER: protein folding, quality control, degradation, and related human diseases, Physiol Rev, 87, 1377, 10.1152/physrev.00050.2006

Riemer, 2009, Disulfide formation in the ER and mitochondria: two solutions to a common process, Science, 324, 1284, 10.1126/science.1170653

Sideris, 2010, Oxidative protein folding in the mitochondrial intermembrane space, Antioxid Redox Signal, 13, 1189, 10.1089/ars.2010.3157

Inaba, 2009, Disulfide bond formation system in Escherichia coli, J Biochem, 146, 591, 10.1093/jb/mvp102

Kadokura, 2010, Mechanisms of oxidative protein folding in the bacterial cell envelope, Antioxid Redox Signal, 13, 1231, 10.1089/ars.2010.3187

Kadokura, 2009, Detecting folding intermediates of a protein as it passes through the bacterial translocation channel, Cell, 138, 1164, 10.1016/j.cell.2009.07.030

Tapley, 2010, Protein refolding by pH-triggered chaperone binding and release, Proc Natl Acad Sci U S A, 107, 1071, 10.1073/pnas.0911610107

Wang, 2008, The cotranslational maturation program for the type II membrane glycoprotein influenza neuraminidase, J Biol Chem, 283, 33826, 10.1074/jbc.M806897200

Feige, 2009, An unfolded CH1 domain controls the assembly and secretion of IgG antibodies, Mol Cell, 34, 569, 10.1016/j.molcel.2009.04.028

Feige, 2010, How antibodies fold, Trends Biochem Sci, 35, 189, 10.1016/j.tibs.2009.11.005

Ghaemmaghami, 2001, Quantitative protein stability measurement in vivo, Nat Struct Biol, 8, 879, 10.1038/nsb1001-879

Ignatova, 2004, Monitoring protein stability and aggregation in vivo by real-time fluorescent labeling, Proc Natl Acad Sci U S A, 101, 523, 10.1073/pnas.0304533101

Ignatova, 2007, From the test tube to the cell: exploring the folding and aggregation of a β-clam protein, Biopolymers, 88, 157, 10.1002/bip.20665

Ebbinghaus, 2010, Protein folding stability and dynamics imaged in a living cell, Nat Methods, 7, 319, 10.1038/nmeth.1435

Philipps, 2003, FRET-based in vivo screening for protein folding and increased protein stability, J Mol Biol, 327, 239, 10.1016/S0022-2836(03)00077-9

Pielak, 2009, Protein nuclear magnetic resonance under physiological conditions, Biochemistry, 48, 226, 10.1021/bi8018948

Ito, 2010, Cellular structural biology, Curr Opin Struct Biol, 20, 640, 10.1016/j.sbi.2010.07.006

Inomata, 2009, High-resolution multi-dimensional NMR spectroscopy of proteins in human cells, Nature, 458, 106, 10.1038/nature07839

Stidham, 2003, Assessment of protein folding/solubility in live cells, Methods Mol Biol, 205, 155

Cabantous, 2008, New molecular reporters for rapid protein folding assays, PLoS ONE, 3, e2387, 10.1371/journal.pone.0002387

Foit, 2009, Optimizing protein stability in vivo, Mol Cell, 36, 861, 10.1016/j.molcel.2009.11.022

Mansell, 2010, A rapid protein folding assay for the bacterial periplasm, Protein Sci, 19, 1079, 10.1002/pro.388

Lyngsø, 2010, A versatile selection system for folding competent proteins using genetic complementation in a eukaryotic host, Protein Sci, 19, 579, 10.1002/pro.337

Barakat, 2007, Exploiting elements of transcriptional machinery to enhance protein stability, J Mol Biol, 366, 103, 10.1016/j.jmb.2006.10.091

Barakat, 2010, Combined use of experimental and computational screens to characterize protein stability, Protein Eng Des Sel, 23, 799, 10.1093/protein/gzq052

Powers, 2009, Biological and chemical approaches to diseases of proteostasis deficiency, Annu Rev Biochem, 78, 959, 10.1146/annurev.biochem.052308.114844

Tokuriki, 2009, Stability effects of mutations and protein evolvability, Curr Opin Struct Biol, 19, 596, 10.1016/j.sbi.2009.08.003

Zeldovich, 2008, Understanding protein evolution: from protein physics to Darwinian selection, Annu Rev Phys Chem, 59, 105, 10.1146/annurev.physchem.58.032806.104449

Bogumil, 2010, Chaperonin-dependent accelerated substitution rates in prokaryotes, Genome Biol Evol, 2, 602, 10.1093/gbe/evq044

Williams, 2010, The effect of chaperonin buffering on protein evolution, Genome Biol Evol, 2, 609, 10.1093/gbe/evq045

Counago, 2008, An adaptive mutation in adenylate kinase that increases organismal fitness is linked to stability–activity trade-offs, Protein Eng Des Sel, 21, 19, 10.1093/protein/gzm072

Peña, 2010, Evolutionary fates within a microbial population highlight an essential role for protein folding during natural selection, Mol Syst Biol, 6, 387, 10.1038/msb.2010.43

Vendruscolo, 2008, Towards quantitative predictions in cell biology using chemical properties of proteins, Mol Biosyst, 4, 1170, 10.1039/b805710a

Tartaglia, 2010, Proteome-level relationship between folding and aggregation propensities of proteins, J Mol Biol, 402, 919, 10.1016/j.jmb.2010.08.013

Mayer, 2007, Correlation of levels of folded recombinant p53 in Escherichia coli with thermodynamic stability in vitro, J Mol Biol, 372, 268, 10.1016/j.jmb.2007.06.044