Analysis of Nidogen-1/Laminin γ1 Interaction by Cross-Linking, Mass Spectrometry, and Computational Modeling Reveals Multiple Binding Modes
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{"title"=>"Analysis of nidogen-1/laminin γ1 interaction by cross-linking, mass spectrometry, and computational modeling reveals multiple binding modes", "type"=>"journal", "authors"=>[{"first_name"=>"Philip", "last_name"=>"Lössl", "scopus_author_id"=>"56167777200"}, {"first_name"=>"Knut", "last_name"=>"Kölbel", "scopus_author_id"=>"24822911900"}, {"first_name"=>"Dirk", "last_name"=>"Tänzler", "scopus_author_id"=>"55766270200"}, {"first_name"=>"David", "last_name"=>"Nannemann", "scopus_author_id"=>"36164996600"}, {"first_name"=>"Christian H.", "last_name"=>"Ihling", "scopus_author_id"=>"55444090000"}, {"first_name"=>"Manuel V.", "last_name"=>"Keller", "scopus_author_id"=>"36673263100"}, {"first_name"=>"Marian", "last_name"=>"Schneider", "scopus_author_id"=>"55879697700"}, {"first_name"=>"Frank", "last_name"=>"Zaucke", "scopus_author_id"=>"6602658691"}, {"first_name"=>"Jens", "last_name"=>"Meiler", "scopus_author_id"=>"7004961758"}, {"first_name"=>"Andrea", "last_name"=>"Sinz", "scopus_author_id"=>"6701513466"}], "year"=>2014, "source"=>"PLoS ONE", "identifiers"=>{"pmid"=>"25387007", "sgr"=>"84915819201", "doi"=>"10.1371/journal.pone.0112886", "scopus"=>"2-s2.0-84915819201", "pui"=>"600653199", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "issn"=>"19326203"}, "id"=>"eb60bdbc-2545-39c5-89fd-1cd92ed9450a", "abstract"=>"We describe the detailed structural investigation of nidogen-1/laminin γ1 complexes using full-length nidogen-1 and a number of laminin γ1 variants. The interactions of nidogen-1 with laminin variants γ1 LEb2-4, γ1 LEb2-4 N836D, γ1 short arm, and γ1 short arm N836D were investigated by applying a combination of (photo-)chemical cross-linking, high-resolution mass spectrometry, and computational modeling. In addition, surface plasmon resonance and ELISA studies were used to determine kinetic constants of the nidogen-1/laminin γ1 interaction. Two complementary cross-linking strategies were pursued to analyze solution structures of laminin γ1 variants and nidogen-1. The majority of distance information was obtained with the homobifunctional amine-reactive cross-linker bis(sulfosuccinimidyl)glutarate. In a second approach, UV-induced cross-linking was performed after incorporation of the diazirine-containing unnatural amino acids photo-leucine and photo-methionine into laminin γ1 LEb2-4, laminin γ1 short arm, and nidogen-1. Our results indicate that Asn-836 within laminin γ1 LEb3 domain is not essential for complex formation. Cross-links between laminin γ1 short arm and nidogen-1 were found in all protein regions, evidencing several additional contact regions apart from the known interaction site. Computational modeling based on the cross-linking constraints indicates the existence of a conformational ensemble of both the individual proteins and the nidogen-1/laminin γ1 complex. This finding implies different modes of interaction resulting in several distinct protein-protein interfaces.", "link"=>"http://www.mendeley.com/research/analysis-nidogen1laminin-%CE%B31-interaction-crosslinking-mass-spectrometry-computational-modeling-reveal", "reader_count"=>29, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>1, "Researcher"=>7, "Student > Doctoral Student"=>4, "Student > Ph. D. Student"=>9, "Student > Postgraduate"=>1, "Student > Master"=>4, "Other"=>1, "Student > Bachelor"=>2}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>1, "Researcher"=>7, "Student > Doctoral Student"=>4, "Student > Ph. D. Student"=>9, "Student > Postgraduate"=>1, "Student > Master"=>4, "Other"=>1, "Student > Bachelor"=>2}, "reader_count_by_subject_area"=>{"Unspecified"=>1, "Biochemistry, Genetics and Molecular Biology"=>9, "Agricultural and Biological Sciences"=>9, "Neuroscience"=>1, "Pharmacology, Toxicology and Pharmaceutical Science"=>1, "Chemistry"=>6, "Computer Science"=>1, "Immunology and Microbiology"=>1}, "reader_count_by_subdiscipline"=>{"Neuroscience"=>{"Neuroscience"=>1}, "Chemistry"=>{"Chemistry"=>6}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>9}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>9}, "Unspecified"=>{"Unspecified"=>1}, "Pharmacology, Toxicology and Pharmaceutical Science"=>{"Pharmacology, Toxicology and Pharmaceutical Science"=>1}}, "reader_count_by_country"=>{"United Kingdom"=>1, "Spain"=>2}, "group_count"=>1}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1787737"], "description"=>"<p>The domains are color-coded with respect to the availability of crystal structures (green), template structures for comparative modeling (yellow) or neither of both (red). PDB IDs of the respective crystal structures are indicated in italics. (A) Nidogen-1 domain assignments are according to the UniProt KB entry P10493. Additionally, the historic domain names (G1–link–G2–rod–G3) are given. (B) Laminin domain designations follow the nomenclature of Aumailley <i>et al.