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Lake JA, Larsen J, Tran DT, Sinsheimer JS. Uncovering the Genomic Origins of Life. Genome Biol Evol 2018; 10:1705-1714. [PMID: 29947758 PMCID: PMC6047450 DOI: 10.1093/gbe/evy129] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/25/2018] [Indexed: 11/14/2022] Open
Abstract
The Origin of Life Domain (OLD) is the period during which life on Earth began. Here, we derive and use a new phylogenetic algorithm to analyze Protein Families in order to reconstruct the chronological steps by which the OLD evolved. During this period, life began with the appearance of the fundamental components of life such as RNAs, DNAs, amino acids, and membranes. Chronologically, the Origin of Life preceded the Last Universal Common Ancestor, which then subsequently engendered modern life on Earth. Our phylogenetic algorithm allows us to explicitly answer previously unknown origin of life questions. Specifically, we explain and illustrate our computational methods by reconstructing the rings describing the evolution of the RNA and DNA worlds. We phylogenetically reconstruct how the RNA and DNA worlds evolved, infer the origins and chronological order of appearance of the first genetic codes, test whether the Ribosomal RNA world preceded the Membrane world, and interpret these new findings with respect to the experimental and theoretical origin of life studies by others.
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Affiliation(s)
- James A Lake
- Molecular, Cell and Developmental Biology, University of California, Los Angeles.,Molecular Biology Institute, University of California, Los Angeles.,Human Genetics, University of California, Los Angeles
| | - Joseph Larsen
- Molecular, Cell and Developmental Biology, University of California, Los Angeles.,Molecular Biology Institute, University of California, Los Angeles.,Biomathematics, University of California, Los Angeles
| | - Dan Thy Tran
- Molecular, Cell and Developmental Biology, University of California, Los Angeles.,Molecular Biology Institute, University of California, Los Angeles
| | - Janet S Sinsheimer
- Human Genetics, University of California, Los Angeles.,Biomathematics, University of California, Los Angeles
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2
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Mutation. Evol Bioinform Online 2016. [DOI: 10.1007/978-3-319-28755-3_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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3
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Abstract
The bacterial ribosome is a complex macromolecular machine that deciphers the genetic code with remarkable fidelity. During the elongation phase of protein synthesis, the ribosome selects aminoacyl-tRNAs as dictated by the canonical base pairing between the anticodon of the tRNA and the codon of the messenger RNA. The ribosome's participation in tRNA selection is active rather than passive, using conformational changes of conserved bases of 16S rRNA to directly monitor the geometry of codon-anticodon base pairing. The tRNA selection process is divided into an initial selection step and a subsequent proofreading step, with the utilization of two sequential steps increasing the discriminating power of the ribosome far beyond that which could be achieved based on the thermodynamics of codon-anticodon base pairing stability. The accuracy of decoding is impaired by a number of antibiotics and can be either increased or decreased by various mutations in either subunit of the ribosome, in elongation factor Tu, and in tRNA. In this chapter we will review our current understanding of various forces that determine the accuracy of decoding by the bacterial ribosome.
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4
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Atkins JF, Björk GR. A gripping tale of ribosomal frameshifting: extragenic suppressors of frameshift mutations spotlight P-site realignment. Microbiol Mol Biol Rev 2009; 73:178-210. [PMID: 19258537 PMCID: PMC2650885 DOI: 10.1128/mmbr.00010-08] [Citation(s) in RCA: 111] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mutants of translation components which compensate for both -1 and +1 frameshift mutations showed the first evidence for framing malleability. Those compensatory mutants isolated in bacteria and yeast with altered tRNA or protein factors are reviewed here and are considered to primarily cause altered P-site realignment and not altered translocation. Though the first sequenced tRNA mutant which suppressed a +1 frameshift mutation had an extra base in its anticodon loop and led to a textbook "yardstick" model in which the number of anticodon bases determines codon size, this model has long been discounted, although not by all. Accordingly, the reviewed data suggest that reading frame maintenance and translocation are two distinct features of the ribosome. None of the -1 tRNA suppressors have anticodon loops with fewer than the standard seven nucleotides. Many of the tRNA mutants potentially affect tRNA bending and/or stability and can be used for functional assays, and one has the conserved C74 of the 3' CCA substituted. The effect of tRNA modification deficiencies on framing has been particularly informative. The properties of some mutants suggest the use of alternative tRNA anticodon loop stack conformations by individual tRNAs in one translation cycle. The mutant proteins range from defective release factors with delayed decoding of A-site stop codons facilitating P-site frameshifting to altered EF-Tu/EF1alpha to mutant ribosomal large- and small-subunit proteins L9 and S9. Their study is revealing how mRNA slippage is restrained except where it is programmed to occur and be utilized.
