Application of Ni(II)-Assisted Peptide Bond Hydrolysis to Non-Enzymatic Affinity Tag Removal
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{"title"=>"Application of Ni(II)-assisted peptide bond hydrolysis to non-enzymatic affinity tag removal", "type"=>"journal", "authors"=>[{"first_name"=>"Edyta", "last_name"=>"Kopera", "scopus_author_id"=>"6506351777"}, {"first_name"=>"Agnieszka", "last_name"=>"Belczyk-Ciesielska", "scopus_author_id"=>"36445264000"}, {"first_name"=>"Wojciech", "last_name"=>"Bal", "scopus_author_id"=>"7006002984"}], "year"=>2012, "source"=>"PLoS ONE", "identifiers"=>{"pmid"=>"22574150", "doi"=>"10.1371/journal.pone.0036350", "sgr"=>"84860524464", "scopus"=>"2-s2.0-84860524464", "issn"=>"19326203", "pui"=>"364730685"}, "id"=>"2431ed8c-ab9e-39b0-a8de-ceb1feb2c58e", "abstract"=>"In this study, we demonstrate a non-enzymatic method for hydrolytic peptide bond cleavage, applied to the removal of an affinity tag from a recombinant fusion protein, SPI2-SRHWAP-His(6). This method is based on a highly specific Ni(II) reaction with (S/T)XHZ peptide sequences. It can be applied for the protein attached to an affinity column or to the unbound protein in solution. We studied the effect of pH, temperature and Ni(II) concentration on the efficacy of cleavage and developed an analytical protocol, which provides active protein with a 90% yield and ∼100% purity. The method works well in the presence of non-ionic detergents, DTT and GuHCl, therefore providing a viable alternative for currently used techniques.", "link"=>"http://www.mendeley.com/research/application-niiiassisted-peptide-bond-hydrolysis-nonenzymatic-affinity-tag-removal", "reader_count"=>20, "reader_count_by_academic_status"=>{"Student > Doctoral Student"=>2, "Researcher"=>7, "Student > Ph. D. Student"=>6, "Student > Master"=>4, "Student > Bachelor"=>1}, "reader_count_by_user_role"=>{"Student > Doctoral Student"=>2, "Researcher"=>7, "Student > Ph. D. Student"=>6, "Student > Master"=>4, "Student > Bachelor"=>1}, "reader_count_by_subject_area"=>{"Biochemistry, Genetics and Molecular Biology"=>5, "Agricultural and Biological Sciences"=>8, "Pharmacology, Toxicology and Pharmaceutical Science"=>1, "Physics and Astronomy"=>1, "Chemistry"=>5}, "reader_count_by_subdiscipline"=>{"Chemistry"=>{"Chemistry"=>5}, "Physics and Astronomy"=>{"Physics and Astronomy"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>8}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>5}, "Pharmacology, Toxicology and Pharmaceutical Science"=>{"Pharmacology, Toxicology and Pharmaceutical Science"=>1}}, "reader_count_by_country"=>{"Hong Kong"=>1, "United States"=>1}, "group_count"=>0}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/642119"], "description"=>"<p>A, temperature dependence; B, pH dependence. The red line indicates the molar fraction of the hydrolytic Ni(II) complex of the Ac-GASRHWKFL-NH<sub>2</sub> peptide <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0036350#pone.0036350-Kopera1\" target=\"_blank\">[17]</a>, calculated for 20 µM peptide and 0.5 mM Ni(II).</p>", "links"=>[], "tags"=>["hydrolysis", "constants", "20", "fusion", "mm", "100", "hepes"], "article_id"=>312606, "categories"=>["Molecular Biology", "Biochemistry", "Chemistry", "Biological Sciences", "Biophysics"], "users"=>["Edyta Kopera", "Agnieszka Belczyk-Ciesielska", "Wojciech Bal"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0036350.g003", "stats"=>{"downloads"=>0, "page_views"=>23, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_hydrolysis_rate_constants_of_20_M_SPI2_SRHWAP_His_6_fusion_protein_in_the_presence_of_0_5_mM_NiCl_2_and_100_mM_Hepes_buffer_/312606", "title"=>"The hydrolysis rate constants of 20 µM SPI2-SRHWAP-His<sub>6</sub> fusion protein in the presence of 0.5 mM NiCl<sub>2</sub> and 100 mM Hepes buffer.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 05:30:27"}
