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Štambuk N, Konjevoda P, Štambuk A. How ambiguity codes specify molecular descriptors and information flow in Code Biology. Biosystems 2023; 233:105034. [PMID: 37739308 DOI: 10.1016/j.biosystems.2023.105034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 09/12/2023] [Accepted: 09/12/2023] [Indexed: 09/24/2023]
Abstract
The article presents IUPAC ambiguity codes for incomplete nucleic acid specification, and their use in Code Biology. It is shown how to use this nomenclature in order to extract accurate information on different properties of the biological systems. We investigated the use of ambiguity codes, as mathematical and logical operators and truth table elements, for the encoding of amino acids by means of the Standard Genetic Code. It is explained how to use ambiguity codes and truth functions in order to obtain accurate information on different properties of the biological systems. Nucleotide ambiguity codes could be applied to: 1. encoding descriptive information of nucleotides, amino acids and proteins (e.g., of polarity, relative solvent accessibility, atom depth, etc.), and 2. system modelling ranging from standard bioinformatics tools to classic evolutionary models (i.e. from Miyazawa-Jernigan statistical potential to Kimura three-substitution-type model, respectively). It is shown that the algorithms based on IUPAC ambiguity codes, Boolean functions and truth table, Probabilistic Square of Opposition/Semiotic Square and Klein 4-groups-could be used for the bioinformatics analyses and Relational data modelling in natural science. Underlying mathematical, logical and semiotic concepts of interest are presented and addressed.
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Affiliation(s)
- Nikola Štambuk
- Centre for Nuclear Magnetic Resonance, Ruđer Bošković Institute, Bijenička cesta 54, HR-10000, Zagreb, Croatia.
| | - Paško Konjevoda
- Laboratory for Epigenomics, Division of Molecular Medicine, Ruđer Bošković Institute, Bijenička cesta 54, HR-10000, Zagreb, Croatia.
| | - Albert Štambuk
- Faculty of Kinesiology, University of Zagreb, Horvaćanski zavoj 15, HR-10000 Zagreb, Croatia
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Gupta S, Azadvari N, Hosseinzadeh P. Design of Protein Segments and Peptides for Binding to Protein Targets. BIODESIGN RESEARCH 2022; 2022:9783197. [PMID: 37850124 PMCID: PMC10521657 DOI: 10.34133/2022/9783197] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 03/16/2022] [Indexed: 10/19/2023] Open
Abstract
Recent years have witnessed a rise in methods for accurate prediction of structure and design of novel functional proteins. Design of functional protein fragments and peptides occupy a small, albeit unique, space within the general field of protein design. While the smaller size of these peptides allows for more exhaustive computational methods, flexibility in their structure and sparsity of data compared to proteins, as well as presence of noncanonical building blocks, add additional challenges to their design. This review summarizes the current advances in the design of protein fragments and peptides for binding to targets and discusses the challenges in the field, with an eye toward future directions.
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Affiliation(s)
- Suchetana Gupta
- Knight Campus Center for Accelerating Scientific Impact, University of Oregon, Eugene OR 97403, USA
| | - Noora Azadvari
- Knight Campus Center for Accelerating Scientific Impact, University of Oregon, Eugene OR 97403, USA
| | - Parisa Hosseinzadeh
- Knight Campus Center for Accelerating Scientific Impact, University of Oregon, Eugene OR 97403, USA
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3
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Štambuk N, Konjevoda P, Pavan J. Antisense Peptide Technology for Diagnostic Tests and Bioengineering Research. Int J Mol Sci 2021; 22:9106. [PMID: 34502016 PMCID: PMC8431130 DOI: 10.3390/ijms22179106] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 08/10/2021] [Accepted: 08/13/2021] [Indexed: 01/01/2023] Open
Abstract
Antisense peptide technology (APT) is based on a useful heuristic algorithm for rational peptide design. It was deduced from empirical observations that peptides consisting of complementary (sense and antisense) amino acids interact with higher probability and affinity than the randomly selected ones. This phenomenon is closely related to the structure of the standard genetic code table, and at the same time, is unrelated to the direction of its codon sequence translation. The concept of complementary peptide interaction is discussed, and its possible applications to diagnostic tests and bioengineering research are summarized. Problems and difficulties that may arise using APT are discussed, and possible solutions are proposed. The methodology was tested on the example of SARS-CoV-2. It is shown that the CABS-dock server accurately predicts the binding of antisense peptides to the SARS-CoV-2 receptor binding domain without requiring predefinition of the binding site. It is concluded that the benefits of APT outweigh the costs of random peptide screening and could lead to considerable savings in time and resources, especially if combined with other computational and immunochemical methods.
