Ligation Tunes Protein Reactivity in an Ancient Haemoglobin: Kinetic Evidence for an Allosteric Mechanism in Methanosarcina acetivorans Protoglobin
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{"title"=>"Ligation tunes protein reactivity in an ancient haemoglobin: Kinetic evidence for an allosteric mechanism in methanosarcina acetivorans protoglobin", "type"=>"journal", "authors"=>[{"first_name"=>"Stefania", "last_name"=>"Abbruzzetti", "scopus_author_id"=>"6602268418"}, {"first_name"=>"Lesley", "last_name"=>"Tilleman", "scopus_author_id"=>"36099428300"}, {"first_name"=>"Stefano", "last_name"=>"Bruno", "scopus_author_id"=>"7101967954"}, {"first_name"=>"Cristiano", "last_name"=>"Viappiani", "scopus_author_id"=>"7003293984"}, {"first_name"=>"Filip", "last_name"=>"Desmet", "scopus_author_id"=>"24465135900"}, {"first_name"=>"Sabine", "last_name"=>"van Doorslaer", "scopus_author_id"=>"55663128600"}, {"first_name"=>"Massimo", "last_name"=>"Coletta", "scopus_author_id"=>"35447556000"}, {"first_name"=>"Chiara", "last_name"=>"Ciaccio", "scopus_author_id"=>"6701718271"}, {"first_name"=>"Paolo", "last_name"=>"Ascenzi", "scopus_author_id"=>"7101910325"}, {"first_name"=>"Marco", "last_name"=>"Nardini", "scopus_author_id"=>"7006788064"}, {"first_name"=>"Martino", "last_name"=>"Bolognesi", "scopus_author_id"=>"35433930400"}, {"first_name"=>"Luc", "last_name"=>"Moens", "scopus_author_id"=>"35419687800"}, {"first_name"=>"Sylvia", "last_name"=>"Dewilde", "scopus_author_id"=>"7004292719"}], "year"=>2012, "source"=>"PLoS ONE", "identifiers"=>{"sgr"=>"84858958591", "pui"=>"364514398", "pmid"=>"22479420", "issn"=>"19326203", "scopus"=>"2-s2.0-84858958591", "doi"=>"10.1371/journal.pone.0033614"}, "id"=>"26e5f4c7-5b85-38e4-8911-63b748fd4792", "abstract"=>"Protoglobin from Methanosarcina acetivorans (MaPgb) is a dimeric globin with peculiar structural properties such as a completely buried haem and two orthogonal tunnels connecting the distal cavity to the solvent. CO binding to and dissociation from MaPgb occur through a biphasic kinetics. We show that the heterogenous kinetics arises from binding to (and dissociation from) two tertiary conformations in ligation-dependent equilibrium. Ligation favours the species with high binding rate (and low dissociation rate). The equilibrium is shifted towards the species with low binding (and high dissociation) rates for the unliganded molecules. A quantitative model is proposed to describe the observed carbonylation kinetics.", "link"=>"http://www.mendeley.com/research/ligation-tunes-protein-reactivity-ancient-haemoglobin-kinetic-evidence-allosteric-mechanism-methanos", "reader_count"=>4, "reader_count_by_academic_status"=>{"Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>2, "Other"=>1}, "reader_count_by_user_role"=>{"Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>2, "Other"=>1}, "reader_count_by_subject_area"=>{"Chemistry"=>4}, "reader_count_by_subdiscipline"=>{"Chemistry"=>{"Chemistry"=>4}}, "group_count"=>0}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/663516"], "description"=>"<p>(A) Comparison between the CO rebinding kinetics after photolysis of CO<i>Ma</i>Pgb* solutions (red curve), CO<i>Ma</i>Pgb* gels (black curve) and <i>Ma</i>Pgb* + CO gels (green curve). All displayed curves were measured at <i>T</i> = 20°C and 1 atm CO. (B) Lifetime distributions retrieved from fitting with the MEM in panel A (color code as in panel A).</p>", "links"=>[], "tags"=>["rebinding", "gels", "nanosecond"], "article_id"=>333985, "categories"=>["Physics", "Biochemistry", "Biophysics"], "users"=>["Stefania Abbruzzetti", "Lesley Tilleman", "Stefano Bruno", "Cristiano Viappiani", "Filip Desmet", "Sabine Van Doorslaer", "Massimo Coletta", "Chiara Ciaccio", "Paolo Ascenzi", "Marco Nardini", "Martino Bolognesi", "Luc Moens", "Sylvia Dewilde"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0033614.g006", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_CO_rebinding_to_Ma_Pgb_gels_after_nanosecond_laser_photolysis_/333985", "title"=>"CO rebinding to <i>Ma</i>Pgb* gels after nanosecond laser photolysis.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-03-27 01:06:25"}
