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Afzelius BA, Maunsbach AB. Biological ultrastructure research; the first 50 years. Tissue Cell 2004; 36:83-94. [PMID: 15041410 DOI: 10.1016/j.tice.2003.11.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2003] [Revised: 10/30/2003] [Accepted: 11/12/2003] [Indexed: 11/26/2022]
Abstract
The second half of the 20th century has witnessed the birth and growth of biological ultrastructure research--a branch of cell biology in which electron microscopy plays an important role. After a humble start in around 1950, when only a limited arsenal of instrumentation was available, a wealth of auxiliary methodologies were developed and gradually put in use. Here we review these techniques: ultramicrotomy of "optimally" fixed and prepared samples, histochemical methods such as immuno-electron microscopy and electron microscope autoradiography, negative staining techniques, freeze-fracturing and other techniques. Closer to the millennium shift, various cryotechniques have gradually developed. Together with computer-based reconstruction methods they are likely to play increasingly more important roles in the future.
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Affiliation(s)
- Björn A Afzelius
- Wenner-Gren Institute, Stockholm University, SE-106 91 Stockholm, Sweden.
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2
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Abstract
PURPOSE OF REVIEW Structural biology is one of the most informative disciplines available to biochemical research. It unites technologies that can reveal high-resolution (often atomic) details of the inner workings of biochemical systems. These insights are crucial for an understanding of basic life processes, such as the reaction mechanism of a drug-converting enzyme, signal transduction from one protein to another, activation of a metabolic pathway by a gene effector, action modes of drugs, or the consequences of a mutation on the function of an enzyme. Structural biology is also vital for characterizing the molecular basis of many diseases and often provides a starting platform for the development of specifically tuned therapies, for example by designing drugs that bind to particular targets in order to affect their functionality. An overview of the main techniques as well as some selected case studies are presented. RECENT FINDINGS Recent advances in the three major structure determination techniques (X-ray crystallography, nuclear magnetic resonance spectroscopy, and electron microscopy) have made it possible to obtain three-dimensional structural information on larger systems, at higher resolution and with much less effort than in the past. Because these techniques often provide complementary information, combining them is particularly powerful for gaining comprehensive insights into complex systems, as illustrated by the recent structure determinations of the low-density lipoprotein receptor and the ribosome. SUMMARY Structural biology is no longer exclusive to a few dedicated specialists. Many of its techniques are now easily accessible and can be used as tools in general life science research.
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Affiliation(s)
- Mischa Machius
- Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, USA.
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3
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Abstract
Cryoelectron microscopy has made a number of significant contributions to our understanding of the translation process. The method of single-particle reconstruction is particularly well suited for the study of the dynamics of ribosome-ligand interactions. This review follows the events of the functional cycle and discusses the findings in the context provided by the recently published x-ray structures.
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Affiliation(s)
- Joachim Frank
- Howard Hughes Medical Institute, Health Research, Inc, at the Wadsworth Center, and Department of Biomedical Sciences, State University of New York at Albany, Empire State Plaza, Albany, NY 12201-0509, USA.
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4
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Kirillov SV, Wower J, Hixson SS, Zimmermann RA. Transit of tRNA through the Escherichia coli ribosome: cross-linking of the 3' end of tRNA to ribosomal proteins at the P and E sites. FEBS Lett 2002; 514:60-6. [PMID: 11904182 DOI: 10.1016/s0014-5793(02)02302-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Photoreactive derivatives of yeast tRNA(Phe) containing 2-azidoadenosine at their 3' termini were used to trace the movement of tRNA across the 50S subunit during its transit from the P site to the E site of the 70S ribosome. When bound to the P site of poly(U)-programmed ribosomes, deacylated tRNA(Phe), Phe-tRNA(Phe) and N-acetyl-Phe-tRNA(Phe) probes labeled protein L27 and two main sites within domain V of the 23S RNA. In contrast, deacylated tRNA(Phe) bound to the E site in the presence of poly(U) labeled protein L33 and a single site within domain V of the 23S rRNA. In the absence of poly(U), the deacylated tRNA(Phe) probe also labeled protein L1. Cross-linking experiments with vacant 70S ribosomes revealed that deacylated tRNA enters the P site through the E site, progressively labeling proteins L1, L33 and, finally, L27. In the course of this process, tRNA passes through the intermediate P/E binding state. These findings suggest that the transit of tRNA from the P site to the E site involves the same interactions, but in reverse order. Moreover, our results indicate that the final release of deacylated tRNA from the ribosome is mediated by the F site, for which protein L1 serves as a marker. The results also show that the precise placement of the acceptor end of tRNA on the 50S subunit at the P and E sites is influenced in subtle ways both by the presence of aminoacyl or peptidyl moieties and, more surprisingly, by the environment of the anticodon on the 30S subunit.
