A Structure-Based Approach for Detection of Thiol Oxidoreductases and Their Catalytic Redox-Active Cysteine Residues
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{"title"=>"A structure-based approach for detection of thiol oxidoreductases and their catalytic redox-active cysteine residues", "type"=>"journal", "authors"=>[{"first_name"=>"Stefano M.", "last_name"=>"Marino", "scopus_author_id"=>"25632524600"}, {"first_name"=>"Vadim N.", "last_name"=>"Gladyshev", "scopus_author_id"=>"7004407393"}], "year"=>2009, "source"=>"PLoS Computational Biology", "identifiers"=>{"scopus"=>"2-s2.0-67049132601", "isbn"=>"1553-7358 (Electronic)\\r1553-734X (Linking)", "doi"=>"10.1371/journal.pcbi.1000383", "pui"=>"354725649", "sgr"=>"67049132601", "issn"=>"1553734X", "pmid"=>"19424433"}, "id"=>"f085637a-685b-3aef-b0ed-9b9348c764ae", "abstract"=>"Cysteine (Cys) residues often play critical roles in proteins, for example, in the formation of structural disulfide bonds, metal binding, targeting proteins to the membranes, and various catalytic functions. However, the structural determinants for various Cys functions are not clear. Thiol oxidoreductases, which are enzymes containing catalytic redox-active Cys residues, have been extensively studied, but even for these proteins there is little understanding of what distinguishes their catalytic redox Cys from other Cys functions. Herein, we characterized thiol oxidoreductases at a structural level and developed an algorithm that can recognize these enzymes by (i) analyzing amino acid and secondary structure composition of the active site and its similarity to known active sites containing redox Cys and (ii) calculating accessibility, active site location, and reactivity of Cys. For proteins with known or modeled structures, this method can identify proteins with catalytic Cys residues and distinguish thiol oxidoreductases from the enzymes containing other catalytic Cys types. Furthermore, by applying this procedure to Saccharomyces cerevisiae proteins containing conserved Cys, we could identify the majority of known yeast thiol oxidoreductases. This study provides insights into the structural properties of catalytic redox-active Cys and should further help to recognize thiol oxidoreductases in protein sequence and structure databases.", "link"=>"http://www.mendeley.com/research/structurebased-approach-detection-thiol-oxidoreductases-catalytic-redoxactive-cysteine-residues", "reader_count"=>38, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>3, "Researcher"=>11, "Student > Ph. D. Student"=>14, "Student > Master"=>3, "Other"=>2, "Student > Bachelor"=>3, "Lecturer"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>3, "Researcher"=>11, "Student > Ph. D. Student"=>14, "Student > Master"=>3, "Other"=>2, "Student > Bachelor"=>3, "Lecturer"=>1}, "reader_count_by_subject_area"=>{"Engineering"=>1, "Unspecified"=>4, "Environmental Science"=>1, "Biochemistry, Genetics and Molecular Biology"=>5, "Agricultural and Biological Sciences"=>19, "Medicine and Dentistry"=>2, "Neuroscience"=>1, "Physics and Astronomy"=>2, "Chemistry"=>2, "Computer Science"=>1}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>2}, "Neuroscience"=>{"Neuroscience"=>1}, "Chemistry"=>{"Chemistry"=>2}, "Physics and Astronomy"=>{"Physics and Astronomy"=>2}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>19}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>5}, "Unspecified"=>{"Unspecified"=>4}, "Environmental Science"=>{"Environmental Science"=>1}}, "reader_count_by_country"=>{"Japan"=>1, "United Arab Emirates"=>1, "Switzerland"=>1, "Portugal"=>1, "India"=>1}, "group_count"=>1}

Scopus | Further Information

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  • {"files"=>["https://ndownloader.figshare.com/files/898882"], "description"=>"<p>(A) Overview of the complete method for prediction of thiol\n oxidoreductases. Red rectangles correspond to the Active Site Similarity\n portion of the method, and blue rectangles to the Cys Reactivity\n portion, each composed of several steps as discussed in the text. Each\n step was carried out independently converging into the final scoring\n function (SF) that ranged from 0 to 6.0. For each of step, the range of\n values in the final SF is reported in brackets, reflecting the different\n weights of the components. (B) The Active Site Similarity method. This\n part of the complete procedure is illustrated with an example of a Cys\n (represented in sticks)-containing protein. The active site (AS) around\n the Cys is analyzed in the following independent steps: (i) amino acid\n composition; (ii) secondary structure content; (iii) 3D structural\n profile analysis. For each of the three steps, the range of values in\n the final scoring function (SF) is reported in brackets. The amino acid\n composition step is further subdivided in three subparts, as detailed in\n the text.