  • {"files"=>["https://ndownloader.figshare.com/files/663611"], "description"=>"<p>(A) Analysis of the CO rebinding kinetics to <i>Ma</i>Pgb<i>*</i> in solution equilibrated at 10°C with 1 atm CO (black circles) and 0.1 atm CO (red circles). The fits (yellow lines) are superimposed to the experimental data (circles). In the figure we have also reported the time course of the other relevant species in Scheme 1 of main text: (<i>MaPgb*<sup>r</sup>:CO</i>)<sub>1</sub> (black), (<i>MaPgb*<sup>t</sup>:CO</i>)<sub>1</sub> (red), (<i>MaPgb*<sup>r</sup>:CO</i>)<sub>2</sub> (green), (<i>MaPgb*<sup>t</sup>:CO</i>)<sub>2</sub> (blue), (<i>MaPgb*<sup>r</sup></i>) (cyan), (<i>MaPgb*<sup>t</sup></i>) (magenta). Solid lines, 1 atm CO; dotted lines, 0.1 atm CO. (B) Analysis of the CO rebinding kinetics to <i>Ma</i>Pgb<i>*</i> in solution equilibrated with 1 atm CO at 10°C (black circles) and 25°C (red circles). The fits and the time courses of the other relevant species are also displayed with the same color code as in Panel A (solid lines, 10°C; dotted lines, 25°C).</p>", "links"=>[], "tags"=>["co", "rebinding", "kinetics"], "article_id"=>334082, "categories"=>["Physics", "Biochemistry", "Biophysics"], "users"=>["Stefania Abbruzzetti", "Lesley Tilleman", "Stefano Bruno", "Cristiano Viappiani", "Filip Desmet", "Sabine Van Doorslaer", "Massimo Coletta", "Chiara Ciaccio", "Paolo Ascenzi", "Marco Nardini", "Martino Bolognesi", "Luc Moens", "Sylvia Dewilde"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0033614.g007", "stats"=>{"downloads"=>1, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Representative_analysis_of_CO_rebinding_kinetics_to_Ma_Pgb_/334082", "title"=>"Representative analysis of CO rebinding kinetics to <i>Ma</i>Pgb*.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-03-27 01:08:02"}
  • {"files"=>["https://ndownloader.figshare.com/files/663927"], "description"=>"<p>Activation free energies were estimated from the linear Eyring plots for each rate constant <i>k</i><sub>i</sub> in the temperature range 10–40°C.</p>*<p>The value of these rates and their associated temperature dependence are difficult to estimate given the small amplitude of the processes.</p>**<p>the present analysis did not allow to appreciate a difference in <i>k<sub>out</sub></i> for the two conformations.</p><p>The numerical reliability of each parameter was defined by evaluating the dependence of the fitness function on changes of the parameter, assuming the others as constant. <i>k</i><sub>−1</sub>≈; <i>k</i><sub>2</sub> , <i>k</i><sub>−2</sub>≈10%; <i>k</i><sub>3</sub> , <i>k</i><sub>−3</sub>≈10%.</p><p>The rate equations for CO binding are very poorly sentitive to <i>k<sub>d,r</sub></i> and <i>k<sub>d,t</sub></i>, which are held constant to the values determined by the following equation: <i>k<sub>OFF,1/2</sub></i> = <i>k<sub>d,r/t</sub></i>×<i>k<sub>out</sub></i>/(<i>k<sub>out</sub></i>+<i>k<sub>g,r/t</sub></i>).</p>", "links"=>[], "tags"=>["constants", "photolysis"], "article_id"=>334403, "categories"=>["Physics", "Biochemistry", "Biophysics"], "users"=>["Stefania Abbruzzetti", "Lesley Tilleman", "Stefano Bruno", "Cristiano Viappiani", "Filip Desmet", "Sabine Van Doorslaer", "Massimo Coletta", "Chiara Ciaccio", "Paolo Ascenzi", "Marco Nardini", "Martino Bolognesi", "Luc Moens", "Sylvia Dewilde"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0033614.t001", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Microscopic_rate_constants_for_Ma_Pgb_from_the_fit_of_the_flash_photolysis_data_at_20_C_/334403", "title"=>"Microscopic rate constants for <i>Ma</i>Pgb<sup>*</sup> from the fit of the flash photolysis data, at 20°C.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-03-27 01:13:23"}