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Affiliation(s)
- Nikola Štambuk
- Center for Nuclear Magnetic Resonance, Ruđer Bošković Institute, Bijenička cesta 54, HR-10000 Zagreb, Croatia
| | - Paško Konjevoda
- Laboratory for Epigenomics, Division of Molecular Medicine, Ruđer Bošković Institute, Bijenička cesta 54, HR-10000 Zagreb, Croatia
| | - Josip Pavan
- Department of Ophthalmology, University Hospital Dubrava, Avenija Gojka Šuška 6, HR-10000 Zagreb, Croatia
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Targeting Tumor Markers with Antisense Peptides: An Example of Human Prostate Specific Antigen. Int J Mol Sci 2019; 20:ijms20092090. [PMID: 31035335 PMCID: PMC6540241 DOI: 10.3390/ijms20092090] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 04/05/2019] [Accepted: 04/25/2019] [Indexed: 12/20/2022] Open
Abstract
The purpose of this paper was to outline the development of short peptide targeting of the human prostate specific antigen (hPSA), and to evaluate its effectiveness in staining PSA in human prostate cancer tissue. The targeting of the hPSA antigen by means of antisense peptide AVRDKVG was designed according to a three-step method involving: 1. The selection of the molecular target (hPSA epitope), 2. the modeling of an antisense peptide (paratope) based on the epitope sequence, and 3. the spectroscopic evaluation of sense–antisense peptide binding. We then modified standard hPSA immunohistochemical staining practice by using a biotinylated antisense peptide instead of the standard monoclonal antibody and compared the results of both procedures. Immunochemical testing on human tissue showed the applicability of the antisense peptide technology to human molecular targets. This methodology represents a new approach to deriving peptide ligands and potential lead compounds for the development of novel diagnostic substances, biopharmaceuticals and vaccines.
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Li HM, Dong ZP, Wang QY, Liu LX, Li BX, Ma XN, Lin MS, Lu T, Wang Y. De Novo Computational Design for Development of a Peptide Ligand Oriented to VEGFR-3 with High Affinity and Long Circulation. Mol Pharm 2017; 14:2236-2244. [DOI: 10.1021/acs.molpharmaceut.7b00070] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Hong M. Li
- Key
Laboratory of Biomedical Functional Materials, School of Sciences, China Pharmaceutical University, Nanjing 211198, China
| | - Zhi P. Dong
- Key
Laboratory of Biomedical Functional Materials, School of Sciences, China Pharmaceutical University, Nanjing 211198, China
| | - Qi Y. Wang
- Key
Laboratory of Biomedical Functional Materials, School of Sciences, China Pharmaceutical University, Nanjing 211198, China
| | - Li X. Liu
- Key
Laboratory of Biomedical Functional Materials, School of Sciences, China Pharmaceutical University, Nanjing 211198, China
| | - Bing X. Li
- Key
Laboratory of Biomedical Functional Materials, School of Sciences, China Pharmaceutical University, Nanjing 211198, China
| | - Xiao N. Ma
- Cellular and Molecular Biology Center of China Pharmaceutical University, Nanjing 211198, China
| | - Ming S. Lin
- TA Instruments-Waters LLC, Shanghai 200233, China
| | - Tao Lu
- State
Key Laboratory of Natural Medicines, School of Sciences, China Pharmaceutical University, Nanjing 211198, China
| | - Yue Wang
- Key
Laboratory of Biomedical Functional Materials, School of Sciences, China Pharmaceutical University, Nanjing 211198, China
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Martinić R, Sošić H, Turčić P, Konjevoda P, Fučić A, Stojković R, Aralica G, Gabričević M, Weitner T, Stambuk N. Hepatoprotective effects of Met-enkephalin on acetaminophen-induced liver lesions in male CBA mice. Molecules 2014; 19:11833-45. [PMID: 25105920 PMCID: PMC6270943 DOI: 10.3390/molecules190811833] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Revised: 07/22/2014] [Accepted: 07/31/2014] [Indexed: 11/16/2022] Open
Abstract
Recent histopathological investigations in patients with hepatitis suggested possible involvement of Met-enkephalin and its receptors in the pathophysiology of hepatitis. Consequently, we evaluated the potential hepatoprotective effects of this endogenous opioid pentapeptide in the experimental model of acetaminophen induced hepatotoxicity in male CBA mice. Met-enkephalin exhibited strong hepatoprotective effects in a dose of 7.5 mg/kg, which corresponds to the protective dose reported for several different animal disease models. In this group plasma alanine aminotransferase and aspartate aminotransferase enzyme activities, as well as liver necrosis score were significantly reduced in comparison to control animals treated with physiological saline (p>0.01). The specificity of the peptide hepatoprotection was investigated from the standpoint of the receptor and peptide blockade. It was concluded that Met-enkephalin effects on the liver were mediated via δ and ζ opioid receptors. Genotoxic testing of Met-enkephalin confirmed the safety of the peptide.
