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Cimicata G, Fridkin G, Bose T, Eyal Z, Halfon Y, Breiner-Goldstein E, Fox T, Zimmerman E, Bashan A, de Val N, Wlodawer A, Yonath A. Structural Studies Reveal the Role of Helix 68 in the Elongation Step of Protein Biosynthesis. mBio 2022; 13:e0030622. [PMID: 35348349 PMCID: PMC9040758 DOI: 10.1128/mbio.00306-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 02/14/2022] [Indexed: 02/04/2023] Open
Abstract
The ribosome, a multicomponent assembly consisting of RNA and proteins, is a pivotal macromolecular machine that translates the genetic code into proteins. The large ribosomal subunit rRNA helix 68 (H68) is a key element in the protein synthesis process, as it coordinates the coupled movements of the actors involved in translocation, including the tRNAs and L1 stalk. Examination of cryo-electron microscopy (cryo-EM) structures of ribosomes incubated for various time durations at physiological temperatures led to the identification of functionally relevant H68 movements. These movements assist the transition of the L1 stalk between its open and closed states. H68 spatial flexibility and its significance to the protein synthesis process were confirmed through its effective targeting with antisense PNA oligomers. Our results suggest that H68 is actively involved in ribosome movements that are central to the elongation process. IMPORTANCE The mechanism that regulates the translocation step in ribosomes during protein synthesis is not fully understood. In this work, cryo-EM techniques used to image ribosomes from Staphylococcus aureus after incubation at physiological temperature allowed the identification of a conformation of the helix 68 that has never been observed so far. We then propose a mechanism in which such helix, switching between two different conformations, actively coordinates the translocation step, shedding light on the dynamics of ribosomal components. In addition, the relevance of helix 68 to ribosome function and its potential as an antibiotic target was proved by inhibiting Staphylococcus aureus ribosomes activity in vitro using oligomers with sequence complementarity.
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Affiliation(s)
- Giuseppe Cimicata
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, Israel
| | - Gil Fridkin
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, Israel
- Department of Organic Chemistry, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Tanaya Bose
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, Israel
| | - Zohar Eyal
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, Israel
| | - Yehuda Halfon
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, Israel
| | - Elinor Breiner-Goldstein
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, Israel
| | - Tara Fox
- Center for Molecular Microscopy, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland, USA
| | - Ella Zimmerman
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, Israel
| | - Anat Bashan
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, Israel
| | - Natalia de Val
- Center for Molecular Microscopy, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland, USA
| | - Alexander Wlodawer
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - Ada Yonath
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot, Israel
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Hensley MP, Tierney DL, Crowder MW. Zn(II) binding to Escherichia coli 70S ribosomes. Biochemistry 2011; 50:9937-9. [PMID: 22026583 DOI: 10.1021/bi200619w] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Escherichia coli 70S ribosomes tightly bind 8 equiv of Zn(II), and EXAFS spectra indicate that Zn(II) may be protein-bound. Ribosomes were incubated with EDTA and Zn(II), and after dialysis, the resulting ribosomes bound 5 and 11 equiv of Zn(II), respectively. EXAFS studies show that the additional Zn(II) in the zinc-supplemented ribosomes binds in part to the phosphate backbone of the ribosome. Lastly, in vitro translation studies demonstrate that EDTA-treated ribosomes do not synthesize an active Zn(II)-bound metalloenzyme, while the as-isolated ribosomes do. These studies demonstrate that the majority of intracellular Zn(II) resides in the ribosome.
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Affiliation(s)
- M Patrick Hensley
- Department of Chemistry and Biochemistry, 160 Hughes Hall, Miami University, Oxford, Ohio 45056, USA
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Affiliation(s)
- M Nomura
- Laboratory of Genetics, University of Wisconsin, Madison, Wisconsin 53706
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White GA, Wood T, Hill WE. Probing the alpha-sarcin region of Escherichia coli 23S rRNA with a cDNA oligomer. Nucleic Acids Res 1988; 16:10817-31. [PMID: 3060850 PMCID: PMC338941 DOI: 10.1093/nar/16.22.10817] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The cause of 50S ribosomal subunit collapse reportedly triggered by hybridization of a 14-base cDNA probe to the alpha-sarcin region of 23S rRNA was investigated by physical measurement of probe-subunit complexes in varying buffer conditions. The results reported here show that this probe was unable to hybridize to its target site in the intact 50S subunit and the physical characteristics of 50S subunits remained unchanged in its presence. Subunit collapse was induced in buffer containing 20mM Tris-HCl (pH 7.5), 600 mM NH4Cl, 1 mM MgCl2, 1 mM DTT, and 0.1 mM EDTA in the absence of probe. The probe bound specifically to its target site in the collapsed particle, but did not promote further unfolding. The results demonstrate that a DNA probe bound to the alpha-sarcin region cannot cause the 50S subunit to unfold or cause 23S rRNA to degrade. We suggest that the previously reported collapse was most probably the result of the ionic conditions used.