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Affiliation(s)
- Stanislav V Kirillov
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA 01003, USA
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5
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Sloma MS, Nygård O. Possible interaction sites of mRNA, tRNA, translation factors and the nascent peptide in 5S, 5.8S and 28S rRNA in in vivo assembled eukaryotic ribosomal complexes. BIOCHIMICA ET BIOPHYSICA ACTA 2001; 1521:30-8. [PMID: 11690633 DOI: 10.1016/s0167-4781(01)00286-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
We have investigated possible interaction sites for mRNA, tRNA, translation factors and the nascent peptide on 5S, 5.8S and 28S rRNA in in vivo assembled translational active mouse ribosomes by comparing the chemical footprinting patterns derived from native polysomes, salt-washed polysomes (mainly lacking translational factors) and salt-washed runoff ribosomes (lacking mRNA, tRNA and translational factors). Several ligand-induced footprints were observed in 28S rRNA while no reactivity changes were seen in 5S and 5.8S rRNA. Footprints derived from mRNA, tRNA and/or the nascent peptide chain were observed in domain I of 28S rRNA (hairpin 23), in domain II (helix 37/38 and helices 42 and 43 and in the eukaryotic expansion segment 15), in domain IV (helices 67 and 74) and in domain V (helices 94 and 96 and in the peptidyl transferase ring). Some of the protected sites were homologous to sites previously suggested to be involved in mRNA, tRNA and/or peptide binding in in vitro assembled prokaryotic complexes. Additional footprints were located in regions that have not previously been found involved in ligand binding. Part of these sites could derive from the nascent peptide in the exit channel of the ribosome.
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MESH Headings
- Animals
- Binding Sites
- CME-Carbodiimide/analogs & derivatives
- Eukaryotic Cells/chemistry
- Eukaryotic Cells/metabolism
- Ligands
- Liver/chemistry
- Liver/metabolism
- Mice
- Peptide Initiation Factors/chemistry
- Polyribosomes/chemistry
- Polyribosomes/metabolism
- Protein Structure, Secondary
- Protein Structure, Tertiary
- RNA, Messenger/chemistry
- RNA, Ribosomal, 28S/chemistry
- RNA, Ribosomal, 5.8S/chemistry
- RNA, Ribosomal, 5S/chemistry
- RNA, Transfer/chemistry
- Sulfuric Acid Esters
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Affiliation(s)
- M S Sloma
- Natural Science Section, Södertörns högskola, Huddinge, Sweden
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6
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Abstract
Cryo-electron microscopy allows the visualization of macromolecules in their native state. Combined with techniques of three-dimensional reconstruction, cryo-EM images of single molecules can be used to study macromolecular interactions. The ribosome, a large RNA-protein complex with multiple binding interactions, is an excellent test case illustrating the power of these new techniques. Conformational changes during the binding of tRNA and protein factors to the ribosome can now be studied without the interference of crystal packing. Now that the first X-ray structures of ribosomal subunits have become available, conformational changes observed by cryo-EM in different functional states can be traced back to internal rearrangements of the underlying structural framework. Electron microscopy, X-ray crystallography, and modeling should be used together in the endeavor to understand the functioning of the translational machinery.
