Publications
2008
Simonetti A, Marzi S, Myasnikov A G, Fabbretti A, Yusupov M, Gualerzi C O, Klaholz B P
Structure of the 30S translation initiation complex Journal Article
In: Nature, vol. 455, no. 7211, pp. 416-420, 2008, ISBN: 18758445, (1476-4687 (Electronic) Journal Article Research Support, Non-U.S. Gov't).
Abstract | Links | BibTeX | Tags: Cryoelectron Microscopy Crystallography, Messenger/chemistry/genetics/metabolism RNA, Met/chemistry/genetics/metabolism/ultrastructure Ribosome Subunits/chemistry/metabolism/ultrastructure Ribosomes/chemistry/*metabolism/*ultrastructure Thermus thermophilus/*enzymology/genetics/*ultrastructure, Molecular Multiprotein Complexes/*chemistry/genetics/metabolism/*ultrastructure *Peptide Chain Initiation, ROMBY, Transfer, Translational Prokaryotic Initiation Factor-1/chemistry/genetics/metabolism/ultrastructure Prokaryotic Initiation Factor-2/chemistry/genetics/metabolism/ultrastructure Protein Conformation RNA, Unité ARN, X-Ray Guanosine Triphosphate/chemistry/metabolism Models
@article{,
title = {Structure of the 30S translation initiation complex},
author = {A Simonetti and S Marzi and A G Myasnikov and A Fabbretti and M Yusupov and C O Gualerzi and B P Klaholz},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18758445},
isbn = {18758445},
year = {2008},
date = {2008-01-01},
journal = {Nature},
volume = {455},
number = {7211},
pages = {416-420},
abstract = {Translation initiation, the rate-limiting step of the universal process of protein synthesis, proceeds through sequential, tightly regulated steps. In bacteria, the correct messenger RNA start site and the reading frame are selected when, with the help of initiation factors IF1, IF2 and IF3, the initiation codon is decoded in the peptidyl site of the 30S ribosomal subunit by the fMet-tRNA(fMet) anticodon. This yields a 30S initiation complex (30SIC) that is an intermediate in the formation of the 70S initiation complex (70SIC) that occurs on joining of the 50S ribosomal subunit to the 30SIC and release of the initiation factors. The localization of IF2 in the 30SIC has proved to be difficult so far using biochemical approaches, but could now be addressed using cryo-electron microscopy and advanced particle separation techniques on the basis of three-dimensional statistical analysis. Here we report the direct visualization of a 30SIC containing mRNA, fMet-tRNA(fMet) and initiation factors IF1 and GTP-bound IF2. We demonstrate that the fMet-tRNA(fMet) is held in a characteristic and precise position and conformation by two interactions that contribute to the formation of a stable complex: one involves the transfer RNA decoding stem which is buried in the 30S peptidyl site, and the other occurs between the carboxy-terminal domain of IF2 and the tRNA acceptor end. The structure provides insights into the mechanism of 70SIC assembly and rationalizes the rapid activation of GTP hydrolysis triggered on 30SIC-50S joining by showing that the GTP-binding domain of IF2 would directly face the GTPase-activated centre of the 50S subunit.},
note = {1476-4687 (Electronic)
Journal Article
Research Support, Non-U.S. Gov't},
keywords = {Cryoelectron Microscopy Crystallography, Messenger/chemistry/genetics/metabolism RNA, Met/chemistry/genetics/metabolism/ultrastructure Ribosome Subunits/chemistry/metabolism/ultrastructure Ribosomes/chemistry/*metabolism/*ultrastructure Thermus thermophilus/*enzymology/genetics/*ultrastructure, Molecular Multiprotein Complexes/*chemistry/genetics/metabolism/*ultrastructure *Peptide Chain Initiation, ROMBY, Transfer, Translational Prokaryotic Initiation Factor-1/chemistry/genetics/metabolism/ultrastructure Prokaryotic Initiation Factor-2/chemistry/genetics/metabolism/ultrastructure Protein Conformation RNA, Unité ARN, X-Ray Guanosine Triphosphate/chemistry/metabolism Models},
pubstate = {published},
tppubtype = {article}
}
2000
Klinck R, Westhof E, Walker S, Afshar M, Collier A, Aboul-Ela F
A potential RNA drug target in the hepatitis C virus internal ribosomal entry site Journal Article
In: RNA, vol. 6, no. 10, pp. 1423-1431, 2000, ISBN: 11073218, (1355-8382 Journal Article).
