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Gisdon FJ, Kynast JP, Ayyildiz M, Hine AV, Plückthun A, Höcker B. Modular peptide binders - development of a predictive technology as alternative for reagent antibodies. Biol Chem 2022; 403:535-543. [PMID: 35089661 DOI: 10.1515/hsz-2021-0384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 01/11/2022] [Indexed: 11/15/2022]
Abstract
Current biomedical research and diagnostics critically depend on detection agents for specific recognition and quantification of protein molecules. Monoclonal antibodies have been used for this purpose over decades and facilitated numerous biological and biomedical investigations. Recently, however, it has become apparent that many commercial reagent antibodies lack specificity or do not recognize their target at all. Thus, synthetic alternatives are needed whose complex designs are facilitated by multidisciplinary approaches incorporating experimental protein engineering with computational modeling. Here, we review the status of such an engineering endeavor based on the modular armadillo repeat protein scaffold and discuss challenges in its implementation.
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Affiliation(s)
- Florian J Gisdon
- Department of Biochemistry, University of Bayreuth, D-95447 Bayreuth, Germany
| | - Josef P Kynast
- Department of Biochemistry, University of Bayreuth, D-95447 Bayreuth, Germany
| | - Merve Ayyildiz
- Department of Biochemistry, University of Bayreuth, D-95447 Bayreuth, Germany
| | - Anna V Hine
- College of Health and Life Sciences, Aston University, Birmingham B4 7ET, UK
| | - Andreas Plückthun
- Department of Biochemistry, University of Zurich, CH-8057 Zürich, Switzerland
| | - Birte Höcker
- Department of Biochemistry, University of Bayreuth, D-95447 Bayreuth, Germany
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2
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Chembath A, Wagstaffe BPG, Ashraf M, Amaral MMF, Frigotto L, Hine AV. Nondegenerate Saturation Mutagenesis: Library Construction and Analysis via MAX and ProxiMAX Randomization. Methods Mol Biol 2022; 2461:19-41. [PMID: 35727442 DOI: 10.1007/978-1-0716-2152-3_3] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Protein engineering can enhance desirable features and improve performance outside of the natural context. Several strategies have been adopted over the years for gene diversification, and engineering of modular proteins in particular is most effective when a high-throughput, library-based approach is employed. Nondegenerate saturation mutagenesis plays a dynamic role in engineering proteins by targeting multiple codons to generate massively diverse gene libraries. Herein, we describe the nondegenerate saturation mutagenesis techniques that we have developed for contiguous (ProxiMAX) and noncontiguous (MAX) randomized codon generation to create precisely defined, diverse gene libraries, in the context of other fully nondegenerate strategies. ProxiMAX randomization comprises saturation cycling with repeated cycles of blunt-ended ligation, type IIS restriction, and PCR amplification, and is now a commercially automated process predominantly used for antibody library generation. MAX randomization encompasses a manual process of selective hybridisation between individual custom oligonucleotide mixes and a conventionally randomized template and is principally employed in the research laboratory setting, to engineer alpha helical proteins and active sites of enzymes. DNA libraries generated using either technology create high-throughput amino acid substitutions via codon randomization, to generate genetically diverse clones.
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Affiliation(s)
- Anupama Chembath
- College of Health and Life Sciences, Aston University, Aston Triangle, Birmingham, UK
| | | | - Mohammed Ashraf
- College of Health and Life Sciences, Aston University, Aston Triangle, Birmingham, UK
| | - Marta M Ferreira Amaral
- College of Health and Life Sciences, Aston University, Aston Triangle, Birmingham, UK
- Bicycle Therapeutics, Cambridge, UK
| | | | - Anna V Hine
- College of Health and Life Sciences, Aston University, Aston Triangle, Birmingham, UK.
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3
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Allsop TDP, Neal R, Wang C, Nagel DA, Hine AV, Culverhouse P, Ania Castañón JD, Webb DJ, Scarano S, Minunni M. An ultra-sensitive aptasensor on optical fibre for the direct detection of bisphenol A. Biosens Bioelectron 2019; 135:102-110. [PMID: 31004920 DOI: 10.1016/j.bios.2019.02.043] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 02/10/2019] [Accepted: 02/15/2019] [Indexed: 12/14/2022]
Abstract
We present a plasmonic biosensor capable of detecting the presence of bisphenol A in ultra-low concentrations, yielding a wavelength shift of 0.15 ± 0.01 nm in response to a solution of 1 fM concentration with limit of detection of 330 ± 70 aM The biosensing device consists of an array of gold nano-antennae with a total length of 2.3 cm that generate coupled localised surface plasmons (cLSPs) and is covalently modified with an aptamer specific for bisphenol A recognition. The array of nano-antennae is fabricated on a lapped section of standard telecommunication optical fibre, allowing for potential multiplexing and its use in remote sensing applications. These results have been achieved without the use of enhancement techniques and therefore the approach allows the direct detection of bisphenol A, a low molecular weight (228 Da) target usually detectable only by indirect detection strategies. Its detection at such levels is a significant step forward in measuring small molecules at ultra-low concentrations. Furthermore, this new sensing platform paves the way for the development of portable systems for in-situ agricultural measurements capable of retrieving data on a substance of very high concern at ultra-low concentrations.
