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Elliott & Elliott: Biochemistry and Molecular Biology 4e

Chapter 24

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Transfer RNA

Schimmel, P. and de Pouplana, L. R. (1995). Transfer RNA: from minihelix to genetic code. Cell 81, 983-6 [DOI: 10.1016/S0092-8674(05)80002-9].
This review addresses the question of why particular nucleotide triplets correspond to specific amino acids. tRNA can be thought of as comprising of two informational domains: the operational RNA code for amino acids, and the anticodon-containing domain with the trinucleotides of the genetic code.

Trifonov, E. N. (2000). Consensus temporal order of amino acids and evolution of the triplet code. Gene 261, 139-51 [DOI: 10.1016/S0378-1119(00)00476-5] [PubMed: 11164045].

Ogle, J. M., Carter, A. P., and Ramakrishnan, V. (2003) Insights into the decoding mechanism from recent ribosome structures. Trends Biochem. Sci., 28, 259-66 [DOI: 10.1016/S0968-0004(03)00066-5].

Initiation

Preiss, T. and Hentze, M. W. (2003). Starting the protein synthesis machine. BioEssays, 25, 1201-11 [DOI: 10.1002/bies.10362].
The ribosome as the ultimate protein-synthesis machine in initiation.

Hinnebusch, A. G. (2006). eiF3: a versatile scaffold for translation initiation complexes. Trends Biochem. Sci., 31, 553-62 [DOI: 10.1016/j.tibs.2006.08.005].

The ribosome

Powers, T. and Noller, H. F. (1994). The 530 loop of 16S rRNA - a signal to EF-Tu? Trends Genet., 10, 27-31 [DOI: 10.1016/0168-9525(94)90016-7].
A penetrating discussion of how fidelity in protein synthesis is achieved.

Stadtman, T. C. (1996). Selenocysteine. Annu. Rev. Biochem., 65, 83 [DOI: 10.1146/annurev.bi.65.070196.000503].

Bock, A. (2000). Biosynthesis of selenoproteins - an overview. Biofactor 11, 77.

Wilson, K. S. and Noller, H. F. (1998). Molecular movement inside the translational engine. Cell 92, 337-49 [DOI: 10.1016/S0092-8674(00)80927-7] [PubMed: 9476894].
An authoritative review of how the ribosome works. It gives more information than most students would require but is listed for anyone taking a special interest in the area.

Rodnina, M. V. and Wintermeyer, W. (2001). Fidelity of aminoacyl-tRNA selection on the ribosome: kinetic and structural mechanisms. Annu. Rev. Biochem., 70, 415-35 [DOI: 10.1146/annurev.biochem.70.1.415].
Advanced research-level review

Dever, T. E. (2002). Gene-specific regulation by general translation factors. Cell 108, 545-56 [DOI: 10.1016/S0092-8674(02)00642-6] [PubMed: 11909525].
Reviews initiation of translation in eukaryotes

Doudna, J. A. and Rath, V. L. (2002). Structure and function of the eukaryotic ribosome: the next frontier. Cell 109, 153-6 [DOI: 10.1016/S0092-8674(02)00725-0] [PubMed: 12007402].
A mini-review on the unique properties of the ribosome.

Ramakrishnan, V. (2002). Ribosome structure and the mechanism of translation. Cell 108, 557-72 [DOI: 10.1016/S0092-8674(02)00619-0] [PubMed: 11909526].
Readable review of all aspects of protein synthesis and ribosome formation.

Joseph, S. (2003). After the ribosome structure: how does translocation work? rna, 9, 160-4 [DOI: 10.1261/rna.2163103] [PubMed: 12554856].

Maden, B. E. H. (2003). Historical review: peptidyl transfer, the Monro era. Trends Biochem. Sci., 28, 619-24 [DOI: 10.1016/j.tibs.2003.09.008].
Review of developments that have led to our current knowledge of the peptide-bond-forming reaction.

Moore, P. B. and Steitz, T. A. (2003). The structural basis of large ribosomal subunit function. Annu. Rev. Biochem., 72, 813-50 [DOI: 10.1146/annurev.biochem.72.110601.135450].
Crystal structures of the ribosome discussed in relation to its peptide-bond-forming activity, the way antibiotics inhibit large subunit function, and the ribosome as an RNA enzyme.

Ogle, J. M. and Ramakrishnan, V. (2005). Structural insights into translational fidelity. Annu. Rev. Biochem., 74, 129 [DOI: 10.1146/annurev.biochem.74.061903.155440].

Mankin, A. S. (2006). Nascent peptide in the ?birth canal? of the ribosome. Trends Biochem. Sci., 31, 11-3 [DOI: 10.1016/j.tibs.2005.11.007].

