Birth, life and death of nascent polypeptide chains
暂无分享,去创建一个
[1] A. Komar,et al. A pause for thought along the co-translational folding pathway. , 2009, Trends in biochemical sciences.
[2] B. D. Davis,et al. Interaction of secreted nascent chains with surrounding membrane in Bacillus subtilis. , 1978, Proceedings of the National Academy of Sciences of the United States of America.
[3] J. Lake,et al. Nascent polypeptide chains emerge from the exit domain of the large ribosomal subunit: immune mapping of the nascent chain. , 1982, Proceedings of the National Academy of Sciences of the United States of America.
[4] A. Brown,et al. The efficiency of folding of some proteins is increased by controlled rates of translation in vivo. A hypothesis. , 1987, Journal of molecular biology.
[5] H. Patzelt,et al. Trigger Factor Peptidyl-prolyl cis/trans Isomerase Activity Is Not Essential for the Folding of Cytosolic Proteins in Escherichia coli* , 2004, Journal of Biological Chemistry.
[6] Jianli Lu,et al. Mapping the electrostatic potential within the ribosomal exit tunnel. , 2007, Journal of molecular biology.
[7] H. Bernstein,et al. The plasticity of a translation arrest motif yields insights into nascent polypeptide recognition inside the ribosome tunnel. , 2009, Molecular cell.
[8] M. Gautschi,et al. The Yeast Nα-Acetyltransferase NatA Is Quantitatively Anchored to the Ribosome and Interacts with Nascent Polypeptides , 2003, Molecular and Cellular Biology.
[9] A. Spirin,et al. Cotranslational Folding of Globin* , 1997, The Journal of Biological Chemistry.
[10] J. Flanagan,et al. Signal Recognition Particle Binds to Ribosome-bound Signal Sequences with Fluorescence-detected Subnanomolar Affinity That Does Not Diminish as the Nascent Chain Lengthens* , 2003, The Journal of Biological Chemistry.
[11] C. Kurland,et al. Growth rate-optimised tRNA abundance and codon usage. , 1997, Journal of molecular biology.
[12] F. Hartl,et al. Identification of Nascent Chain Interaction Sites on Trigger Factor* , 2007, Journal of Biological Chemistry.
[13] Ruth Nussinov,et al. Synonymous mutations and ribosome stalling can lead to altered folding pathways and distinct minima. , 2008, Journal of molecular biology.
[14] William J. Lennarz,et al. Encyclopedia of biological chemistry , 2004 .
[15] C. Yanofsky,et al. Conserved Residues Asp16 and Pro24 of TnaC-tRNAPro Participate in Tryptophan Induction of tna Operon Expression , 2008, Journal of bacteriology.
[16] A Yonath,et al. A tunnel in the large ribosomal subunit revealed by three-dimensional image reconstruction. , 1987, Science.
[17] J. Soppa. Protein Acetylation in Archaea, Bacteria, and Eukaryotes , 2010, Archaea.
[18] M. Paetzel,et al. Signal peptidases. , 2002, Chemical reviews.
[19] M. Gautschi,et al. Nascent-polypeptide-associated complex , 2002, Cellular and Molecular Life Sciences CMLS.
[20] Daniel N. Wilson,et al. Localization of eukaryote-specific ribosomal proteins in a 5.5-Å cryo-EM map of the 80S eukaryotic ribosome , 2010, Proceedings of the National Academy of Sciences.
[21] C. Dobson,et al. Three-dimensional structures of translating ribosomes by Cryo-EM. , 2004, Molecular cell.
[22] N. Ban,et al. A peptide deformylase–ribosome complex reveals mechanism of nascent chain processing , 2008, Nature.
[23] Peter J McCormick,et al. Nascent Membrane and Secretory Proteins Differ in FRET-Detected Folding Far inside the Ribosome and in Their Exposure to Ribosomal Proteins , 2004, Cell.
[24] A. Komar,et al. Activities of Ligatin and MCT-1/DENR in eukaryotic translation initiation and ribosomal recycling. , 2010, Genes & development.