</i><a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0112886#pone.0112886-Aumailley1\" target=\"_blank\">[5]</a>. Laminin γ1 short arm is part of the heterotrimeric protein laminin-111, the overall structure of which is schematically depicted.</p>", "links"=>[], "tags"=>["nidogen", "computational modeling", "solution structures", "mass spectrometry", "protein regions", "ELISA studies", "laminin γ1", "arm N 836D", "Multiple Binding Modes", "interaction site", "contact regions", "surface plasmon resonance", "laminin γ1 LEb 3 domain", "laminin γ1 variants", "distance information"], "article_id"=>1235950, "categories"=>["Biological Sciences"], "users"=>["Philip Lössl", "Knut Kölbel", "Dirk Tänzler", "David Nannemann", "Christian H. Ihling", "Manuel V. Keller", "Marian Schneider", "Frank Zaucke", "Jens Meiler", "Andrea Sinz"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0112886.g001", "stats"=>{"downloads"=>0, "page_views"=>14, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Arrangement_of_A_nidogen_1_and_B_laminin_947_1_short_arm_/1235950", "title"=>"Arrangement of (A) nidogen-1 and (B) laminin γ1 short arm.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-11-11 03:10:39"}
  • {"files"=>["https://ndownloader.figshare.com/files/1787738"], "description"=>"<p>Cross-links are assigned to domains based on the UniProt KB entry P10493 (nidogen-1) and the laminin nomenclature of Aumailley <i>et al.</i><a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0112886#pone.0112886-Aumailley1\" target=\"_blank\">[5]</a>. Unannotated areas within the sequences are named ‘ua’. Corresponding to the number of inter-domain contacts, areas of intersection are color-coded from white (none) to dark grey (maximum). (A) Intramolecular cross-links within nidogen-1. The globular domains G1, G2, and G3 are denoted by dotted lines. Cross-links located nearby the diagonal border represent contacts between domains being close to each other in the protein sequence. (B) Cross-links between nidogen-1 and laminin γ1 wild type (upper panel) as well as N836D variants (lower panel). The LEb3 domain, bearing the N836D mutation, is marked with an asterisk.</p>", "links"=>[], "tags"=>["nidogen", "computational modeling", "solution structures", "mass spectrometry", "protein regions", "ELISA studies", "laminin γ1", "arm N 836D", "Multiple Binding Modes", "interaction site", "contact regions", "surface plasmon resonance", "laminin γ1 LEb 3 domain", "laminin γ1 variants", "distance information"], "article_id"=>1235951, "categories"=>["Biological Sciences"], "users"=>["Philip Lössl", "Knut Kölbel", "Dirk Tänzler", "David Nannemann", "Christian H. Ihling", "Manuel V. Keller", "Marian Schneider", "Frank Zaucke", "Jens Meiler", "Andrea Sinz"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0112886.g002", "stats"=>{"downloads"=>0, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Diagonal_plots_of_all_cross_links_identified_/1235951", "title"=>"Diagonal plots of all cross-links identified.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-11-11 03:10:39"}