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Affiliation(s)
- John F Atkins
- BioSciences Institute, University College, Cork, Ireland.
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5
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Taliaferro DL, Farabaugh PJ. Testing constraints on rRNA bases that make nonsequence-specific contacts with the codon-anticodon complex in the ribosomal A site. RNA (NEW YORK, N.Y.) 2007; 13:1279-86. [PMID: 17592040 PMCID: PMC1924888 DOI: 10.1261/rna.552007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
During protein synthesis, interactions between the decoding center of the ribosome and the codon-anticodon complexes maintain translation accuracy. Correct aminoacyl-tRNAs induce the ribosome to shift into a "closed" conformation that both blocks tRNA dissociation and accelerates the process of tRNA acceptance. As part of the ribosomal recognition of cognate tRNAs, the rRNA nucleotides G530 and A1492 form a hydrogen-bonded pair that interacts with the middle position of the codon.anticodon complex and recognizes correct Watson-Crick base pairs. Exchanging these two nucleotides (A530 and G1492) would not disrupt these interactions, suggesting that such a double mutant ribosome might properly recognize tRNAs and support viability. We find, however, that exchange mutants retain little ribosomal activity. We suggest that even though the exchanged nucleotides might function properly during tRNA recruitment, they might disrupt one or more other functions of the nucleotides during other stages of protein synthesis.
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Affiliation(s)
- Dwayne L Taliaferro
- Program in Molecular and Cell Biology, Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, MD 21250, USA
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6
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Rospert S, Rakwalska M, Dubaquié Y. Polypeptide chain termination and stop codon readthrough on eukaryotic ribosomes. REVIEWS OF PHYSIOLOGY BIOCHEMISTRY AND PHARMACOLOGY 2006; 155:1-30. [PMID: 15928926 DOI: 10.1007/3-540-28217-3_1] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
During protein translation, a variety of quality control checks ensure that the resulting polypeptides deviate minimally from their genetic encoding template. Translational fidelity is central in order to preserve the function and integrity of each cell. Correct termination is an important aspect of translational fidelity, and a multitude of mechanisms and players participate in this exquisitely regulated process. This review explores our current understanding of eukaryotic termination by highlighting the roles of the different ribosomal components as well as termination factors and ribosome-associated proteins, such as chaperones.
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Affiliation(s)
- S Rospert
- Universität Freiburg, Institut für Biochemie und Molekularbiologie, Hermann-Herder-Strasse 7, 79104 Freiburg, Germany.
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7
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Forsdyke DR. Species Survival and Arrival. Evol Bioinform Online 2006. [DOI: 10.1007/978-0-387-33419-6_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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8
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Abstract
The underlying basis for the accuracy of protein synthesis has been the subject of over four decades of investigation. Recent biochemical and structural data make it possible to understand at least in outline the structural basis for tRNA selection, in which codon recognition by cognate tRNA results in the hydrolysis of GTP by EF-Tu over 75 A away. The ribosome recognizes the geometry of codon-anticodon base pairing at the first two positions but monitors the third, or wobble position, less stringently. Part of the additional binding energy of cognate tRNA is used to induce conformational changes in the ribosome that stabilize a transition state for GTP hydrolysis by EF-Tu and subsequently result in accelerated accommodation of tRNA into the peptidyl transferase center. The transition state for GTP hydrolysis is characterized, among other things, by a distorted tRNA. This picture explains a large body of data on the effect of antibiotics and mutations on translational fidelity. However, many fundamental questions remain, such as the mechanism of activation of GTP hydrolysis by EF-Tu, and the relationship between decoding and frameshifting.
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Affiliation(s)
- James M Ogle
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 2QH, United Kingdom.