[25] N. Ban,et al. Trigger factor in complex with the ribosome forms a molecular cradle for nascent proteins , 2004, Nature.
[26] A. Rich,et al. Partial resistance of nascent polypeptide chains to proteolytic digestion due to ribosomal shielding. , 1967, Journal of molecular biology.
[27] J. Frydman. Folding of newly translated proteins in vivo: the role of molecular chaperones. , 2001, Annual review of biochemistry.
[28] Y. Pilpel,et al. An Evolutionarily Conserved Mechanism for Controlling the Efficiency of Protein Translation , 2010, Cell.
[29] C. Joazeiro,et al. Role of a ribosome-associated E3 ubiquitin ligase in protein quality control , 2010, Nature.
[30] J. Leeds,et al. Peptide deformylase as an antibacterial target: a critical assessment. , 2006, Current opinion in pharmacology.
[31] Klaus Schulten,et al. Structural Insight into Nascent Polypeptide Chain–Mediated Translational Stalling , 2009, Science.
[32] I. Adzhubei,et al. [Role of the code redundancy in determining cotranslational protein folding]. , 1989, Biokhimiia.
[33] K. Shokat,et al. Human Catechol-O-Methyltransferase Haplotypes Modulate Protein Expression by Altering mRNA Secondary Structure , 2006, Science.
[34] E. Craig,et al. Human Mpp11 J Protein: Ribosome-Tethered Molecular Chaperones Are Ubiquitous , 2005, Science.
[35] C. Deutsch,et al. Secondary structure formation of a transmembrane segment in Kv channels. , 2005, Biochemistry.
[36] L. Brill,et al. The eIF3 interactome reveals the translasome, a supercomplex linking protein synthesis and degradation machineries. , 2009, Molecular cell.
[37] S. Chowdhury,et al. Protein Folding by Domain V of Escherichia coli 23S rRNA: Specificity of RNA-Protein Interactions , 2008, Journal of bacteriology.
[38] G Chelvanayagam,et al. An analysis of the helix‐to‐strand transition between peptides with identical sequence , 2000, Proteins.
[39] Lippincott-Schwartz,et al. Supporting Online Material Materials and Methods Som Text Figs. S1 to S8 Table S1 Movies S1 to S3 a " Silent " Polymorphism in the Mdr1 Gene Changes Substrate Specificity Corrected 30 November 2007; See Last Page , 2022 .
[40] M. Wiedmann,et al. NAC covers ribosome-associated nascent chains thereby forming a protective environment for regions of nascent chains just emerging from the peptidyl transferase center , 1995, The Journal of cell biology.
[41] D C Shields,et al. Codon usage patterns in Escherichia coli, Bacillus subtilis, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Drosophila melanogaster and Homo sapiens; a review of the considerable within-species diversity. , 1988, Nucleic acids research.
[42] S. Sanyal,et al. 23S rRNA assisted folding of cytoplasmic malate dehydrogenase is distinctly different from its self-folding. , 2002, Nucleic acids research.
[43] P. Jenö,et al. The chaperones MPP11 and Hsp70L1 form the mammalian ribosome-associated complex. , 2005, Proceedings of the National Academy of Sciences of the United States of America.
[44] R. Brimacombe,et al. The path of the growing peptide chain through the 23S rRNA in the 50S ribosomal subunit; a comparative cross-linking study with three different peptide families. , 1998, Nucleic acids research.
[45] T. Meinnel,et al. Organellar peptide deformylases: universality of the N-terminal methionine cleavage mechanism. , 2001, Trends in plant science.
[46] T. Meinnel,et al. Protein N-terminal methionine excision , 2004, Cellular and Molecular Life Sciences CMLS.
[47] Joachim Frank,et al. The Ribosome Comes Alive. , 2010, Israel journal of chemistry.
[48] Michele Vendruscolo,et al. Transient tertiary structure formation within the ribosome exit port. , 2010, Journal of the American Chemical Society.
[49] Richard Brimacombe,et al. Mapping the path of the nascent peptide chain through the 23S RNA in the 50S ribosomal subunit , 1995, Nucleic Acids Res..