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Affiliation(s)
- Thomas D P Allsop
- Non-linear Dynamics and Fiber Optics, Instituto de Óptica "Daza de Valdés" (IO-CSIC), Calle de Serrano, 121, 28006 Madrid, Spain; Aston Institute of Photonic Technologies, Aston University, Aston Triangle, Birmingham B47ET, UK.
| | - Ronald Neal
- Dept of Maths and Computing, Faculty of Science and Technology, University of Plymouth, Plymouth PL4 8AA, UK
| | - Changle Wang
- Aston Institute of Photonic Technologies, Aston University, Aston Triangle, Birmingham B47ET, UK.
| | - David A Nagel
- School of Life and Health Sciences, Aston University, Aston Triangle, Birmingham B47ET, UK
| | - Anna V Hine
- School of Life and Health Sciences, Aston University, Aston Triangle, Birmingham B47ET, UK
| | - Philip Culverhouse
- Dept of Maths and Computing, Faculty of Science and Technology, University of Plymouth, Plymouth PL4 8AA, UK
| | - Juan D Ania Castañón
- Non-linear Dynamics and Fiber Optics, Instituto de Óptica "Daza de Valdés" (IO-CSIC), Calle de Serrano, 121, 28006 Madrid, Spain
| | - David J Webb
- Aston Institute of Photonic Technologies, Aston University, Aston Triangle, Birmingham B47ET, UK
| | - Simona Scarano
- Dipartimento di Chimica "Ugo Schiff" and CSGI, Università degli Studi di Firenze, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Maria Minunni
- Dipartimento di Chimica "Ugo Schiff" and CSGI, Università degli Studi di Firenze, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
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4
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Abstract
Beyond the natural proteome, high-throughput mutagenesis offers the protein engineer an opportunity to "tweak" the wild-type activity of a protein to create a recombinant protein with required attributes. Of the various approaches available, saturation mutagenesis is one of the core techniques employed by protein engineers, and in recent times, nondegenerate saturation mutagenesis is emerging as the approach of choice. This review compares the current methodologies available for conducting nondegenerate saturation mutagenesis with traditional, degenerate saturation and briefly outlines the options available for screening the resulting libraries, to discover a novel protein with the required activity and/or specificity.
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Affiliation(s)
- M M Ferreira Amaral
- School of Life and Health Sciences, Aston University, Birmingham, United Kingdom
| | - L Frigotto
- Isogenica Ltd., The Mansion, Chesterford Research Park, Essex, United Kingdom
| | - A V Hine
- School of Life and Health Sciences, Aston University, Birmingham, United Kingdom.
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5
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Abstract
Discovering the function of an unknown protein, particularly one with neither structural nor functional correlates, is a daunting task. Interaction analyses determine binding partners, whereas DNA transfection, either transient or stable, leads to intracellular expression, though not necessarily at physiologically relevant levels. In theory, direct intracellular protein delivery (protein transduction) provides a conceptually simpler alternative, but in practice the approach is problematic. Domains such as HIV TAT protein are valuable, but their effectiveness is protein specific. Similarly, the delivery of intact proteins via endocytic pathways (e.g. using liposomes) is problematic for functional analysis because of the potential for protein degradation in the endosomes/lysosomes. Consequently, recent reports that microspheres can deliver bio-cargoes into cells via a non-endocytic, energy-independent pathway offer an exciting and promising alternative for in vitro delivery of functional protein. In order for such promise to be fully exploited, microspheres are required that (i) are stably linked to proteins, (ii) can deliver those proteins with good efficiency, (iii) release functional protein once inside the cells, and (iv) permit concomitant tracking. Herein, we report the application of microspheres to successfully address all of these criteria simultaneously, for the first time. After cellular uptake, protein release was autocatalyzed by the reducing cytoplasmic environment. Outside of cells, the covalent microsphere–protein linkage was stable for ≥90 h at 37 °C. Using conservative methods of estimation, 74.3% ± 5.6% of cells were shown to take up these microspheres after 24 h of incubation, with the whole process of delivery and intracellular protein release occurring within 36 h. Intended for in vitro functional protein research, this approach will enable study of the consequences of protein delivery at physiologically relevant levels, without recourse to nucleic acids, and offers a useful alternative to commercial protein transfection reagents such as Chariot™. We also provide clear immunostaining evidence to resolve residual controversy surrounding FACS-based assessment of microsphere uptake.