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Affiliation(s)
- G A White
- Department of Chemistry, University of Montana, Missoula 59812
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Abstract
Two bands of RNAase activity were observed on gel electrophoresis of fractions obtained during partial purification of the RNAase of Entamoeba invadens. The faster migrating band which was responsible for most of the RNAase activity was isolated by gel electrophoresis. A pI of 5.5 was determined for this RNAase activity and estimates of its molecular weight and sedimentation coefficient gave values of about 25 000 and approximately 2.8 S. It exhibited maximum activity around pH 6, and digestion of RNA showed a pattern expected of an endoribonuclease.
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Abstract
The 30 S ribosomal subunit from Escherichia coli was unfolded into discrete particles upon which physical studies were carried out. These particles were found to be homogeneous and were characterized using sedimentation velocity, diffusion, density and viscosity measurements. The results of these studies clearly certify two distinct stages of unfolding, neither involving a significant loss of protein. However, the results also clearly show that the measurement of only one characteristic (e.g., the sedimentation coefficient) is not sufficient to suggest a structural change. The significance and importance of the apparent specific volume are stressed.
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Belli M, Onori G, Araco A, Giorgi C. Letter: Changes in the ultraviolet absorption of E. coli rRNA on ribosome unfolding. Biopolymers 1976; 15:1229-32. [PMID: 773445 DOI: 10.1002/bip.1976.360150615] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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8
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Olenick JG. Antibacterial action of primaquine: effects in vitro on polypeptide synthesis and in vivo on ribosomes and ribosomal ribonucleic acid. Antimicrob Agents Chemother 1975; 8:754-6. [PMID: 813574 PMCID: PMC429459 DOI: 10.1128/aac.8.6.754] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Primaquine inhibited polyphenylalanine formation directed by poly(U) in a cell-free system obtained from Bacillus megaterium only when the drug was preincubated with transfer ribonucleic acid (tRNA), poly(U), or ribosomes. Considerably less inhibition was produced when the ionic strength of the preincubation mixture of tRNA or poly(U) plus primaquine was increased; with ribosomes, the extent of inhibition was only slightly reduced. In cultures of B. megaterium, primaquine induced the breakdown of ribosomes and their RNA.
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Garrett RA, Schulte C, Stöffler G, Gray P, Monier R. The release of proteins and 5S RNA during the unfolding of Escherichia coli ribosomes. FEBS Lett 1974; 49:1-4. [PMID: 4216514 DOI: 10.1016/0014-5793(74)80617-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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10
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Spirin AS. Structural transformations of ribosomes (dissociation, unfolding and disassembly). FEBS Lett 1974; 40:suppl:S38-47. [PMID: 4605150 DOI: 10.1016/0014-5793(74)80687-3] [Citation(s) in RCA: 31] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Robinson A, Sykes J. A comparison of the unfolding and dissociation of the large ribosome subunits from Rhodopseudomonas spheroides N.C.I.B. 8253 and Escherichia coli M.R.E. 600. Biochem J 1973; 133:739-47. [PMID: 4201305 PMCID: PMC1177764 DOI: 10.1042/bj1330739] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
1. The behaviour of the large ribosomal subunit from Rhodopseudomonas spheroides (45S) has been compared with the 50S ribosome from Escherichia coli M.R.E. 600 (and E. coli M.R.E. 162) during unfolding by removal of Mg(2+) and detachment of ribosomal proteins by high univalent cation concentrations. The extent to which these processes are reversible with these ribosomes has also been examined. 2. The R. spheroides 45S ribosome unfolds relatively slowly but then gives rise directly to two ribonucleoprotein particles (16.6S and 13.7S); the former contains the intact primary structure of the 16.25S rRNA species and the latter the 15.00S rRNA species of the original ribosome. No detectable protein loss occurs during unfolding. The E. coli ribosome unfolds via a series of discrete intermediates to a single, unfolded ribonucleoprotein unit (19.1S) containing the 23S rRNA and all the protein of the original ribosome. 3. The two unfolded R. spheroides ribonucleoproteins did not recombine when the original conditions were restored but each simply assumed a more compact configuration. Similar treatments reversed the unfolding of the E. coli 50S ribosomes; replacement of Mg(2+) caused the refolding of the initial products of unfolding and in the presence of Ni(2+) the completely unfolded species (19.1S) again sedimented at the same rate as the original ribosomes (44S). 4. Ribosomal proteins (25%) were dissociated from R. spheroides 45S ribosomes by dialysis against a solution with a Na(+)/Mg(2+) ratio of 250:1. During this process two core particles were formed (21.2S and 14.2S) and the primary structures of the two original rRNA species were conserved. This dissociation was not reversed. With E. coli 50S approximately 15% of the original ribosomal protein was dissociated, a single 37.6S core particle was formed, the 23S rRNA remained intact and the ribosomal proteins would reassociate with the core particle to give a 50S ribosome. 5. The ribonuclease activities in R. spheroides 45S and E. coli M.R.E. 600 and E. coli M.R.E. 162 50S ribosomes are compared. 6. The observations concerning unfolding and dissociation are consistent with previous reports showing the unusual rRNA complement of the mature R. spheroides 45S ribosome and show the dependence of these events upon the rRNA and the importance of protein-protein interactions in the structure of the R. spheroides ribosome.
