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Torkington J, Harries R, O'Connell S, Knight L, Islam S, Bashir N, Watkins A, Fegan G, Cornish J, Rees B, Cole H, Jarvis H, Jones S, Russell I, Bosanquet D, Cleves A, Sewell B, Farr A, Zbrzyzna N, Fiera N, Ellis-Owen R, Hilton Z, Parry C, Bradbury A, Wall P, Hill J, Winter D, Cocks K, Harris D, Hilton J, Vakis S, Hanratty D, Rajagopal R, Akbar F, Ben-Sassi A, Francis N, Jones L, Williamson M, Lindsey I, West R, Smart C, Ziprin P, Agarwal T, Faulkner G, Pinkney T, Vimalachandran D, Lawes D, Faiz O, Nisar P, Smart N, Wilson T, Myers A, Lund J, Smolarek S, Acheson A, Horwood J, Ansell J, Phillips S, Davies M, Davies L, Bird S, Palmer N, Williams M, Galanopoulos G, Rao PD, Jones D, Barnett R, Tate S, Wheat J, Patel N, Rahmani S, Toynton E, Smith L, Reeves N, Kealaher E, Williams G, Sekaran C, Evans M, Beynon J, Egan R, Qasem E, Khot U, Ather S, Mummigati P, Taylor G, Williamson J, Lim J, Powell A, Nageswaran H, Williams A, Padmanabhan J, Phillips K, Ford T, Edwards J, Varney N, Hicks L, Greenway C, Chesters K, Jones H, Blake P, Brown C, Roche L, Jones D, Feeney M, Shah P, Rutter C, McGrath C, Curtis N, Pippard L, Perry J, Allison J, Ockrim J, Dalton R, Allison A, Rendell J, Howard L, Beesley K, Dennison G, Burton J, Bowen G, Duberley S, Richards L, Giles J, Katebe J, Dalton S, Wood J, Courtney E, Hompes R, Poole A, Ward S, Wilkinson L, Hardstaff L, Bogden M, Al-Rashedy M, Fensom C, Lunt N, McCurrie M, Peacock R, Malik K, Burns H, Townley B, Hill P, Sadat M, Khan U, Wignall C, Murati D, Dhanaratne M, Quaid S, Gurram S, Smith D, Harris P, Pollard J, DiBenedetto G, Chadwick J, Hull R, Bach S, Morton D, Hollier K, Hardy V, Ghods M, Tyrrell D, Ashraf S, Glasbey J, Ashraf M, Garner S, Whitehouse A, Yeung D, Mohamed SN, Wilkin R, Suggett N, Lee C, Bagul A, McNeill C, Eardley N, Mahapatra R, Gabriel C, Datt P, Mahmud S, Daniels I, McDermott F, Nodolsk M, Park L, Scott H, Trickett J, Bearn P, Trivedi P, Frost V, Gray C, Croft M, Beral D, Osborne J, Pugh R, Herdman G, George R, Howell AM, Al-Shahaby S, Narendrakumar B, Mohsen Y, Ijaz S, Nasseri M, Herrod P, Brear T, Reilly JJ, Sohal A, Otieno C, Lai W, Coleman M, Platt E, Patrick A, Pitman C, Balasubramanya S, Dickson E, Warman R, Newton C, Tani S, Simpson J, Banerjee A, Siddika A, Campion D, Humes D, Randhawa N, Saunders J, Bharathan B, Hay O. Incisional hernia following colorectal cancer surgery according to suture technique: Hughes Abdominal Repair Randomized Trial (HART). Br J Surg 2022; 109:943-950. [PMID: 35979802 PMCID: PMC10364691 DOI: 10.1093/bjs/znac198] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 05/09/2022] [Accepted: 05/13/2022] [Indexed: 11/14/2022]
Abstract
BACKGROUND Incisional hernias cause morbidity and may require further surgery. HART (Hughes Abdominal Repair Trial) assessed the effect of an alternative suture method on the incidence of incisional hernia following colorectal cancer surgery. METHODS A pragmatic multicentre single-blind RCT allocated patients undergoing midline incision for colorectal cancer to either Hughes closure (double far-near-near-far sutures of 1 nylon suture at 2-cm intervals along the fascia combined with conventional mass closure) or the surgeon's standard closure. The primary outcome was the incidence of incisional hernia at 1 year assessed by clinical examination. An intention-to-treat analysis was performed. RESULTS Between August 2014 and February 2018, 802 patients were randomized to either Hughes closure (401) or the standard mass closure group (401). At 1 year after surgery, 672 patients (83.7 per cent) were included in the primary outcome analysis; 50 of 339 patients (14.8 per cent) in the Hughes group and 57 of 333 (17.1 per cent) in the standard closure group had incisional hernia (OR 0.84, 95 per cent c.i. 0.55 to 1.27; P = 0.402). At 2 years, 78 patients (28.7 per cent) in the Hughes repair group and 84 (31.8 per cent) in the standard closure group had incisional hernia (OR 0.86, 0.59 to 1.25; P = 0.429). Adverse events were similar in the two groups, apart from the rate of surgical-site infection, which was higher in the Hughes group (13.2 versus 7.7 per cent; OR 1.82, 1.14 to 2.91; P = 0.011). CONCLUSION The incidence of incisional hernia after colorectal cancer surgery is high. There was no statistical difference in incidence between Hughes closure and mass closure at 1 or 2 years. REGISTRATION NUMBER ISRCTN25616490 (http://www.controlled-trials.com).