  • {"files"=>["https://ndownloader.figshare.com/files/339795", "https://ndownloader.figshare.com/files/339848", "https://ndownloader.figshare.com/files/339894", "https://ndownloader.figshare.com/files/339921", "https://ndownloader.figshare.com/files/339951", "https://ndownloader.figshare.com/files/339989", "https://ndownloader.figshare.com/files/340025"], "description"=>"<div><p>Protoglobin from <em>Methanosarcina acetivorans</em> (<em>Ma</em>Pgb) is a dimeric globin with peculiar structural properties such as a completely buried haem and two orthogonal tunnels connecting the distal cavity to the solvent. CO binding to and dissociation from <em>Ma</em>Pgb occur through a biphasic kinetics. We show that the heterogenous kinetics arises from binding to (and dissociation from) two tertiary conformations in ligation-dependent equilibrium. Ligation favours the species with high binding rate (and low dissociation rate). The equilibrium is shifted towards the species with low binding (and high dissociation) rates for the unliganded molecules. A quantitative model is proposed to describe the observed carbonylation kinetics.</p> </div>", "links"=>[], "tags"=>["ligation", "tunes", "reactivity", "kinetic", "allosteric", "protoglobin"], "article_id"=>127172, "categories"=>["Physics", "Biochemistry", "Biophysics"], "users"=>["Stefania Abbruzzetti", "Lesley Tilleman", "Stefano Bruno", "Cristiano Viappiani", "Filip Desmet", "Sabine Van Doorslaer", "Massimo Coletta", "Chiara Ciaccio", "Paolo Ascenzi", "Marco Nardini", "Martino Bolognesi", "Luc Moens", "Sylvia Dewilde"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0033614.s001", "https://dx.doi.org/10.1371/journal.pone.0033614.s002", "https://dx.doi.org/10.1371/journal.pone.0033614.s003", "https://dx.doi.org/10.1371/journal.pone.0033614.s004", "https://dx.doi.org/10.1371/journal.pone.0033614.s005", "https://dx.doi.org/10.1371/journal.pone.0033614.s006", "https://dx.doi.org/10.1371/journal.pone.0033614.s007"], "stats"=>{"downloads"=>3, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Ligation_Tunes_Protein_Reactivity_in_an_Ancient_Haemoglobin_Kinetic_Evidence_for_an_Allosteric_Mechanism_in_Methanosarcina_acetivorans_Protoglobin/127172", "title"=>"Ligation Tunes Protein Reactivity in an Ancient Haemoglobin: Kinetic Evidence for an Allosteric Mechanism in <em>Methanosarcina acetivorans</em> Protoglobin", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2012-03-27 01:59:32"}
  • {"files"=>["https://ndownloader.figshare.com/files/663171"], "description"=>"<p>(<b>A</b>) Representative CO binding kinetics as measured through the normalized absorbance changes at 418 nm for <i>Ma</i>Pgb* in 0.1 M phosphate pH 7.0 at 20°C (blue dots). CO concentration was 25 µM. Solid red line is the non-linear least-squares fitting to a double exponential relaxation. Inset. CO concentration dependence of the apparent rate constants obtained from the fitting with a double exponential relaxation to the progress curves at 418 nm. (<b>B</b>) CO dissociation kinetics induced by mixing a CO<i>Ma</i>Pgb* solution with a NO-equilibrated solution as measured through the normalized absorbance changes at 421 nm for <i>Ma</i>Pgb* in 0.1 M phosphate pH 7.0 at 20°C (blue dots). Solid red line is the non-linear least-squares fitting to a double exponential relaxation. (<b>C</b>) O<sub>2</sub> dissociation kinetics (blue circles, monitored at 411 nm) from Fe<sup>2+</sup> O<sub>2</sub><i>Ma</i>Pgb* after addition of sodium dithionite (10 mM final concentration) at 20°C. The red solid line is the fit to a double exponential relaxation. Black vertical lines indicate the time at which mixing with CO was performed.</p>", "links"=>[], "tags"=>["binding", "dissociation", "stopped"], "article_id"=>333642, "categories"=>["Physics", "Biochemistry", "Biophysics"], "users"=>["Stefania Abbruzzetti", "Lesley Tilleman", "Stefano Bruno", "Cristiano Viappiani", "Filip Desmet", "Sabine Van Doorslaer", "Massimo Coletta", "Chiara Ciaccio", "Paolo Ascenzi", "Marco Nardini", "Martino Bolognesi", "Luc Moens", "Sylvia Dewilde"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0033614.g003", "stats"=>{"downloads"=>1, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_CO_binding_to_and_dissociation_from_Ma_Pgb_from_stopped_flow_/333642", "title"=>"CO binding to and dissociation from <i>Ma</i>Pgb* from stopped flow.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-03-27 01:00:42"}