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12
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Weller DL, Heaney A, Franceschi RT, Boudreau RE, Shaw DE. Isoelectric focusing and study of ribosomal proteins and lactate dehydrogenase. Ann N Y Acad Sci 1973; 209:258-80. [PMID: 4577169 DOI: 10.1111/j.1749-6632.1973.tb47533.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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15
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Maruyama HB, Okamura S. Ribosome degradation and the degradation products in starved Escherichia coli. V. Ribonucleoprotein particles from glucose-starved cells. J Bacteriol 1972; 110:442-6. [PMID: 4553002 PMCID: PMC247426 DOI: 10.1128/jb.110.1.442-446.1972] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The properties of the abnormal ribonucleoprotein particles produced by Escherichia coli Q-13 starved for glucose were studied. Smaller species of these partially deproteinized particles separable to six distinct sizes contained partially degraded ribonucleic acids. The mode of ribosome degradation under this condition is discussed in terms of differential appearance of these intermediate particles.
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16
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Khawaja JA. Interaction of ribosomes and ribosomal subparticles with endoplasmic reticulum membranes in vitro: effect of spermine and magnesium. BIOCHIMICA ET BIOPHYSICA ACTA 1971; 254:117-28. [PMID: 5134203 DOI: 10.1016/0005-2787(71)90118-3] [Citation(s) in RCA: 44] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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17
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Shires TK, Narurkar L, Pitot HC. The association in vitro of polyribosomes with ribonuclease-treated derivatives of hepatic rough endoplasmic reticulum. Characteristics of the membrane binding sites and factors influencing association. Biochem J 1971; 125:67-79. [PMID: 5158923 PMCID: PMC1178026 DOI: 10.1042/bj1250067] [Citation(s) in RCA: 59] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
1. Pancreatic ribonuclease in dilute EDTA has been shown to condition rough-microsomal membranes from adult rat liver to accept exogenously added rat liver polyribosomes in vitro at 0-4 degrees C. Treated smooth membranes would not significantly interact with polyribosomes. 2. The conditioning process decreased the membrane RNA content and removed polyribosomes from vesicle surfaces as viewed electron-microscopically. 3. Binding to these conditioned membranes was shown to be uninfluenced by changes of temperature (0-37 degrees C) and pH (6.9-7.8) or the presence of cell sap, but was inhibited by increasing the concentration of potassium chloride. 4. Possession of a polyribosome-binding capacity by conditioned rough membranes was not dependent on adventitious materials that could be dislodged by high ionic strengths. 5. Trypsin treatment under mild conditions destroyed the binding capacity of ribonuclease-conditioned rough membranes. 6. A 2-10S residual RNA was recovered from ribonuclease-conditioned membranes, but its partial removal had no effect on the capacity of membranes to accept polyribosomes. However, some role for this residual RNA in attaching polyribosomes could not be discounted. 7. Evidence is considered that polyribosome-binding sites are intrinsic features of conditioned membranes isolated from rough-microsomal fractions, and that long-range ionic bonding is a primary factor in polyribosome interaction with these binding sites.