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Olaniyi P, Whiteland H, Shah U, Bodger O, Verma J, Haboubi H, Rees B, Kynaston H, Doak S. Prostate Cancer Progression: Aspirin Induces Toxicity in Prostate Cancer Cell. Int J Surg 2017. [DOI: 10.1016/j.ijsu.2017.08.084] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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James C, Rees B, Cuming T. Anal skin tags excision, decision or indecision? Int J Surg 2016. [DOI: 10.1016/j.ijsu.2016.08.142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Cornish J, Harries RL, Bosanquet D, Rees B, Ansell J, Frewer N, Dhruva Rao PK, Parry C, Ellis-Owen R, Phillips SM, Morris C, Horwood J, Davies ML, Davies MM, Hargest R, Davies Z, Hilton J, Harris D, Ben-Sassi A, Rajagopal R, Hanratty D, Islam S, Watkins A, Bashir N, Jones S, Russell IR, Torkington J. Hughes Abdominal Repair Trial (HART) - Abdominal wall closure techniques to reduce the incidence of incisional hernias: study protocol for a randomised controlled trial. Trials 2016; 17:454. [PMID: 27634489 PMCID: PMC5025615 DOI: 10.1186/s13063-016-1573-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 08/14/2016] [Indexed: 01/05/2023] Open
Abstract
Background Incisional hernias are common complications of midline closure following abdominal surgery and cause significant morbidity, impaired quality of life and increased health care costs. The ‘Hughes Repair’ combines a standard mass closure with a series of horizontal and two vertical mattress sutures within a single suture. This theoretically distributes the load along the incision length as well as across it. There is evidence to suggest that this technique is as effective as mesh repair for the operative management of incisional hernias; however, no trials have compared the Hughes Repair with standard mass closure for the prevention of incisional hernia formation following a midline incision. Methods/design This is a 1:1 randomised controlled trial comparing two suture techniques for the closure of the midline abdominal wound following surgery for colorectal cancer. Full ethical approval has been gained (Wales REC 3, MREC 12/WA/0374). Eight hundred patients will be randomised from approximately 20 general surgical units within the United Kingdom. Patients undergoing open or laparoscopic (more than a 5-cm midline incision) surgery for colorectal cancer, elective or emergency, are eligible. Patients under the age of 18 years, those having mesh inserted or undergoing musculofascial flap closure of the perineal defect in abdominoperineal wound closure, and those unable to give informed consent will be excluded. Patients will be randomised intraoperatively to either the Hughes Repair or standard mass closure. The primary outcome measure is the incidence of incisional hernias at 1 year as assessed by standardised clinical examination. The secondary outcomes include quality of life patient-reported outcome measures, cost-utility analysis, incidence of complete abdominal wound dehiscence and C-POSSUM scores. The incidence of incisional hernia at 1 year, assessed by computerised tomography, will form a tertiary outcome. Discussion A feasibility phase has been completed. The results of the study will be used to inform current and future practice and potentially reduce the risk of incisional hernia formation following midline incisions. Trial registration Trial Registration Number: ISRCTN 25616490. Registered on 1 January 2012. Electronic supplementary material The online version of this article (doi:10.1186/s13063-016-1573-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- J Cornish
- Department of Surgery, University Hospital of Wales, Heath Park, Cardiff, CF14 4XW, UK
| | - R L Harries
- Department of Surgery, University Hospital of Wales, Heath Park, Cardiff, CF14 4XW, UK
| | - D Bosanquet
- Department of Surgery, University Hospital of Wales, Heath Park, Cardiff, CF14 4XW, UK
| | - B Rees
- Department of Surgery, University Hospital of Wales, Heath Park, Cardiff, CF14 4XW, UK
| | - J Ansell
- Department of Surgery, University Hospital of Wales, Heath Park, Cardiff, CF14 4XW, UK
| | - N Frewer
- Department of Surgery, University Hospital of Wales, Heath Park, Cardiff, CF14 4XW, UK
| | - P K Dhruva Rao
- Department of Surgery, University Hospital of Wales, Heath Park, Cardiff, CF14 4XW, UK
| | - C Parry
- Department of Surgery, University Hospital of Wales, Heath Park, Cardiff, CF14 4XW, UK
| | - R Ellis-Owen
- Department of Surgery, University Hospital of Wales, Heath Park, Cardiff, CF14 4XW, UK
| | - S M Phillips
- Department of Surgery, University Hospital of Wales, Heath Park, Cardiff, CF14 4XW, UK
| | - C Morris
- Department of Surgery, University Hospital of Wales, Heath Park, Cardiff, CF14 4XW, UK
| | - J Horwood
- Department of Surgery, University Hospital of Wales, Heath Park, Cardiff, CF14 4XW, UK
| | - M L Davies
- Department of Surgery, University Hospital of Wales, Heath Park, Cardiff, CF14 4XW, UK
| | - M M Davies
- Department of Surgery, University Hospital of Wales, Heath Park, Cardiff, CF14 4XW, UK
| | - R Hargest
- Department of Surgery, University Hospital of Wales, Heath Park, Cardiff, CF14 4XW, UK
| | - Z Davies
- Department of Surgery, University Hospital of Wales, Heath Park, Cardiff, CF14 4XW, UK
| | - J Hilton
- Princess of Wales Hospital, Bridgend, UK
| | | | | | | | - D Hanratty
- Royal Glamorgan Hospital, Llantrisant, UK
| | - S Islam
- Swansea Clinical Trials Unit, Swansea University, Swansea, UK
| | - A Watkins
- Swansea Clinical Trials Unit, Swansea University, Swansea, UK
| | - N Bashir
- Swansea Clinical Trials Unit, Swansea University, Swansea, UK
| | - S Jones
- Involving People, Health and Care Research Wales, Cardiff, UK
| | - I R Russell
- Swansea Clinical Trials Unit, Swansea University, Swansea, UK
| | - J Torkington
- Department of Surgery, University Hospital of Wales, Heath Park, Cardiff, CF14 4XW, UK.
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Abdel-Fatah TMA, Ball G, Miles AK, Moseley P, Green A, Rees B, Ellis IO, Chan SYT. Abstract P6-07-18: Identification of Sperm Associated Antigen 5 (SPAG5) as a novel biological and predictive biomarker in Breast cancer. Cancer Res 2012. [DOI: 10.1158/0008-5472.sabcs12-p6-07-18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Introduction: SPAG5 has been found to be involved in the functional and dynamic regulation of mitotic spindles, and to be essential for chromosome segregation fidelity. Recently we found by using neural network and pathways analysis of a gene expression array data that SPAG5 was among top 10 ranked genes out of 48,000 of transcripts, that accurately predicted worse clinical outcome based on a 10-fold external cross-validation analysis with an average classification accuracy of >99.999%. Moreover we found that 5% of BC showed amplification of SPAG5 locus at chromosome 17q11.2 and SPAG5 mRNA expression levels displayed a statistically significant correlation with its copy number.
Methods: In the current study the molecular and clinicopathological features of SPAG5 expression and its effect on management of BC have been investigated in 2800 BC patients with primary operable invasive BCs constituted four cohorts: 1) A series of 1650 BC patients received adjuvant endocrine and/or CMF chemotherapy according to NPI.2) A series of 256 BC received adjuvant anthracycline-based chemotherapy (ATC-CT)3) A series of 140 primary BC HER2+ patients treated with ATC-CT+ Herceptin 4) To validate SPAG5 as a predictor factor for ATC-CT, 260 patients with locally advanced primary breast cancer treated with neoadjuvant ATC-CT were included and the pathological complete response (pCR) was used to evaluate the response to chemotherapy.
Immunohistochemical staining was performed using Anti–SPAG5 rabbit polyclonal (HPA022479; Sigma).
