Large facilities and the evolving ribosome, the cellular machine for genetic-code translation

Yonath, Ada

doi:10.1098/rsif.2009.0167.focus

Cited by 23 publications

(29 citation statements)

References 117 publications

(150 reference statements)

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“…The pocket-like protoribosome proposed previously (Davidovich et al, 2009;Krupkin et al, 2011) is as small as 120-180 nucleotides and might actually be constructed by hybridization of several smaller pieces as well as by ligation or duplication of RNA chains. It is also possible that an even smaller RNA entity could provide the same core functionality as the modern version, which is clearly an optimized ancient entity (Yonath, 2009). Importantly, efforts to demonstrate the existence of an RNA-based RNA replicase have been difficult, with the best working models (Lincoln and Joyce, 2009;Wochner et al, 2011) no less complex than the pocket-like protoribosome considered here.…”

Section: Fox Et Almentioning

confidence: 99%

“…In conjunction with this rotation, the nascent peptide is directed into the exit tunnel (Bashan et al, 2003;Yonath, 2003Yonath, , 2009Zarivach et al, 2004;Agmon et al, 2005). In the absence of the tunnel, for example, when it is blocked, the modern machine stalls, as the nascent peptide does not have anywhere to go.…”

Section: Fox Et Almentioning

confidence: 99%

“…It is involved in protein biosynthesis stalling that occurs in association with cellular events, and antibiotic sensitivity is caused by blockage of the tunnel (Nakatogawa and Ito, 2002;Lu and Deutsch, 2005;Yonath, 2005;Ito et al, 2010;Ramu et al, 2009Ramu et al, , 2011Chiba et al, 2011). In addition, the modern ribosome provides an optimized center for its polymerase function (Yonath, 2009). In particular, in the modern ribosome, the 3¢ end of the A-site tRNA rotates into the P-site while the peptide bond is being formed (Gindulyte et al, 2006).…”

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confidence: 99%

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An Exit Cavity Was Crucial to the Polymerase Activity of the Early Ribosome

Fox

Tran²,

Yonath³

2012

Astrobiology

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The emergence of an RNA entity capable of synthesizing peptides was a key prebiotic development. It is hypothesized that a precursor of the modern ribosomal exit tunnel was associated with this RNA entity (e.g., ''protoribosome'' or ''bonding entity'') from the earliest time and played an essential role. Various compounds that can bind and activate amino acids, including extremely short RNA chains carrying amino acids, and possibly di-or tripeptides, would have associated with the internal cavity of the protoribosome. This cavity hosts the site for peptide bond formation and adjacent to it a relatively elongated feature that could have evolved to the modern ribosomal exit tunnel, as it is wide enough to allow passage of an oligopeptide. When two of the compounds carrying amino acids or di-or tripeptides (to which we refer, for simplicity, as small aminoacylated RNAs) were in proximity within the heart of the protoribosome, a peptide bond could form spontaneously. The growing peptide would enter the nearby cavity and would not disrupt the attachment of the substrates to the protoribosome or interfere with the subsequent attachment of additional small aminoacylated RNAs. Additionally, the presence of the peptide in the cavity would increase the lifetime of the oligopeptide in the protoribosome. Thus, subsequent addition of another amino acid would be more likely than detachment from the protoribosome, and synthesis could continue. The early ability to synthesize peptides may have resulted in an abbreviated RNA World.

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Section: Fox Et Almentioning

confidence: 99%

Section: Fox Et Almentioning

confidence: 99%

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confidence: 99%

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An Exit Cavity Was Crucial to the Polymerase Activity of the Early Ribosome

Fox

Tran²,

Yonath³

2012

Astrobiology

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“…For example, proteins are synthesized inside the tunnel of a ribosome (31) - (33) . One of the most important features of the BetaMol is the recognition of tunnels using the beta-complex and the quasi-triangulation.…”

Section: Tunnelmentioning

confidence: 99%

BetaMol: A Molecular Modeling, Analysis and Visualization Software Based on the Beta-Complex and the Quasi-Triangulation

Cho

Kim

Ryu

et al. 2012

JAMDSM

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Molecular shape is one of the most critical factors that determines molecular function. Therefore, it is frequently desirable to understand geometric characteristics of a molecule more precisely and efficiently. In this paper, we introduce the BetaMol, a molecular modeling, analysis, and visualization software based on the recent theory of the beta-complex and the quasi-triangulation that are derived from the Voronoi diagram of three-dimensional spherical atoms. The powerful features of the BetaMol are solely based on a unified, single framework of the mathematically rigorous and computationally efficient beta-complex theory. The BetaMol is implemented in the standard C++ language with OpenGL graphics library and freely available at Voronoi Diagram Research Center web site (http://voronoi.hanyang.ac.kr).

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“…The limitations of high-resolution protein crystallography due not only to cell dimension, but also to crystal size and quality, are being pushed back. A paper by Yonath (2009) …”

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confidence: 99%