Exploring the mechanism of protein synthesis with modified substrates and novel intermediate mimics

Blood Cells, Molecules, and Diseases - Tập 38 - Trang 110-116 - 2007
Joshua S. Weinger1, Scott A. Strobel2
1Laboratory of Chemistry and Cell Biology, Rockefeller University, New York, NY 10021, USA
2Department of Molecular Biophysics and Biochemistry, Yale University, 260 Whitney Avenue, New Haven, CT 06520-8114, USA

Tài liệu tham khảo

Green, 1997, Ribosomes and translation, Annu. Rev. Biochem., 66, 679, 10.1146/annurev.biochem.66.1.679 Fersht, 1970, Reactions of nucleophilic reagents with acylating agents of extreme reactivity and unreactivity—Correlation of beta values for attacking and leaving group variation, J. Am. Chem. Soc., 92, 5442, 10.1021/ja00721a024 Rodnina, 2003, Peptide bond formation on the ribosome: structure and mechanism, Curr. Opin. Struct. Biol., 13, 334, 10.1016/S0959-440X(03)00065-4 Fersht, 1985 Palade, 1955, A small particulate component of the cytoplasm, J. Biophys. Biochem. Cytol., 1, 59, 10.1083/jcb.1.1.59 Lake, 1976, Ribosome structure determined by electron microscopy of Escherichia coli small subunits, large subunits and monomeric ribosomes, J. Mol. Biol., 105, 131, 10.1016/0022-2836(76)90200-X Stark, 1995, The 70S Escherichia coli ribosome at 23 A resolution: fitting the ribosomal RNA, Structure, 3, 815, 10.1016/S0969-2126(01)00216-7 Frank, 1995, A model of protein synthesis based on cryo-electron microscopy of the E. coli ribosome, Nature, 376, 441, 10.1038/376441a0 Ban, 2000, The complete atomic structure of the large ribosomal subunit at 2.4 A resolution, Science, 289, 905, 10.1126/science.289.5481.905 Nissen, 2000, The structural basis of ribosome activity in peptide bond synthesis, Science, 289, 920, 10.1126/science.289.5481.920 Schlunzen, 2001, Structural basis for the interaction of antibiotics with the peptidyl transferase centre in eubacteria, Nature, 413, 814, 10.1038/35101544 Harms, 2001, High resolution structure of the large ribosomal subunit from a mesophilic eubacterium, Cell, 107, 679, 10.1016/S0092-8674(01)00546-3 Welch, 1995, An inhibitor of ribosomal peptidyl transferase using transition-state analogy, Biochemistry, 34, 385, 10.1021/bi00002a001 Parnell, 2002, Evidence against stabilization of the transition state oxyanion by a pKa-perturbed RNA base in the peptidyl transferase center, Proc. Natl. Acad. Sci. U. S. A., 99, 11658, 10.1073/pnas.182210099 Xiong, 2001, pKa of adenine 2451 in the ribosomal peptidyl transferase center remains elusive, RNA, 7, 1365 Hansen, 2002, Structural insights into peptide bond formation, Proc. Natl. Acad. Sci. U. S. A., 99, 11670, 10.1073/pnas.172404099 Youngman, 2004, The active site of the ribosome is composed of two layers of conserved nucleotides with distinct roles in peptide bond formation and peptide release, Cell, 117, 589, 10.1016/S0092-8674(04)00411-8 Polacek, 2001, Ribosomal peptidyl transferase can withstand mutations at the putative catalytic nucleotide, Nature, 411, 498, 10.1038/35078113 Sievers, 2004, The ribosome as an entropy trap, Proc. Natl. Acad. Sci. U. S. A., 101, 7897, 10.1073/pnas.0402488101 Thompson, 2001, Analysis of mutations at residues A2451 and G2447 of 23S rRNA in the peptidyltransferase active site of the 50S ribosomal subunit, Proc. Natl. Acad. Sci. U. S. A., 98, 9002, 10.1073/pnas.151257098 Beringer, 2003, The G2447A mutation does not affect ionization