[50] J. Onuchic,et al. Theory of Protein Folding This Review Comes from a Themed Issue on Folding and Binding Edited Basic Concepts Perfect Funnel Landscapes and Common Features of Folding Mechanisms , 2022 .
[51] C. Oubridge,et al. Recognition of a signal peptide by the signal recognition particle , 2010, Nature.
[52] A. Mankin,et al. Nascent peptide in the "birth canal" of the ribosome. , 2006, Trends in biochemical sciences.
[53] T. Ikemura. Codon usage and tRNA content in unicellular and multicellular organisms. , 1985, Molecular biology and evolution.
[54] E. Angov,et al. Adjustment of codon usage frequencies by codon harmonization improves protein expression and folding. , 2011, Methods in molecular biology.
[55] S. Sanyal,et al. Role of the ribosome in protein folding. , 2008, Biotechnology journal.
[56] B. Bukau,et al. Structure and function of the molecular chaperone Trigger Factor. , 2010, Biochimica et biophysica acta.
[57] B. Matthews,et al. Structure and function of the methionine aminopeptidases. , 2000, Biochimica et biophysica acta.
[58] Kim Sneppen,et al. The functional half-life of an mRNA depends on the ribosome spacing in an early coding region. , 2011, Journal of molecular biology.
[59] T. Steitz,et al. The complete atomic structure of the large ribosomal subunit at 2.4 A resolution. , 2000, Science.
[60] Marco Gartmann,et al. α-Helical nascent polypeptide chains visualized within distinct regions of the ribosomal exit tunnel , 2010, Nature Structural &Molecular Biology.
[61] C. Yanofsky,et al. Instruction of Translating Ribosome by Nascent Peptide , 2002, Science.
[62] Tao Pan,et al. Tissue-Specific Differences in Human Transfer RNA Expression , 2006, PLoS genetics.
[63] C. Deutsch,et al. A folding zone in the ribosomal exit tunnel for Kv1.3 helix formation. , 2010, Journal of molecular biology.
[64] A. Spirin,et al. Stereochemical analysis of ribosomal transpeptidation. Conformation of nascent peptide. , 1986, Journal of molecular biology.
[65] Bernd Bukau,et al. The ribosome as a platform for co-translational processing, folding and targeting of newly synthesized proteins , 2009, Nature Structural &Molecular Biology.
[66] E. Deuerling,et al. Molecular guardians for newborn proteins: ribosome-associated chaperones and their role in protein folding , 2005, Cellular and Molecular Life Sciences CMLS.
[67] David B. Williams,et al. Participation of lectin chaperones and thiol oxidoreductases in protein folding within the endoplasmic reticulum. , 2011, Current opinion in cell biology.
[68] Steven P. Brown,et al. Yeast Nα‐terminal acetyltransferases are associated with ribosomes , 2008 .
[69] A. Komar,et al. Synonymous codon substitutions affect ribosome traffic and protein folding during in vitro translation , 1999, FEBS letters.
[70] T. Schwartz. Origins and evolution of cotranslational transport to the ER. , 2007, Advances in experimental medicine and biology.
[71] David J F du Plessis,et al. The Sec translocase. , 2011, Biochimica et biophysica acta.
[72] N. Ban,et al. L23 protein functions as a chaperone docking site on the ribosome , 2002, Nature.
[73] Klaus Schulten,et al. Structure of Monomeric Yeast and Mammalian Sec61 Complexes Interacting with the Translating Ribosome , 2009, Science.
[74] M. Yusupov,et al. Crystal Structure of the Eukaryotic Ribosome , 2010, Science.
[75] M. Marín,et al. Folding at the rhythm of the rare codon beat , 2008, Biotechnology journal.
[76] Zoya Ignatova,et al. Transient ribosomal attenuation coordinates protein synthesis and co-translational folding , 2009, Nature Structural &Molecular Biology.
[77] Malte Beringer,et al. The ribosomal peptidyl transferase. , 2007, Molecular cell.
[78] I. Adzhubei,et al. Nonuniform size distribution of nascent globin peptides, evidence for pause localization sites, and a cotranslational protein-folding model , 1991, Journal of protein chemistry.