Rodnina, M. V., Beringa, M., and Wintermyer, W. (2007). How ribosomes make peptide bonds. Trends Biochem. Sci., 32, 20-6 [DOI: 10.1016/j.tibs.2006.11.007].

Caban, K. and Copeland, P. R. (2006). Size matters: a view of selenocysteine incorporation from the ribosome. Cell Mol. Life Sci., 63, 73-81 [DOI: 10.1007/s00018-005-5402-y].

Korostelev, A. and Noller, H. F. (2007). The ribosome in focus: new structures bring new insights. Trends Bochem. Sci., 32, 434 [DOI: 10.1016/j.tibs.2007.08.002].

Riboswitches

Wakeman, C. A., Winkler, W. C., and Dann, C. E. (2007). Structural features of metabolite-sensing riboswitches. Trends Biochem. Sci., 32, 415-24 [DOI: 10.1016/j.tibs.2007.08.005].

Molecular chaperones and protein folding

Hortl, F.-U., Hlodon, R., and Langer, T. (1994). Molecular chaperones in protein folding: the art of avoiding sticky situations. Trends Biochem. Sci., 19, 20-5 [DOI: 10.1016/0968-0004(94)90169-4].
A general review of protein folding

Horwich, A. L. (1995). Resurrection or destruction? Curr. Biol., 5, 455-8 [DOI: 10.1016/S0960-9822(95)00089-3
Discusses how chaperones are involved both in rescuing proteins and directing them towards proteolytic destruction.

Netzer, W. J. and Hartl, F. U. (1998). Protein folding in the cytosol: chaperonin-dependent and independent mechanisms. Trends Biochem. Sci., 23, 68-73 [DOI: 10.1016/S0968-0004(97)01171-7].
A comprehensive account of protein folding and the mechanism of chaperone action.

Bukau, B. and Horwich, A. L. (1998). The Hsp 70 and Hsp 60 chaperone machines. Cell 92, 351-66 [DOI: 10.1016/S0092-8674(00)80928-9] [PubMed: 9476895].
An authoritative clear review, with structural models.

Pfanner, N. (1999). Protein folding: who chaperones nascent chains in bacteria? Curr. Biol., 9, R722 [DOI: 10.1016/S0960-9822(99)80467-9].
Summarizes the actions of Hsp 60 and Hsp 70.

Rye, H. S. et al. (1999). GroEL-GroES cycling ATP and non-native polypeptide direct alternation of folding-active rings. Cell 97, 325-38 [DOI: 10.1016/S0092-8674(00)80742-4] [PubMed: 10319813].

Gottesman, M. E. and Hendrickson, W. A. (2000). Protein folding and unfolding by E. coli chaperones and chaperonins. Curr. Opin. Microbiol., 3, 197-202 [DOI: 10.1016/S1369-5274(00)00075-8].
Summarizes the structures and functions of these molecular machines.

Prion diseases

Weissmann, C. (1995). Yielding under the strain. Nature, 375, 628-9 [DOI: 10.1038/375628a0] [PubMed: 7791890].
A concise summary of the molecular basis of prion diseases.

Prusiner, S. B. (1995). The prion diseases. Sci. Am., 272(1), 30-7.
General review of the field

Thomas, P. J., Qu, B.-H., and Pedersen, P. L. (1995). Defective protein folding as a basis of human disease. Trends Biochem. Sci., 20, 456-9 [DOI: 10.1016/S0968-0004(00)89100-8].
Discusses the possibility that a large number of diseases, in addition to prion diseases, may be due to protein-folding abnormalities.

Taubes, G. (1996). Misfolding the way to disease. Science, 272, 1493-5 [DOI: 10.1126/science.271.5255.1493].
A research news item presents the general hypothesis that protein misfolding may cause amyloid diseases such as Alzheimer?s disease as well as the prion diseases. Introduces the concept that aggregation of proteins into insoluble complexes may be more prevalent and more important than hitherto suspected.

Dobson, C. M. (1999). Protein misfolding, evolution and disease. Trends Biochem. Sci., 24, 329-32 [DOI: 10.1016/S0968-0004(99)01445-0].
Reviews diseases in which protein misfolding leads to amyloid or fibrillar aggregates.

Hunter, N. (1999). Prion diseases and the central dogma of molecular biology. Trends Microbiol., 7, 265-6 [DOI: 10.1016/S0966-842X(99)01543-7].
A ?Comment? article summarizing the nature of prions.

Manson, J. C. (1999). Understanding transmission of the prion diseases. Trends Microbiol., 7, 465-7 [DOI: 10.1016/S0966-842X(99)01619-4].
A ?Comment? article summarizing this topic

Hope, J. (1999). Prions. Curr. Biol., 9, R763-4 [DOI: 10.1016/S0960-9822(99)80435-7].
A quick guide to the essential facts.