Results: i) By using dual immunoflurescent in BC cell lines, co-expression of SPAG5 and proliferating cell nuclear antigen (PCNA) was detected in 4 out of 5 of the breast cancer cell lines screened (MCF7, T47D, MDA468 and MDA231) providing evidence for the importance of SPAG5 in cell proliferation. ii) 20% of breast cancer showed SPAG5 protein overexpression. SPAG5 overexpression showed a statistically significant association with ER−, PR−, triple negative phenotype, high grade tumour, high ki67, basal like phenotype and epithelial mesenchymal transition phenotype, p53 mutation and absence of DNA repair genes (BRCA1, ATM and XRCC1); p values <0.0001. iii) In high risk ER− BC patients who did not received any adjuvant therapy or received ineffective CMF chemotherapy, SPAG5+ protein expression had a similar risk of death and recurrence. Receiving ATC-CT had a positive impact on high risk ER− BC patients with SPAG5 protein + expression as SPAG5+ protein expression showed 72–65% less of death, recurrence and metastases compared to SPAG5−; p < 0.0001. The positive impact of ATC-CT on SPAG5+BC has also been confirmed in HER2+ who either received ATC-CT only or ACT-CT plus Herceptin. iv) Moreover, BC received neoadjuvantATC-CT, SPAG5+ BC achieved 39% pCR vs., 6% of SPAG5-negative BC (p < 0.00001). After controlling to other validated predictors for pCR, SPAG5 remained as a powerful independent predictor (HR; 2.4, CI 95%; 1.5–3.9; p = 0.00001).
Conclusion: SPAG5 is an important novel gene implicated in the survival of BC cells and its protein expression is an independent predictor for ATC- CT. SPAG5 may provide new avenues for the discovery of new predictive marker to guide therapeutic intervention.
Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr P6-07-18.
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Affiliation(s)
- TMA Abdel-Fatah
- Nottingham City Hospital NHS Trust, Nottingham; The John van Geest Cancer Research Centre, Nottingham Trent University; University of Nottingham
| | - G Ball
- Nottingham City Hospital NHS Trust, Nottingham; The John van Geest Cancer Research Centre, Nottingham Trent University; University of Nottingham
| | - AK Miles
- Nottingham City Hospital NHS Trust, Nottingham; The John van Geest Cancer Research Centre, Nottingham Trent University; University of Nottingham
| | - P Moseley
- Nottingham City Hospital NHS Trust, Nottingham; The John van Geest Cancer Research Centre, Nottingham Trent University; University of Nottingham
| | - A Green
- Nottingham City Hospital NHS Trust, Nottingham; The John van Geest Cancer Research Centre, Nottingham Trent University; University of Nottingham
| | - B Rees
- Nottingham City Hospital NHS Trust, Nottingham; The John van Geest Cancer Research Centre, Nottingham Trent University; University of Nottingham
| | - IO Ellis
- Nottingham City Hospital NHS Trust, Nottingham; The John van Geest Cancer Research Centre, Nottingham Trent University; University of Nottingham
| | - SYT Chan
- Nottingham City Hospital NHS Trust, Nottingham; The John van Geest Cancer Research Centre, Nottingham Trent University; University of Nottingham
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McMillan DM, Rees B, Irschick DJ. Thermal tolerance and Hsp70 expression in the Western fence lizard,
Sceloporus occidentalis
: Geographic variation in measures of acute stress and their role in selection on sprint speeds. FASEB J 2009. [DOI: 10.1096/fasebj.23.1_supplement.lb121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | - Bernard Rees
- Biological SciencesUniversity of New OrleansNew OrleansLA
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Moran D, Macleod M, Wall E, Eory V, Mcvittie A, Barnes A, Rees B, Pajot G, Matthews R, Smith P, Moxey A. Marginal abatement cost curves for UK agriculture, forestry, land-use and land-use change sector out to 2022. ACTA ACUST UNITED AC 2009. [DOI: 10.1088/1755-1307/6/24/242002] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Yusupov M, Yusupova G, Jenner L, Moras D, Rees B. Structures of the ribosome on different functional states. Acta Crystallogr A 2008. [DOI: 10.1107/s010876730809956x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Jenner L, Rees B, Yusupov M, Yusupova G. Messenger RNA conformations in the ribosomal E site revealed by X-ray crystallography. EMBO Rep 2007; 8:846-50. [PMID: 17721443 PMCID: PMC1973951 DOI: 10.1038/sj.embor.7401044] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2007] [Revised: 06/27/2007] [Accepted: 07/03/2007] [Indexed: 01/02/2023] Open
Abstract
A comparison of messenger RNA in X-ray crystal structures of 70S ribosomal complexes in the initiation, post-initiation and elongation states of translation shows distinct conformational differences in the exit (E) codon. Here, we present structural evidence indicating that, after the initiation event, the E codon nucleotides relax and form a classical A-helical conformation. This conformation is similar to that of the P and A codons, and is favourable for establishing Watson-Crick interactions with the anticodon of E-site transfer RNA.
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Affiliation(s)
- Lasse Jenner
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 1, rue Laurent Fries, Illkirch 67404, France
| | - Bernard Rees
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 1, rue Laurent Fries, Illkirch 67404, France
| | - Marat Yusupov
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 1, rue Laurent Fries, Illkirch 67404, France
| | - Gulnara Yusupova
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 1, rue Laurent Fries, Illkirch 67404, France
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Jenner L, Yusupova G, Rees B, Yusupov M. Structural basis for messenger RNA movement on the ribosome. Acta Crystallogr A 2007. [DOI: 10.1107/s0108767307099643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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Yusupova G, Jenner L, Rees B, Moras D, Yusupov M. Structural basis for messenger RNA movement on the ribosome. Nature 2006; 444:391-4. [PMID: 17051149 DOI: 10.1038/nature05281] [Citation(s) in RCA: 217] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2006] [Accepted: 09/27/2006] [Indexed: 11/09/2022]
Abstract
Translation initiation is a major determinant of the overall expression level of a gene. The translation of functionally active protein requires the messenger RNA to be positioned on the ribosome such that the start/initiation codon will be read first and in the correct frame. Little is known about the molecular basis for the interaction of mRNA with the ribosome at different states of translation. Recent crystal structures of the ribosomal subunits, the empty 70S ribosome and the 70S ribosome containing functional ligands have provided information about the general organization of the ribosome and its functional centres. Here we compare the X-ray structures of eight ribosome complexes modelling the translation initiation, post-initiation and elongation states. In the initiation and post-initiation complexes, the presence of the Shine-Dalgarno (SD) duplex causes strong anchoring of the 5'-end of mRNA onto the platform of the 30S subunit, with numerous interactions between mRNA and the ribosome. Conversely, the 5' end of the 'elongator' mRNA lacking SD interactions is flexible, suggesting a different exit path for mRNA during elongation. After the initiation of translation, but while an SD interaction is still present, mRNA moves in the 3'-->5' direction with simultaneous clockwise rotation and lengthening of the SD duplex, bringing it into contact with ribosomal protein S2.