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Affiliation(s)
- David Nagel
- From the ‡School of Life and Health Sciences, Aston University, Aston Triangle, Birmingham, B4 7ET, UK
| | - Jonathan M Behrendt
- §School of Engineering and Applied Science, Aston University, Aston Triangle, Birmingham, B4 7ET, UK
| | - Gwen F Chimonides
- §School of Engineering and Applied Science, Aston University, Aston Triangle, Birmingham, B4 7ET, UK
| | - Elizabeth E Torr
- From the ‡School of Life and Health Sciences, Aston University, Aston Triangle, Birmingham, B4 7ET, UK
| | - Andrew Devitt
- From the ‡School of Life and Health Sciences, Aston University, Aston Triangle, Birmingham, B4 7ET, UK; ‖Aston Research Centre for Healthy Aging, Aston University, Aston Triangle, Birmingham, B4 7ET, UK
| | - Andrew J Sutherland
- §School of Engineering and Applied Science, Aston University, Aston Triangle, Birmingham, B4 7ET, UK
| | - Anna V Hine
- From the ‡School of Life and Health Sciences, Aston University, Aston Triangle, Birmingham, B4 7ET, UK;
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Behrendt JM, Nagel D, Chundoo E, Alexander LM, Dupin D, Hine AV, Bradley M, Sutherland AJ. Synthesis and characterization of dual-functionalized core-shell fluorescent microspheres for bioconjugation and cellular delivery. PLoS One 2013; 8:e50713. [PMID: 23526923 PMCID: PMC3602537 DOI: 10.1371/journal.pone.0050713] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Accepted: 10/23/2012] [Indexed: 01/15/2023] Open
Abstract
The efficient transport of micron-sized beads into cells, via a non-endocytosis mediated mechanism, has only recently been described. As such there is considerable scope for optimization and exploitation of this procedure to enable imaging and sensing applications to be realized. Herein, we report the design, synthesis and characterization of fluorescent microsphere-based cellular delivery agents that can also carry biological cargoes. These core-shell polymer microspheres possess two distinct chemical environments; the core is hydrophobic and can be labeled with fluorescent dye, to permit visual tracking of the microsphere during and after cellular delivery, whilst the outer shell renders the external surfaces of the microspheres hydrophilic, thus facilitating both bioconjugation and cellular compatibility. Cross-linked core particles were prepared in a dispersion polymerization reaction employing styrene, divinylbenzene and a thiol-functionalized co-monomer. These core particles were then shelled in a seeded emulsion polymerization reaction, employing styrene, divinylbenzene and methacrylic acid, to generate orthogonally functionalized core-shell microspheres which were internally labeled via the core thiol moieties through reaction with a thiol reactive dye (DY630-maleimide). Following internal labeling, bioconjugation of green fluorescent protein (GFP) to their carboxyl-functionalized surfaces was successfully accomplished using standard coupling protocols. The resultant dual-labeled microspheres were visualized by both of the fully resolvable fluorescence emissions of their cores (DY630) and shells (GFP). In vitro cellular uptake of these microspheres by HeLa cells was demonstrated conventionally by fluorescence-based flow cytometry, whilst MTT assays demonstrated that 92% of HeLa cells remained viable after uptake. Due to their size and surface functionalities, these far-red-labeled microspheres are ideal candidates for in vitro, cellular delivery of proteins.
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Affiliation(s)
- Jonathan M. Behrendt
- Chemical Engineering & Applied Chemistry, School of Engineering & Applied Science, Aston University, Birmingham, United Kingdom
| | - David Nagel
- School of Life & Health Sciences, Aston University, Birmingham, United Kingdom
| | - Evita Chundoo
- Chemical Engineering & Applied Chemistry, School of Engineering & Applied Science, Aston University, Birmingham, United Kingdom
| | - Lois M. Alexander
- School of Chemistry, Edinburgh University, Edinburgh, United Kingdom
| | - Damien Dupin
- Department of Chemistry, Dainton Building, the University of Sheffield, Brook Hill, Sheffield, United Kingdom
| | - Anna V. Hine
- School of Life & Health Sciences, Aston University, Birmingham, United Kingdom
| | - Mark Bradley
- School of Chemistry, Edinburgh University, Edinburgh, United Kingdom
| | - Andrew J. Sutherland
- Chemical Engineering & Applied Chemistry, School of Engineering & Applied Science, Aston University, Birmingham, United Kingdom
- * E-mail:
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7
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Behrendt JM, Afzaal M, Alexander LM, Bradley M, Hine AV, Nagel D, O'Brien P, Presland K, Sutherland AJ. Thiol-containing microspheres as polymeric ligands for the immobilisation of quantum dots. ACTA ACUST UNITED AC 2009. [DOI: 10.1039/b814261k] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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8
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Barbosa H, Hine AV, Brocchini S, Slater NKH, Marcos JC. Affinity partitioning of plasmid DNA with a zinc finger protein. J Chromatogr A 2008; 1206:105-12. [PMID: 18760786 DOI: 10.1016/j.chroma.2008.07.095] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2008] [Revised: 07/22/2008] [Accepted: 07/23/2008] [Indexed: 10/21/2022]
Abstract
The affinity isolation of pre-purified plasmid DNA (pDNA) from model buffer solutions using native and poly(ethylene glycol) (PEG) derivatized zinc finger-GST (Glutathione-S-Transferase) fusion protein was examined in PEG-dextran (DEX) aqueous two-phase systems (ATPSs). In the absence of pDNA, partitioning of unbound PEGylated fusion protein into the PEG-rich phase was confirmed with 97.5% of the PEGylated fusion protein being detected in the PEG phase of a PEG 600-DEX 40 ATPS. This represents a 1322-fold increase in the protein partition coefficient in comparison to the non-PEGylated protein (Kc = 0.013). In the presence of pDNA containing a specific oligonucleotide recognition sequence, the zinc finger moiety of the PEGylated fusion protein bound to the plasmid and steered the complex to the PEG-rich phase. An increase in the proportion of pDNA that partitioned to the PEG-rich phase was observed as the concentration of PEGylated fusion protein was increased. Partitioning of the bound complex occurred to such an extent that no DNA was detected by the picogreen assay in the dextran phase. It was also possible to partition pDNA using a non-PEGylated (native) zinc finger-GST fusion protein in a PEG 1000-DEX 500 ATPS. In this case the native ligand accumulated mainly in the PEG phase. These results indicate good prospects for the design of new plasmid DNA purification methods using fusion proteins as affinity ligands.