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Affiliation(s)
- Roko Martinić
- Department for Clinical Pathophysiology, Clinical Hospital Centre Split, Šoltanska 1, 21000 Split, Croatia.
| | - Hrvoje Sošić
- Department of Urology, University Clinical Hospital Centre Zagreb, Kišpatićeva 12, 10000 Zagreb, Croatia.
| | - Petra Turčić
- Department of Pharmacology, Faculty of Pharmacy and Biochemistry, University of Zagreb, Domagojeva 2, 10000 Zagreb, Croatia.
| | - Paško Konjevoda
- Center for Nuclear Magnetic Resonance, Ruđer Bošković Institute, Bijenička cesta 54, 10002 Zagreb, Croatia.
| | - Aleksandra Fučić
- Institute for Medical Research and Occupational Health, Ksaverska cesta 2, 10001 Zagreb, Croatia.
| | - Ranko Stojković
- Division of Molecular Medicine, Ruđer Bošković Institute, Bijenička cesta 54, 10002 Zagreb, Croatia.
| | - Gorana Aralica
- University Hospital Dubrava, Avenija Gojka Šuška 6, 10000 Zagreb, Croatia.
| | - Mario Gabričević
- Department of General and Inorganic Chemistry, Faculty of Pharmacy and Biochemistry, University of Zagreb, Ante Kovačića 1, 10000 Zagreb, Croatia.
| | - Tin Weitner
- Department of General and Inorganic Chemistry, Faculty of Pharmacy and Biochemistry, University of Zagreb, Ante Kovačića 1, 10000 Zagreb, Croatia.
| | - Nikola Stambuk
- Center for Nuclear Magnetic Resonance, Ruđer Bošković Institute, Bijenička cesta 54, 10002 Zagreb, Croatia.
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Štambuk N, Manojlović Z, Turčić P, Martinić R, Konjevoda P, Weitner T, Wardega P, Gabričević M. A simple three-step method for design and affinity testing of new antisense peptides: an example of erythropoietin. Int J Mol Sci 2014; 15:9209-23. [PMID: 24865486 PMCID: PMC4100090 DOI: 10.3390/ijms15069209] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2014] [Revised: 05/09/2014] [Accepted: 05/12/2014] [Indexed: 11/16/2022] Open
Abstract
Antisense peptide technology is a valuable tool for deriving new biologically active molecules and performing peptide-receptor modulation. It is based on the fact that peptides specified by the complementary (antisense) nucleotide sequences often bind to each other with a higher specificity and efficacy. We tested the validity of this concept on the example of human erythropoietin, a well-characterized and pharmacologically relevant hematopoietic growth factor. The purpose of the work was to present and test simple and efficient three-step procedure for the design of an antisense peptide targeting receptor-binding site of human erythropoietin. Firstly, we selected the carboxyl-terminal receptor binding region of the molecule (epitope) as a template for the antisense peptide modeling; Secondly, we designed an antisense peptide using mRNA transcription of the epitope sequence in the 3'→5' direction and computational screening of potential paratope structures with BLAST; Thirdly, we evaluated sense-antisense (epitope-paratope) peptide binding and affinity by means of fluorescence spectroscopy and microscale thermophoresis. Both methods showed similar Kd values of 850 and 816 µM, respectively. The advantages of the methods were: fast screening with a small quantity of the sample needed, and measurements done within the range of physicochemical parameters resembling physiological conditions. Antisense peptides targeting specific erythropoietin region(s) could be used for the development of new immunochemical methods. Selected antisense peptides with optimal affinity are potential lead compounds for the development of novel diagnostic substances, biopharmaceuticals and vaccines.