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MESH Headings
- Bacterial Proteins/chemistry
- Bacterial Proteins/genetics
- Bacterial Proteins/metabolism
- Escherichia coli/genetics
- Models, Molecular
- Molecular Conformation
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Messenger/chemistry
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Transfer/chemistry
- RNA, Transfer/genetics
- RNA, Transfer/metabolism
- Ribosomal Proteins/chemistry
- Ribosomal Proteins/genetics
- Ribosomal Proteins/metabolism
- Ribosomes/chemistry
- Ribosomes/genetics
- Ribosomes/metabolism
- Thermus thermophilus
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Affiliation(s)
- Gulnara Yusupova
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch cedex, France
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Jenner L, Romby P, Rees B, Moras D, Yusupova G, Yusupov M. The thrSmessenger path on the ribosome. Acta Crystallogr A 2005. [DOI: 10.1107/s0108767305090318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Rees B, Jenner L, Yusupov M. Bulk-solvent correction in large macromolecular structures. Acta Crystallogr D Biol Crystallogr 2005; 61:1299-301. [PMID: 16131764 DOI: 10.1107/s0907444905019591] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2005] [Accepted: 06/21/2005] [Indexed: 11/10/2022]
Abstract
The estimation of the bulk-solvent contribution to the diffraction of a macromolecular crystal makes use of a solvent mask which delimits the bulk-solvent regions in the crystal. It is shown that the way this mask is usually defined in CNS contains a bias which can lead to absurd results in the case of very large structures, where the calculations can only be made on relatively coarse grids. A modified procedure is described and applied to 70S ribosome data at 5.5 A resolution. The B factor affecting the bulk solvent is also discussed. Even in this case of very high and widely variable atomic B factors, it seems sufficient to consider a constant and isotropic B factor for the bulk solvent. This is initially set to the average value of the atomic B factor, but can be refined.
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Affiliation(s)
- Bernard Rees
- Laboratoire de Biologie et Génomique Structurales, IGBMC, 1 Rue Laurent Fries, BP 10142, 67400 Illkirch Cedex, France.
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Jenner L, Romby P, Rees B, Schulze-Briese C, Springer M, Ehresmann C, Ehresmann B, Moras D, Yusupova G, Yusupov M. Translational operator of mRNA on the ribosome: how repressor proteins exclude ribosome binding. Science 2005; 308:120-3. [PMID: 15802605 DOI: 10.1126/science.1105639] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The ribosome of Thermus thermophilus was cocrystallized with initiator transfer RNA (tRNA) and a structured messenger RNA (mRNA) carrying a translational operator. The path of the mRNA was defined at 5.5 angstroms resolution by comparing it with either the crystal structure of the same ribosomal complex lacking mRNA or with an unstructured mRNA. A precise ribosomal environment positions the operator stem-loop structure perpendicular to the surface of the ribosome on the platform of the 30S subunit. The binding of the operator and of the initiator tRNA occurs on the ribosome with an unoccupied tRNA exit site, which is expected for an initiation complex. The positioning of the regulatory domain of the operator relative to the ribosome elucidates the molecular mechanism by which the bound repressor switches off translation. Our data suggest a general way in which mRNA control elements must be placed on the ribosome to perform their regulatory task.
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MESH Headings
- Bacterial Proteins/metabolism
- Base Pairing
- Binding Sites
- Crystallization
- Crystallography, X-Ray
- Fourier Analysis
- Models, Molecular
- Nucleic Acid Conformation
- Protein Biosynthesis
- RNA, Bacterial/chemistry
- RNA, Bacterial/metabolism
- RNA, Messenger/chemistry
- RNA, Messenger/metabolism
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 16S/metabolism
- RNA, Transfer, Met/chemistry
- RNA, Transfer, Met/metabolism
- Regulatory Sequences, Ribonucleic Acid
- Repressor Proteins/metabolism
- Ribosomal Proteins/metabolism
- Ribosomes/metabolism
- Thermus thermophilus/genetics
- Thermus thermophilus/metabolism
- Threonine-tRNA Ligase/genetics
- Threonine-tRNA Ligase/metabolism
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Affiliation(s)
- Lasse Jenner
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
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Dock-Bregeon AC, Rees B, Torres-Larios A, Bey G, Caillet J, Moras D. Achieving error-free translation; the mechanism of proofreading of threonyl-tRNA synthetase at atomic resolution. Mol Cell 2004; 16:375-86. [PMID: 15525511 DOI: 10.1016/j.molcel.2004.10.002] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2004] [Revised: 08/06/2004] [Accepted: 08/17/2004] [Indexed: 10/26/2022]
Abstract
The fidelity of aminoacylation of tRNA(Thr) by the threonyl-tRNA synthetase (ThrRS) requires the discrimination of the cognate substrate threonine from the noncognate serine. Misacylation by serine is corrected in a proofreading or editing step. An editing site has been located 39 A away from the aminoacylation site. We report the crystal structures of this editing domain in its apo form and in complex with the serine product, and with two nonhydrolyzable analogs of potential substrates: the terminal tRNA adenosine charged with serine, and seryl adenylate. The structures show how serine is recognized, and threonine rejected, and provide the structural basis for the editing mechanism, a water-mediated hydrolysis of the mischarged tRNA. When the adenylate analog binds in the editing site, a phosphate oxygen takes the place of one of the catalytic water molecules, thereby blocking the reaction. This rules out a correction mechanism that would occur before the binding of the amino acid on the tRNA.
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MESH Headings
- Amino Acid Sequence
- Aminoacylation
- Binding Sites
- Escherichia coli/chemistry
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Hydrolysis
- Molecular Sequence Data
- Mutagenesis, Site-Directed
- Oxygen/chemistry
- Phosphates/chemistry
- Protein Biosynthesis
- RNA Editing
- RNA, Transfer, Ser/chemistry
- RNA, Transfer, Ser/metabolism
- RNA, Transfer, Thr/chemistry
- RNA, Transfer, Thr/metabolism
- Sequence Homology, Amino Acid
- Threonine-tRNA Ligase/chemistry
- Threonine-tRNA Ligase/genetics
- Threonine-tRNA Ligase/metabolism
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Affiliation(s)
- Anne-Catherine Dock-Bregeon
- IGBMC (CNRS/INSERM/Université Louis Pasteur), Laboratoire de Biologie et Génomique Structurales, 1, rue Laurent Fries, BP 10142, 67400 Illkirch, France
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18
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Affiliation(s)
- A D Podjarny
- UPR de Biologie Structurale, Universite Louis Pasteur, Illkirch, C.U. de Strasbourg, France
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19
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Torres-Larios A, Sankaranarayanan R, Rees B, Dock-Bregeon AC, Moras D. Conformational movements and cooperativity upon amino acid, ATP and tRNA binding in threonyl-tRNA synthetase. J Mol Biol 2003; 331:201-11. [PMID: 12875846 DOI: 10.1016/s0022-2836(03)00719-8] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The crystal structures of threonyl-tRNA synthetase (ThrRS) from Staphylococcus aureus, with ATP and an analogue of threonyl adenylate, are described. Together with the previously determined structures of Escherichia coli ThrRS with different substrates, they allow a comprehensive analysis of the effect of binding of all the substrates: threonine, ATP and tRNA. The tRNA, by inserting its acceptor arm between the N-terminal domain and the catalytic domain, causes a large rotation of the former. Within the catalytic domain, four regions surrounding the active site display significant conformational changes upon binding of the different substrates. The binding of threonine induces the movement of as much as 50 consecutive amino acid residues. The binding of ATP triggers a displacement, as large as 8A at some C(alpha) positions, of a strand-loop-strand region of the core beta-sheet. Two other regions move in a cooperative way upon binding of threonine or ATP: the motif 2 loop, which plays an essential role in the first step of the aminoacylation reaction, and the ordering loop, which closes on the active site cavity when the substrates are in place. The tRNA interacts with all four mobile regions, several residues initially bound to threonine or ATP switching to a position in which they can contact the tRNA. Three such conformational switches could be identified, each of them in a different mobile region. The structural analysis suggests that, while the small substrates can bind in any order, they must be in place before productive tRNA binding can occur.