  • {"files"=>["https://ndownloader.figshare.com/files/1787739"], "description"=>"<p>The cross-linked product comprises amino acids 407–420 of the G2 domain (α-peptide, red) and 939–949 of the G3 domain (β-peptide, green), in which K-407 is connected to K-948/949.</p>", "links"=>[], "tags"=>["nidogen", "computational modeling", "solution structures", "mass spectrometry", "protein regions", "ELISA studies", "laminin γ1", "arm N 836D", "Multiple Binding Modes", "interaction site", "contact regions", "surface plasmon resonance", "laminin γ1 LEb 3 domain", "laminin γ1 variants", "distance information"], "article_id"=>1235952, "categories"=>["Biological Sciences"], "users"=>["Philip Lössl", "Knut Kölbel", "Dirk Tänzler", "David Nannemann", "Christian H. Ihling", "Manuel V. Keller", "Marian Schneider", "Frank Zaucke", "Jens Meiler", "Andrea Sinz"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0112886.g003", "stats"=>{"downloads"=>3, "page_views"=>82, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Nano_HPLC_nano_ESI_LTQ_Orbitrap_MS_MS_analysis_of_cross_linked_peptides_derived_from_nidogen_1_G2_and_G3_domain_/1235952", "title"=>"Nano-HPLC/nano-ESI-LTQ-Orbitrap-MS/MS analysis of cross-linked peptides derived from nidogen-1 G2 and G3 domain.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-11-11 03:10:39"}
  • {"files"=>["https://ndownloader.figshare.com/files/1787740"], "description"=>"<p>Shown are the two best-scoring models generated by comparative modeling based on 13 structural homologues that have been identified by fold recognition. The residues are colored according to their Rosetta total score. Scores below zero (yellow-green color) indicate energetically favorable conformations.</p>", "links"=>[], "tags"=>["nidogen", "computational modeling", "solution structures", "mass spectrometry", "protein regions", "ELISA studies", "laminin γ1", "arm N 836D", "Multiple Binding Modes", "interaction site", "contact regions", "surface plasmon resonance", "laminin γ1 LEb 3 domain", "laminin γ1 variants", "distance information"], "article_id"=>1235953, "categories"=>["Biological Sciences"], "users"=>["Philip Lössl", "Knut Kölbel", "Dirk Tänzler", "David Nannemann", "Christian H. Ihling", "Manuel V. Keller", "Marian Schneider", "Frank Zaucke", "Jens Meiler", "Andrea Sinz"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0112886.g004", "stats"=>{"downloads"=>0, "page_views"=>20, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Structural_models_for_laminin_947_1_L4_/1235953", "title"=>"Structural models for laminin γ1 L4.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-11-11 03:10:39"}
  • {"files"=>["https://ndownloader.figshare.com/files/1787741"], "description"=>"<p>The ten best-scoring structures among the final models were all derived from four initial centroid models of the G1 domain. Structures representing three of these centroid models are shown here. These models comply with the single distance constraint in this region that was identified by cross-linking/MS. Cross-linked residues are displayed as black sticks. Cα–Cα distances are given in Å. The residues are colored according to their Rosetta total score. Scores below zero (yellow-green color) indicate energetically favorable conformations. The identifiers of the underlying centroid models are indicated.</p>", "links"=>[], "tags"=>["nidogen", "computational modeling", "solution structures", "mass spectrometry", "protein regions", "ELISA studies", "laminin γ1", "arm N 836D", "Multiple Binding Modes", "interaction site", "contact regions", "surface plasmon resonance", "laminin γ1 LEb 3 domain", "laminin γ1 variants", "distance information"], "article_id"=>1235954, "categories"=>["Biological Sciences"], "users"=>["Philip Lössl", "Knut Kölbel", "Dirk Tänzler", "David Nannemann", "Christian H. Ihling", "Manuel V. Keller", "Marian Schneider", "Frank Zaucke", "Jens Meiler", "Andrea Sinz"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0112886.g005", "stats"=>{"downloads"=>0, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_De_novo_folded_models_of_nidogen_1_G1_/1235954", "title"=>"<i>De novo</i> folded models of nidogen-1 G1.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-11-11 03:10:39"}
  • {"files"=>["https://ndownloader.figshare.com/files/1787742"], "description"=>"<p>Based on PDB entry 1NPE and the identified cross-links, modified structural models for the high-affinity interaction region of laminin γ1 and nidogen-1 were generated. Cross-linked residues are displayed as spheres. Cα–Cα distances are given in Å. (A) Model with the best Rosetta total score and a Rosetta atom-pair constraint score ranking among the top 2.5%. (B) Model with the best Rosetta atom-pair constraint score and a Rosetta total score ranking among the top 2.5%. (C) Alignment of both models and the unmodified crystal structure 1NPE (black). The orientation of LEb2–4 clearly has changed during structural refinement. The β-propeller fold of the G3 domain is still intact.