Molecular mimicry: Quantitative methods to study structural similarity between protein and RNA

Liang, Han; Landweber, Laura F.

doi:10.1261/rna.7207205

Cited by 8 publications

(7 citation statements)

References 28 publications

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“…This intriguing connection highlights the importance of molecular mimicry in the RNA-RNP (RNA plus protein) transition (Nakamura, 2001;Liang and Landweber, 2005;Delarue, 2007), and strongly supports our earlier hypothesis that the two complementary recognition patterns of acceptor stems by the class I and class II p-aaRSs were inherited from the two isofunctional ribozymes (Rodin et al, 1996). This is also relevant to the possible origin of the two p-aaRSs from the complementary strands of the same ancestral gene (Rodin and Ohno, 1995) that conceivably, directly recapitulates the preceding complementarity of the two r-aaRSs.…”

Section: Sn Rodin and As Rodinmentioning

confidence: 92%

On the origin of the genetic code: signatures of its primordial complementarity in tRNAs and aminoacyl-tRNA synthetases

Rodin

2008

Heredity

103

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If the table of the genetic code is rearranged to put complementary codons face-to-face, it becomes apparent that the code displays latent mirror symmetry with respect to two sterically different modes of tRNA recognition. These modes involve distinct classes of aminoacyl-tRNA synthetases (aaRSs I and II) with recognition from the minor or major groove sides of the acceptor stem, respectively. We analyze the anticodon pairs complementary to the face-toface codon couplets. Taking into account the invariant nucleotides on either side (5 0 and 3 0 ), we consider the risk of anticodon confusion and subsequent erroneous aminoacylation in the ancestral coding system. This logic leads to the conclusion that ribozymic precursors of tRNA synthetases had the same two complementary modes of tRNA aminoacylation. This surprising case of molecular mimicry (1) shows a key potential selective advantage arising from the partitioning of aaRSs into two classes, (2) is consistent with the hypothesis that the two aaRS classes were originally encoded by the complementary strands of the same primordial gene and (3) provides a 'missing link' between the classic genetic code, embodied in the anticodon, and the second, or RNA operational, code that is embodied mostly in the acceptor stem and is directly responsible for proper tRNA aminoacylation.

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Section: Sn Rodin and As Rodinmentioning

confidence: 92%

On the origin of the genetic code: signatures of its primordial complementarity in tRNAs and aminoacyl-tRNA synthetases

Rodin

2008

Heredity

103

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“…The fact that the extant aaRS mode of tRNA aminoacylation is used to extract clues to a mechanism that is postulated to have been done solely by RNA in the beginning is justified a posteriori by the fact that there are several situations where such a molecular mimicry phenomenon between proteins and tRNA, in e.g., RF1 and RF2 and EF-Tu, is known and documented (Liang and Landweber 2005).…”

Section: Invasion Of the Codon Table: A Two-step Model?mentioning

confidence: 99%

An asymmetric underlying rule in the assignment of codons: Possible clue to a quick early evolution of the genetic code via successive binary choices

Delarue¹

2006

RNA

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Aminoacyl-tRNA synthetases (aaRSs) are responsible for creating the pool of correctly charged aminoacyl-tRNAs that are necessary for the translation of genetic information (mRNA) by the ribosome. Each aaRS belongs to either one of only two classes with two different mechanisms of aminoacylation, making use of either the 29OH (Class I) or the 39OH (Class II) of the terminal A76 of the tRNA and approaching the tRNA either from the minor groove (29OH) or the major groove (39OH). Here, an asymmetric pattern typical of differentiation is uncovered in the partition of the codon repertoire, as defined by the mechanism of aminoacylation of each corresponding tRNA. This pattern can be reproduced in a unique cascade of successive binary decisions that progressively reduces codon ambiguity. The deduced order of differentiation is manifestly driven by the reduction of translation errors. A simple rule can be defined, decoding each codon sequence in its binary class, thereby providing both the code and the key to decode it. Assuming that the partition into two mechanisms of tRNA aminoacylation is a relic that dates back to the invention of the genetic code in the RNA World, a model for the assignment of amino acids in the codon table can be derived. The model implies that the stop codon was always there, as the codon whose tRNA cannot be charged with any amino acid, and makes the prediction of an ultimate differentiation step, which is found to correspond to the codon assignment of the 22nd amino acid pyrrolysine in archaebacteria.

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“…Molecular mimicry refers to the process that a molecule evolves to resemble another molecule in terms of the structure, and thus also mimics the function ( Liang and Landweber, 2005 ; Pasteur, 1982 ). For example, translation initiation factor 2A (eIF2A) is mimicked by K3L from poxviruses ( Katz et al , 2014 ).…”

Section: Structure Alignment Of Protein–rna Mimicrymentioning

confidence: 99%

Finding optimal interaction interface alignments between biological complexes

2015

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Motivation: Biological molecules perform their functions through interactions with other molecules. Structure alignment of interaction interfaces between biological complexes is an indispensable step in detecting their structural similarities, which are keys to understanding their evolutionary histories and functions. Although various structure alignment methods have been developed to successfully access the similarities of protein structures or certain types of interaction interfaces, existing alignment tools cannot directly align arbitrary types of interfaces formed by protein, DNA or RNA molecules. Specifically, they require a ‘blackbox preprocessing’ to standardize interface types and chain identifiers. Yet their performance is limited and sometimes unsatisfactory.Results: Here we introduce a novel method, PROSTA-inter, that automatically determines and aligns interaction interfaces between two arbitrary types of complex structures. Our method uses sequentially remote fragments to search for the optimal superimposition. The optimal residue matching problem is then formulated as a maximum weighted bipartite matching problem to detect the optimal sequence order-independent alignment. Benchmark evaluation on all non-redundant protein–DNA complexes in PDB shows significant performance improvement of our method over TM-align and iAlign (with the ‘blackbox preprocessing’). Two case studies where our method discovers, for the first time, structural similarities between two pairs of functionally related protein–DNA complexes are presented. We further demonstrate the power of our method on detecting structural similarities between a protein–protein complex and a protein–RNA complex, which is biologically known as a protein–RNA mimicry case.Availability and implementation: The PROSTA-inter web-server is publicly available at http://www.cbrc.kaust.edu.sa/prosta/.Contact: xin.gao@kaust.edu.sa

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Molecular mimicry: Quantitative methods to study structural similarity between protein and RNA

Cited by 8 publications

References 28 publications

On the origin of the genetic code: signatures of its primordial complementarity in tRNAs and aminoacyl-tRNA synthetases

On the origin of the genetic code: signatures of its primordial complementarity in tRNAs and aminoacyl-tRNA synthetases

An asymmetric underlying rule in the assignment of codons: Possible clue to a quick early evolution of the genetic code via successive binary choices

Finding optimal interaction interface alignments between biological complexes

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