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Affiliation(s)
- H Barbosa
- Department of Chemistry, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
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9
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Abstract
We have shown previously that a sequence-specific DNA-binding protein based on the Lac repressor protein can isolate pre-purified DNA efficiently from simple buffer solution but our attempts to purify plasmids directly from crude starting materials were disappointing with impractically low DNA yields. We have optimized the procedure and present a simple affinity methodology whereby plasmid DNA is purified directly by mixing two crude cell lysates, one cell lysate containing the plasmid and the other the protein affinity ligand, without the need for treatment by RNaseA. After IMAC chromatography, high purity supercoiled DNA is recovered in good yields of 100-150 microg plasmid per 200 mL shake flask culture. Moreover, the resulting DNA is free from linear or open-circular plasmid DNA, genomic DNA, RNA, and protein, to the limits of our detection. Furthermore, we show that lyophilized affinity ligand can be stored at room temperature and re-hydrated for use when required.
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Affiliation(s)
- Richard A J Darby
- School of Life and Health Sciences, Aston University, Aston Triangle, Birmingham, B4 7ET, United Kingdom
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10
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McCairn MC, Hughes MD, Hine AV, Sutherland AJ. A platform for both solid-phase peptide nucleic acid oligomer synthesis and subsequent in situ detection and quantification of nucleic acid sequences. ACTA ACUST UNITED AC 2006; 8:639-42. [PMID: 16961397 DOI: 10.1021/cc060035g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Mark C McCairn
- Department of Chemical Engineering & Applied Chemistry and School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham, B4 7ET, United Kingdom
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11
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McCairn MC, Hughes MD, Hine AV, Sutherland AJ. Solid-phase PNA synthesis and in situ scintillation proximity assay for the detection of PNA-DNA hybridization. ACTA ACUST UNITED AC 2006; 8:1-3. [PMID: 16398544 DOI: 10.1021/cc050051y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mark C McCairn
- Department of Chemical Engineering and Applied Chemistry, Aston University, Aston Triangle, Birmingham, B4 7ET United Kingdom
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Abstract
Current approaches for purifying plasmids from bacterial production systems exploit the physiochemical properties of nucleic acids in non-specific capture systems. In this study, an affinity system for plasmid DNA (pDNA) purification has been developed utilizing the interaction between the lac operon (lacO) sequence contained in the pDNA and a 64mer synthetic peptide representing the DNA-binding domain of the lac repressor protein, LacI. Two plasmids were evaluated, the native pUC19 and pUC19 with dual lacO3/lacOs operators (pUC19(lacO3/lacOs)), where the lacOs operator is perfectly symmetrical. The DNA-protein affinity interaction was evaluated by surface plasmon resonance using a Biacore system. The affinity capture of DNA in a chromatography system was evaluated using LacI peptide that had been immobilized to Streamline adsorbent. The KD-values for double stranded DNA (dsDNA) fragments containing lacO1 and lacO3 and lacOS and lacO3 were 5.7 +/- 0.3 x 10(-11) M and 4.1 +/- 0.2 x 10(-11) M respectively, which compare favorably with literature reports of 5 x 10(-10)-1 x 10(-9) M for native lacO1 and 1-1.2 x 10(-10) M for lacO1 in a saline buffer. Densitometric analysis of the gel bands from the affinity chromatography run clearly showed a significant preference for capture of the supercoiled fraction from the feed pDNA sample. The results indicate the feasibility of the affinity approach for pDNA capture and purification using native protein-DNA interaction.