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Affiliation(s)
- Alfredo Torres-Larios
- Laboratoire de Biologie et Génomique Structurales, IGBMC, 1 rue Laurent Fries, BP 10142, 67400 Illkirch Cedex, France
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20
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Mitschler A, Rees B, Wiest R, Benard M. Electron deformation density for the "supershort" chromium-chromium quadruple bond: a joint experimental and theoretical study. J Am Chem Soc 2002. [DOI: 10.1021/ja00390a019] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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21
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Mitschler A, Rees B, Lehmann MS. Electron density in bis(dicarbonyl-.pi.-cyclopentadienyliron) at liquid nitrogen temperature by x-ray and neutron diffraction. J Am Chem Soc 2002. [DOI: 10.1021/ja00479a022] [Citation(s) in RCA: 106] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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22
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Clemente DA, Biagini MC, Rees B, Herrmann WA. Molecular structure and experimental electron density of (.mu.-methylene)bis[dicarbonyl(.eta.5-cyclopentadienyl)manganese] at 130 K. Inorg Chem 2002. [DOI: 10.1021/ic00140a029] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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23
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Rees B, Bilwes A. Three-dimensional structures of neurotoxins and cardiotoxins. [Erratum to document cited in CA119(7):64994k]. Chem Res Toxicol 2002. [DOI: 10.1021/tx00036a024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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24
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Rees B, Mitschler A. Electronic structure of chromium hexacarbonyl at liquid nitrogen temperature. 2. Experimental study (x-ray and neutron diffraction) of .sigma. and .pi. bonding. J Am Chem Soc 2002. [DOI: 10.1021/ja00441a005] [Citation(s) in RCA: 104] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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25
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Wiest R, Rees B, Mitschler A, Mathey F. Molecular structure of phosphaferrocene and charge-density distribution at low temperature. Inorg Chem 2002. [DOI: 10.1021/ic50223a042] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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26
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Torres-Larios A, Dock-Bregeon AC, Romby P, Rees B, Sankaranarayanan R, Caillet J, Springer M, Ehresmann C, Ehresmann B, Moras D. Structural basis of translational control by Escherichia coli threonyl tRNA synthetase. Nat Struct Biol 2002; 9:343-7. [PMID: 11953757 DOI: 10.1038/nsb789] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Escherichia coli threonyl-tRNA synthetase (ThrRS) represses the translation of its own messenger RNA by binding to an operator located upstream of the initiation codon. The crystal structure of the complex between the core of ThrRS and the essential domain of the operator shows that the mRNA uses the recognition mode of the tRNA anticodon loop to initiate binding. The final positioning of the operator, upon which the control mechanism is based, relies on a characteristic RNA motif adapted to the enzyme surface. The finding of other thrS operators that have this conserved motif leads to a generalization of this regulatory mechanism to a subset of Gram-negative bacteria.
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MESH Headings
- Anticodon/genetics
- Base Sequence
- Crystallography, X-Ray
- Escherichia coli/enzymology
- Escherichia coli/genetics
- Models, Molecular
- Molecular Sequence Data
- Nucleic Acid Conformation
- Protein Biosynthesis
- Protein Conformation
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Messenger/chemistry
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Transfer/chemistry
- RNA, Transfer/genetics
- RNA, Transfer/metabolism
- Sequence Alignment
- Structure-Activity Relationship
- Threonine-tRNA Ligase/chemistry
- Threonine-tRNA Ligase/metabolism
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Affiliation(s)
- Alfredo Torres-Larios
- Laboratoire de Biologie et Génomique Structurales, IGBMC, BP163, 67404 Illkirch Cedex, France
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27
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Abstract
BACKGROUND This study assesses the transfer of laparoscopic skills to a group of Basic Surgical Trainees (BST) attending the Basic Surgical Skills (BSS) course. METHODS The virtual reality simulator MIST-VR was used to assess 13 trainees before and after the course and again 3 weeks and 3 months later. Analysis of kinematic data using the Imperial College Surgical Assessment Device gave measures of distance traveled, distance efficiency ratio, time taken, number of errors made, and number of movements made in completing a virtual laparoscopic task. The performance of the group was compared to a control group who underwent no training. RESULTS All parameters improved significantly after the course, with the exception of distance traveled by the instruments. All outcome measures were significantly improved at 3 weeks. The control group showed a nonsignificant trend toward improvement in all parameters. CONCLUSIONS The Basic Surgical Skills course produces quantifiable improvements in laparoscopic skill that are measurable by MIST-VR. There is a learning effect associated with using MIST-VR alone.
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Affiliation(s)
- J Torkington
- Academic Surgical Unit, Imperial College School of Medicine, St. Mary's Hospital, London, W2 1NY, Englan
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28
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Rees B, Prando P. Documentation and log keeping: ensuring your work does what you intend it to do. Health Phys 2001; 81:265-268. [PMID: 11513459 DOI: 10.1097/00004032-200109000-00007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Maintaining regular documentation, such as a log-book, can be an organization's most important asset when dealing with radiation protection issues, both normal and abnormal. When an organization is faced with litigation, proper documentation of events can ensure that a record is acceptable and, by extension, that the data itself is acceptable. A record of events will not preclude litigation, nor will it guarantee that an organization will prevail in a court of law, but it will provide evidence and credibility that could favorably affect the outcome of litigation. An organization can ensure that the documents it creates and maintains are as effective as possible by being aware of the legal consequences of documenting events and taking appropriate steps to conform to standards for admission of documentation. Misconceptions about log keeping such as recording only events that are likely to result in litigation, rather than recording all events, can prevent a record from being admissible as evidence. Because of the amount of effort and time put into documentation, and the reliance placed on its contents, it is important for an organization to ensure that a record will do what it is intended to do, namely to accurately record activities. Issues discussed in this article include the legal basis of documentary evidence, what and what not to record, when and how to record it, and how to strengthen the records kept.
