Structural Modeling of a Novel CAPN5 Mutation that Causes Uveitis and Neovascular Retinal Detachment
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{"title"=>"Structural modeling of a novel CAPN5 mutation that causes uveitis and neovascular retinal detachment", "type"=>"journal", "authors"=>[{"first_name"=>"Alexander G.", "last_name"=>"Bassuk", "scopus_author_id"=>"6701838698"}, {"first_name"=>"Steven", "last_name"=>"Yeh", "scopus_author_id"=>"7402085804"}, {"first_name"=>"Shu", "last_name"=>"Wu", "scopus_author_id"=>"35084727600"}, {"first_name"=>"Daniel F.", "last_name"=>"Martin", "scopus_author_id"=>"7406285308"}, {"first_name"=>"Stephen H.", "last_name"=>"Tsang", "scopus_author_id"=>"34870998900"}, {"first_name"=>"Lokesh", "last_name"=>"Gakhar", "scopus_author_id"=>"23027783900"}, {"first_name"=>"Vinit B.", "last_name"=>"Mahajan", "scopus_author_id"=>"7102215618"}], "year"=>2015, "source"=>"PLoS ONE", "identifiers"=>{"pmid"=>"25856303", "sgr"=>"84928902596", "doi"=>"10.1371/journal.pone.0122352", "scopus"=>"2-s2.0-84928902596", "pui"=>"604108228", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "issn"=>"19326203"}, "id"=>"2d6fff79-ede5-3e92-bd73-c55df75d5a26", "abstract"=>"CAPN5 mutations have been linked to autosomal dominant neovascular inflammatory vitreoretinopathy (ADNIV), a blinding autoimmune eye disease. Here, we link a new CAPN5 mutation to ADNIV and model the three-dimensional structure of the resulting mutant protein. In our study, a kindred with inflammatory vitreoretinopathy was evaluated by clinical eye examinations, DNA sequencing, and protein structural modeling to investigate the disease-causing mutation. Two daughters of an affected mother demonstrated symptoms of stage III ADNIV, with posterior uveitis, cystoid macular edema, intraocular fibrosis, retinal neovascularization, retinal degeneration, and cataract. The women also harbored a novel guanine to thymine (c.750G>T, p.Lys250Asn) missense mutation in exon 6 of CAPN5, a gene that encodes a calcium-activated cysteine protease, calpain-5. Modeling based on the structures of all known calpains revealed the mutation falls within a calcium-sensitive flexible gating loop that controls access to the catalytic groove. Three-dimensional modeling placed the new mutation in a region adjacent to two previously identified disease-causing mutations, all three of which likely disrupt hydrogen bonding within the gating loop, yielding a CAPN5 with altered enzymatic activity. This is the third case of a CAPN5 mutation leading to inherited uveitis and neovascular vitreoretinopathy, suggesting patients with ADNIV features should be tested for CAPN5 mutations. Structural modeling of novel variants can be used to support mechanistic consequences of the disease-causing variants.", "link"=>"http://www.mendeley.com/research/structural-modeling-novel-capn5-mutation-causes-uveitis-neovascular-retinal-detachment", "reader_count"=>10, "reader_count_by_academic_status"=>{"Student > Doctoral Student"=>2, "Researcher"=>1, "Student > Ph. D. Student"=>1, "Other"=>3, "Student > Master"=>1, "Lecturer > Senior Lecturer"=>1, "Professor"=>1}, "reader_count_by_user_role"=>{"Student > Doctoral Student"=>2, "Researcher"=>1, "Student > Ph. D. Student"=>1, "Other"=>3, "Student > Master"=>1, "Lecturer > Senior Lecturer"=>1, "Professor"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>2, "Biochemistry, Genetics and Molecular Biology"=>1, "Medicine and Dentistry"=>2, "Agricultural and Biological Sciences"=>1, "Pharmacology, Toxicology and Pharmaceutical Science"=>1, "Business, Management and Accounting"=>1, "Computer Science"=>1, "Linguistics"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>2}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>1}, "Computer Science"=>{"Computer Science"=>1}, "Business, Management and Accounting"=>{"Business, Management and Accounting"=>1}, "Linguistics"=>{"Linguistics"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>1}, "Unspecified"=>{"Unspecified"=>2}, "Pharmacology, Toxicology and Pharmaceutical Science"=>{"Pharmacology, Toxicology and Pharmaceutical Science"=>1}}, "reader_count_by_country"=>{"Mexico"=>1}, "group_count"=>0}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/2011581"], "description"=>"<p><b>A</b>. Chromatogram of proband showed a heterozygous c.750G>T DNA sequence mutation (arrow) in exon 6 of <i>CAPN5</i>. <b>B</b>. Calpain-5 is composed of four domains, and the mutation was located in catalytic domain IIb (green). <b>C</b>. Primary protein sequence alignment of calpain-5 orthologs shows high evolutionary conservation of the new mutated p.Lys250Asn residue, along with the two prior ADNIV mutations, p.Arg243Leu and p.Leu244Pro (red arrow/box) in catalytic domain IIb. The two previously identified ADNIV mutations and the newly identified ADNIV mutation are 2 to 9 amino acids upstream of the histidine catalytic residue (blue box). Amino acid mismatches are color-highlighted. <b>D</b>. Twelve human calpain family paralogs show the p.Lys250Asn is highly conserved. (Black, 100% similarity; dark grey, 80 to 100% similarity; light grey, 60 to 80% similarity; white, less than 60% similarity).</p>", "links"=>[], "tags"=>["gating loop", "CAPN 5 mutations", "stage III ADNIV", "cystoid macular edema", "c .750G p.Lys 250Asn missense mutation", "dna", "CAPN 5 mutation", "Neovascular Retinal Detachment CAPN 5 mutations", "Novel CAPN 5 Mutation"], "article_id"=>1372645, "categories"=>["Uncategorised"], "users"=>["Alexander G. Bassuk", "Steven Yeh", "Shu Wu", "Daniel F. Martin", "Stephen H. Tsang", "Lokesh Gakhar", "Vinit B. Mahajan"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0122352.g002", "stats"=>{"downloads"=>0, "page_views"=>17, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_CAPN5_gene_harbors_a_novel_mutation_in_exon_6_/1372645", "title"=>"The <i>CAPN5</i> gene harbors a novel mutation in exon-6.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-04-09 02:50:22"}
  • {"files"=>["https://ndownloader.figshare.com/files/2011579"], "description"=>"<p><b>A</b>. The pedigree of a family with clinical features of ADNIV did not show a specific pattern of inheritance. Black symbols represent clinically affected subjects. Open symbols represent unaffected subjects. <b>B</b>. A color fundus photo of the proband’s (II:1) left macula. <b>C</b>. A fluorescein angiogram reveals CME (arrow) and temporal window defects. <b>D</b>. Fundus autofluorescence showed a central hyperreflective ring in the macula and hypofluorescence temporal to the macula (arrows). <b>E, F</b>. Optical coherence tomography (OCT) shows CME greater in the left eye. <b>G</b>. A color fundus photo of the sister’s (II:2) right macula shows a dense epiretinal membrane (ERM, arrow) over the nerve and macula. <b>H, I</b>. OCT shows an ERM and CME OU. (ADNIV, autosomal dominant neovascular inflammatory vitreoretinopathy; CME, cystoid macular edema; OCT, optical coherence tomography; OD, right eye; OS left eye; OU, both eyes.)</p>", "links"=>[], "tags"=>["gating loop", "CAPN 5 mutations", "stage III ADNIV", "cystoid macular edema", "c .750G p.Lys 250Asn missense mutation", "dna", "CAPN 5 mutation", "Neovascular Retinal Detachment CAPN 5 mutations", "Novel CAPN 5 Mutation"], "article_id"=>1372643, "categories"=>["Uncategorised"], "users"=>["Alexander G. Bassuk", "Steven Yeh", "Shu Wu", "Daniel F. Martin", "Stephen H. Tsang", "Lokesh Gakhar", "Vinit B. Mahajan"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0122352.g001", "stats"=>{"downloads"=>0, "page_views"=>30, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Clinical_Imaging_/1372643", "title"=>"Clinical Imaging.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-04-09 02:50:22"}
  • {"files"=>["https://ndownloader.figshare.com/files/2011585"], "description"=>"<p>The flexible gating loop (colored differently in each panel) can be observed in different conformations across the known structures of the calpain family. The loops shown here are from the crystal structures of calpain-1 (<b>A-E</b>; pdb ids 2ARY, 1ZCM, 1TL9, 1KXR, 1KFX), calpain-2 (<b>F-H</b>; 1U5I, 1MDW, 3DF0), calpain-8 (<b>I</b>; 2NQA), calpain-9 (<b>J, K</b>; 1ZIV, 2P0R) and the homology model of calpain-5 (<b>L</b>). The loop in its most ordered form tends to have a short alpha helix (<b>C, G, I, J, K, L</b>) and a short beta sheet (<b>D, L</b>). Often the loop is disordered and cannot be located in the crystal structure due to lack of sufficient electron density (<b>E, F, H</b>). The catalytic residues are shown in yellow and the residues at the site of the calpain-5 ADNIV mutations are shown in magenta.