</p>", "links"=>[], "tags"=>["thiol", "oxidoreductases", "structure"], "article_id"=>569342, "categories"=>["Biochemistry"], "users"=>["Stefano M. Marino", "Vadim N. Gladyshev"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1000383.g001", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_A_method_for_prediction_of_thiol_oxidoreductases_in_structure____databases_/569342", "title"=>"A method for prediction of thiol oxidoreductases in structure\n databases.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-05-08 02:35:42"}
  • {"files"=>["https://ndownloader.figshare.com/files/899333"], "description"=>"<p>The calculated curves are shown in red and the corresponding standard\n Henderson-Hasselbach (HH) titration curves in blue. (A) An example of a\n highly deviating theoretical titration. (B) An example of no deviation\n (this is the most common situation since most Cys behave in this\n manner).</p>", "links"=>[], "tags"=>["titration"], "article_id"=>569801, "categories"=>["Biochemistry"], "users"=>["Stefano M. Marino", "Vadim N. Gladyshev"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1000383.g005", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Theoretical_titration_curves_/569801", "title"=>"Theoretical titration curves.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-05-08 02:43:21"}
  • {"files"=>["https://ndownloader.figshare.com/files/899046"], "description"=>"<p>An average composition at 6Å (A) and 8 Å (B)\n distances from Cys for proteins in the thiol oxidoreductase and control\n datasets, separated by function and fold as described in the text.\n Abbreviations: Trx fold OxR, thioredoxin-fold thiol oxidoreductases; Non\n Trx fold OxR, other thiol oxidoreductases; FAD OxR, FAD-containing thiol\n oxidoreductases and Non OxR, proteins in the control dataset (<a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000383#pcbi.1000383.s008\" target=\"_blank\">Table\n S2</a>). Random Cys refers to a set of 1800 proteins randomly\n selected from PDB, mentioned in the text. The calculated standard\n deviations are also shown.</p>", "links"=>[], "tags"=>["thiol", "oxidoreductases"], "article_id"=>569512, "categories"=>["Biochemistry"], "users"=>["Stefano M. Marino", "Vadim N. Gladyshev"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1000383.g002", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Amino_acid_composition_of_thiol_oxidoreductases_and_control_proteins_/569512", "title"=>"Amino acid composition of thiol oxidoreductases and control proteins.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-05-08 02:38:32"}
  • {"files"=>["https://ndownloader.figshare.com/files/899284"], "description"=>"<p>Benchmarking of five publicly available programs for prediction of active\n site residues: Q-site finder, Pocket finder, THEMATICS, FOD and SARIG.\n For Q-site finder and Pocket finder, the percentage of correctly\n predicted proteins is shown wherein only the first three ranked sites\n (dark grey cylinder) or all 10 sites (light grey cylinder) are\n considered. For FOD, the dark grey bar shows a true positive rate using\n the standard cutoff, while the light grey bar represents a true positive\n rate when a more permissive cutoff is employed (i.e., active site\n residues have a normalized ΔH score>0.5). For SARIG, the\n dark grey bar bar represents a true positive rate with the standard\n cutoff, while the light grey bar shows a true positive rate when a more\n permissive cutoff values (closeness Z-score>0.75 and 3\n Å<sup>2</sup>2) are employed.</p>", "links"=>[], "tags"=>["methods", "thiol"], "article_id"=>569748, "categories"=>["Biochemistry"], "users"=>["Stefano M. Marino", "Vadim N. Gladyshev"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1000383.g004", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Application_of_methods_for_active_site_recognition_to_thiol____oxidoreductases_/569748", "title"=>"Application of methods for active site recognition to thiol\n oxidoreductases.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-05-08 02:42:28"}