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19
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The effect of monovalent cations on the sedimentation behavior of Escherichia coli ribosomes. ACTA ACUST UNITED AC 1971. [DOI: 10.1016/0005-2787(71)90534-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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20
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Eilam Y, Elson D. Unfolding of the 30S ribosomal subunit of Escherichia coli and the conformation of the unfolded subunit. Parallel sedimentation and optical rotatory dispersion studies. Biochemistry 1971; 10:1489-95. [PMID: 4996353 DOI: 10.1021/bi00784a034] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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21
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Kaiser II, Haffley JL, Weller DL, Horowitz J. Interaction of bacterial ribosomes with bentonite. BIOCHIMICA ET BIOPHYSICA ACTA 1971; 232:388-402. [PMID: 4928716 DOI: 10.1016/0005-2787(71)90592-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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22
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Hill WE, Anderegg JW, Van Holde KE. Effects of solvent environment and mode of preparation on the physical properties of ribosomes fron Escherichia coli. J Mol Biol 1970; 53:107-21. [PMID: 4922219 DOI: 10.1016/0022-2836(70)90048-3] [Citation(s) in RCA: 37] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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23
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Adler AJ, Fasman GD, Tal M. Circular dichroism of Escherichia coli ribosomes: effect of heating and metal ions. BIOCHIMICA ET BIOPHYSICA ACTA 1970; 213:424-36. [PMID: 4994395 DOI: 10.1016/0005-2787(70)90050-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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24
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Huston RL, Schrader LE, Honold GR, Beecher GR, Cooper WK, Sauberlich HE. Factors influencing the isolation of a polyribosomal system from rat liver and its ability to incorporate [14C]amino acids. BIOCHIMICA ET BIOPHYSICA ACTA 1970; 209:220-39. [PMID: 5421968 DOI: 10.1016/0005-2787(70)90678-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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25
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Cammack KA, Miller DS, Grinstead KH. Physical properties of ribosomal ribonucleic acid isolated from bacteria deficient in ribonuclease I. Biochem J 1970; 117:745-55. [PMID: 4915439 PMCID: PMC1179027 DOI: 10.1042/bj1170745] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
1. Bacteria deficient in ribonuclease I were used as a source of stable ribosomal RNA. RNA was isolated from a ribosome fraction of Pseudomonas fluorescens N.C.I.B. 8248 and acetone-treated cells of Escherichia coli M.R.E. 600 by the method developed by Robinson & Wade (1968). 2. The s(20,w) of the 16S and 23S components can vary from 21S and 28S down to 4S depending on the RNA macro-ion concentration and the extent to which charge is suppressed by univalent Na(+) and tris(+) counter-ions or neutralized through the binding of bivalent Mg(2+) to phosphate groups. 3. The primary charge effect in sedimentation and the frictional coefficient (which increases as the molecular conformation expands) both increase with charge and cause a decrease in s value. 4. RNA solutions heated to 80 degrees C for 10min show minor changes in s value and a detectable increase in polydispersity. Millimolar concentrations of Mg(2+) promote heat-instability and so does treatment of RNA solutions with the nuclease adsorbent macaloid, which was found to contaminate the solutions with Mg(2+). 5. The stabilization of secondary structure by univalent and bivalent cations was investigated by optical methods. 6. The sedimentation properties of 30S and 50S ribosomal subunits and their constituent 16S and 23S RNA components were compared and discussed from the viewpoint of unfolding.
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Weiss RL, Morris DR. The inality of polyamines to maintain ribosome structure and function. BIOCHIMICA ET BIOPHYSICA ACTA 1970; 204:502-11. [PMID: 4909655 DOI: 10.1016/0005-2787(70)90170-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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Maruyama H, Ono M, Mizuno D. Ribosome degradation and the degradation products in starved Escherichia coli. 3. Ribosomal RNA degradation during the complete deprivation of nutrients. BIOCHIMICA ET BIOPHYSICA ACTA 1970; 199:176-83. [PMID: 4905132 DOI: 10.1016/0005-2787(70)90706-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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29
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Traub P. Structure, function and in vitro reconstitution of escherichia coli ribosomes. Curr Top Microbiol Immunol 1970; 52:1-93. [PMID: 4915756 DOI: 10.1007/978-3-642-95130-5_1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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Atsmon A, Spitnik-Elson P, Elson D. Detachment of ribosomal proteins by salt. II. Some properties of protein-deficient particles formed by the detachment of ribosomal proteins. J Mol Biol 1969; 45:125-35. [PMID: 4898841 DOI: 10.1016/0022-2836(69)90215-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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