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Chen K, Eargle J, Lai J, Kim H, Abeysirigunawardena S, Mayerle M, Woodson S, Ha T, Luthey-Schulten Z. Assembly of the five-way junction in the ribosomal small subunit using hybrid MD-Gō simulations. J Phys Chem B 2012; 116:6819-31. [PMID: 22458631 DOI: 10.1021/jp212614b] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Assembly of the bacterial ribosomal small subunit (SSU) begins with the folding of the five-way junction upon interaction with the primary binding protein S4. This complex contains the largest contiguous molecular signature, which is a conserved feature in all bacterial 16S rRNAs. In a previous study, we used all-atom molecular dynamics simulations to demonstrate that the co-evolving signature in the N-terminus of S4 is intrinsically disordered and capable of accelerating the binding process through a fly casting mechanism. In this paper, comparisons between the all-atom MD simulations and FRET experiments identify multiple metastable conformations of the naked five-way junction without the presence of S4. Furthermore, we capture the simultaneous folding and binding of the five-way junction and r-protein S4 by use of a structure-based Gō potential implemented within the framework of the all-atom molecular dynamics CHARMM force field. Different folding pathways are observed for the refolding of the five-way junction upon partial binding of S4. Our simulations illustrate the complex nature of RNA folding in the presence of a protein binding partner and provide insight into the role of population shift and the induced fit mechanisms in the protein:RNA folding and binding process.
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Affiliation(s)
- Ke Chen
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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2
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Abstract
Ribosomal protein S4 from Escherichia coli binds a large domain of 16 S ribosomal RNA and also a pseudoknot structure in the alpha operon mRNA, where it represses its own synthesis. No similarity between the two RNA binding sites has been detected. To find out whether separate protein regions are responsible for rRNA and mRNA recognition, proteins with N-terminal or C-terminal deletions have been overexpressed and purified. Protein-mRNA interactions were detected by (i) a nitrocellulose filter binding assay, (ii) inhibition of primer extension by reverse transcriptase, and (iii) a gel shift assay. Circular dichroism spectra were taken to determine whether the proteins adopted stable secondary structures. From these studies it is concluded that amino acids 48-104 make specific contacts with the mRNA, although residues 105-177 (out of 205) are required to observe the same toeprint pattern as full-length protein and may stabilize a specific portion of the mRNA structure. These results parallel ribosomal RNA binding properties of similar fragments (Conrad, R. C., and Craven, G. R. (1987) Nucleic Acids Res. 15, 10331-10343, and references therein). It appears that the same protein domain is responsible for both mRNA and rRNA binding activities.
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Affiliation(s)
- A M Baker
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, USA
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3
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Cachia C, Flamion PJ, Schreiber JP. Fast preparative separation of 'native' core E coli 30S ribosomal proteins. Biochimie 1991; 73:607-10. [PMID: 1764505 DOI: 10.1016/0300-9084(91)90029-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We have developed an ion-exchange high performance liquid chromatographic method for preparative separation of 'core' proteins from E coli 30S ribosomal subunits, extracted with salt under non-denaturing conditions. This method yields individual proteins in pure and native form at high concentrations, (5 to 25 mg/ml) suitable for direct use in 1D-, 2D- or 3D-NMR studies.
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Affiliation(s)
- C Cachia
- Laboratoire de Biophysique, UFR des Sciences Pharmaceutiques et Biologiques, Dijon, France
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4
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Liljas A. Comparative biochemistry and biophysics of ribosomal proteins. INTERNATIONAL REVIEW OF CYTOLOGY 1991; 124:103-36. [PMID: 2001915 DOI: 10.1016/s0074-7696(08)61525-9] [Citation(s) in RCA: 71] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- A Liljas
- Department of Molecular Biophysics, Lund University, Sweden
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5
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Capel MS, Kjeldgaard M, Engelman DM, Moore PB. Positions of S2, S13, S16, S17, S19 and S21 in the 30 S ribosomal subunit of Escherichia coli. J Mol Biol 1988; 200:65-87. [PMID: 3288761 DOI: 10.1016/0022-2836(88)90334-8] [Citation(s) in RCA: 93] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Neutron scattering distance data are presented for 33 protein pairs in the 30 S ribosomal subunit from Escherichia coli, along with the methods used for measuring distances between its exchangeable components. When combined with prior data, these new results permit the positioning of S2, S13, S16, S17, S19 and S21 in the 30 S ribosomal subunit, completing the mapping of its proteins by neutron scattering. Comparisons with other data suggest that the neutron map is a reliable guide to the quaternary structure of the 30 S subunit.