  • {"files"=>["https://ndownloader.figshare.com/files/642829"], "description"=>"<p>The temperature dependence of the 1<sup>st</sup> order rate constant and reaction half-time for the on-column SPI2-SRHWAP-His<sub>6</sub> hydrolysis, at pH 8.2, determined by HPLC.</p>", "links"=>[], "tags"=>["dependence", "half-time", "on-column", "ph"], "article_id"=>313319, "categories"=>["Molecular Biology", "Biochemistry", "Chemistry", "Biological Sciences", "Biophysics"], "users"=>["Edyta Kopera", "Agnieszka Belczyk-Ciesielska", "Wojciech Bal"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0036350.t003", "stats"=>{"downloads"=>1, "page_views"=>14, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_temperature_dependence_of_the_1_st_order_rate_constant_and_reaction_half_time_for_the_on_column_SPI2_SRHWAP_His_6_hydrolysis_at_pH_8_2_determined_by_HPLC_/313319", "title"=>"The temperature dependence of the 1<sup>st</sup> order rate constant and reaction half-time for the on-column SPI2-SRHWAP-His<sub>6</sub> hydrolysis, at pH 8.2, determined by HPLC.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-20 05:34:11"}
  • {"files"=>["https://ndownloader.figshare.com/files/641846"], "description"=>"<p>Incubation times are indicated on the plot. Peak labels denote reaction substrate and products, identified using ESI-MS: <b><i>S</i></b>, substrate (5868 Da); <b><i>P</i></b>, pure SPI2 protein (4310 Da); <b><i>T</i></b>, the SRHWAP-His<sub>6</sub> tag (1574 Da); <b><i>I</i></b>, the intermediate product of hydrolysis (5868 Da).</p>", "links"=>[], "tags"=>["examples", "chromatograms", "containing", "20", "fusion", "mm", "100", "hepes", "ph", "incubated"], "article_id"=>312328, "categories"=>["Molecular Biology", "Biochemistry", "Chemistry", "Biological Sciences", "Biophysics"], "users"=>["Edyta Kopera", "Agnieszka Belczyk-Ciesielska", "Wojciech Bal"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0036350.g001", "stats"=>{"downloads"=>1, "page_views"=>15, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_examples_of_chromatograms_of_reaction_mixture_containing_initially_20_M_SPI2_SRHWAP_His_6_fusion_protein_0_5_mM_NiCl_2_and_100_mM_Hepes_buffer_pH_8_2_incubated_and_45_176_C_/312328", "title"=>"The examples of chromatograms of reaction mixture containing initially 20 µM SPI2-SRHWAP-His<sub>6</sub> fusion protein, 0.5 mM NiCl<sub>2</sub> and 100 mM Hepes buffer, pH 8.2 incubated and 45°C.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 05:28:57"}
  • {"files"=>["https://ndownloader.figshare.com/files/642240"], "description"=>"<p>The tag can be removed in solution (left) or when immobilized at the affinity column (right).</p>", "links"=>[], "tags"=>["approaches", "affinity", "cleavage"], "article_id"=>312737, "categories"=>["Molecular Biology", "Biochemistry", "Chemistry", "Biological Sciences", "Biophysics"], "users"=>["Edyta Kopera", "Agnieszka Belczyk-Ciesielska", "Wojciech Bal"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0036350.g004", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Alternative_approaches_to_Ni_II_dependent_affinity_tag_cleavage_in_protein_purification_/312737", "title"=>"Alternative approaches to Ni(II)-dependent affinity tag cleavage in protein purification.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 05:31:08"}
  • {"files"=>["https://ndownloader.figshare.com/files/641967"], "description"=>"<p>The main plot shows peak integrals normalized to molar fractions of the initial SPI2-SRHWAP-His<sub>6</sub> fusion protein concentration, and the inset presents 1st order rate constant fits to the substrate decay and product formation. Species are labeled according to <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0036350#pone-0036350-g001\" target=\"_blank\">Fig. 1</a>.</p>", "links"=>[], "tags"=>["hydrolysis", "illustrated"], "article_id"=>312464, "categories"=>["Molecular Biology", "Biochemistry", "Chemistry", "Biological Sciences", "Biophysics"], "users"=>["Edyta Kopera", "Agnieszka Belczyk-Ciesielska", "Wojciech Bal"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0036350.g002", "stats"=>{"downloads"=>1, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_example_of_hydrolysis_rate_constant_calculation_using_the_data_illustrated_in_Fig_1_/312464", "title"=>"The example of hydrolysis rate constant calculation using the data illustrated in <b>Fig. 1</b>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 05:29:44"}