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Affiliation(s)
- Nikola Štambuk
- Center for Nuclear Magnetic Resonance, Ruđer Bošković Institute, Bijenička cesta 54, 10002 Zagreb, Croatia.
| | - Zoran Manojlović
- Croatian Institute for Toxicology and Antidoping, Borongajska 83 g, 10000 Zagreb, Croatia.
| | - Petra Turčić
- Department of Pharmacology, Faculty of Pharmacy and Biochemistry, University of Zagreb, Domagojeva 2, 10000 Zagreb, Croatia.
| | - Roko Martinić
- Department for Clinical Pathophysiology, Clinical Hospital Centre Split, Šoltanska 1, 21000 Split, Croatia.
| | - Paško Konjevoda
- Center for Nuclear Magnetic Resonance, Ruđer Bošković Institute, Bijenička cesta 54, 10002 Zagreb, Croatia.
| | - Tin Weitner
- Department of General and Inorganic Chemistry, Faculty of Pharmacy and Biochemistry, University of Zagreb, Ante Kovačića 1, 10000 Zagreb, Croatia.
| | - Piotr Wardega
- NanoTemper Technologies GmbH, Flößergasse 4, 81369 Munich, Germany.
| | - Mario Gabričević
- Department of General and Inorganic Chemistry, Faculty of Pharmacy and Biochemistry, University of Zagreb, Ante Kovačića 1, 10000 Zagreb, Croatia.
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Stemmer N, Strekalova E, Djogo N, Plöger F, Loers G, Lutz D, Buck F, Michalak M, Schachner M, Kleene R. Generation of amyloid-β is reduced by the interaction of calreticulin with amyloid precursor protein, presenilin and nicastrin. PLoS One 2013; 8:e61299. [PMID: 23585889 PMCID: PMC3621835 DOI: 10.1371/journal.pone.0061299] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Accepted: 03/11/2013] [Indexed: 12/28/2022] Open
Abstract
Dysregulation of the proteolytic processing of amyloid precursor protein by γ-secretase and the ensuing generation of amyloid-β is associated with the pathogenesis of Alzheimer's disease. Thus, the identification of amyloid precursor protein binding proteins involved in regulating processing of amyloid precursor protein by the γ-secretase complex is essential for understanding the mechanisms underlying the molecular pathology of the disease. We identified calreticulin as novel amyloid precursor protein interaction partner that binds to the γ-secretase cleavage site within amyloid precursor protein and showed that this Ca2+- and N-glycan-independent interaction is mediated by amino acids 330–344 in the C-terminal C-domain of calreticulin. Co-immunoprecipitation confirmed that calreticulin is not only associated with amyloid precursor protein but also with the γ-secretase complex members presenilin and nicastrin. Calreticulin was detected at the cell surface by surface biotinylation of cells overexpressing amyloid precursor protein and was co-localized by immunostaining with amyloid precursor protein and presenilin at the cell surface of hippocampal neurons. The P-domain of calreticulin located between the N-terminal N-domain and the C-domain interacts with presenilin, the catalytic subunit of the γ-secretase complex. The P- and C-domains also interact with nicastrin, another functionally important subunit of this complex. Transfection of amyloid precursor protein overexpressing cells with full-length calreticulin leads to a decrease in amyloid-β42 levels in culture supernatants, while transfection with the P-domain increases amyloid-β40 levels. Similarly, application of the recombinant P- or C-domains and of a synthetic calreticulin peptide comprising amino acid 330–344 to amyloid precursor protein overexpressing cells result in elevated amyloid-β40 and amyloid-β42 levels, respectively. These findings indicate that the interaction of calreticulin with amyloid precursor protein and the γ-secretase complex regulates the proteolytic processing of amyloid precursor protein by the γ-secretase complex, pointing to calreticulin as a potential target for therapy in Alzheimer's disease.