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Affiliation(s)
- Gareth M Forde
- Department of Chemical Engineering, Cambridge Unit for Bioscience Engineering (CUBE), Pembroke Street, University of Cambridge, Cambridge CB2 3RA, UK
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13
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Abstract
Muscle protein degradation is thought to play a major role in muscle atrophy in cancer cachexia. To investigate the importance of the ubiquitin-proteasome pathway, which has been suggested to be the main degradative pathway mediating progressive protein loss in cachexia, the expression of mRNA for proteasome subunits C2 and C5 as well as the ubiquitin-conjugating enzyme, E214k, has been determined in gastrocnemius and pectoral muscles of mice bearing the MAC16 adenocarcinoma, using competitive quantitative reverse transcriptase polymerase chain reaction. Protein levels of proteasome subunits and E214k were determined by immunoblotting, to ensure changes in mRNA were reflected in changes in protein expression. Muscle weights correlated linearly with weight loss during the course of the study. There was a good correlation between expression of C2 and E214k mRNA and protein levels in gastrocnemius muscle with increases of 6–8-fold for C2 and two-fold for E214k between 12 and 20% weight loss, followed by a decrease in expression at weight losses of 25–27%, although loss of muscle protein continued. In contrast, expression of C5 mRNA only increased two-fold and was elevated similarly at all weight losses between 7.5 and 27%. Both proteasome functional activity, and proteasome-specific tyrosine release as a measure of total protein degradation was also maximal at 18–20% weight loss and decreased at higher weight loss. Proteasome expression in pectoral muscle followed a different pattern with increases in C2 and C5 and E214k mRNA only being seen at weight losses above 17%, although muscle loss increased progressively with increasing weight loss. These results suggest that activation of the ubiquitin-proteasome pathway plays a major role in protein loss in gastrocnemius muscle, up to 20% weight loss, but that other factors such as depression in protein synthesis may play a more important role at higher weight loss.
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Affiliation(s)
- J Khal
- Pharmaceutical Sciences Research Institute, Aston University, Birmingham B4 7ET, UK
| | - S M Wyke
- Pharmaceutical Sciences Research Institute, Aston University, Birmingham B4 7ET, UK
| | - S T Russell
- Pharmaceutical Sciences Research Institute, Aston University, Birmingham B4 7ET, UK
| | - A V Hine
- Pharmaceutical Sciences Research Institute, Aston University, Birmingham B4 7ET, UK
| | - M J Tisdale
- Pharmaceutical Sciences Research Institute, Aston University, Birmingham B4 7ET, UK
- Pharmaceutical Sciences Research Institute, Aston University, Birmingham B4 7ET, UK. E-mail:
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Khal J, Hine AV, Fearon KCH, Dejong CHC, Tisdale MJ. Increased expression of proteasome subunits in skeletal muscle of cancer patients with weight loss. Int J Biochem Cell Biol 2005; 37:2196-206. [PMID: 16125116 DOI: 10.1016/j.biocel.2004.10.017] [Citation(s) in RCA: 101] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2004] [Revised: 10/22/2004] [Accepted: 10/28/2004] [Indexed: 11/21/2022]
Abstract
Atrophy of skeletal muscle is common in patients with cancer and results in increased morbidity and mortality. In order to design effective therapy the mechanism by which this occurs needs to be elucidated. Most studies suggest that the ubiquitin-proteasome proteolytic pathway is most important in intracellular proteolysis, although there have been no reports on the activity of this pathway in patients with different extents of weight loss. In this report the expression of the ubiquitin-proteasome pathway in rectus abdominis muscle has been determined in cancer patients with weight loss of 0-34% using a competitive reverse transcriptase polymerase chain reaction to measure expression of mRNA for proteasome subunits C2 and C5, while protein expression has been determined by western blotting. Overall, both C2 and C5 gene expression was increased by about three-fold in skeletal muscle of cachectic cancer patients (average weight loss 14.5+/-2.5%), compared with that in patients without weight loss, with or without cancer. The level of gene expression was dependent on the amount of weight loss, increasing maximally for both proteasome subunits in patients with weight loss of 12-19%. Further increases in weight loss reduced expression of mRNA for both proteasome subunits, although it was still elevated in comparison with patients with no weight loss. There was no evidence for an increase in expression at weight losses less than 10%. There was a good correlation between expression of proteasome 20Salpha subunits, detected by western blotting, and C2 and C5 mRNA, showing that increased gene expression resulted in increased protein synthesis. Expression of the ubiquitin conjugating enzyme, E2(14k), with weight loss followed a similar pattern to that of proteasome subunits. These results suggest variations in the expression of key components of the ubiquitin-proteasome pathway with weight loss of cancer patients, and suggest that another mechanism of protein degradation must be operative for patients with weight loss less than 10%.