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9
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Rospert S, Rakwalska M, Dubaquié Y. Polypeptide chain termination and stop codon readthrough on eukaryotic ribosomes. Rev Physiol Biochem Pharmacol 2005. [DOI: 10.1007/s10254-005-0039-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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10
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Xue HY, Forsdyke DR. Low-complexity segments in Plasmodium falciparum proteins are primarily nucleic acid level adaptations. Mol Biochem Parasitol 2003; 128:21-32. [PMID: 12706793 DOI: 10.1016/s0166-6851(03)00039-2] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Protein segments that contain few of the possible 20 amino acids, sometimes in tandem repeat arrays, are referred to as containing "simple" or "low-complexity" sequence. Many Plasmodium falciparum proteins are longer than their homologs in other species by virtue of their content of such low-complexity segments that have no known function; these are interspersed among segments of higher complexity to which function can often be ascribed. If there is low complexity at the protein level, there is likely to be low complexity at the corresponding nucleic acid level (departure from equifrequency of the four bases). Thus, low complexity may have been selected primarily at the nucleic acid level and low complexity at the protein level may be secondary. In this case, the amino acid composition of low-complexity segments should be more reflective than that of high complexity segments on forces operating at the nucleic acid level, which include GC-pressure and AG-pressure. Consistent with this, for amino acid determining first and second codon positions, open reading frames containing low-complexity segments show increased contributions to downward GC-pressure (revealed as decreased percentage of G+C) and to upward AG-pressure (revealed as increased percentage A+G). When not countermanded by high contributions to AG-pressure, low-complexity segments can contribute to base order-dependent fold potential; in this respect, they resemble introns. Thus, in P. falciparum, low-complexity segments appear as adaptations primarily serving nucleic acid level functions.
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Affiliation(s)
- H Y Xue
- Department of Biochemistry, Queen's University, Kingston, Ont, K7L3N6, Canada
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11
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Sanbonmatsu KY, Joseph S. Understanding discrimination by the ribosome: stability testing and groove measurement of codon-anticodon pairs. J Mol Biol 2003; 328:33-47. [PMID: 12683995 DOI: 10.1016/s0022-2836(03)00236-5] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The ribosome must discriminate between correct and incorrect tRNAs with sufficient speed and accuracy to sustain an adequate rate of cell growth. Here, we report the results of explicit solvent molecular dynamics simulations, which address the mechanism of discrimination by the ribosome. The universally conserved 16S rRNA base A1493 and the kink in mRNA between A and P sites amplify differences in stability between cognate and near-cognate codon-anticodon pairs. Destabilization by the mRNA kink also provides a geometric explanation for the higher error rates observed for mismatches in the first codon position relative to mismatches in the second codon position. For more stable near-cognates, the repositioning of the universally conserved bases A1492 and G530 results in increased solvent exposure and an uncompensated loss of hydrogen bonds, preventing correct codon-anticodon-ribosome interactions from forming.
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Affiliation(s)
- K Y Sanbonmatsu
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
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12
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Plant EP, Jacobs KLM, Harger JW, Meskauskas A, Jacobs JL, Baxter JL, Petrov AN, Dinman JD. The 9-A solution: how mRNA pseudoknots promote efficient programmed -1 ribosomal frameshifting. RNA (NEW YORK, N.Y.) 2003; 9:168-74. [PMID: 12554858 PMCID: PMC1237042 DOI: 10.1261/rna.2132503] [Citation(s) in RCA: 115] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
There is something special about mRNA pseudoknots that allows them to elicit efficient levels of programmed -1 ribosomal frameshifting. Here, we present a synthesis of recent crystallographic, molecular, biochemical, and genetic studies to explain this property. Movement of 9 A by the anticodon loop of the aminoacyl-tRNA at the accommodation step normally pulls the downstream mRNA a similar distance along with it. We suggest that the downstream mRNA pseudoknot provides resistance to this movement by becoming wedged into the entrance of the ribosomal mRNA tunnel. These two opposing forces result in the creation of a local region of tension in the mRNA between the A-site codon and the mRNA pseudoknot. This can be relieved by one of two mechanisms; unwinding the pseudoknot, allowing the downstream region to move forward, or by slippage of the proximal region of the mRNA backwards by one base. The observed result of the latter mechanism is a net shift of reading frame by one base in the 5' direction, that is, a -1 ribosomal frameshift.
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Affiliation(s)
- Ewan P Plant
- Department of Cell Biology and Molecular Genetics, Microbiology Building, University of Maryland, College Park, MD 20742, USA
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13
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Abstract
Expression of the tryptophanase operon of Escherichia coli is regulated by catabolite repression and tryptophan-induced transcription antitermination. An induction site activated by l-tryptophan is created in the translating ribosome during synthesis of TnaC, the 24-residue leader peptide. Replacing the tnaC stop codon with a tryptophan codon allows tryptophan-charged tryptophan transfer RNA to substitute for tryptophan as inducer. This suggests that the ribosomal A site occupied by the tryptophanyl moiety of the charged transfer RNA is the site of induction. The location of tryptophan-12 of nascent TnaC in the peptide exit tunnel was crucial for induction. These results show that a nascent peptide sequence can influence translation continuation and termination within a translating ribosome.