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Affiliation(s)
- Nina Stemmer
- Zentrum für Molekulare Neurobiologie, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Elena Strekalova
- Zentrum für Molekulare Neurobiologie, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Nevena Djogo
- Zentrum für Molekulare Neurobiologie, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Frank Plöger
- Zentrum für Molekulare Neurobiologie, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Gabriele Loers
- Zentrum für Molekulare Neurobiologie, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - David Lutz
- Zentrum für Molekulare Neurobiologie, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Friedrich Buck
- Institut für Klinische Chemie, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Marek Michalak
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Melitta Schachner
- Zentrum für Molekulare Neurobiologie, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
- Keck Center for Collaborative Neuroscience and Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, New Jersey, United States of America
- Center for Neuroscience, Shantou University Medical College, Shantou, China
- * E-mail:
| | - Ralf Kleene
- Zentrum für Molekulare Neurobiologie, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
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Interaction of α-melanocortin and its pentapeptide antisense LVKAT: effects on hepatoprotection in male CBA mice. Molecules 2011; 16:7331-43. [PMID: 21873934 PMCID: PMC6264190 DOI: 10.3390/molecules16097331] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2011] [Revised: 08/23/2011] [Accepted: 08/23/2011] [Indexed: 11/17/2022] Open
Abstract
The genetic code defines nucleotide patterns that code for individual amino acids and their complementary, i.e., antisense, pairs. Peptides specified by the complementary mRNAs often bind to each other with a higher specificity and efficacy. Applications of this genetic code property in biomedicine are related to the modulation of peptide and hormone biological function, selective immunomodulation, modeling of discontinuous and linear epitopes, modeling of mimotopes, paratopes and antibody mimetics, peptide vaccine development, peptidomimetic and drug design. We have investigated sense-antisense peptide interactions and related modulation of the peptide function by modulating the effects of α-MSH on hepatoprotection with its antisense peptide LVKAT. First, transcription of complementary mRNA sequence of α-MSH in 3’→5’ direction was used to design antisense peptide to the central motif that serves as α-MSH pharmacophore for melanocortin receptors. Second, tryptophan spectrofluorometric titration was applied to evaluate the binding of α-MSH and its central pharmacophore motif to the antisense peptide, and it was concluded that this procedure represents a simple and efficient method to evaluate sense-antisense peptide interaction in vitro. Third, we showed that antisense peptide LVKAT abolished potent hepatoprotective effects of α-MSH in vivo.
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Martínez-Ceron MC, Targovnik AM, Urtasun N, Cascone O, Miranda MV, Camperi SA. Recombinant protein purification using complementary peptides as affinity tags. N Biotechnol 2011; 29:206-10. [PMID: 21664994 DOI: 10.1016/j.nbt.2011.05.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2010] [Revised: 05/18/2011] [Accepted: 05/24/2011] [Indexed: 11/27/2022]
Abstract
Affinity tags have become highly popular tools for purifying recombinant proteins from crude extracts by affinity chromatography. Besides, short peptides are excellent ligands for affinity chromatography, as they are not likely to cause an immune response in case of leakage into the product, they are more stable than antibodies to elution and cleaning conditions and they usually have very acceptable selectivity. Hydropathically complementary peptides designed de novo show enough selectivity to be used successfully as peptide ligands for protein purification from crude extracts. Recognition specificity and selectivity in the interaction between the complementary peptide pair His-Leu-Leu-Phe-Pro-Ile-Ile-Ile-Ala-Ala-Ser-Leu and Lys-Asn-Tyr-Pro-Lys-Lys-Lys-Met-Glu-Lys-Arg-Phe have been demonstrated by other authors. In this work, we designed a recombinant protein purification method using a peptide affinity tag that binds to a peptide-binding partner immobilized on a chromatographic matrix. The enhanced green fluorescent protein expressed (EGFP) in Escherichia coli was used as the model. The peptide Gly-Gly-Gly-His-Leu-Leu-Phe-Pro-Ile-Ile-Ile-Ala-Ala-Ser-Leu was synthesized by solid phase using the Fmoc chemistry and immobilized in NHS-Sepharose (PC-Sepharose). Gly residues were added as a spacer arm at the N terminus. The EGFP was expressed either with the fusion tag Lys-Asn-Tyr-Pro-Lys-Lys-Lys-Met-Glu-Lys-Arg-Phe on the C terminus (EGFP-CPTag) or without any fusion tag. After cell disruption, the extract was directly applied to the PC-Sepharose column equilibrated with 20mM sodium phosphate buffer, pH 7.0. The adsorbed EGFP-CPTag was then eluted with 1M Tris. The yield was 98% and the purification factor 4.6. By contrast, EGFP without tag pass through without interacting with the PC-Sepharose column. The method designed can be applied for the purification of other recombinant proteins.
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Affiliation(s)
- María C Martínez-Ceron
- Cátedra de Microbiología Industrial y Biotecnología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956, (1113) Buenos Aires, Argentina
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