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Affiliation(s)
- B Rees
- Los Alamos National Laboratory, NM 87545, USA.
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29
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Dock-Bregeon A, Sankaranarayanan R, Romby P, Caillet J, Springer M, Rees B, Francklyn CS, Ehresmann C, Moras D. Transfer RNA-mediated editing in threonyl-tRNA synthetase. The class II solution to the double discrimination problem. Cell 2000; 103:877-84. [PMID: 11136973 DOI: 10.1016/s0092-8674(00)00191-4] [Citation(s) in RCA: 152] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Threonyl-tRNA synthetase, a class II synthetase, uses a unique zinc ion to discriminate against the isosteric valine at the activation step. The crystal structure of the enzyme with an analog of seryl adenylate shows that the noncognate serine cannot be fully discriminated at that step. We show that hydrolysis of the incorrectly formed ser-tRNA(Thr) is performed at a specific site in the N-terminal domain of the enzyme. The present study suggests that both classes of synthetases use effectively the ability of the CCA end of tRNA to switch between a hairpin and a helical conformation for aminoacylation and editing. As a consequence, the editing mechanism of both classes of synthetases can be described as mirror images, as already seen for tRNA binding and amino acid activation.
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Affiliation(s)
- A Dock-Bregeon
- UPR 9004 Biologie Structurale IGBMC, CNRS/INSERM/ULP BP163 67404 Cedex, Illkirch, France
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30
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Sankaranarayanan R, Dock Bregeon AC, Rees B, Bovee M, Caillet J, Romby P, Francklyn C, Moras D. Zinc ion mediated amino acid recognition by threonyl-tRNA synthetase. Acta Crystallogr A 2000. [DOI: 10.1107/s0108767300022595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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31
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Abstract
The crystal structure of aspartyl-tRNA synthetase from Escherichia coli has been determined to a resolution of 2.7 A. The structure is compared to the same enzyme co-crystallized with tRNA(Asp) and containing aspartyl adenylate or ATP. The asymmetric unit contains three monomers of the enzyme. While most parts of the protein show no significant differences in the three monomers, a few regions cannot be superimposed. Those regions are characterized by a high B-factor, and consist mostly of loops that make contacts with the tRNA in the complexes. The flexibility of the protein is seen at a global level, by the observation of a 10 to 15 degrees rotation of the N-terminal and insertion domains upon tRNA binding, and at the level of the individual amino acid residues, by main-chain and side-chain rearrangements. In contrast to these induced-fit conformational changes, a few residues essential for the tRNA anticodon or aspartyl-adenylate recognition exist in a predefined conformation, ensured by specific interactions within the protein.
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MESH Headings
- Adenosine Monophosphate/analogs & derivatives
- Adenosine Monophosphate/metabolism
- Adenosine Triphosphate/metabolism
- Anticodon/chemistry
- Anticodon/genetics
- Anticodon/metabolism
- Aspartate-tRNA Ligase/chemistry
- Aspartate-tRNA Ligase/metabolism
- Aspartic Acid/analogs & derivatives
- Aspartic Acid/metabolism
- Base Pairing/genetics
- Binding Sites
- Crystallography, X-Ray
- Dimerization
- Escherichia coli/enzymology
- Models, Molecular
- Molecular Sequence Data
- Pliability
- Protein Structure, Secondary
- Protein Structure, Tertiary
- RNA, Transfer, Amino Acyl/chemistry
- RNA, Transfer, Amino Acyl/genetics
- RNA, Transfer, Amino Acyl/metabolism
- Rotation
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Affiliation(s)
- B Rees
- UPR 9004, Laboratoire de Biologie et de Génomique Structurales, Institut de Génétique et de Biologie Moléculaire et Cellulaire, 1 rue Laurent Fries, Illkirch, 67400, France
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32
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Sankaranarayanan R, Dock-Bregeon AC, Rees B, Bovee M, Caillet J, Romby P, Francklyn CS, Moras D. Zinc ion mediated amino acid discrimination by threonyl-tRNA synthetase. Nat Struct Biol 2000; 7:461-5. [PMID: 10881191 DOI: 10.1038/75856] [Citation(s) in RCA: 129] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Accurate translation of the genetic code depends on the ability of aminoacyl-tRNA synthetases to distinguish between similar amino acids. In order to investigate the basis of amino acid recognition and to understand the role played by the zinc ion present in the active site of threonyl-tRNA synthetase, we have determined the crystal structures of complexes of an active truncated form of the enzyme with a threonyl adenylate analog or threonine. The zinc ion is directly involved in threonine recognition, forming a pentacoordinate intermediate with both the amino group and the side chain hydroxyl. Amino acid activation experiments reveal that the enzyme shows no activation of isosteric valine, and activates serine at a rate 1,000-fold less than that of cognate threonine. This study demonstrates that the zinc ion is neither strictly catalytic nor structural and suggests how the zinc ion ensures that only amino acids that possess a hydroxyl group attached to the beta-position are activated.
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33
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Torkington J, Smith S, Rees B, Darzi A. Optimising the acquisition of laparoscopic skill. MINIM INVASIV THER 2000. [DOI: 10.3109/13645700009061450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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34
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Sankaranarayanan R, Dock-Bregeon AC, Romby P, Caillet J, Springer M, Rees B, Ehresmann C, Ehresmann B, Moras D. The structure of threonyl-tRNA synthetase-tRNA(Thr) complex enlightens its repressor activity and reveals an essential zinc ion in the active site. Cell 1999; 97:371-81. [PMID: 10319817 DOI: 10.1016/s0092-8674(00)80746-1] [Citation(s) in RCA: 258] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
E. coli threonyl-tRNA synthetase (ThrRS) is a class II enzyme that represses the translation of its own mRNA. We report the crystal structure at 2.9 A resolution of the complex between tRNA(Thr) and ThrRS, whose structural features reveal novel strategies for providing specificity in tRNA selection. These include an amino-terminal domain containing a novel protein fold that makes minor groove contacts with the tRNA acceptor stem. The enzyme induces a large deformation of the anticodon loop, resulting in an interaction between two adjacent anticodon bases, which accounts for their prominent role in tRNA identity and translational regulation. A zinc ion found in the active site is implicated in amino acid recognition/discrimination.