  • {"files"=>["https://ndownloader.figshare.com/files/642889"], "description"=>"<p>The temperature dependence of the 1<sup>st</sup> order rate constant and reaction half-times for SPI2-SRHWAP-His<sub>6</sub> hydrolysis in solution, at H 8.2, determined by HPLC.</p>", "links"=>[], "tags"=>["dependence", "half-times", "hydrolysis"], "article_id"=>313387, "categories"=>["Molecular Biology", "Biochemistry", "Chemistry", "Biological Sciences", "Biophysics"], "users"=>["Edyta Kopera", "Agnieszka Belczyk-Ciesielska", "Wojciech Bal"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0036350.t001", "stats"=>{"downloads"=>1, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_temperature_dependence_of_the_1_st_order_rate_constant_and_reaction_half_times_for_SPI2_SRHWAP_His_6_hydrolysis_in_solution_at_H_8_2_determined_by_HPLC_/313387", "title"=>"The temperature dependence of the 1<sup>st</sup> order rate constant and reaction half-times for SPI2-SRHWAP-His<sub>6</sub> hydrolysis in solution, at H 8.2, determined by HPLC.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-20 05:34:32"}
  • {"files"=>["https://ndownloader.figshare.com/files/642430"], "description"=>"<p>The effect of Ni(II) ions concentration, pH and various detergents on the hydrolysis of SPI2-SRHWAP-His<sub>6</sub> fusion protein.</p>", "links"=>[], "tags"=>["ions", "ph", "detergents", "hydrolysis", "fusion"], "article_id"=>312924, "categories"=>["Molecular Biology", "Biochemistry", "Chemistry", "Biological Sciences", "Biophysics"], "users"=>["Edyta Kopera", "Agnieszka Belczyk-Ciesielska", "Wojciech Bal"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0036350.g006", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_effect_of_Ni_II_ions_concentration_pH_and_various_detergents_on_the_hydrolysis_of_SPI2_SRHWAP_His_6_fusion_protein_/312924", "title"=>"The effect of Ni(II) ions concentration, pH and various detergents on the hydrolysis of SPI2-SRHWAP-His<sub>6</sub> fusion protein.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 05:32:06"}
  • {"files"=>["https://ndownloader.figshare.com/files/642736"], "description"=>"<p><a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0036350#pone.0036350-Kopera1\" target=\"_blank\">[<b>17</b>]</a><b>.</b> Lines represent linear fits to experimental points.</p>", "links"=>[], "tags"=>["demonstrating", "dependence", "hydrolysis", "rates", "ph", "fusion", "hydrolysed", "in-solution", "on-column", "compared", "ac-gasrhwkfl-amide", "peptide"], "article_id"=>313221, "categories"=>["Molecular Biology", "Biochemistry", "Chemistry", "Biological Sciences", "Biophysics"], "users"=>["Edyta Kopera", "Agnieszka Belczyk-Ciesielska", "Wojciech Bal"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0036350.g009", "stats"=>{"downloads"=>1, "page_views"=>54, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Arrhenius_plots_demonstrating_the_temperature_dependence_of_hydrolysis_reaction_rates_at_pH_8_2_for_SPI2_SRHWAP_His_6_fusion_protein_hydrolysed_in_solution_black_and_on_column_blue_compared_to_that_of_the_Ac_GASRHWKFL_amide_peptide_red_/313221", "title"=>"Arrhenius plots, demonstrating the temperature dependence of hydrolysis reaction rates at pH 8.2 for SPI2-SRHWAP-His<sub>6</sub> fusion protein hydrolysed in-solution (black), and on-column (blue), compared to that of the Ac-GASRHWKFL-amide peptide (red)", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 05:33:39"}
  • {"files"=>["https://ndownloader.figshare.com/files/642312"], "description"=>"<p>From top to bottom: control fusion protein (incubated without Ni(II) ions), incubation buffer, and two pooled wash fractions (250 mM imidazole) after 22 h of incubation.</p>", "links"=>[], "tags"=>["examples", "chromatograms", "containing", "80", "fusion", "loaded", "ni-nta-agarose", "incubated", "mm", "100", "hepes", "ph"], "article_id"=>312792, "categories"=>["Molecular Biology", "Biochemistry", "Chemistry", "Biological Sciences", "Biophysics"], "users"=>["Edyta Kopera", "Agnieszka Belczyk-Ciesielska", "Wojciech Bal"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0036350.g005", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_examples_of_chromatograms_of_reaction_mixture_containing_initially_80_M_SPI2_SRHWAP_His_6_fusion_protein_loaded_on_the_Ni_NTA_agarose_column_incubated_with_4_mM_NiCl_2_in_100_mM_Hepes_buffer_pH_8_2_at_50_176_C_/312792", "title"=>"The examples of chromatograms of reaction mixture containing initially 80 µM SPI2-SRHWAP-His<sub>6</sub> fusion protein loaded on the Ni-NTA-agarose column, incubated with 4 mM NiCl<sub>2</sub> in 100 mM Hepes buffer, pH 8.2 at 50°C.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 05:31:25"}