[79] C. Anfinsen. Principles that govern the folding of protein chains. , 1973, Science.
[80] P. Walter,et al. Signal sequence recognition and protein targeting to the endoplasmic reticulum membrane. , 1994, Annual review of cell biology.
[81] S. Marzi,et al. A structural view of translation initiation in bacteria , 2009, Cellular and Molecular Life Sciences.
[82] H. Bernstein,et al. Translation arrest requires two-way communication between a nascent polypeptide and the ribosome. , 2006, Molecular cell.
[83] J. Nyborg,et al. 3 The Protein Biosynthesis, Elongation Cycle , 2000 .
[84] K. Kannan,et al. The key function of a conserved and modified rRNA residue in the ribosomal response to the nascent peptide , 2010, The EMBO journal.
[85] S. Rospert,et al. The ribosome-bound Hsp70 homolog Ssb of Saccharomyces cerevisiae. , 2010, Biochimica et biophysica acta.
[86] Koreaki Ito,et al. The Ribosomal Exit Tunnel Functions as a Discriminating Gate , 2002, Cell.
[87] Nicol N. Schraudolph,et al. A Role for Codon Order in Translation Dynamics , 2010, Cell.
[88] Holger Stark,et al. Three-dimensional electron cryomicroscopy of ribosomes. , 2002, Current protein & peptide science.
[89] M. Gautschi,et al. A functional chaperone triad on the yeast ribosome , 2002, Proceedings of the National Academy of Sciences of the United States of America.
[90] Steven P. Brown,et al. Yeast N(alpha)-terminal acetyltransferases are associated with ribosomes. , 2008, Journal of cellular biochemistry.
[91] Johannes Söding,et al. Cryo-EM structure and rRNA model of a translating eukaryotic 80S ribosome at 5.5-Å resolution , 2010, Proceedings of the National Academy of Sciences.
[92] J. Frydman,et al. Systems Analyses Reveal Two Chaperone Networks with Distinct Functions in Eukaryotic Cells , 2006, Cell.
[93] R. Jackson,et al. The mechanism of eukaryotic translation initiation and principles of its regulation , 2010, Nature Reviews Molecular Cell Biology.
[94] N. Ban,et al. Crystal Structure of the Eukaryotic 40S Ribosomal Subunit in Complex with Initiation Factor 1 , 2011, Science.
[95] M. Sachs,et al. Sequence Requirements for Ribosome Stalling by the Arginine Attenuator Peptide* , 2010, The Journal of Biological Chemistry.
[96] Joseph A. Vetro,et al. Yeast methionine aminopeptidase type 1 is ribosome‐associated and requires its N‐terminal zinc finger domain for normal function in vivo * , 2002, Journal of cellular biochemistry.
[97] Yoko Ino,et al. N(α)-Acetylation of yeast ribosomal proteins and its effect on protein synthesis. , 2011, Journal of proteomics.
[98] Koreaki Ito,et al. Control of SecA and SecM translation by protein secretion. , 2004, Current opinion in microbiology.
[99] N. Ban,et al. Multiple conformational switches in a GTPase complex control co-translational protein targeting , 2009, Proceedings of the National Academy of Sciences.
[100] G. Kramer,et al. Ribosomes and ribosomal RNA as chaperones for folding of proteins. , 1997, Folding & design.
[101] Alexander Varshavsky,et al. N-Terminal Acetylation of Cellular Proteins Creates Specific Degradation Signals , 2010, Science.
[102] N. Ban,et al. Crystal Structure of the Eukaryotic 60S Ribosomal Subunit in Complex with Initiation Factor 6 , 2011, Science.
[103] F. Képès,et al. The "+70 pause": hypothesis of a translational control of membrane protein assembly. , 1996, Journal of molecular biology.
[104] Markus Aebi,et al. N-glycan structures: recognition and processing in the ER. , 2010, Trends in biochemical sciences.
[105] T. Arnesen,et al. A synopsis of eukaryotic Nα-terminal acetyltransferases: nomenclature, subunits and substrates , 2009, BMC proceedings.