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Affiliation(s)
- Feng Gong
- Department of Biological Sciences, Stanford University, Stanford, CA 94305, USA
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14
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Rodnina MV, Daviter T, Gromadski K, Wintermeyer W. Structural dynamics of ribosomal RNA during decoding on the ribosome. Biochimie 2002; 84:745-54. [PMID: 12457562 DOI: 10.1016/s0300-9084(02)01409-8] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Decoding is a multistep process by which the ribosome accurately selects aminoacyl-tRNA (aa-tRNA) that matches the mRNA codon in the A site. The correct geometry of the codon-anticodon complex is monitored by the ribosome, resulting in conformational changes in the decoding center of the small (30S) ribosomal subunit by an induced-fit mechanism. The recognition of aa-tRNA is modulated by changes of the ribosome conformation in regions other than the decoding center that may either affect the architecture of the latter or alter the communication of the 30S subunit with the large (50S) subunit where the GTPase and peptidyl transferase centers are located. Correct codon-anticodon complex formation greatly accelerates the rates of GTP hydrolysis and peptide bond formation, indicating the importance of crosstalk between the subunits and the role of the 50S subunit in aa-tRNA selection. In the present review, recent results of the ribosome crystallography, cryoelectron microscopy (cryo-EM), genetics, rapid kinetics and biochemical approaches are reviewed which show that the dynamics of the structure of ribosomal RNA (rRNA) play a crucial role in decoding.
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Affiliation(s)
- Marina V Rodnina
- Institute of Physical Biochemistry, University of Witten/Herdecke, Stockumer Str 10, 58448, Witten, Germany.
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15
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Valle M, Sengupta J, Swami NK, Grassucci RA, Burkhardt N, Nierhaus KH, Agrawal RK, Frank J. Cryo-EM reveals an active role for aminoacyl-tRNA in the accommodation process. EMBO J 2002; 21:3557-67. [PMID: 12093756 PMCID: PMC126079 DOI: 10.1093/emboj/cdf326] [Citation(s) in RCA: 252] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
During the elongation cycle of protein biosynthesis, the specific amino acid coded for by the mRNA is delivered by a complex that is comprised of the cognate aminoacyl-tRNA, elongation factor Tu and GTP. As this ternary complex binds to the ribosome, the anticodon end of the tRNA reaches the decoding center in the 30S subunit. Here we present the cryo- electron microscopy (EM) study of an Escherichia coli 70S ribosome-bound ternary complex stalled with an antibiotic, kirromycin. In the cryo-EM map the anticodon arm of the tRNA presents a new conformation that appears to facilitate the initial codon-anticodon interaction. Furthermore, the elbow region of the tRNA is seen to contact the GTPase-associated center on the 50S subunit of the ribosome, suggesting an active role of the tRNA in the transmission of the signal prompting the GTP hydrolysis upon codon recognition.