</p>", "links"=>[], "tags"=>["nidogen", "computational modeling", "solution structures", "mass spectrometry", "protein regions", "ELISA studies", "laminin γ1", "arm N 836D", "Multiple Binding Modes", "interaction site", "contact regions", "surface plasmon resonance", "laminin γ1 LEb 3 domain", "laminin γ1 variants", "distance information"], "article_id"=>1235955, "categories"=>["Biological Sciences"], "users"=>["Philip Lössl", "Knut Kölbel", "Dirk Tänzler", "David Nannemann", "Christian H. Ihling", "Manuel V. Keller", "Marian Schneider", "Frank Zaucke", "Jens Meiler", "Andrea Sinz"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0112886.g006", "stats"=>{"downloads"=>1, "page_views"=>23, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Refined_models_of_the_nidogen_1_G3_laminin_947_1_LEb2_8211_4_complex_/1235955", "title"=>"Refined models of the nidogen-1 G3/laminin γ1 LEb2–4 complex.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-11-11 03:10:39"}
  • {"files"=>["https://ndownloader.figshare.com/files/1787743"], "description"=>"<p>The LEb2–4 structure (red) is taken from PDB entry 1NPE. Nidogen-1 (grey) is schematically depicted as a combination of the crystal structures 1GL4 (G2 domain) and 1NPE (G3 domain) and representative models of the remaining domains. Residues involved in intermolecular contacts are shown as spheres. Gray dotted lines represent verified cross-links.</p>", "links"=>[], "tags"=>["nidogen", "computational modeling", "solution structures", "mass spectrometry", "protein regions", "ELISA studies", "laminin γ1", "arm N 836D", "Multiple Binding Modes", "interaction site", "contact regions", "surface plasmon resonance", "laminin γ1 LEb 3 domain", "laminin γ1 variants", "distance information"], "article_id"=>1235956, "categories"=>["Biological Sciences"], "users"=>["Philip Lössl", "Knut Kölbel", "Dirk Tänzler", "David Nannemann", "Christian H. Ihling", "Manuel V. Keller", "Marian Schneider", "Frank Zaucke", "Jens Meiler", "Andrea Sinz"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0112886.g007", "stats"=>{"downloads"=>0, "page_views"=>15, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Contacts_of_laminin_947_1_LEb2_8211_4_wild_type_with_nidogen_1_/1235956", "title"=>"Contacts of laminin γ1 LEb2–4 wild type with nidogen-1.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-11-11 03:10:39"}
  • {"files"=>["https://ndownloader.figshare.com/files/1787744"], "description"=>"<p>Cα–Cα distances of cross-linked residues were determined for the unmodified crystal structure (PDB entry 1NPE) as well as for the Rosetta models with the best Rosetta total score and atom-pair constraint score, respectively (shown in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0112886#pone-0112886-g006\" target=\"_blank\">Figure 6</a>). For intermolecular contacts, residues are assigned to the respective protein. All other cross-links are located within nidogen-1.</p><p>Overview of cross-links within the nidogen-1 G3/laminin γ1 LEb2–4 complex.</p>", "links"=>[], "tags"=>["nidogen", "computational modeling", "solution structures", "mass spectrometry", "protein regions", "ELISA studies", "laminin γ1", "arm N 836D", "Multiple Binding Modes", "interaction site", "contact regions", "surface plasmon resonance", "laminin γ1 LEb 3 domain", "laminin γ1 variants", "distance information"], "article_id"=>1235957, "categories"=>["Biological Sciences"], "users"=>["Philip Lössl", "Knut Kölbel", "Dirk Tänzler", "David Nannemann", "Christian H. Ihling", "Manuel V. Keller", "Marian Schneider", "Frank Zaucke", "Jens Meiler", "Andrea Sinz"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0112886.t001", "stats"=>{"downloads"=>4, "page_views"=>20, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Overview_of_cross_links_within_the_nidogen_1_G3_laminin_947_1_LEb2_8211_4_complex_/1235957", "title"=>"Overview of cross-links within the nidogen-1 G3/laminin γ1 LEb2–4 complex.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-11-11 03:10:39"}