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MESH Headings
- Amino Acyl-tRNA Synthetases/chemistry
- Amino Acyl-tRNA Synthetases/genetics
- Amino Acyl-tRNA Synthetases/metabolism
- Bacterial Proteins/chemistry
- Bacterial Proteins/genetics
- Bacterial Proteins/metabolism
- Base Sequence
- Binding Sites/genetics
- Catalytic Domain
- Dimerization
- Enzyme Activation/physiology
- Escherichia coli/enzymology
- Escherichia coli/genetics
- Genetic Complementation Test
- Molecular Mimicry
- Molecular Sequence Data
- Nucleic Acid Conformation
- Protein Structure, Secondary
- Protein Structure, Tertiary
- RNA, Messenger/genetics
- RNA, Transfer, Amino Acyl/chemistry
- RNA, Transfer, Amino Acyl/genetics
- RNA, Transfer, Amino Acyl/metabolism
- Sequence Homology, Amino Acid
- Zinc/chemistry
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Affiliation(s)
- R Sankaranarayanan
- UPR 9004 Biologie Structurale, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, Illkirch, France
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35
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Lowenthal R, Tuck D, Tegg E, Marsden K, Rees B, Luck J, Ragg S, Parker N, Kotlovsky N. Hemopoietic stem-cell harvesting and transplantation using G-CSF-primed BM: comparison with unprimed BM and G-CSF-primed PBSC. Cytotherapy 1999; 1:409-16. [DOI: 10.1080/0032472031000141285] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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36
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Locher KP, Rees B, Koebnik R, Mitschler A, Moulinier L, Rosenbusch JP, Moras D. Transmembrane signaling across the ligand-gated FhuA receptor: crystal structures of free and ferrichrome-bound states reveal allosteric changes. Cell 1998; 95:771-8. [PMID: 9865695 DOI: 10.1016/s0092-8674(00)81700-6] [Citation(s) in RCA: 390] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
FhuA protein facilitates ligand-gated transport of ferrichrome-bound iron across Escherichia coli outer membranes. X-ray analysis at 2.7 A resolution reveals two distinct conformations in the presence and absence of ferrichrome. The monomeric protein consists of a hollow, 22-stranded, antiparallel beta barrel (residues 160-714), which is obstructed by a plug (residues 19-159). The binding site of ferrichrome, an aromatic pocket near the cell surface, undergoes minor changes upon association with the ligand. These are propagated and amplified across the plug, eventually resulting in substantially different protein conformations at the periplasmic face. Our findings reveal the mechanism of signal transmission and suggest how the energy-transducing TonB complex senses ligand binding.
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Affiliation(s)
- K P Locher
- Department of Microbiology, Biozentrum, University of Basel, Switzerland
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37
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Rees B, Kelly K, Forbes J. P110 The role of nurse counsellor support groups for women diagnosed with breast cancer at hunter breast screen. Eur J Cancer 1998. [DOI: 10.1016/s0959-8049(97)89481-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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38
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Rhodes M, Gompertz H, Armstrong K, Lennard T, Rees B. Randomised trial of laparoscopic versus small-incision cholecystectomy. Lancet 1996; 347:1621-2; author reply 1623-4. [PMID: 8667886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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39
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Abstract
This article reports a meta-analysis of 84 studies of quality of life (QOL) in cardiac patient populations published in the 5-year period 1987-1991. Selected methodologies and substantive characteristics of the studies are described. An overall effect size of .31 indicated a small but significant positive effect of pharmacologic, mechanical, surgical, nursing, or other treatment on QOL. No negative effect of treatment was found for any cardiovascular diagnostic category. Homogeneity analysis revealed eight potential moderators of the overall effect size: quality of study, gender of sample, time dimension, sampling method, intervention, marital status of subjects, quality-of-life dimension measured, and sample size.
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Affiliation(s)
- M R Kinney
- Center for Nursing Research, University of Alabama School of Nursing, Birmingham, USA
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40
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Abstract
Microbiology and cell biology researchers make extensive use of beta emitting nuclides. Because of the short half-lives or difficulty of direct measurement some researchers do not view radionuclide use with proper care and respect. Radionuclide use in microbiology and cell biology research is unique. Review of the isotopes and processes may be useful to the health physicist and research alike.
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Affiliation(s)
- B Rees
- Los Alamos National Laboratory, NM 87545, USA
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41
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Abstract
The availability of several X-ray structures at atomic resolution of tRNA(Asp) from yeast, both in its free state and complexed with its cognate tRNA-synthetase, enables a detailed examination of the conformational changes due to interaction with the enzyme. Although the molecule conserves its general L shape, its conformation undergoes important modifications. They may be described as a bending of the two arms which brings the 3' acceptor end and the anticodon part closer together, completed by a drastic change of the anticodon loop, which puts the anticodon bases in a more exposed position, facilitating their interaction with the synthetase. The packing interactions in the crystals are also discussed. Finally, the results of protection studies by chemical probes in solution are discussed in view of the RNA-protein contacts observed in the crystals.
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Affiliation(s)
- B Rees
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, Illkirch, France
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42
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Arnez JG, Harris DC, Mitschler A, Rees B, Francklyn CS, Moras D. Crystal structure of histidyl-tRNA synthetase from Escherichia coli complexed with histidyl-adenylate. EMBO J 1995; 14:4143-55. [PMID: 7556055 PMCID: PMC394497 DOI: 10.1002/j.1460-2075.1995.tb00088.x] [Citation(s) in RCA: 106] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
The crystal structure at 2.6 A of the histidyl-tRNA synthetase from Escherichia coli complexed with histidyl-adenylate has been determined. The enzyme is a homodimer with a molecular weight of 94 kDa and belongs to the class II of aminoacyl-tRNA synthetases (aaRS). The asymmetric unit is composed of two homodimers. Each monomer consists of two domains. The N-terminal catalytic core domain contains a six-stranded antiparallel beta-sheet sitting on two alpha-helices, which can be superposed with the catalytic domains of yeast AspRS, and GlyRS and SerRS from Thermus thermophilus with a root-mean-square difference on the C alpha atoms of 1.7-1.9 A. The active sites of all four monomers are occupied by histidyl-adenylate, which apparently forms during crystallization. The 100 residue C-terminal alpha/beta domain resembles half of a beta-barrel, and provides an independent domain oriented to contact the anticodon stem and part of the anticodon loop of tRNA(His). The modular domain organization of histidyl-tRNA synthetase reiterates a repeated theme in aaRS, and its structure should provide insight into the ability of certain aaRS to aminoacylate minihelices and other non-tRNA molecules.
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43
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Eriani G, Cavarelli J, Martin F, Ador L, Rees B, Thierry JC, Gangloff J, Moras D. The class II aminoacyl-tRNA synthetases and their active site: evolutionary conservation of an ATP binding site. J Mol Evol 1995; 40:499-508. [PMID: 7783225 DOI: 10.1007/bf00166618] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Previous sequence analyses have suggested the existence of two distinct classes of aminoacyl-tRNA synthetase. The partition was established on the basis of exclusive sets of sequence motifs (Eriani et al. [1990] Nature 347:203-306). X-ray studies have now well defined the structural basis of the two classes: the class I enzymes share with dehydrogenases and kinases the classic nucleotide binding fold called the Rossmann fold, whereas the class II enzymes possess a different fold, not found elsewhere, built around a six-stranded antiparallel beta-sheet. The two classes of synthetases catalyze the same global reaction that is the attachment of an amino acid to the tRNA, but differ as to where on the terminal adenosine of the tRNA the amino acid is placed: class I enzymes act on the 2' hydroxyl whereas the class II enzymes prefer the 3' hydroxyl group. The three-dimensional structure of aspartyl-tRNA synthetase from yeast, a typical class II enzyme, is described here, in relation to its function. The crucial role of the sequence motifs in substrate binding and enzyme structure is high-lighted. Overall these results underline the existence of an intimate evolutionary link between the aminoacyl-tRNA synthetases, despite their actual structural diversity.