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Affiliation(s)
- J Khal
- Pharmaceutical Sciences Research Institute, Aston University, Birmingham B4 7ET, UK
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15
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Abstract
Affinity purification of plasmid DNA is an attractive option for the biomanufacture of therapeutic plasmids, which are strictly controlled for levels of host protein, DNA, RNA, and endotoxin. Plasmid vectors are considered to be a safer alternative than viruses for gene therapy, but milligram quantities of DNA are required per dose. Previous affinity approaches have involved triplex DNA formation and a sequence-specific zinc finger protein. We present a more generically applicable protein-based approach, which exploits the lac operator, present in a wide diversity of plasmids, as a target sequence. We used a GFP/His-tagged LacI protein, which is precomplexed with the plasmid, and the resulting complex was immobilized on a solid support (TALON resin). Ensuing elution gives plasmid DNA, in good yield (>80% based on recovered starting material, 35-50% overall process), free from detectable RNA and protein and with minimal genomic DNA contamination. Such an affinity-based process should enhance plasmid purity and ultimately, after appropriate development, may simplify the biomanufacturing process of therapeutic plasmids.
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Affiliation(s)
- Richard A J Darby
- School of Life and Health Sciences, Aston University, Birmingham, UK
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16
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Hughes MD, Zhang ZR, Sutherland AJ, Santos AF, Hine AV. Discovery of active proteins directly from combinatorial randomized protein libraries without display, purification or sequencing: identification of novel zinc finger proteins. Nucleic Acids Res 2005; 33:e32. [PMID: 15722478 PMCID: PMC549430 DOI: 10.1093/nar/gni031] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
We have successfully linked protein library screening directly with the identification of active proteins, without the need for individual purification, display technologies or physical linkage between the protein and its encoding sequence. By using 'MAX' randomization we have rapidly constructed 60 overlapping gene libraries that encode zinc finger proteins, randomized variously at the three principal DNA-contacting residues. Expression and screening of the libraries against five possible target DNA sequences generated data points covering a potential 40,000 individual interactions. Comparative analysis of the resulting data enabled direct identification of active proteins. Accuracy of this library analysis methodology was confirmed by both in vitro and in vivo analyses of identified proteins to yield novel zinc finger proteins that bind to their target sequences with high affinity, as indicated by low nanomolar apparent dissociation constants.
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Affiliation(s)
- Marcus D. Hughes
- School of Life and Health Sciences, Aston UniversityAston Triangle, Birmingham B4 7ET, UK
- ProtaMAX Ltd55 Colmore Row, Birmingham B3 2AS, UK
| | - Zhan-Ren Zhang
- School of Life and Health Sciences, Aston UniversityAston Triangle, Birmingham B4 7ET, UK
| | - Andrew J. Sutherland
- Chemical Engineering and Applied Chemistry, School of Engineering & Applied Science, Aston UniversityAston Triangle, Birmingham B4 7ET, UK
| | - Albert F. Santos
- GE Healthcare, Cardiff LaboratoriesForest Farm, Whitchurch, Cardiff CF14 7YT, UK
| | - Anna V. Hine
- School of Life and Health Sciences, Aston UniversityAston Triangle, Birmingham B4 7ET, UK
- ProtaMAX Ltd55 Colmore Row, Birmingham B3 2AS, UK
- To whom correspondence should be addressed. Tel: +44 121 204 3961; Fax: +44 121 359 0733;
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Zhang ZR, Palfrey D, Nagel DA, Lambert PA, Jessop RA, Santos AF, Hine AV. Fluorescent microplate-based analysis of protein-DNA interactions. I: Immobilized protein. Biotechniques 2004; 35:980-2, 984, 986. [PMID: 14628672 DOI: 10.2144/03355st06] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [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: 11/23/2022] Open
Abstract
A simple protein-DNA interaction analysis has been developed using a high-affinity/high-specificity zinc finger protein. In essence, purified protein samples are immobilized directly onto the surface of microplate wells, and fluorescently labeled DNA is added in solution. After incubation and washing, bound DNA is detected in a standard microplate reader. The minimum sensitivity of the assay is approximately 0.2 nM DNA. Since the detection of bound DNA is noninvasive and the protein-DNA interaction is not disrupted during detection, iterative readings may be taken from the same well, after successive alterations in interaction conditions, if required. In this respect, the assay may therefore be considered real time and permits appropriate interaction conditions to be determined quantitatively. The assay format is ideally suited to investigate the interactions of purified unlabeled DNA binding proteins in a high-throughput format.
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Zhang ZR, Hughes MD, Morgan LJ, Santos AF, Hine AV. Fluorescent microplate-based analysis of protein-DNA interactions II: immobilized DNA. Biotechniques 2003; 35:988-90, 992, 994 passim. [PMID: 14628673 DOI: 10.2144/03355st07] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [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: 11/23/2022] Open
Abstract
A simple protein-DNA interaction analysis has been developed using both a high-affinity/high-specificity zinc finger protein and a low-specificity zinc finger protein with nonspecific DNA binding capability. The latter protein is designed to mimic background binding by proteins generated in randomized or shuffled gene libraries. In essence, DNA is immobilized onto the surface of microplate wells via streptavidin capture, and green fluorescent protein (GFP)-labeled protein is added in solution as part of a crude cell lysate or protein mixture. After incubation and washing, bound protein is detected in a standard microplate reader. The minimum sensitivity of the assay is approximately 0.4 nM protein. The assay format is ideally suited to investigate the interactions of DNA binding proteins from within crude cell extracts and/or mixtures of proteins that may be encountered in protein libraries generated by codon randomization or gene shuffling.