  • {"files"=>["https://ndownloader.figshare.com/files/899178"], "description"=>"<p>(A) p-values for occurrence of each amino acid within 6 Å of\n the catalytic Cys (<a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000383#pcbi-1000383-g002\" target=\"_blank\">Figure\n 2A</a>) for different types of proteins in our dataset. Values\n were obtained using t-test (comparing the whole population of each type\n with the whole population of the Random Cys set) using GraphPad. (B)\n p-values for occurrence of each amino acid within 8 Å of the\n catalytic Cys (<a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000383#pcbi-1000383-g002\" target=\"_blank\">Figure\n 2B</a>) for different types of proteins in our dataset. Residues with\n most significant p-values are highlighted in bold.</p>", "links"=>[], "tags"=>["p-values", "occurrence", "amino"], "article_id"=>569630, "categories"=>["Biochemistry"], "users"=>["Stefano M. Marino", "Vadim N. Gladyshev"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1000383.g003", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Calculated_p_values_for_average_occurrence_of_amino_acids_/569630", "title"=>"Calculated p-values for average occurrence of amino acids.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-05-08 02:40:30"}
  • {"files"=>["https://ndownloader.figshare.com/files/899422"], "description"=>"<p>In the figure, the difference between True Positive Rate (TPR) and False\n Positive Rate (FPR) for each parameter weight is plotted. True positives\n included correctly predicted thiol oxidoreductases from the Test Case\n (<a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000383#pcbi.1000383.s009\" target=\"_blank\">Table S3</a>), and false positives control proteins (<a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000383#pcbi.1000383.s009\" target=\"_blank\">Table\n S3</a>) predicted as thiol oxidoreductases (i.e., containing a Cys\n scoring higher than the cut-off). A Y-axis value of 1 indicates complete\n separation of the dataset. Starting from the optimized weights described\n in the text, each parameter was varied separately in the range\n 0–4 (X-axis values). The graph should be read as follows: each\n parameter is represented by a curve, and each point represents the\n TPR-FPR value (the higher the better) for a specific weight. Maxima\n represent the best scoring values (compare to <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000383#pcbi-1000383-g001\" target=\"_blank\">Figure 1A</a>). Decreased values to the\n right of the maximum reflect a tendency of the parameter to give False\n Positive predictions when over-weighted, while when on the left, it\n corresponds to a tendency to underestimate the number of True Positives\n when the parameter is under-weighted. This analysis provides insights\n into variability introduced in the performance when the parameter\n weights are changed, in particular showing that the optimized parameters\n cannot vary in a broad range of values. However, for two parameters\n alternative values were possible: the Profile scoring (values could vary\n in the range 2.5-÷2.75) and the H++\n contribution (1÷1.25). For all other parameters, clear maxima\n (corresponding to the optimized values described in the text) were\n observed.</p>", "links"=>[], "tags"=>["parameter"], "article_id"=>569884, "categories"=>["Biochemistry"], "users"=>["Stefano M. Marino", "Vadim N. Gladyshev"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1000383.g006", "stats"=>{"downloads"=>0, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Effect_of_variation_in_parameter_used_on_method_performance_/569884", "title"=>"Effect of variation in parameter used on method performance.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-05-08 02:44:44"}
  • {"files"=>["https://ndownloader.figshare.com/files/444987", "https://ndownloader.figshare.com/files/445001", "https://ndownloader.figshare.com/files/445017", "https://ndownloader.figshare.com/files/445034", "https://ndownloader.figshare.com/files/445049", "https://ndownloader.figshare.com/files/445063", "https://ndownloader.figshare.com/files/445079", "https://ndownloader.figshare.com/files/445086", "https://ndownloader.figshare.com/files/445095", "https://ndownloader.figshare.com/files/445102", "https://ndownloader.figshare.com/files/445111", "https://ndownloader.figshare.com/files/445120"], "description"=>"<div><p>Cysteine (Cys) residues often play critical roles in proteins, for example, in the formation of structural disulfide bonds, metal binding, targeting proteins to the membranes, and various catalytic functions. However, the structural determinants for various Cys functions are not clear. Thiol oxidoreductases, which are enzymes containing catalytic redox-active Cys residues, have