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Affiliation(s)
- G Eriani
- UPR 9002, Structure des Macromolécules Biologiques et Mécanismes de Reconnaissance, Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg, France
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Abstract
The transgenic TGR(mRen-2)27 rat, in which the Ren-2 mouse renin gene is transfected into the genome of the Sprague-Dawley rat, develops severe hypertension at a young age that responds to inhibitors of angiotensin-converting enzyme and to antagonists of the type 1 angiotensin II (Ang II) receptor. Despite this evidence that the hypertension is Ang II dependent, TGR(mRen-2)27 rats have suppressed renal renin and renin mRNA content, and there is controversy concerning the plasma levels of renin and Ang II in these rats. We investigated the effect of the transgene on circulating and tissue levels of angiotensin and bradykinin peptides in 6-week-old male homozygous TGR(mRen-2)27 rats. Systolic blood pressure of TGR(mRen-2)27 rats was 212 +/- 4 mm Hg (mean +/- SEM, n = 25) compared with 108 +/- 2 mm Hg (n = 29) for age- and sex-matched Sprague-Dawley rats. Compared with control rats, TGR(mRen-2)27 rats had increased plasma levels of active renin (4.5-fold), prorenin (300-fold), and Ang II (fourfold) as well as tissue levels of Ang II (twofold to fourfold in kidney, adrenal, heart, aorta, brown adipose tissue, and lung and 18-fold in brain). Plasma angiotensinogen levels were reduced to 73% of control, and plasma aldosterone levels were increased fourfold. Plasma angiotensin-converting enzyme was reduced to 64% of control. Compared with control rats, TGR(mRen-2)27 rats had increased bradykinin levels in brown adipose tissue (1.9-fold) and lung (1.6-fold).(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- D J Campbell
- St Vincent's Institute of Medical Research, Fitzroy, Australia
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Tsunoda M, Takenaka A, Cavarelli J, Rees B, Thierry JC, Moras D. Electrostatic potential in aminoacylation by aspartyl-tRNAs synthetase. Nucleic Acids Symp Ser 1995:65-66. [PMID: 8841554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Based upon the X-ray structures of complexes between tRNAAsp and aspRS including ATP or Asp-AMP, several electrostatic potentials were calculated by solving the Poisson-Boltzmann equation. The potentials indicate clearly that a Mg2+ ion is essential for binding of ATP and that aspartate is identified electrostatically. The alpha-carboxyl group is forced to contact with the alpha-phosphorus atom of ATP, suggesting its inversion to form an Asp-AMP. When the cognate tRNA is bound to the aspRS:Asp-AMP complex, the 3'-hydroxyl group is located in an electrostatically favorable position to transfer the amino acid as a class II aminoacylation.
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Affiliation(s)
- M Tsunoda
- Faculty of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Japan
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Bilwes A, Rees B, Moras D, Ménez R, Ménez A. X-ray structure at 1.55 A of toxin gamma, a cardiotoxin from Naja nigricollis venom. Crystal packing reveals a model for insertion into membranes. J Mol Biol 1994; 239:122-36. [PMID: 8196041 DOI: 10.1006/jmbi.1994.1357] [Citation(s) in RCA: 79] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The crystal structure of toxin gamma from Naja nigricollis has been solved and refined to 1.55 A resolution. The final R-factor, computed with all X-ray data available, is 17.9%. The three-dimensional structure is characterized by a core formed by two beta-sheets organized in three extended loops. It is similar to that of cardiotoxin V4II from Naja mossambica mossambica, with the exception of the hydrophobic loop I. The flexibility and variability of the loops contrast sharply with the rigidity of the molecular core and its high degree of structural conservation among the cardiotoxin family. The most flexible loop II adopts different conformations in the three monomers forming the crystal asymmetric unit. These monomers form a trimer around an approximate 3-fold axis, with conserved hydrophobic side-chains on the outside and hydrophilic residues in the central channel or involved in interactions with the other molecules. The trimer thus resembles a membrane protein with a central channel that could allow the passage of small ions. It is proposed as a model for the insertion of cardiotoxin into a membrane.
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Affiliation(s)
- A Bilwes
- UPR de Biologie Structurale, Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg, France
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Cavarelli J, Eriani G, Rees B, Ruff M, Boeglin M, Mitschler A, Martin F, Gangloff J, Thierry JC, Moras D. The active site of yeast aspartyl-tRNA synthetase: structural and functional aspects of the aminoacylation reaction. EMBO J 1994; 13:327-37. [PMID: 8313877 PMCID: PMC394812 DOI: 10.1002/j.1460-2075.1994.tb06265.x] [Citation(s) in RCA: 182] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
The crystal structures of the various complexes formed by yeast aspartyl-tRNA synthetase (AspRS) and its substrates provide snapshots of the active site corresponding to different steps of the aminoacylation reaction. Native crystals of the binary complex tRNA-AspRS were soaked in solutions containing the two other substrates, ATP (or its analog AMPPcP) and aspartic acid. When all substrates are present in the crystal, this leads to the formation of the aspartyl-adenylate and/or the aspartyl-tRNA. A class II-specific pathway for the aminoacylation reaction is proposed which explains the known functional differences between the two classes while preserving a common framework. Extended signature sequences characteristic of class II aaRS (motifs 2 and 3) constitute the basic functional unit. The ATP molecule adopts a bent conformation, stabilized by the invariant Arg531 of motif 3 and a magnesium ion coordinated to the pyrophosphate group and to two class-invariant acidic residues. The aspartic acid substrate is positioned by a class II invariant acidic residue, Asp342, interacting with the amino group and by amino acids conserved in the aspartyl synthetase family. The amino acids in contact with the substrates have been probed by site-directed mutagenesis for their functional implication.
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Affiliation(s)
- J Cavarelli
- UPR 9004, Laboratoire de Biologie Structurale, Strasbourg, France
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Cavarelli J, Rees B, Ruff M, Thierry JC, Moras D. tRNA Aspaspartyl-tRNA synthetase recognition. Acta Crystallogr A 1993. [DOI: 10.1107/s010876737809827x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Cavarelli J, Rees B, Boeglin M, Ruff M, Thierry JC, Moras D. The active site of yeast aspartyl-tRNA synthetase. Acta Crystallogr A 1993. [DOI: 10.1107/s010876737809769x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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Affiliation(s)
- B Rees
- UPR de Biologie Structurale, Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg, France
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