  • {"files"=>["https://ndownloader.figshare.com/files/663298"], "description"=>"<p>(A) CO rebinding kinetics to CO<i>Ma</i>Pgb* solutions at T = 10°C (green, 1 atm CO; red, 0.1 atm CO) and T = 30°C (blue, 1 atm CO; orange, 0.1 atm CO). (B) Lifetime distributions obtained from the MEM analysis of the CO rebinding curves shown in (A).</p>", "links"=>[], "tags"=>["rebinding", "nanosecond"], "article_id"=>333774, "categories"=>["Physics", "Biochemistry", "Biophysics"], "users"=>["Stefania Abbruzzetti", "Lesley Tilleman", "Stefano Bruno", "Cristiano Viappiani", "Filip Desmet", "Sabine Van Doorslaer", "Massimo Coletta", "Chiara Ciaccio", "Paolo Ascenzi", "Marco Nardini", "Martino Bolognesi", "Luc Moens", "Sylvia Dewilde"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0033614.g004", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_CO_rebinding_to_Ma_Pgb_after_nanosecond_laser_photolysis_/333774", "title"=>"CO rebinding to <i>Ma</i>Pgb* after nanosecond laser photolysis.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-03-27 01:02:54"}
  • {"files"=>["https://ndownloader.figshare.com/files/663402"], "description"=>"<p>(A) Comparison of the first (U<sub>1</sub>, black line) and the second (U<sub>2</sub>, red line) components obtained from the SVD analysis on the time-resolved spectra measured for <i>Ma</i>Pgb* in solution. Spectra <i>U</i><sub>i</sub> are multiplied by the corresponding singular value <i>S</i><sub>i</sub>. (B) Time courses of the amplitudes <i>V</i><sub>1</sub> (open black circles) and <i>V</i><sub>2</sub> (open red circles). The pressure of CO was 1 atm, and the spectra were measured at 20°C. The black curve in panel B is the absorbance change measured at 436 nm (in a single wavelength experiment) at the same CO pressure and temperature.</p>", "links"=>[], "tags"=>["resolved", "spectra", "nanosecond", "photolysis"], "article_id"=>333871, "categories"=>["Physics", "Biochemistry", "Biophysics"], "users"=>["Stefania Abbruzzetti", "Lesley Tilleman", "Stefano Bruno", "Cristiano Viappiani", "Filip Desmet", "Sabine Van Doorslaer", "Massimo Coletta", "Chiara Ciaccio", "Paolo Ascenzi", "Marco Nardini", "Martino Bolognesi", "Luc Moens", "Sylvia Dewilde"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0033614.g005", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_SVD_analysis_of_time_resolved_spectra_after_nanosecond_laser_photolysis_of_CO_Ma_Pgb_/333871", "title"=>"SVD analysis of time resolved spectra after nanosecond laser photolysis of CO<i>Ma</i>Pgb*.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-03-27 01:04:31"}
  • {"files"=>["https://ndownloader.figshare.com/files/663850"], "description"=>"<p>The free energy plot for reaction Scheme 1 as calculated from activation free energies for the forward and reverse rate constants reported in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0033614#pone-0033614-t001\" target=\"_blank\">Table 1</a>. Transition states are labelled as ‡. Transitions between <i>r</i> and <i>t</i> conformations are indicated from curves with arrows. Solid lines (red, <i>r</i>; blue, <i>t</i>) connect states within each conformation.</p>", "links"=>[], "tags"=>["biophysics", "physics", "Biochemistry"], "article_id"=>334321, "categories"=>["Physics", "Biochemistry", "Biophysics"], "users"=>["Stefania Abbruzzetti", "Lesley Tilleman", "Stefano Bruno", "Cristiano Viappiani", "Filip Desmet", "Sabine Van Doorslaer", "Massimo Coletta", "Chiara Ciaccio", "Paolo Ascenzi", "Marco Nardini", "Martino Bolognesi", "Luc Moens", "Sylvia Dewilde"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0033614.g009", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Free_energy_plot_/334321", "title"=>"Free energy plot.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-03-27 01:12:01"}