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Affiliation(s)
- M S Capel
- Department of Chemistry, Yale University, New Haven, CT 06511
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6
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Deckman IC, Draper DE. S4-alpha mRNA translation regulation complex. II. Secondary structures of the RNA regulatory site in the presence and absence of S4. J Mol Biol 1987; 196:323-32. [PMID: 2443720 DOI: 10.1016/0022-2836(87)90693-0] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The secondary structure of the Escherichia coli alpha mRNA leader sequence has been determined using nucleases specific for single- or double-stranded RNA. Three different length alpha RNA fragments were studied at 0 degrees C and 37 degrees C. A very stable eight base-pair helix forms upstream from the ribosome initiation site, defining a 29 base loop. There is evidence for base-pairing between nucleotides within this loop and for a "pseudo-knot" interaction of some loop bases with nucleotides just 3' to the initiation codon, forming a region of complex structure. A weak helix also pairs sequences near the 5' terminus of the alpha mRNA with bases near the Shine-Dalgarno sequence. Affinity constants for the translational repressor S4 binding different length alpha mRNA fragments indicate that most of the S4 recognition features must be contained within the main helix and hairpin regions. Binding of S4 to the alpha mRNA alters the structure of the 29 base hairpin region, and probably melts the weak pairing between the 5' and 3' termini of the leader. The pseudo-knot structure and the conformational changes associated with it provide a link between the structures of the S4 binding site and the ribosome binding site. The alpha mRNA may therefore play an active role in mediating translational repression.
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Affiliation(s)
- I C Deckman
- Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218
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7
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Littlechild J, Malcolm A, Paterakis K, Ackermann I, Dijk J. The tertiary structure of salt-extracted ribosomal proteins from Escherichia coli as studied by proton magnetic resonance spectroscopy and limited proteolysis experiments. BIOCHIMICA ET BIOPHYSICA ACTA 1987; 913:245-55. [PMID: 3297162 DOI: 10.1016/0167-4838(87)90336-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Ribosomal proteins from Escherichia coli have been isolated by a mild purification procedure. Their tertiary structure has been explored by two techniques, proton magnetic resonance and limited proteolysis. A number of proteins when subjected to limited proteolysis produce resistant fragments in good yields. In most cases this does not depend on the specificity of the enzyme used. The proteins S15, S16, S17 and L30 are not degraded at all, whereas a few proteins are very susceptible to proteolysis. 1H-NMR experiments show that the majority of the ribosomal proteins have a uniquely folded tertiary structure. This is particularly pronounced in the four proteins mentioned above which resist proteolysis. In general, a good agreement is observed between the degree of proteolytic resistance and the amount of folding indicated by NMR spectroscopy. Similar studies on a few ribosomal proteins purified under denaturing conditions show that, in contrast, these protein preparations are not structurally homogeneous and that they contain a mixture of denatured and renatured molecules. The results are interpreted in terms of a compactly folded tertiary structure for the four proteinase-resistant proteins while the majority of the other proteins appear to have two domains, one compactly folded and resistant to proteinase and the other flexible and susceptible to proteolysis. A few proteins seem to have a completely flexible structure and can therefore be easily degraded.
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9
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Dijk J, Littlechild JA, Freund AM, Pouyet J, Daune M, Provencher SW. The secondary structure of salt-extracted ribosomal proteins from Escherichia coli as studied by circular dichroic spectroscopy. BIOCHIMICA ET BIOPHYSICA ACTA 1986; 874:227-34. [PMID: 3535896 DOI: 10.1016/0167-4838(86)90122-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Ribosomal proteins from Escherichia coli MRE600 have been obtained by a new, mild purification procedure. This involves extraction of the subunits with salt followed by chromatographic fractionation in the presence of salt. The use of urea or other denaturing agents and conditions is avoided. A survey of the secondary structure of the 30 S and 50 S proteins, as observed by circular dichroic spectroscopy, is presented. The spectra have been analysed by a new procedure which uses a library of 16 circular dichroic spectra of proteins with a known three-dimensional structure. This method provides a more reliable analysis, especially of the contribution from beta-sheet. The results show that most of the 30 S proteins have a high alpha-helix content, whereas the 50 S proteins are more diverse. The latter group shows a larger contribution from beta-sheet. The data presented here are compared with those already published for a number of proteins which were, with one exception, prepared in the presence of urea. In most cases we find higher alpha-helix and beta-sheet values for the salt-extracted proteins than for the corresponding urea-treated proteins. In those cases, however, where special care was taken to renature the urea-treated proteins agreement is found to within the expected experimental error. The results show that salt-extracted ribosomal proteins have a well-defined secondary structure with a relatively small contribution from unordered structure.
