Commentary. in the Article “Genetic Code Origins: Experi- Ments Confirm Phylogenetic Predictions and May Explain a Puzzle” B
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5890 Corrections Proc. Natl. Acad. Sci. USA 96 (1999) Commentary. In the article “Genetic code origins: Experi- Neurobiology. In the article “Growth factor-mediated Fyn ments confirm phylogenetic predictions and may explain a signaling regulates a-amino-3-hydroxy-5-methyl-4-isox- puzzle” by Paul Schimmel and Lluis Ribas de Pouplana, which azolepropionic acid (AMPA) receptor expression in rodent appeared in number 2, January 19, 1999 of Proc. Natl. Acad. neocortical neurons” by Mako Narisawa-Saito, Alcino J. Silva, Sci. USA (96, 327–328), the following corrections should be Tsuyoshi Yamaguchi, Takashi Hayashi, Tadashi Yamamoto, noted. The fifth and sixth sentences of the first paragraph on and Hiroyuki Nawa, which appeared in number 5, March 2, page 328 should read as follows (changes are indicated by bold 1999, of Proc. Natl. Acad. Sci. USA (96, 2461–2466), due to a type): “This base pair is found in the spirochetes T. pallidum printer’s error, there were several errors in the author and and B. burgdorferi that contain a class I enzyme. In contrast, affiliations lines. The correct affiliations are as follows: Ibba et al. (1) show that the class II E. coli enzyme cannot MAKO NARISAWA-SAITO*†,ALCINO J. SILVA‡,TSUYOSHI accept G2-U71.” Also, the word “spirocytes” in the sixth YAMAGUCHI*, TAKASHI HAYASHI§,TADASHI YAMAMOTO§, sentence of the second paragraph on page 328 should read AND HIROYUKI NAWA*†‡ spirochetes. Finally, the sixth sentence of the last paragraph on page 328 should read as follows: “So multiple lateral gene *Department of Molecular Neurobiology, Brain Research Institute, Niigata University, Niigata 951-8585, Japan; ‡Cold Spring Harbor Laboratory, Cold transfer from archaebacteria to certain bacteria could account Spring Harbor, NY 11724; and §Institute of Medical Science, University of for the presence of class I LysRS in bacterial organisms such Tokyo, Tokyo 108-8639, Japan as T. pallidum, B. burgdorferi, and R. prowacekii.” †To whom reprint requests should be addressed. Perspective. In the article “Active galactic nuclei” by Andrew Fabian, which appeared in number 9, April 27, 1999, of Proc. Pharmacology. In the article “Systemic biosynthesis of pros- Natl. Acad. Sci. USA (96, 4749–4751), the following statement tacyclin by cyclooxygenase (COX)-2: The human pharmacol- ogy of a selective inhibitor of COX-2” by B. F. McAdam, was omitted from the legend to Fig. 1: “Fig. 1 was reprinted F. Catella-Lawson, I. A. Mardini, S. Kapoor, J. A. Lawson, and with permission from ref. 18 (Copyright 1997, Mon. Not. R. G. A. FitzGerald, which appeared in number 1, January 5, Astron. Soc.).” 1999, of Proc. Natl. Acad. Sci. USA (96, 272–277), the authors inadvertently omitted the acknowledgment of the support Applied Biological Sciences. In the article “Multiple genetic from the General Clinical Research Center where these stud- modifications of the erythromycin polyketide synthase to ies were performed. The relevant grant is NIH-MO1RR produce a library of novel “unnatural” natural products” by 00040. Robert McDaniel, Arinthip Thamchaipenet, Claes Gustafs- son, Hong Fu, Melanie Betlach, Mary Betlach, and Gary Ashley, which appeared in number 5, March 2, 1999, of Proc. Natl. Acad. Sci. USA (96, 1846–1851), the following correction should be noted. A.T. was supported by a fellowship from the National Center for Genetic Engineering and Biotechnology (BIOTEC), the National Science and Technology Develop- ment Agency (NSTDA), Thailand. Biochemistry. In the article “Minimal and optimal mecha- nisms for GroE-mediated protein folding” by Anat Peres Ben-Zvi, Jean Chatellier, Alan R. Fersht, and Pierre Golou- binoff, which appeared in number 26, December 22, 1998, of Proc. Natl. Acad. Sci. USA (95, 15275–15280), the following correction should be noted. The legend of Fig. 4 should read as follows: “Effect of Mn21 ions on GroELyGroES-mediated refolding of mtMDH. The time-dependent reactivation of GroEL-bound mtMDH (4 mM GroEL, 0.3 mM mtMDH) was measured in the presence of 1 mM ATP and an ATP- regeneration system [equimolar (4 mM) GroES] in folding buffer as in Figs. 1–3, but with a near-limiting 6 mM concen- tration of divalent ions instead of 20 mM Mg21. Open symbols: 6mMMg21. Filled symbols: 4 mM Mg21 and2mMMn21.A 6.25-fold excess of free GroEL (22 mM) was added (E, Œ)or not (h, }) to the reaction 11 min after initiation of reactivation at 25°C with ATP.” Downloaded by guest on October 1, 2021 Proc. Natl. Acad. Sci. USA Vol. 95, pp. 15275–15280, December 1998 Biochemistry Minimal and optimal mechanisms for GroE-mediated protein folding (heat-shockyminichaperoneymalate dehydrogenase) ANAT PERES BEN-ZVI*, JEAN CHATELLIER†,ALAN