[106] C. Yanofsky,et al. Features of ribosome-peptidyl-tRNA interactions essential for tryptophan induction of tna operon expression. , 2005, Molecular cell.
[107] L. Berthiaume,et al. Post-translational myristoylation: Fat matters in cellular life and death. , 2011, Biochimie.
[108] Michael K Gilson,et al. Protein folding and binding: from biology to physics and back again. , 2011, Current opinion in structural biology.
[109] Jonathan W. Yewdell,et al. Rapid degradation of a large fraction of newly synthesized proteins by proteasomes , 2000, Nature.
[110] L. Lindahl,et al. Effects on Translation Pausing of Alterations in Protein and RNA Components of the Ribosome Exit Tunnel , 2008, Journal of bacteriology.
[111] T. Inada,et al. Nascent Peptide-dependent Translation Arrest Leads to Not4p-mediated Protein Degradation by the Proteasome* , 2009, Journal of Biological Chemistry.
[112] V. Ramakrishnan,et al. What recent ribosome structures have revealed about the mechanism of translation , 2009, Nature.
[113] R. Brimacombe,et al. Flexibility of the nascent polypeptide chain within the ribosome--contacts from the peptide N-terminus to a specific region of the 30S subunit. , 1998, European Journal of Biochemistry.
[114] D. Sabatini,et al. CONTROLLED PROTEOLYSIS OF NASCENT POLYPEPTIDES IN RAT LIVER CELL FRACTIONS , 1970, The Journal of cell biology.
[115] A. Spirin,et al. Does the channel for nascent peptide exist inside the ribosome? Immune electron microscopy study , 1988, FEBS letters.
[116] A. Varshavsky,et al. Detecting and measuring cotranslational protein degradation in vivo. , 2000, Science.
[117] Ryan Hunt,et al. Silent (synonymous) SNPs: should we care about them? , 2009, Methods in molecular biology.
[118] M Gerstein,et al. The geometry of the ribosomal polypeptide exit tunnel. , 2006, Journal of molecular biology.
[119] H. Taguchi,et al. Co-translational Binding of GroEL to Nascent Polypeptides Is Followed by Post-translational Encapsulation by GroES to Mediate Protein Folding* , 2006, Journal of Biological Chemistry.
[120] E. Bibi. Early targeting events during membrane protein biogenesis in Escherichia coli. , 2011, Biochimica et biophysica acta.
[121] A. Palmenberg. Proteolytic processing of picornaviral polyprotein. , 1990, Annual review of microbiology.
[122] Patricia L. Clark,et al. Rare Codons Cluster , 2008, PloS one.
[123] Gel chromatographic analysis of nascent globin chains. Evidence of nonuniform size distribution. , 1974, The Journal of biological chemistry.
[124] J. Schneider-Mergener,et al. Binding specificity of Escherichia coli trigger factor , 2001, Proceedings of the National Academy of Sciences of the United States of America.
[125] W. Lennarz,et al. Unraveling the Mechanism of Protein N-Glycosylation* , 2005, Journal of Biological Chemistry.
[126] D. Klepacki,et al. Nascent peptide in the ribosome exit tunnel affects functional properties of the A-site of the peptidyl transferase center. , 2011, Molecular cell.
[127] T. Lithgow,et al. RAC, a stable ribosome-associated complex in yeast formed by the DnaK-DnaJ homologs Ssz1p and zuotin , 2001, Proceedings of the National Academy of Sciences of the United States of America.
[128] Thierry Meinnel,et al. Cotranslational processing mechanisms: towards a dynamic 3D model. , 2009, Trends in biochemical sciences.
[129] Jun O. Liu,et al. Identification of an SH3-binding motif in a new class of methionine aminopeptidases from Mycobacterium tuberculosis suggests a mode of interaction with the ribosome. , 2005, Biochemistry.
[130] M. Wiedmann,et al. A protein complex required for signal-sequence-specific sorting and translocation , 1994, Nature.
[131] Jianli Lu,et al. Folding zones inside the ribosomal exit tunnel , 2005, Nature Structural &Molecular Biology.