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MESH Headings
- Anticodon/genetics
- Codon/genetics
- Cryoelectron Microscopy
- Escherichia coli/chemistry
- Escherichia coli Proteins/chemistry
- Escherichia coli Proteins/ultrastructure
- Guanosine Diphosphate/chemistry
- Guanosine Triphosphate/metabolism
- Image Processing, Computer-Assisted
- Macromolecular Substances
- Models, Molecular
- Nucleic Acid Conformation
- Peptide Chain Elongation, Translational
- Peptide Elongation Factor Tu/chemistry
- Peptide Elongation Factor Tu/ultrastructure
- Protein Conformation
- Pyridones/pharmacology
- RNA, Transfer/chemistry
- RNA, Transfer, Amino Acyl/chemistry
- RNA, Transfer, Amino Acyl/metabolism
- RNA, Transfer, Amino Acyl/physiology
- RNA, Transfer, Amino Acyl/ultrastructure
- RNA, Transfer, Phe/chemistry
- RNA, Transfer, Phe/metabolism
- Ribosomes/chemistry
- Ribosomes/drug effects
- Ribosomes/ultrastructure
- Structure-Activity Relationship
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Affiliation(s)
- Mikel Valle
- Howard Hughes Medical Institute, Health Research, Inc., at the Wadsworth Center, New York State Department of Health, Empire State Plaza, Albany, NY 12201-0509, Columbia High School, 962 Luther Road, East Greenbush, NY 12061, Department of Biomedical Sciences, State University of New York at Albany, Empire State Plaza, Albany, NY 12201-0509, USA and Max-Planck-Institut für Molekulare Genetik, Ihnestrasse 73, D-14195 Berlin, Germany Corresponding author e-mail:
| | - Jayati Sengupta
- Howard Hughes Medical Institute, Health Research, Inc., at the Wadsworth Center, New York State Department of Health, Empire State Plaza, Albany, NY 12201-0509, Columbia High School, 962 Luther Road, East Greenbush, NY 12061, Department of Biomedical Sciences, State University of New York at Albany, Empire State Plaza, Albany, NY 12201-0509, USA and Max-Planck-Institut für Molekulare Genetik, Ihnestrasse 73, D-14195 Berlin, Germany Corresponding author e-mail:
| | - Neil K. Swami
- Howard Hughes Medical Institute, Health Research, Inc., at the Wadsworth Center, New York State Department of Health, Empire State Plaza, Albany, NY 12201-0509, Columbia High School, 962 Luther Road, East Greenbush, NY 12061, Department of Biomedical Sciences, State University of New York at Albany, Empire State Plaza, Albany, NY 12201-0509, USA and Max-Planck-Institut für Molekulare Genetik, Ihnestrasse 73, D-14195 Berlin, Germany Corresponding author e-mail:
| | - Robert A. Grassucci
- Howard Hughes Medical Institute, Health Research, Inc., at the Wadsworth Center, New York State Department of Health, Empire State Plaza, Albany, NY 12201-0509, Columbia High School, 962 Luther Road, East Greenbush, NY 12061, Department of Biomedical Sciences, State University of New York at Albany, Empire State Plaza, Albany, NY 12201-0509, USA and Max-Planck-Institut für Molekulare Genetik, Ihnestrasse 73, D-14195 Berlin, Germany Corresponding author e-mail:
| | - Nils Burkhardt
- Howard Hughes Medical Institute, Health Research, Inc., at the Wadsworth Center, New York State Department of Health, Empire State Plaza, Albany, NY 12201-0509, Columbia High School, 962 Luther Road, East Greenbush, NY 12061, Department of Biomedical Sciences, State University of New York at Albany, Empire State Plaza, Albany, NY 12201-0509, USA and Max-Planck-Institut für Molekulare Genetik, Ihnestrasse 73, D-14195 Berlin, Germany Corresponding author e-mail:
| | - Knud H. Nierhaus
- Howard Hughes Medical Institute, Health Research, Inc., at the Wadsworth Center, New York State Department of Health, Empire State Plaza, Albany, NY 12201-0509, Columbia High School, 962 Luther Road, East Greenbush, NY 12061, Department of Biomedical Sciences, State University of New York at Albany, Empire State Plaza, Albany, NY 12201-0509, USA and Max-Planck-Institut für Molekulare Genetik, Ihnestrasse 73, D-14195 Berlin, Germany Corresponding author e-mail:
| | - Rajendra K. Agrawal
- Howard Hughes Medical Institute, Health Research, Inc., at the Wadsworth Center, New York State Department of Health, Empire State Plaza, Albany, NY 12201-0509, Columbia High School, 962 Luther Road, East Greenbush, NY 12061, Department of Biomedical Sciences, State University of New York at Albany, Empire State Plaza, Albany, NY 12201-0509, USA and Max-Planck-Institut für Molekulare Genetik, Ihnestrasse 73, D-14195 Berlin, Germany Corresponding author e-mail:
| | - Joachim Frank
- Howard Hughes Medical Institute, Health Research, Inc., at the Wadsworth Center, New York State Department of Health, Empire State Plaza, Albany, NY 12201-0509, Columbia High School, 962 Luther Road, East Greenbush, NY 12061, Department of Biomedical Sciences, State University of New York at Albany, Empire State Plaza, Albany, NY 12201-0509, USA and Max-Planck-Institut für Molekulare Genetik, Ihnestrasse 73, D-14195 Berlin, Germany Corresponding author e-mail:
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16
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Metzler DE, Metzler CM, Sauke DJ. Ribosomes and the Synthesis of Proteins. Biochemistry 2001. [DOI: 10.1016/b978-012492543-4/50032-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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