R. FERSHT†‡, AND PIERRE GOLOUBINOFF*‡ *Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel; and †Medical Research Centre for Protein Engineering and Cambridge University Chemical Laboratory, Hills Road, Cambridge CB2 2QH, United Kingdom Contributed by Alan R. Fersht, October 8, 1998 ABSTRACT We have analyzed the effects of different face the central cavity of the GroEL14 cylinder. When nucle- components of the GroE chaperonin system on protein folding otides bind to the GroEL14.GroES7 complex, the volume of the by using a nonpermissive substrate (i.e., one that has very low cavity is dramatically increased, and the binding sites become spontaneous refolding yield) for which rate data can be cryptic (6, 7). In the holochaperonin, refolding of protein acquired. In the absence of GroES and nucleotides, the rate of substrates has been shown to occur underneath the GroES7 GroEL-mediated refolding of heat- and DTT-denatured mi- cap inside a unique ‘‘cis’’ chamber of the GroEL14.GroES7 tochondrial malate dehydrogenase was extremely low, but oligomer (8), or, more efficiently, inside two chambers of the some three times higher than the spontaneous rate. This highly active symmetrical GroEL14.(GroES7)2 oligomer (5, 9, GroEL-mediated rate was increased 17-fold by saturating 10). Although GroEL functions as a double-ring complex (11), concentrations of ATP, 11-fold by ADP and GroES, and a single ring suffices for the mammalian mitochondrial homo- 465-fold by ATP and GroES. Optimal refolding activity was logue Hsp60 in vivo (12). In addition, minichaperones (frag- observed when the dissociation of GroES from the chaperonin ments encompassing the apical domain of GroEL) are effec- complex was dramatically reduced. Although GroEL tive in refolding several protein substrates in vitro, calling into minichaperones were able to bind denatured mitochondrial question the importance of the encapsulation within the active malate dehydrogenase, they were ineffective in enhancing the GroEL14.GroES7 complexes for all substrates (13). Moreover, refolding rate. The spectrum of mechanisms for GroE- the smallest minichaperones (residues 193–335 and 191–345) mediated protein folding depends on the nature of the sub- can, to varying extents, complement temperature-sensitive E. strate. The minimal mechanism for permissive substrates coli groEL alleles and supplement low levels of GroEL activity (i.e., having significant yields of spontaneous refolding), re- in transformants of E. coli in which the groEL gene has been quires only binding to the apical domain of GroEL. Slow deleted (14). folding rates of nonpermissive substrates are limited by the Strict GroEL-, GroES-, and ATP-dependent refolding of a transitions between high- and low-affinity states of GroEL nonnative protein in vitro was discovered for urea-denatured alone. The optimal mechanism, which requires holoGroEL, RubisCO (2). However, chaperonin-mediated refolding of physiological amounts of GroES, and ATP hydrolysis, is proteins such as enolase, tryptophanase, rhodanese, and glu- necessary for the chaperonin-mediated folding of nonpermis- tamine synthetase can take place in the presence of ADP and sive substrates at physiologically relevant rates under condi- nonhydrolyzable ATP analogs (15–17). GroEL-mediated re- tions in which retention of bound GroES prevents the pre- folding of lactate dehydrogenase, enolase, tryptophanase, and mature release of aggregation-prone folding intermediates dehydrofolate reductase can occur with ATP but without from the chaperonin complex. The different mechanisms are GroES (15, 16, 18, 19). GroEL minichaperones, despite being described in terms of the structural features of mini- and monomeric and non-nucleotide-binding, efficiently mediate holo-chaperones. the refolding of some proteins, such as rhodanese and cyclo- philin A (13, 14). Noticeably, the different chaperonin require- Heat-shock proteins GroEL and GroES (the GroE chaperonin ments of the various protein substrates were addressed under system) from Escherichia coli are involved in the folding and in vitro conditions that often allowed significant levels of assembly of newly synthesized polypeptide chains released spontaneous refolding (15, 20). This has led to various, seem- from the translation machinery and the refolding of stress- ingly contradictory models for a minimal mechanism of denatured proteins (1). In vitro, GroEL and GroES carry two GroEL- or minichaperone-mediated protein refolding, some complementary activities that prevent heat- and chemical- including, or specifically excluding l GroES interactions denatured polypeptides from irreversible aggregation and andyor nucleotide interactions andyor ATP hydrolysis (15– assist their refolding into native proteins (1–3). 22). In vivo, the GroE-assisted refolding reaction also depends GroEL