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Affiliation(s)
- J Frank
- Howard Hughes Medical Institute, Health Research, Inc. at the Wadsworth Center, Empire State Plaza, Albany, New York 12201-0509, USA
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7
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Jiang QX, Chester DW, Sigworth FJ. Spherical reconstruction: a method for structure determination of membrane proteins from cryo-EM images. J Struct Biol 2001; 133:119-31. [PMID: 11472084 DOI: 10.1006/jsbi.2001.4376] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
We propose a new method for single-particle reconstruction, which should be generally applicable to structure determination for membrane proteins. After reconstitution into a small spherical vesicle, a membrane protein takes a particular orientation relative to the membrane normal, and its position in the projected image of the vesicle directly defines two of its three Euler angles of orientation. The spherical constraint imposed by the vesicle effectively reduces the dimensionality of the alignment search from 5 to 3 and simplifies the detection of the particle. Projection images of particles in vesicles collectively take all possible orientations and therefore cover the whole Fourier space. Analysis of images of vesicles in ice showed that the vesicle density is well described by a simple model for membrane electron scattering density. In fitting this model we found that osmotically swollen vesicles remain nearly spherical through the freezing process. These results satisfy the basic experimental requirements for spherical reconstruction. A computer simulation of particles in vesicles showed that this method provides good estimates of the two Euler angles and thus may improve single-particle reconstruction and extend it to smaller membrane proteins.
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Affiliation(s)
- Q X Jiang
- Department of Cellular and Molecular Physiology, Yale University, 333 Cedar Street, New Haven, Connecticut 06520, USA
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8
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Wower J, Kirillov SV, Wower IK, Guven S, Hixson SS, Zimmermann RA. Transit of tRNA through the Escherichia coli ribosome. Cross-linking of the 3' end of tRNA to specific nucleotides of the 23 S ribosomal RNA at the A, P, and E sites. J Biol Chem 2000; 275:37887-94. [PMID: 10961994 DOI: 10.1074/jbc.m005031200] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
When bound to Escherichia coli ribosomes and irradiated with near-UV light, various derivatives of yeast tRNA(Phe) containing 2-azidoadenosine at the 3' terminus form cross-links to 23 S rRNA and 50 S subunit proteins in a site-dependent manner. A and P site-bound tRNAs, whose 3' termini reside in the peptidyl transferase center, label primarily nucleotides U2506 and U2585 and protein L27. In contrast, E site-bound tRNA labels nucleotide C2422 and protein L33. The cross-linking patterns confirm the topographical separation of the peptidyl transferase center from the E site domain. The relative amounts of label incorporated into the universally conserved residues U2506 and U2585 depend on the occupancy of the A and P sites by different tRNA ligands and indicates that these nucleotides play a pivotal role in peptide transfer. In particular, the 3'-adenosine of the peptidyl-tRNA analogue, AcPhe-tRNA(Phe), remains in close contact with U2506 regardless of whether its anticodon is located in the A site or P site. Our findings, therefore, modify and extend the hybrid state model of tRNA-ribosome interaction. We show that the 3'-end of the deacylated tRNA that is formed after transpeptidation does not immediately progress to the E site but remains temporarily in the peptidyl transferase center. In addition, we demonstrate that the E site, defined by the labeling of nucleotide C2422 and protein L33, represents an intermediate state of binding that precedes the entry of deacylated tRNA into the F (final) site from which it dissociates into the cytoplasm.