[132] R Dustin Schaeffer,et al. Combining experiment and simulation in protein folding: closing the gap for small model systems. , 2008, Current opinion in structural biology.
[133] Jonathan Weissman,et al. Molecular Chaperones and Protein Quality Control , 2006, Cell.
[134] Lisa D. Cabrita,et al. Protein folding on the ribosome. , 2010, Current opinion in structural biology.
[135] W. Fiers,et al. Folding of the MS2 coat protein in Escherichia coli is modulated by translational pauses resulting from mRNA secondary structure and codon usage: a hypothesis. , 1993, Journal of theoretical biology.
[136] Koreaki Ito,et al. Divergent stalling sequences sense and control cellular physiology. , 2010, Biochemical and biophysical research communications.
[137] Malte Beringer,et al. Modulating the activity of the peptidyl transferase center of the ribosome. , 2008, RNA.
[138] S. Napthine,et al. Ribosomal Pausing at a Frameshifter RNA Pseudoknot Is Sensitive to Reading Phase but Shows Little Correlation with Frameshift Efficiency , 2001, Molecular and Cellular Biology.
[139] T.J.P. Hubbard,et al. Gathering them in to the fold , 1996, Nature Structural Biology.
[140] D. Boehringer,et al. Cryo-EM structure of the E. coli translating ribosome in complex with SRP and its receptor , 2011, Nature Structural &Molecular Biology.
[141] A. Morris,et al. Nonuniform size distribution of nascent peptides. The effect of messenger RNA structure upon the rate of translation. , 1979, Archives of biochemistry and biophysics.
[142] R. Deshaies,et al. RING domain E3 ubiquitin ligases. , 2009, Annual review of biochemistry.
[143] A. Komar,et al. Eukaryotic Protein Biosynthesis: The Elongation Cycle , 2013 .
[144] Andrey Kosolapov,et al. Tertiary Interactions within the Ribosomal Exit Tunnel , 2009, Nature Structural &Molecular Biology.
[145] J E Mullet,et al. Ribosomes pause at specific sites during synthesis of membrane-bound chloroplast reaction center protein D1. , 1991, The Journal of biological chemistry.
[146] K. D. Hartman,et al. Human N-Myristoyltransferase Amino-terminal Domain Involved in Targeting the Enzyme to the Ribosomal Subcellular Fraction* , 1997, The Journal of Biological Chemistry.
[147] R. Brimacombe,et al. Contacts between the growing peptide chain and the 23S RNA in the 50S ribosomal subunit. , 1994, Nucleic acids research.
[148] Daniel N. Wilson,et al. The ribosomal tunnel as a functional environment for nascent polypeptide folding and translational stalling. , 2011, Current opinion in structural biology.
[149] D. Kelleher,et al. An evolving view of the eukaryotic oligosaccharyltransferase. , 2006, Glycobiology.
[150] I. Adzhubei,et al. [Role of the rare codon clusters in defining the boundaries of polypeptide chain regions with identical secondary structures in the process of co-translational folding of proteins]. , 1988, Doklady Akademii nauk SSSR.
[151] L. Hurst,et al. Hearing silence: non-neutral evolution at synonymous sites in mammals , 2006, Nature Reviews Genetics.
[152] Wolfgang Wintermeyer,et al. Recent mechanistic insights into eukaryotic ribosomes. , 2009, Current opinion in cell biology.
[153] F. Sherman,et al. N-terminal acetyltransferases and sequence requirements for N-terminal acetylation of eukaryotic proteins. , 2003, Journal of molecular biology.
[154] E. Olson,et al. Acylation of proteins with myristic acid occurs cotranslationally. , 1987, Science.
[155] S. Liebhaber,et al. Translationally associated helix-destabilizing activity in rabbit reticulocyte lysate. , 1984, The Journal of biological chemistry.
[156] T. Inada,et al. Translation of the poly(A) tail plays crucial roles in nonstop mRNA surveillance via translation repression and protein destabilization by proteasome in yeast. , 2007, Genes & development.