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Abstract
Amino acid substitution plays a vital role in both the molecular engineering of proteins and analysis of structure-activity relationships. High-throughput substitution is achieved by codon randomisation, which generates a library of mutants (a randomised gene library) in a single experiment. For full randomisation, key codons are typically replaced with NNN (64 sequences) or NN(G)(CorT) (32 sequences). This obligates cloning of redundant codons alongside those required to encode the 20 amino acids. As the number of randomised codons increases, there is therefore a progressive loss of randomisation efficiency; the number of genes required per protein rises exponentially. The redundant codons cause amino acids to be represented unevenly; for example, methionine is encoded just once within NNN, whilst arginine is encoded six times. Finally, the organisation of the genetic code makes it impossible to encode functional subsets of amino acids (e.g. polar residues only) in a single experiment. Here, we present a novel solution to randomisation where genetic redundancy is eliminated; the number of different genes equals the number of encoded proteins, regardless of codon number. There is no inherent amino acid bias and any required subset of amino acids may be encoded in one experiment. This generic approach should be widely applicable in studies involving randomisation of proteins.
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Affiliation(s)
- Marcus D Hughes
- School of Life and Health Sciences, Aston University, Aston Triangle, B4 7ET, Birmingham, UK
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McCairn MC, Hine AV, Sutherland AJ. Synthesis and evaluation of scintillant-containing poly(oxyethylene glycol) polymer (POP-Sc) supports. ACTA ACUST UNITED AC 2002. [DOI: 10.1039/b210421k] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Woodgate J, Palfrey D, Nagel DA, Hine AV, Slater NKH. Protein-mediated isolation of plasmid DNA by a zinc finger-glutathione S-transferase affinity linker. Biotechnol Bioeng 2002; 79:450-6. [PMID: 12115408 DOI: 10.1002/bit.10296] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.5] [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: 11/11/2022]
Abstract
The sequence-specific affinity chromatographic isolation of plasmid DNA from crude lysates of E. coli DH5alpha fermentations is addressed. A zinc finger-GST fusion protein that binds a synthetic oligonucleotide cassette containing the appropriate DNA recognition sequence is described. This cassette was inserted into the SmaI site of pUC19 to enable the affinity isolation of the plasmid. It is shown that zinc finger-GST fusion proteins can bind both their DNA recognition sequence and a glutathione-derivatized solid support simultaneously. Furthermore, a simple procedure for the isolation of such plasmids from clarified cell lysates is demonstrated. Cell lysates were clarified by cross-flow Dean vortex microfiltration, and the permeate was incubated with zinc finger-GST fusion protein. The resulting complex was adsorbed directly onto glutathione-Sepharose. Analysis of the glutathione-eluted complex showed that plasmid DNA had been recovered, largely free from contamination by genomic DNA or bacterial cell proteins.
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Affiliation(s)
- John Woodgate
- School of Engineering and Applied Science, Aston University, Aston Triangle, Birmingham, United Kingdom
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Palfrey D, Picardo M, Hine AV. A new randomization assay reveals unexpected elements of sequence bias in model 'randomized' gene libraries: implications for biopanning. Gene 2000; 251:91-9. [PMID: 10863100 DOI: 10.1016/s0378-1119(00)00206-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [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: 11/24/2022]
Abstract
Although techniques such as biopanning rely heavily upon the screening of randomized gene libraries, there is surprisingly little information available on the construction of those libraries. In general, it is based on the cloning of 'randomized' synthetic oligonucleotides, in which given position(s) contain an equal mixture of all four bases. Yet, many supposedly 'randomized' libraries contain significant elements of bias and/or omission. Here, we report the development and validation of a new, PCR-based assay that enables rapid examination of library composition both prior to and after cloning. By using our assay to analyse model libraries, we demonstrate that the cloning of a given distribution of sequences does not necessarily result in a similarly composed library of clones. Thus, while bias in randomized synthetic oligonucleotide mixtures can be virtually eliminated by using unequal ratios of the four phosphoramidites, the use of such mixtures does not ensure retrieval of a truly randomized library. We propose that in the absence of a technique to control cloning frequencies, the ability to analyse the composition of libraries after cloning will enhance significantly the quality of information derived from those libraries.