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Affiliation(s)
- J Wower
- Department of Animal and Dairy Sciences, Program in Cell and Molecular Biosciences, Auburn University, Auburn, Alabama 36849-5415, USA
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9
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Frank J, Penczek P, Agrawal RK, Grassucci RA, Heagle AB. Three-dimensional cryoelectron microscopy of ribosomes. Methods Enzymol 2000; 317:276-91. [PMID: 10829286 DOI: 10.1016/s0076-6879(00)17020-x] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- J Frank
- Howard Hughes Medical Institute, Wadsworth Center, New York, USA
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10
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Morgan DG, Ménétret JF, Radermacher M, Neuhof A, Akey IV, Rapoport TA, Akey CW. A comparison of the yeast and rabbit 80 S ribosome reveals the topology of the nascent chain exit tunnel, inter-subunit bridges and mammalian rRNA expansion segments. J Mol Biol 2000; 301:301-21. [PMID: 10926511 DOI: 10.1006/jmbi.2000.3947] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Protein synthesis in eukaryotes is mediated by both cytoplasmic and membrane-bound ribosomes. During the co-translational translocation of secretory and membrane proteins, eukaryotic ribosomes dock with the protein conducting channel of the endoplasmic reticulum. An understanding of these processes will require the detailed structure of a eukaryotic ribosome. To this end, we have compared the three-dimensional structures of yeast and rabbit ribosomes at 24 A resolution. In general, we find that the active sites for protein synthesis and translocation have been highly conserved. It is interesting that a channel was visualized in the neck of the small subunit whose entrance is formed by a deep groove. By analogy with the prokaryotic small subunit, this channel may provide a conserved portal through which mRNA is threaded into the decoding center. In addition, both the small and large subunits are built around a dense tubular network. Our analysis further suggests that the nascent chain exit tunnel and the docking surface for the endoplasmic reticulum channel are formed by this network. We surmise that many of these features correspond to rRNA, based on biochemical and structural data. Ribosomal function is critically dependent on the specific association of small and large subunits. Our analysis of eukaryotic ribosomes reveals four conserved inter-subunit bridges with a geometry similar to that found in prokaryotes. In particular, a double-bridge connects the small subunit platform with the interface canyon on the large subunit. Moreover, a novel bridge is formed between the platform and the base of the L1 domain. Finally, size differences between mammalian and yeast large subunit rRNAs have been correlated with five expansion segments that form two large spines and three extended fingers. Overall, we find that expansion segments within the large subunit rRNA have been incorporated at positions distinct from the active sites for protein synthesis and translocation.
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Affiliation(s)
- D G Morgan
- Department of Physiology and Structural Biology, Boston University School of Medicine, 700 Albany St., Boston, MA 02218-2526, USA
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11
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Agrawal RK, Spahn CM, Penczek P, Grassucci RA, Nierhaus KH, Frank J. Visualization of tRNA movements on the Escherichia coli 70S ribosome during the elongation cycle. J Cell Biol 2000; 150:447-60. [PMID: 10931859 PMCID: PMC2175196 DOI: 10.1083/jcb.150.3.447] [Citation(s) in RCA: 130] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2000] [Accepted: 06/16/2000] [Indexed: 11/22/2022] Open
Abstract
Three-dimensional cryomaps have been reconstructed for tRNA-ribosome complexes in pre- and posttranslocational states at 17-A resolution. The positions of tRNAs in the A and P sites in the pretranslocational complexes and in the P and E sites in the posttranslocational complexes have been determined. Of these, the P-site tRNA position is the same as seen earlier in the initiation-like fMet-tRNA(f)(Met)-ribosome complex, where it was visualized with high accuracy. Now, the positions of the A- and E-site tRNAs are determined with similar accuracy. The positions of the CCA end of the tRNAs at the A site are different before and after peptide bond formation. The relative positions of anticodons of P- and E-site tRNAs in the posttranslocational state are such that a codon-anticodon interaction at the E site appears feasible.
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Affiliation(s)
- Rajendra K. Agrawal
- Wadsworth Center, Department of Biomedical Sciences, State University of New York, Albany, New York 12201
| | - Christian M.T. Spahn
- Howard Hughes Medical Institute, Health Research, Incorporated at Wadsworth Center, Albany, New York 12201
- Max-Planck-Institut für Molekulare Genetik, Ihnestrasse 73, D-14195 Berlin, Germany
| | - Pawel Penczek
- Wadsworth Center, Department of Biomedical Sciences, State University of New York, Albany, New York 12201
| | - Robert A. Grassucci
- Howard Hughes Medical Institute, Health Research, Incorporated at Wadsworth Center, Albany, New York 12201
| | - Knud H. Nierhaus
- Max-Planck-Institut für Molekulare Genetik, Ihnestrasse 73, D-14195 Berlin, Germany
| | - Joachim Frank
- Wadsworth Center, Department of Biomedical Sciences, State University of New York, Albany, New York 12201
- Howard Hughes Medical Institute, Health Research, Incorporated at Wadsworth Center, Albany, New York 12201
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12
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Abstract
The ribosome is the site in the cell where proteins are synthesized. Cryo-electron microscopy and X-ray crystallography have revealed the ribosome as a particle made of two subunits, each formed as an intricate mesh of RNAs and many proteins. Ligand-binding experiments followed by cryo-electron microscopy have helped to determine some of the key stages of interaction between the ribosome and the main ligand molecules.