</p>", "links"=>[], "tags"=>["gating loop", "CAPN 5 mutations", "stage III ADNIV", "cystoid macular edema", "c .750G p.Lys 250Asn missense mutation", "dna", "CAPN 5 mutation", "Neovascular Retinal Detachment CAPN 5 mutations", "Novel CAPN 5 Mutation"], "article_id"=>1372651, "categories"=>["Uncategorised"], "users"=>["Alexander G. Bassuk", "Steven Yeh", "Shu Wu", "Daniel F. Martin", "Stephen H. Tsang", "Lokesh Gakhar", "Vinit B. Mahajan"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0122352.g004", "stats"=>{"downloads"=>0, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Structure_and_modeling_of_the_Calpain_5_gating_loop_/1372651", "title"=>"Structure and modeling of the Calpain-5 gating loop.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-04-09 02:50:22"}
  • {"files"=>["https://ndownloader.figshare.com/files/2011590"], "description"=>"<p><b>A</b>. In the crystal structure of calpain-9, Lys252 forms a salt bridge with Glu241, which in turn hydrogen bonds with the backbone nitrogen of Arg237 and locks the flexible gating loop in place. <b>B</b>. The same set of interactions are observed in the homology model of calpain-5, where Lys250 is well positioned to form a salt bridge with Asp239, which in turn can form a hydrogen bond with the backbone nitrogen of Val235. <b>C</b>. The p.Lys250Asn (purple) mutation modeled here indicates that Asn250, with altered hydrogen bonding capability, will interact differently with Asp239 and affect the conformation and flexibility that this catalytically important gating loop adopts. Changes in the conformation of the gating loop would subsequently alter enzymatic activity.</p>", "links"=>[], "tags"=>["gating loop", "CAPN 5 mutations", "stage III ADNIV", "cystoid macular edema", "c .750G p.Lys 250Asn missense mutation", "dna", "CAPN 5 mutation", "Neovascular Retinal Detachment CAPN 5 mutations", "Novel CAPN 5 Mutation"], "article_id"=>1372657, "categories"=>["Uncategorised"], "users"=>["Alexander G. Bassuk", "Steven Yeh", "Shu Wu", "Daniel F. Martin", "Stephen H. Tsang", "Lokesh Gakhar", "Vinit B. Mahajan"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0122352.g005", "stats"=>{"downloads"=>0, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Hydrogen_bonding_salt_bridge_network_at_the_site_of_p_Lys250Asn_ADNIV_mutation_/1372657", "title"=>"Hydrogen bonding/salt bridge network at the site of p.Lys250Asn ADNIV mutation.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-04-09 02:50:22"}
  • {"files"=>["https://ndownloader.figshare.com/files/2011583"], "description"=>"<p>A three dimensional model of the calpain-5 catalytic domain II was generated using calpain-9 (the closest sequence match) as a template. The residues of the catalytic triad (yellow sticks) are located in the catalytic groove (outlined in blue) between domains IIa and IIb. Although the primary sequence (<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0122352#pone.0122352.g002\" target=\"_blank\">Fig 2</a>) showed the ADNIV Lys250Asn mutation was several residues away from the two known ADNIV mutations, the three-dimensional model reveals all three ADNIV mutations (magenta sticks) are adjacent to one another on a flexible gating loop (green) that regulates enzymatic activity by controlling access to the catalytic groove. This loop samples many conformations, including a short beta sheet harboring the ADNIV residues as shown here. The mutations alter charged or hydrophobic residues.</p>", "links"=>[], "tags"=>["gating loop", "CAPN 5 mutations", "stage III ADNIV", "cystoid macular edema", "c .750G p.Lys 250Asn missense mutation", "dna", "CAPN 5 mutation", "Neovascular Retinal Detachment CAPN 5 mutations", "Novel CAPN 5 Mutation"], "article_id"=>1372647, "categories"=>["Uncategorised"], "users"=>["Alexander G. Bassuk", "Steven Yeh", "Shu Wu", "Daniel F. Martin", "Stephen H. Tsang", "Lokesh Gakhar", "Vinit B. Mahajan"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0122352.g003", "stats"=>{"downloads"=>1, "page_views"=>19, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Protein_structure_modeling_of_calpain_5_and_ADNIV_mutants_/1372647", "title"=>"Protein structure modeling of calpain-5 and ADNIV mutants.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-04-09 02:50:22"}

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Relative Metric

{"start_date"=>"2015-01-01T00:00:00Z", "end_date"=>"2015-12-31T00:00:00Z", "subject_areas"=>[]}
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