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Möller W, Maassen JA. On the Structure, Function, and Dynamics of L7/L12 from Escherichia coliRibosomes. ACTA ACUST UNITED AC 1986. [DOI: 10.1007/978-1-4612-4884-2_18] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
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11
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Maassen JA, Schop EN, Möller W. Localization of Lys-51 of L7/L12 on 50S ribosomes from Escherichia coli. EUROPEAN JOURNAL OF BIOCHEMISTRY 1984; 138:131-4. [PMID: 6420152 DOI: 10.1111/j.1432-1033.1984.tb07891.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Ribosomal protein L7/L12 from Escherichia coli was modified specifically at Lys-51 with 4-(6-formyl-3-azido-phenoxy)butyrimidate. Reconstitution of ribosomal cores, lacking L7/L12, with imidate-modified L7/L12 resulted in back formation of 50S particles which were fully active in elongation-factor-dependent processes. By use of the formylazidophenoxy moiety as hapten, the position of Lys-51 of L7/L12 on the 50S ribosome was determined by immune electron microscopy. The results show that an L7/L12 dimer is present in the L7/L12 stalk in such a way that Lys-51 is located at the far cytoplasmic end of the stalk. The experimental data are discussed in relation to a proposed model for the L7/L12 dimer.
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12
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Giri L, Hill WE, Wittmann HG, Wittmann-Liebold B. Ribosomal proteins: their structure and spatial arrangement in prokaryotic ribosomes. ADVANCES IN PROTEIN CHEMISTRY 1984; 36:1-78. [PMID: 6382961 DOI: 10.1016/s0065-3233(08)60295-8] [Citation(s) in RCA: 59] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
During the last 15 years of ribosomal protein study, enormous progress has been made. Each of the proteins from E. coli ribosomes has been isolated, sequenced, and immunologically and physically characterized. Ribosomal proteins from other sources (e.g., from some bacteria, yeast, and rat) have been isolated and studied as well. Several proteins have recently been crystallized, and from the X-ray studies it is expected that much important information on the three-dimensional structure will be forthcoming. Many other proteins can probably be crystallized if suitable preparative procedures and crystallization conditions are found. Tremendous progress has also been made in deciphering the architecture of the ribosome. A battery of different methods has been used to provide the nearest neighbor distances of the ribosomal proteins in situ. Definitive measurements are now emanating from neutron-scattering experiments which also promise to give reasonably accurate radii of gyration of the proteins in situ. In turn, refined immune electron microscopy results supplement the neutron-scattering data and also position the proteins on the subunits themselves. This cannot be done by the other methods. Determination of the three-dimensional RNA structure within the ribosome is still in its infancy. Nonetheless, it is expected that by combining the data from protein-RNA and from RNA-RNA cross-linking studies, the structure of the RNA in situ can be unraveled. Of great interest is the fact that ribosomal subunits and ribosomes themselves have now been crystallized, and low-resolution structural maps have already been obtained. However, to grow suitable crystals and to resolve the ribosomal structure at a sufficiently high resolution remains a great challenge and task to biochemists and crystallographers.
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Winkelmann DA, Kahan L, Lake JA. Ribosomal protein S4 is an internal protein: Localization by immunoelectron microscopy on protein-deficient subribosomal particles. Proc Natl Acad Sci U S A 1982; 79:5184-8. [PMID: 6752941 PMCID: PMC346859 DOI: 10.1073/pnas.79.17.5184] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The location of protein S4 in the small ribosomal subunit has been identified by immunoelectron microscopy. Although intact small subunits are not reactive with antibodies directed against protein S4, subribosomal particles reconstituted without proteins S5 and S12 are reactive. By using these "incomplete" subparticles, we have mapped the position of S4. It is located at a single site on the exterior (cytoplasmic) side of the subunit, at the partition that separates the one-third, or head, from two-thirds, or base, of the subunit. In this location, protein S4 is "beneath" proteins S5 and S12. All three proteins are members of a complex on, or near, the external surface of the small ribosomal subunit that plays an important role in regulation of translational fidelity.