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Affiliation(s)
- D Palfrey
- Pharmaceutical Sciences Research Institute, Aston University, Aston Triangle, Birmingham, UK
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Palfrey D, Cook PJ, Smythe JA, Lip GY, Hine AV. Simplified preparation of human arterial sections for PCR analysis of Chlamydia pneumoniae and human DNA. Mol Pathol 1999; 52:289-94. [PMID: 10748879 PMCID: PMC395712 DOI: 10.1136/mp.52.5.289] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [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: 01/19/2023]
Abstract
AIMS To investigate multiple techniques for the preparation of solid tissue for polymerase chain reaction (PCR) analysis, and to identify the most simple techniques for routine use in the laboratory. METHODS Techniques for the preparation of arterial tissue samples including homogenisation, ultrafiltration, and treatments involving proteinase K, Gene Clean, lectin, and Fe3+ specific chelators were evaluated using the PCR to amplify both Chlamydia pneumoniae and human DNA. RESULTS Treatment with either Gene-Clean or lectin and the Fe3+ specific chelator deferoxamine mesylate removed PCR inhibitors from tissue homogenates. Homogenisation followed by GeneClean treatment resulted in the amplification of C pneumoniae DNA from within a section of atherosclerotic carotid artery, implying that C pneumoniae elementary bodies had been disrupted. In eight further clinical samples from patients not known to have C pneumoniae infection, human DNA was amplified and no cross contamination was observed between samples. These samples contained no evidence of C pneumoniae by PCR. CONCLUSIONS A simple preparation of solid tissue for PCR analysis, involving homogenisation followed by GeneClean treatment has been developed, and is effective for the amplification of both C pneumoniae and human DNA.
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Affiliation(s)
- D Palfrey
- Pharmaceutical Sciences Research Institute, Aston University, Birmingham, UK
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Kusakabe T, Hine AV, Hyberts SG, Richardson CC. The Cys4 zinc finger of bacteriophage T7 primase in sequence-specific single-stranded DNA recognition. Proc Natl Acad Sci U S A 1999; 96:4295-300. [PMID: 10200256 PMCID: PMC16326 DOI: 10.1073/pnas.96.8.4295] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.1] [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: 11/18/2022] Open
Abstract
Bacteriophage T7 DNA primase recognizes 5'-GTC-3' in single-stranded DNA. The primase contains a single Cys4 zinc-binding motif that is essential for recognition. Biochemical and mutagenic analyses suggest that the Cys4 motif contacts cytosine of 5'-GTC-3' and may also contribute to thymine recognition. Residues His33 and Asp31 are critical for these interactions. Biochemical analysis also reveals that T7 primase selectively binds CTP in the absence of DNA. We propose that bound CTP selects the remaining base G, of 5'-GTC-3', by base pairing. Our deduced mechanism for recognition of ssDNA by Cys4 motifs bears little resemblance to the recognition of trinucleotides of double-stranded DNA by Cys2His2 zinc fingers.
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Affiliation(s)
- T Kusakabe
- Department of Biological Chemistry and Molecular Pharmacology, Harvard University Medical School, Boston, MA 02115, USA
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Hine AV, Richardson CC. A functional chimeric DNA primase: the Cys4 zinc-binding domain of bacteriophage T3 primase fused to the helicase of bacteriophage T7. Proc Natl Acad Sci U S A 1994; 91:12327-31. [PMID: 7991626 PMCID: PMC45430 DOI: 10.1073/pnas.91.25.12327] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [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: 01/28/2023] Open
Abstract
Two colinear bacteriophage T7 gene 4 proteins provide helicase and primase functions in vivo. T7 primase differs from T7 helicase by an additional 63 residues at the amino terminus. This terminal domain contains a zinc-binding motif which mediates an interaction with the basic primase recognition sequence 3'-CTG-5'. We have generated a chimeric primase in which the 81 amino-terminal residues are derived from the primase of phage T3 and the 484 carboxyl-terminal residues are those of phage T7 helicase. The amino-terminal domain of T3 primase is 50% homologous with that of T7 primase. The resulting T3/T7 chimeric protein is a functional primase in vivo. While the primase activity of the purified protein is about one-third that of T7 primase, the recognition sites used and the oligoribonucleotides synthesized from these sites are identical. We conclude that the residues responsible for the interaction with the sequence 3'-CTG-5' are conserved between the chimeric and T7 proteins.
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Affiliation(s)
- A V Hine
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115
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Hine AV, Brown TA. Synthesis and expression of a gene encoding a 48-residue repeat in the Pseudomonas syringae ice nucleation protein. Gene 1994; 142:73-8. [PMID: 8181760 DOI: 10.1016/0378-1119(94)90357-3] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The aim of this work was to construct short analogues of the repetitive water-binding domain of the Pseudomonas syringae ice nucleation protein, InaZ. Structural analysis of these analogues might provide data pertaining to the protein-water contacts that underlie ice nucleation. An artificial gene coding for a 48-mer repeat sequence from InaZ was synthesized from four oligodeoxyribonucleotides and ligated into the expression vector, pGEX2T. The recombinant vector was cloned in Escherichia coli and a glutathione S-transferase fusion protein obtained. This fusion protein displayed a low level of ice-nucleating activity when tested by a droplet freezing assay. The fusion protein could be cleaved with thrombin, providing a means for future recovery of the 48-mer peptide in amounts suitable for structural analysis by nuclear magnetic resonance spectroscopy.
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Affiliation(s)
- A V Hine
- Department of Biochemistry and Applied Molecular Biology, UMIST, Manchester, UK
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