been extensively studied, but even for these proteins there is little understanding of what distinguishes their catalytic redox Cys from other Cys functions. Herein, we characterized thiol oxidoreductases at a structural level and developed an algorithm that can recognize these enzymes by (i) analyzing amino acid and secondary structure composition of the active site and its similarity to known active sites containing redox Cys and (ii) calculating accessibility, active site location, and reactivity of Cys. For proteins with known or modeled structures, this method can identify proteins with catalytic Cys residues and distinguish thiol oxidoreductases from the enzymes containing other catalytic Cys types. Furthermore, by applying this procedure to <em>Saccharomyces cerevisiae</em> proteins containing conserved Cys, we could identify the majority of known yeast thiol oxidoreductases. This study provides insights into the structural properties of catalytic redox-active Cys and should further help to recognize thiol oxidoreductases in protein sequence and structure databases.</p> </div>", "links"=>[], "tags"=>["structure-based", "detection", "thiol", "oxidoreductases", "and", "catalytic", "redox-active", "cysteine", "residues"], "article_id"=>147704, "categories"=>["Biochemistry"], "users"=>["Stefano M. Marino", "Vadim N. Gladyshev"], "doi"=>["https://dx.doi.org/10.1371/journal.pcbi.1000383.s001", "https://dx.doi.org/10.1371/journal.pcbi.1000383.s002", "https://dx.doi.org/10.1371/journal.pcbi.1000383.s003", "https://dx.doi.org/10.1371/journal.pcbi.1000383.s004", "https://dx.doi.org/10.1371/journal.pcbi.1000383.s005", "https://dx.doi.org/10.1371/journal.pcbi.1000383.s006", "https://dx.doi.org/10.1371/journal.pcbi.1000383.s007", "https://dx.doi.org/10.1371/journal.pcbi.1000383.s008", "https://dx.doi.org/10.1371/journal.pcbi.1000383.s009", "https://dx.doi.org/10.1371/journal.pcbi.1000383.s010", "https://dx.doi.org/10.1371/journal.pcbi.1000383.s011", "https://dx.doi.org/10.1371/journal.pcbi.1000383.s012"], "stats"=>{"downloads"=>47, "page_views"=>30, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/A_Structure_Based_Approach_for_Detection_of_Thiol_Oxidoreductases_and___Their_Catalytic_Redox_Active_Cysteine_Residues/147704", "title"=>"A Structure-Based Approach for Detection of Thiol Oxidoreductases and\n Their Catalytic Redox-Active Cysteine Residues", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2009-05-08 02:08:24"}
  • {"files"=>["https://ndownloader.figshare.com/files/899525"], "description"=>"<p>Green circles show thiol oxidoreductases and grey circles other proteins\n of the Test Case. The Test Case is described in the text and in <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000383#pcbi.1000383.s009\" target=\"_blank\">Table\n S3</a>.</p>", "links"=>[], "tags"=>["biochemistry/biocatalysis", "biochemistry/bioinformatics", "biochemistry/structural genomics"], "article_id"=>569989, "categories"=>["Biochemistry"], "users"=>["Stefano M. Marino", "Vadim N. Gladyshev"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1000383.g007", "stats"=>{"downloads"=>3, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Analysis_of_the_Test_Case_/569989", "title"=>"Analysis of the Test Case.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-05-08 02:46:29"}
  • {"files"=>["https://ndownloader.figshare.com/files/899608"], "description"=>"<p>The score for each protein of the yeast proteome (i.e., the score for the\n highest scoring Cys) is plotted (model index numbers follow the order in\n <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000383#pcbi.1000383.s011\" target=\"_blank\">Table S5</a>). Green circles represent thiol oxidoreductases,\n and yellow circles show proteins scoring with thiol oxidoreductases but\n not known to be redox catalysts. Gray circles represent other proteins.\n All but one known thiol oxidoreductase were detected.</p>", "links"=>[], "tags"=>["biochemistry/biocatalysis", "biochemistry/bioinformatics", "biochemistry/structural genomics"], "article_id"=>570070, "categories"=>["Biochemistry"], "users"=>["Stefano M. Marino", "Vadim N. Gladyshev"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1000383.g008", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Analysis_of_the_Saccharomyces_cerevisiae_proteome_/570070", "title"=>"Analysis of the <i>Saccharomyces cerevisiae</i> proteome.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-05-08 00:01:10"}

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Relative Metric

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