Butler, D. (2001). Unfolding issues. Nature, 414, 577 [DOI: 10.1038/35102713].
Briefly discusses prions and gives three-dimensional structures

Dobson, C. M. (2002). Getting out of shape. Nature, 418, 729-30 [DOI: 10.1038/418729a] [PubMed: 12181546].
Short article on protein-misfolding diseases

Buxbaum, J. N. (2003). Diseases of protein conformation: what do in vitro experiments tell us about in vivo diseases? Trends Biochem. Sci., 28, 585-92 [DOI: 10.1016/j.tibs.2003.09.009].
Review on human diseases associated with misfolded proteins with decreased solubility.

Soto, C., Estrada, L., and Castilla, J. (2006). Amyloids, prions and the inherent infectious nature of misfolded proteins. Trends Biochem. Sci., 31, 150-5 [DOI: 10.1016/j.tibs.2006.01.002].

Arolas, J. L., and Aviles, F. X., Chang, J., and Ventura, S. (2006). Folding of small disulphide rich proteins: clarifying the puzzle. Trends Biochem. Sci., 31, 292-301 [DOI: 10.1016/j.tibs.2006.03.005].

Chiti, F. and Dobson, C. M. (2006). Protein misfolding, functional amyloid and human disease. Annu. Rev. Biochem., 75, 333-66 [DOI: 10.1146/annurev.biochem.75.101304.123901].

Translational control

Russell, J. E., Morales, J., and Liebhaber, S. A. (1997). The role of mRNA stability in the control of globin gene expression. Prog. Nucleic Acid Res. Mol. Biol., 57, 249-87 [DOI: 10.1016/S0079-6603(08)60283-4].

Gebauer, F. and Hentze, M. W. (2004). Molecular mechanisms of translational control. Nature Reviews, 5, 827-35 [DOI: 10.1038/nrm1488] [PubMed: 15459663].
A comprehensive detailed account

Proud, C. G. (2006). Regulation of protein synthesis by insulin. Biochem. Soc. Trans., 34, 213-6 [DOI: 10.1042/BST20060213].

Translational control of proteins involved in haem synthesis and iron metabolism

Chen, J.-J. and London, I. M. (1995). Regulation of protein synthesis by heme-regulated eIF-2α kinase. Trends Biochem. Sci., 20, 105-8 [DOI: 10.1016/S0968-0004(00)88975-6].
A comprehensive review of the control of haemoglobin synthesis by this mechanism.

May, B. K., et al. (1995). Molecular regulation of heme biosynthesis in higher vertebrates. Prog. Nucleic Acid Res., and mole bio 51, 1-47 [DOI: 10.1016/S0079-6603(08)60875-2].
A comprehensive review of all aspects including the hereditary diseases.

Proteasomes

Coux, O., Tanaka, K., and Goldberg, A. L. (1996). Structure and function of the 20S and 26S proteasomes. Ann. Rev. Biochem., 65, 801-44 [DOI: 10.1146/annurev.bi.65.070196.004101].
A comprehensive review of the subject suitable for advanced students.

Stuart, D. I. and Jones, E. Y. (1997). Cutting complexity down to size. Nature, 386, 437-8 [DOI: 10.1038/386437a0] [PubMed: 9087396].
A News and Views summary of proteasomes and their structure

Ciechanover, A. (1998). The ubiquitin-proteasome pathway: on protein death and cell life. EMBO J., 17, 7151-60 [DOI: 10.1093/emboj/17.24.7151].

De Mot, R., Nagy, I., Walz, J., and Baumeister, W. (1999). Proteasomes and other self-compartmentalizing proteases in prokaryotes. Trends Microbiol., 7, 88-92 [DOI: 10.1016/S0966-842X(98)01432-2].

Kirschner, M. (1999). Intracellular proteolysis. Trends Cell Biol., Trends Biochem. Sci. and Trends Genet., Joint issue. 24, M42-5.
Part of a special millennium issue of the journals, this article reviews the development of an area of biochemistry from what was a relatively dull subject to one of the exciting ones today.

Scheffner, M. and Whitaker, N. J. (2001). Proteolytic relay comes to end. Nature, 410, 882-3 [DOI: 10.1038/35073728] [PubMed: 11309599].

Hooper, N. M., Ed. (2002). Proteases in biology and medicine. Essays Biochem., 36, 1-167.
A complete issue with 12 reviews on many aspects of proteases, including caspases, cancer, proteasomes, and blood clotting.

Gille C., et al. (2003). A comprehensive view on proteasomal sequences: implications for the evolution of the proteasome. J. Mol. Biol., 326, 1437-48 [DOI: 10.1016/S0022-2836(02)01470-5].