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14
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Venyaminov SY, Gogia ZV. Optical characteristics of all individual proteins from the small subunit of Escherichia coli ribosomes. EUROPEAN JOURNAL OF BIOCHEMISTRY 1982; 126:299-309. [PMID: 6751823 DOI: 10.1111/j.1432-1033.1982.tb06779.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The procedure of isolation and renaturation of all ribosomal proteins from the 30-S subunit of Escherichia coli ribosomes is described. Absorption spectra of these proteins in the near-ultraviolet region have been measured and molar absorption coefficients have been determined on the basis of nitrogen content. Molar absorption coefficients have been calculated for 20 proteins with a known amino acid sequence and the calculated values have been compared with the experimentally determined ones. The absorption spectra obtained allow an easy, precise and highly reproducible spectrophotometric determination of the concentration of individual ribosomal proteins. Circular dichroic spectra of 21 individual proteins from the 30-S subunit of E. coli ribosomes were measured in the range 184-310 nm. The secondary structure of the proteins studied was calculated from the spectra in the range 190-240 nm. Almost all proteins (except proteins S12, S17, S18 and S19) are characterized by a high content of secondary structure. Circular dichroic spectra in the near-ultraviolet region (240-310 nm) indicate that the side groups of aromatic amino acids are fixed in the tertiary structure of the proteins studied. Some internal characteristics (independent of the measurement conditions) of the circular dichroic spectrum in the far-ultraviolet region were proposed as a measure of the resemblance to the native state of ribosomal proteins; these characteristics may be useful for comparison of protein preparations obtained by different methods in different laboratories.
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16
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Ramakrishnan VR, Yabuki S, Sillers IY, Schindler DG, Engelman DM, Moore PB. Positions of proteins S6, S11 and S15 in the 30 S ribosomal subunit of Escherichia coli. J Mol Biol 1981; 153:739-60. [PMID: 7040690 DOI: 10.1016/0022-2836(81)90416-2] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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17
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Gogia ZV, Bushuev VN, Spirin AS. Study of the secondary and tertiary structure of ribosomal protein S7 from Escherichia coli in solution. FEBS Lett 1981; 130:279-82. [PMID: 7026290 DOI: 10.1016/0014-5793(81)81139-8] [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: 01/23/2023]
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18
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Serdyuk IN, Sarkisyan MA, Gogia ZV. Compact structure of ribosomal protein S4 in solution as revealed by small-angle x-ray scattering. FEBS Lett 1981; 129:55-8. [PMID: 6268459 DOI: 10.1016/0014-5793(81)80754-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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19
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Tumanova LG, Gudkov AT, Bushuev VN, Okon MS. Study of the tertiary structure of protein L11 from Escherichia coli ribosomes in solution by proton magnetic resonance. FEBS Lett 1981; 127:241-4. [PMID: 6263707 DOI: 10.1016/0014-5793(81)80215-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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20
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Kime MJ, Ratcliffe RG, Moore PB, Williams RJ. A proton NMR study of ribosomal protein L25 from Escherichia coli. EUROPEAN JOURNAL OF BIOCHEMISTRY 1981; 116:269-76. [PMID: 7018905 DOI: 10.1111/j.1432-1033.1981.tb05329.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
A highly folded form of the ribosomal protein L25 from Escherichia coli can be obtained from urea-denatured preparations. Proton NMR data show that this form of the molecule must have a compact, globular tertiary structure. Spectroscopically it is indistinguishable from L25 prepared by methods which avoid denaturing solvents. Thus L25 is a protein which can be reversibly denatured. The stability and solubility of the folded form of the protein are discussed and primary assignments made for a number of resonances in its NMR spectrum. The paper shows that this folded form of the protein can be characterised using NMR spectroscopy. High-resolution NMR spectroscopy provides a sensitive and general way for the characterisation of protein folds.
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21
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Wittmann HG, Dijk J, Brimacombe R. The structure and evolution of ribosomes and their components. CURRENT TOPICS IN CELLULAR REGULATION 1981; 18:487-504. [PMID: 7023857 DOI: 10.1016/b978-0-12-152818-8.50035-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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22
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Kime MJ, Ratcliffe RG, Moore PB, Williams RJ. On the renaturation of ribosomal protein L11. EUROPEAN JOURNAL OF BIOCHEMISTRY 1980; 110:493-8. [PMID: 7002552 DOI: 10.1111/j.1432-1033.1980.tb04891.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
When urea-denatured preparations of protein L11 from the ribosome of Escherichia coli are introduced into physiological buffers, two completely different configurations can be obtained. One form, by NMR criteria, shows little evidence of stable tertiary interactions; the other shows strong indications of a distinctive folding pattern. The configuration obtained depends on minor details of the method used for returning samples to non-denaturing conditions.
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23
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Serdyuk IN, Shpungin JL, Zaccai G. Neutron scattering study of the 13 S fragment of 16 S RNA and its complex with ribosomal protein S4. J Mol Biol 1980; 137:109-21. [PMID: 6154143 DOI: 10.1016/0022-2836(80)90160-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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