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Affiliation(s)
- J Frank
- Department of Biomedical Science, Howard Hughes Medical Institute, Health Research, Inc., Wadsworth Center, State University of New York at Albany, Albany, 12201-0509 ,USA.
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13
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Lieberman KR, Firpo MA, Herr AJ, Nguyenle T, Atkins JF, Gesteland RF, Noller HF. The 23 S rRNA environment of ribosomal protein L9 in the 50 S ribosomal subunit. J Mol Biol 2000; 297:1129-43. [PMID: 10764578 DOI: 10.1006/jmbi.2000.3621] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Ribosomal protein L9 consists of two globular alpha/beta domains separated by a nine-turn alpha-helix. We examined the rRNA environment of L9 by chemical footprinting and directed hydroxyl radical probing. We reconstituted L9, or individual domains of L9, with L9-deficient 50 S subunits, or with deproteinized 23 S rRNA. A footprint was identified in domain V of 23 S rRNA that was mainly attributable to N-domain binding. Fe(II) was tethered to L9 via cysteine residues introduced at positions along the alpha-helix and in the C-domain, and derivatized proteins were reconstituted with L9-deficient subunits. Directed hydroxyl radical probing targeted regions of domains I, III, IV, and V of 23 S rRNA, reinforcing the view that 50 S subunit architecture is typified by interwoven rRNA domains. There was a striking correlation between the cleavage patterns from the Fe(II) probes attached to the alpha-helix and their predicted orientations, constraining both the position and orientation of L9, as well as the arrangement of specific elements of 23 S rRNA, in the 50 S subunit.
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MESH Headings
- Binding Sites
- Edetic Acid/metabolism
- Escherichia coli/chemistry
- Escherichia coli/genetics
- Ferrous Compounds/metabolism
- Genetic Engineering
- Hydroxyl Radical/metabolism
- Models, Molecular
- Molecular Probes/metabolism
- Molecular Weight
- Mutation/genetics
- Nucleic Acid Conformation
- Protein Structure, Secondary
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Ribosomal, 23S/chemistry
- RNA, Ribosomal, 23S/genetics
- RNA, Ribosomal, 23S/metabolism
- RNA-Binding Proteins/chemistry
- RNA-Binding Proteins/genetics
- RNA-Binding Proteins/metabolism
- Ribosomal Proteins/chemistry
- Ribosomal Proteins/genetics
- Ribosomal Proteins/metabolism
- Ribosomes/chemistry
- Ribosomes/genetics
- Ribosomes/metabolism
- Sulfuric Acid Esters/metabolism
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Affiliation(s)
- K R Lieberman
- Center for Molecular Biology of RNA, Sinsheimer Laboratories, University of California, Santa Cruz, CA, 95064, USA
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14
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Ramachandiran V, Willms C, Kramer G, Hardesty B. Fluorophores at the N terminus of nascent chloramphenicol acetyltransferase peptides affect translation and movement through the ribosome. J Biol Chem 2000; 275:1781-6. [PMID: 10636875 DOI: 10.1074/jbc.275.3.1781] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Structurally different fluorescent probes were covalently attached to methionyl-tRNA(f) and tested for their incorporation into nascent peptides and full-length protein using an Escherichia coli cell-free coupled transcription/translation system. Bovine rhodanese and bacterial chloramphenicol acetyltransferase (CAT) were synthesized using derivatives of cascade yellow, eosin, pyrene, or coumarin attached to [(35)S]Met-tRNA(f). All of the probes tested were incorporated into polypeptides, although less efficiently when compared with formyl-methionine. Eosin, the largest of the fluorophores used with estimated dimensions of 20 x 11 A, caused the largest reduction in product formed. The rate of initiation was reduced with the fluorophore-Met-tRNA(f) compared with fMet-tRNA(f) with pyrene having the least and eosin the biggest effect. Analysis of the nascent polypeptides showed that the modifications at the N terminus affected the rate at which nascent CAT peptides were elongated causing accumulation of peptides of about 4 kDa, possibly by steric hindrance inside the tunnel within the 50 S ribosomal subunit. Fluorescence measurements indicate that the probe at the N terminus of nascent pyrene-CAT peptides is in a relatively hydrophilic environment. This finding is in agreement with recent data showing cross-linking of the N terminus of nascent peptides to nucleotides of the 23 S ribosomal RNA.