  • {"files"=>["https://ndownloader.figshare.com/files/663725"], "description"=>"<p>Comparison between the CO rebinding kinetics (circles) and the time courses of <i>MaPgb*<sup>t</sup></i> (solid lines) as retrieved from the numerical analysis after photolysis of CO<i>Ma</i>Pgb* solutions (black), CO<i>Ma</i>Pgb* gels (red), and <i>Ma</i>Pgb* + CO gels (green). Curves were measured at T = 20°C and 1 atm CO. The black dotted curve is the time evolution of the second spectral component obtained from the SVD analysis on transient spectra (see <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0033614#pone-0033614-g005\" target=\"_blank\">Figure 5</a>).</p>", "links"=>[], "tags"=>["relaxation", "resolved", "spectra", "numerical", "co"], "article_id"=>334195, "categories"=>["Physics", "Biochemistry", "Biophysics"], "users"=>["Stefania Abbruzzetti", "Lesley Tilleman", "Stefano Bruno", "Cristiano Viappiani", "Filip Desmet", "Sabine Van Doorslaer", "Massimo Coletta", "Chiara Ciaccio", "Paolo Ascenzi", "Marco Nardini", "Martino Bolognesi", "Luc Moens", "Sylvia Dewilde"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0033614.g008", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Structural_relaxation_from_time_resolved_spectra_and_numerical_analysis_of_CO_rebinding_/334195", "title"=>"Structural relaxation from time resolved spectra and numerical analysis of CO rebinding.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-03-27 01:09:55"}
  • {"files"=>["https://ndownloader.figshare.com/files/662927"], "description"=>"<p>Dithionite-reduced Fe<sup>2+</sup> deoxy form (black line) and the CO-bound form (red line). The protein concentration was 20 µM. Spectra were measured with an optical pathlength of 0.2 cm.</p>", "links"=>[], "tags"=>["absorption", "spectra"], "article_id"=>333399, "categories"=>["Physics", "Biochemistry", "Biophysics"], "users"=>["Stefania Abbruzzetti", "Lesley Tilleman", "Stefano Bruno", "Cristiano Viappiani", "Filip Desmet", "Sabine Van Doorslaer", "Massimo Coletta", "Chiara Ciaccio", "Paolo Ascenzi", "Marco Nardini", "Martino Bolognesi", "Luc Moens", "Sylvia Dewilde"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0033614.g001", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Electronic_absorption_spectra_of_Ma_Pgb_/333399", "title"=>"Electronic absorption spectra of <i>Ma</i>Pgb*.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-03-27 00:56:39"}
  • {"files"=>["https://ndownloader.figshare.com/files/663009"], "description"=>"<p>Low-frequency (<b>A</b>) and high-frequency (<b>B</b>) region of the RR spectrum of Fe<sup>2+</sup><i>Ma</i>Pgb* (a) CO<i>Ma</i>Pgb*. The excitation wavelength was 413.1 nm, laser powers employed were (a) 100 mW, and (b) 1 mW.</p>", "links"=>[], "tags"=>["raman", "spectra"], "article_id"=>333487, "categories"=>["Physics", "Biochemistry", "Biophysics"], "users"=>["Stefania Abbruzzetti", "Lesley Tilleman", "Stefano Bruno", "Cristiano Viappiani", "Filip Desmet", "Sabine Van Doorslaer", "Massimo Coletta", "Chiara Ciaccio", "Paolo Ascenzi", "Marco Nardini", "Martino Bolognesi", "Luc Moens", "Sylvia Dewilde"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0033614.g002", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Resonance_Raman_spectra_of_Ma_Pgb_/333487", "title"=>"Resonance Raman spectra of <i>Ma</i>Pgb*.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-03-27 00:58:07"}

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Relative Metric

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