Abstract | Links | BibTeX | Tags: Base Pairing Base Sequence Computational Biology *Drug Design Endoribonucleases/metabolism Genetic Engineering Hepacivirus/*genetics Models, Biomolecular *Nucleic Acid Conformation RNA, Genetic, Messenger/chemistry/genetics/metabolism RNA, Molecular Molecular Sequence Data Mutation Nuclear Magnetic Resonance, Nucleic Acid/*genetics Reproducibility of Results Ribosomes/*metabolism Ricin/metabolism Structure-Activity Relationship Substrate Specificity Translation, Unité ARN, Viral/*chemistry/genetics/*metabolism Regulatory Sequences
@article{,
title = {A potential RNA drug target in the hepatitis C virus internal ribosomal entry site},
author = {R Klinck and E Westhof and S Walker and M Afshar and A Collier and F Aboul-Ela},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11073218},
isbn = {11073218},
year = {2000},
date = {2000-01-01},
journal = {RNA},
volume = {6},
number = {10},
pages = {1423-1431},
abstract = {Subdomain IlId from the hepatitis C virus (HCV) internal ribosome entry site (IRES) has been shown to be essential for cap-independent translation. We have conducted a structural study of a 27-nt fragment, identical in sequence to IlId, to explore the structural features of this subdomain. The proposed secondary structure of IlId is comprised of two 3 bp helical regions separated by an internal loop and closed at one end by a 6-nt terminal loop. NMR and molecular modeling were used interactively to formulate a validated model of the three-dimensional structure of IlId. We found that this fragment contains several noncanonical structural motifs and non-Watson-Crick base pairs, some of which are common to other RNAs. In particular, a motif characteristic of the rRNA alpha-sarcin/ricin loop was located in the internal loop. The terminal loop, 5'-UUGGGU, was found to fold to form a trinucleotide loop closed by a trans-wobble U.G base pair. The sixth nucleotide was bulged out to allow stacking of this U.G pair on the adjacent helical region. In vivo mutational analysis in the context of the full IRES confirmed the importance of each structural motif within IIId for IRES function. These findings may provide clues as to host cellular proteins that play a role in IRES-directed translation and, in particular, the mechanism through which host ribosomes are sequestered for viral function.},
note = {1355-8382
Journal Article},
keywords = {Base Pairing Base Sequence Computational Biology *Drug Design Endoribonucleases/metabolism Genetic Engineering Hepacivirus/*genetics Models, Biomolecular *Nucleic Acid Conformation RNA, Genetic, Messenger/chemistry/genetics/metabolism RNA, Molecular Molecular Sequence Data Mutation Nuclear Magnetic Resonance, Nucleic Acid/*genetics Reproducibility of Results Ribosomes/*metabolism Ricin/metabolism Structure-Activity Relationship Substrate Specificity Translation, Unité ARN, Viral/*chemistry/genetics/*metabolism Regulatory Sequences},
pubstate = {published},
tppubtype = {article}
}
1992
Lavignon M, Tounekti N, Rayner B, Imbach J L, Keith G, Paoletti J, Malvy C
Inhibition of murine leukemia viruses by nuclease-resistant alpha-oligonucleotides Journal Article
In: Antisense Res Dev, vol. 2, no. 4, pp. 315-324, 1992, ISBN: 1292779, (1050-5261 Journal Article).
Abstract | Links | BibTeX | Tags: 3T3 Cells Animals Base Sequence Binding Sites Culture Media Friend murine leukemia virus/*drug effects/genetics/physiology Mice Molecular Sequence Data Moloney murine leukemia virus/*drug effects/genetics/physiology Oligonucleotides, Antisense/metabolism/*pharmacology RNA, Genetic/drug effects, Genetic/drug effects Translation, Messenger/chemistry/genetics/metabolism RNA, Non-U.S. Gov't Transcription, Unité ARN, Viral/chemistry/genetics/metabolism Support
@article{,
title = {Inhibition of murine leukemia viruses by nuclease-resistant alpha-oligonucleotides},
author = {M Lavignon and N Tounekti and B Rayner and J L Imbach and G Keith and J Paoletti and C Malvy},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1292779},
isbn = {1292779},
year = {1992},
date = {1992-01-01},
journal = {Antisense Res Dev},
volume = {2},
number = {4},
pages = {315-324},
abstract = {We studied the antiviral activity of nuclease-resistant alpha-anomeric oligonucleotides. An alpha-oligonucleotide (20-mer) targeted to the primer binding site (PBS) of murine retroviruses inhibited viral spreading. The inhibition only occurred when the cells had been electropermeabilized in the presence of the oligonucleotide. The PBS sequence is involved in reverse transcription and in translation. The data suggest that the oligonucleotide could perturb reverse transcription activity. Thus, either the oligonucleotide induced a decrease in initiation or it inhibited the extension of the minus or plus strands DNA during reverse transcription. These results show that reverse transcription may be an interesting target for antisense oligonucleotides.},
note = {1050-5261
Journal Article},
keywords = {3T3 Cells Animals Base Sequence Binding Sites Culture Media Friend murine leukemia virus/*drug effects/genetics/physiology Mice Molecular Sequence Data Moloney murine leukemia virus/*drug effects/genetics/physiology Oligonucleotides, Antisense/metabolism/*pharmacology RNA, Genetic/drug effects, Genetic/drug effects Translation, Messenger/chemistry/genetics/metabolism RNA, Non-U.S. Gov't Transcription, Unité ARN, Viral/chemistry/genetics/metabolism Support},
pubstate = {published},
tppubtype = {article}
}