  • {"files"=>["https://ndownloader.figshare.com/files/1787745", "https://ndownloader.figshare.com/files/1787746", "https://ndownloader.figshare.com/files/1787747", "https://ndownloader.figshare.com/files/1787748", "https://ndownloader.figshare.com/files/1787749", "https://ndownloader.figshare.com/files/1787750", "https://ndownloader.figshare.com/files/1787751", "https://ndownloader.figshare.com/files/1787752", "https://ndownloader.figshare.com/files/1787753", "https://ndownloader.figshare.com/files/1787754", "https://ndownloader.figshare.com/files/1787755", "https://ndownloader.figshare.com/files/1787756", "https://ndownloader.figshare.com/files/1787757", "https://ndownloader.figshare.com/files/1787758", "https://ndownloader.figshare.com/files/1787759", "https://ndownloader.figshare.com/files/1787760", "https://ndownloader.figshare.com/files/1787761", "https://ndownloader.figshare.com/files/1787762", "https://ndownloader.figshare.com/files/1787763"], "description"=>"<div><p>We describe the detailed structural investigation of nidogen-1/laminin γ1 complexes using full-length nidogen-1 and a number of laminin γ1 variants. The interactions of nidogen-1 with laminin variants γ1 LEb2–4, γ1 LEb2–4 N836D, γ1 short arm, and γ1 short arm N836D were investigated by applying a combination of (photo-)chemical cross-linking, high-resolution mass spectrometry, and computational modeling. In addition, surface plasmon resonance and ELISA studies were used to determine kinetic constants of the nidogen-1/laminin γ1 interaction. Two complementary cross-linking strategies were pursued to analyze solution structures of laminin γ1 variants and nidogen-1. The majority of distance information was obtained with the homobifunctional amine-reactive cross-linker <i>bis</i>(sulfosuccinimidyl)glutarate. In a second approach, UV-induced cross-linking was performed after incorporation of the diazirine-containing unnatural amino acids photo-leucine and photo-methionine into laminin γ1 LEb2–4, laminin γ1 short arm, and nidogen-1. Our results indicate that Asn-836 within laminin γ1 LEb3 domain is not essential for complex formation. Cross-links between laminin γ1 short arm and nidogen-1 were found in all protein regions, evidencing several additional contact regions apart from the known interaction site. Computational modeling based on the cross-linking constraints indicates the existence of a conformational ensemble of both the individual proteins and the nidogen-1/laminin γ1 complex. This finding implies different modes of interaction resulting in several distinct protein-protein interfaces.</p></div>", "links"=>[], "tags"=>["nidogen", "computational modeling", "solution structures", "mass spectrometry", "protein regions", "ELISA studies", "laminin γ1", "arm N 836D", "Multiple Binding Modes", "interaction site", "contact regions", "surface plasmon resonance", "laminin γ1 LEb 3 domain", "laminin γ1 variants", "distance information"], "article_id"=>1235958, "categories"=>["Biological Sciences"], "users"=>["Philip Lössl", "Knut Kölbel", "Dirk Tänzler", "David Nannemann", "Christian H. Ihling", "Manuel V. Keller", "Marian Schneider", "Frank Zaucke", "Jens Meiler", "Andrea Sinz"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0112886.s001", "https://dx.doi.org/10.1371/journal.pone.0112886.s002", "https://dx.doi.org/10.1371/journal.pone.0112886.s003", "https://dx.doi.org/10.1371/journal.pone.0112886.s004", "https://dx.doi.org/10.1371/journal.pone.0112886.s005", "https://dx.doi.org/10.1371/journal.pone.0112886.s006", "https://dx.doi.org/10.1371/journal.pone.0112886.s007", "https://dx.doi.org/10.1371/journal.pone.0112886.s008", "https://dx.doi.org/10.1371/journal.pone.0112886.s009", "https://dx.doi.org/10.1371/journal.pone.0112886.s010", "https://dx.doi.org/10.1371/journal.pone.0112886.s011", "https://dx.doi.org/10.1371/journal.pone.0112886.s012", "https://dx.doi.org/10.1371/journal.pone.0112886.s013", "https://dx.doi.org/10.1371/journal.pone.0112886.s014", "https://dx.doi.org/10.1371/journal.pone.0112886.s015", "https://dx.doi.org/10.1371/journal.pone.0112886.s016", "https://dx.doi.org/10.1371/journal.pone.0112886.s017", "https://dx.doi.org/10.1371/journal.pone.0112886.s018", "https://dx.doi.org/10.1371/journal.pone.0112886.s019"], "stats"=>{"downloads"=>92, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Analysis_of_Nidogen_1_Laminin_947_1_Interaction_by_Cross_Linking_Mass_Spectrometry_and_Computational_Modeling_Reveals_Multiple_Binding_Modes_/1235958", "title"=>"Analysis of Nidogen-1/Laminin γ1 Interaction by Cross-Linking, Mass Spectrometry, and Computational Modeling Reveals Multiple Binding Modes", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2014-11-11 03:10:39"}

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Relative Metric

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