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Affiliation(s)
- V Ramachandiran
- Department of Chemistry and Biochemistry, University of Texas, Austin, Texas 78712, USA
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15
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Vladimirov SN, Druzina Z, Wang R, Cooperman BS. Identification of 50S components neighboring 23S rRNA nucleotides A2448 and U2604 within the peptidyl transferase center of Escherichia coli ribosomes. Biochemistry 2000; 39:183-93. [PMID: 10625493 DOI: 10.1021/bi991866o] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The 23S rRNA nucleotides 2604-12 and 2448-58 fall within the central loop of domain V, which forms a major part of the peptidyl transferase center of the ribosome. We report the synthesis of radioactive, photolabile 2'-O-methyloligoRNAs, PHONTs 1 and 2, complementary to these nucleotides and their exploitation in identifying 50S ribosomal subunit components neighboring their target sites. Photolysis of the 50S complex with PHONT 1, complementary to nts 2604-12, leads to target site-specific photoincorporation into protein L2 and 23S rRNA nucleotides A886, Alpha1918, A1919, G1922-C1924, U2563, U2586, and C2601. Photolysis of the 50S complex with PHONT 2, complementary to nts 2448-58, leads to target site-specific probe photoincorporation into proteins L2, L3, one or more of proteins L17, L18, L21, and of proteins L9, L15, L16, and 23S rRNA nucleotides C2456 and psi2457. Chemical footprinting studies show that 2'-O-methyloligoRNA binding causes little distortion of the peptidyl transferase center but do provide suggestive evidence for the location of flexible regions within 23S rRNA. The significance of these results for the structure of the peptidyl transferase center is considered.
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Affiliation(s)
- S N Vladimirov
- Department of Chemistry, University of Pennsylvania, Philadelphia 19104-6323, USA
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16
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Bukhtiyarov Y, Druzina Z, Cooperman BS. Identification of 23S rRNA nucleotides neighboring the P-loop in the Escherichia coli 50S subunit. Nucleic Acids Res 1999; 27:4376-84. [PMID: 10536145 PMCID: PMC148719 DOI: 10.1093/nar/27.22.4376] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We report the synthesis of a radioactive, photolabile 2'-O-methyloligoRNA probe, 2258-53/52(SAz)-48, PHONT1, and its exploitation in identifying 23S rRNA nucleotides neighboring the so-called 'P-loop'. The probe is complementary to nt 2248-2258 in Escherichia coli 50S subunits. PHONT1 contains a p-azidophenacyl group attached to a phosphorothioate bridge between the nucleotides complementary to the positions 2252-2253, such that the photogenerated nitrene is maximally 17-19 A from 23S RNA nucleotides G2252 and G2253. PHONT1 binds to the 50S subunit, and photoincorporates within or immediately adjacent to its target site, as well as into several nucleotides falling between G2357 and A2430. The significance of these results for the structure of the peptidyl transferase center is considered. The PHONT approach is generally applicable to studies of complex RNA-containing molecules.
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Affiliation(s)
- Y Bukhtiyarov
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, USA
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