  • {"files"=>["https://ndownloader.figshare.com/files/642856"], "description"=>"<p>The pH dependence of the 1<sup>st</sup> order rate constant and reaction half-time for SPI2-SRHWAP-His<sub>6</sub> hydrolysis in solution, at 50°C, determined by HPLC.</p>", "links"=>[], "tags"=>["ph", "dependence", "half-time", "hydrolysis"], "article_id"=>313349, "categories"=>["Molecular Biology", "Biochemistry", "Chemistry", "Biological Sciences", "Biophysics"], "users"=>["Edyta Kopera", "Agnieszka Belczyk-Ciesielska", "Wojciech Bal"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0036350.t002", "stats"=>{"downloads"=>0, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_pH_dependence_of_the_1_st_order_rate_constant_and_reaction_half_time_for_SPI2_SRHWAP_His_6_hydrolysis_in_solution_at_50_176_C_determined_by_HPLC_/313349", "title"=>"The pH dependence of the 1<sup>st</sup> order rate constant and reaction half-time for SPI2-SRHWAP-His<sub>6</sub> hydrolysis in solution, at 50°C, determined by HPLC.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-20 05:34:21"}
  • {"files"=>["https://ndownloader.figshare.com/files/642628"], "description"=>"<p>Peak labels denote reaction substrate and products, identified using ESI-MS: <b><i>S</i></b>, substrate (5868 Da); <b><i>P</i></b>, pure SPI2 protein (4310 Da); <b><i>P-h</i></b>, SPI2 protein hydroxamate (4326 Da); <b><i>T</i></b>, SRHWAP-His<sub>6</sub> tag (1574 Da); <b><i>I</i></b>, the intermediate product of hydrolysis (5868 Da). * impurity peaks which did not exhibit coherent molecular masses.</p>", "links"=>[], "tags"=>["hplc", "chromatograms", "fusion", "incubated", "ions"], "article_id"=>313121, "categories"=>["Molecular Biology", "Biochemistry", "Chemistry", "Biological Sciences", "Biophysics"], "users"=>["Edyta Kopera", "Agnieszka Belczyk-Ciesielska", "Wojciech Bal"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0036350.g008", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_HPLC_chromatograms_of_the_SPI2_SRHWAP_His_6_fusion_protein_incubated_with_Ni_II_ions_in_the_presence_of_0_25_M_hydroxylamine_/313121", "title"=>"The HPLC chromatograms of the SPI2-SRHWAP-His<sub>6</sub> fusion protein incubated with Ni(II) ions in the presence of 0.25 M hydroxylamine.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 05:33:09"}
  • {"files"=>["https://ndownloader.figshare.com/files/642514"], "description"=>"<p>(A) native conditions, 100 µM Ubi incubated at 50°C in 20 mM Tris, pH 8.2 for 0 h in the absence of Ni(II) (lane 1), 100 µM Ubi incubated at 50°C for 24 h in the presence of 5 mM Ni(II) (lane 2), low-range protein molecular weight marker (lane 3); (B) denaturating conditions, 100 µM Ubi incubated at 50°C and pH 8.2 in the presence of 5 mM Ni(II) and 5 M GuHCl for 0 h (lane 4), 12 h (lane 5), 24 h (lane 6), and 48 h (lane 7); low-range protein molecular weight marker (lane 8) (C) densitometric analysis of gel (B).</p>", "links"=>[], "tags"=>["hydrolysis"], "article_id"=>313010, "categories"=>["Molecular Biology", "Biochemistry", "Chemistry", "Biological Sciences", "Biophysics"], "users"=>["Edyta Kopera", "Agnieszka Belczyk-Ciesielska", "Wojciech Bal"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0036350.g007", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Electrophoretic_analysis_of_Ni_II_hydrolysis_of_Ubi_/313010", "title"=>"Electrophoretic analysis of Ni(II) hydrolysis of Ubi.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 05:32:35"}

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Relative Metric

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