of a ribosomal group taking part in peptide bond formation, RNA, 9, 919, 10.1261/rna.5600503 Weinger, 2006, Participation of the tRNA A76 hydroxyl groups throughout translation, Biochemistry, 45, 5939, 10.1021/bi060183n Weinger, 2004, Substrate-assisted catalysis of peptide bond formation by the ribosome, Nat. Struct. Mol. Biol., 11, 1101, 10.1038/nsmb841 Uesugi, 1979, Linear relationship between electronegativity of 2′-substituents and conformation of adenine nucleosides, Tetrahedron Lett., 20, 4073, 10.1016/S0040-4039(01)86507-2 Herschlag, 1993, Contributions of 2′-hydroxyl groups of the RNA substrate to binding and catalysis by the Tetrahymena ribozyme. An energetic picture of an active site composed of RNA, Biochemistry, 32, 8299, 10.1021/bi00083a034 Katunin, 2002, Important contribution to catalysis of peptide bond formation by a single ionizing group within the ribosome, Mol. Cell, 10, 339, 10.1016/S1097-2765(02)00566-X Brunelle, 2006, The interaction between C75 of tRNA and the A loop of the ribosome stimulates peptidyl transferase activity, RNA, 12, 33, 10.1261/rna.2256706 Schmeing, 2005, An induced-fit mechanism to promote peptide bond formation and exclude hydrolysis of peptidyl-tRNA, Nature, 438, 520, 10.1038/nature04152 Huang, 2006, Regiospecificity of the peptidyl tRNA ester within the ribosomal P site, J. Am. Chem. Soc., 128, 3108, 10.1021/ja0554099 Schmeing, 2005, Structural insights into the roles of water and the 2′ hydroxyl of the P site tRNA in the peptidyl transferase reaction, Mol. Cell, 20, 437, 10.1016/j.molcel.2005.09.006 Reese, 1965, Acyl migration in ribonucleoside derivatives, Tetrahedron Lett., 2467, 10.1016/S0040-4039(01)84008-9 Nathans, 1963, Structural requirements for puromycin inhibition of protein synthesis, Nature, 197, 1076, 10.1038/1971076a0 Ringer, 1974, Inhibition of the peptidyl transferase A-site function by 2′-O-aminoacyloligonucleotides, Biochem. Biophys. Res. Commun., 56, 760, 10.1016/0006-291X(74)90670-6 Bhuta, 1981, Aminoacyl derivatives of nucleosides, nucleotides and polynucleotides .33. Stereochemical control of ribosomal peptidyltransferase reaction—Role of amino-acid side-chain orientation of acceptor substrate, Biochemistry, 20, 8, 10.1021/bi00504a002 Hecht, 1974, Isomeric phenylalanyl-tRNAs. Position of the aminoacyl moiety during protein biosynthesis, Proc. Natl. Acad. Sci. U. S. A., 71, 4317, 10.1073/pnas.71.11.4317 Wagner, 1982, Activity of the 2′ and 3′ isomers of aminoacyl transfer ribonucleic acid in the in vitro peptide elongation on Escherichia coli ribosomes, Biochemistry, 21, 1521, 10.1021/bi00536a009 Oivanen, 1998, Kinetics and mechanisms for the cleavage and isomerization of the phosphodiester bonds of RNA by Bronsted acids and bases, Chem. Rev., 98, 961, 10.1021/cr960425x Lim, 1986, Stereochemical analysis of ribosomal transpeptidation. Conformation of nascent peptide, J. Mol. Biol., 188, 565, 10.1016/S0022-2836(86)80006-7 Das, 1999, A possible mechanism of peptide bond formation on ribosome without mediation of peptidyl transferase, J. Theor. Biol., 200, 193, 10.1006/jtbi.1999.0987 Trobro, 2006, Analysis of predictions for the catalytic mechanism of ribosomal peptidyl transfer, Biochemistry, 45, 7049, 10.1021/bi0605383 Dorner, 2003, Mononucleotide derivatives as ribosomal P-site substrates reveal an important contribution of the 2′-OH to activity, Nucleic Acids Res., 31, 6536, 10.1093/nar/gkg842