Molecular Details of Olfactomedin Domains Provide Pathway to Structure-Function Studies
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{"title"=>"Molecular details of olfactomedin domains provide pathway to structure-function studies", "type"=>"journal", "authors"=>[{"first_name"=>"Shannon E.", "last_name"=>"Hill", "scopus_author_id"=>"29467580600"}, {"first_name"=>"Rebecca K.", "last_name"=>"Donegan", "scopus_author_id"=>"55509389900"}, {"first_name"=>"Elaine", "last_name"=>"Nguyen", "scopus_author_id"=>"56583841600"}, {"first_name"=>"Tanay M.", "last_name"=>"Desai", "scopus_author_id"=>"57198385905"}, {"first_name"=>"Raquel L.", "last_name"=>"Lieberman", "scopus_author_id"=>"9239648000"}], "year"=>2015, "source"=>"PLoS ONE", "identifiers"=>{"sgr"=>"84939203253", "doi"=>"10.1371/journal.pone.0130888", "scopus"=>"2-s2.0-84939203253", "pui"=>"605481225", "isbn"=>"1932-6203", "issn"=>"19326203"}, "id"=>"0b219904-5561-3f0b-9c5d-b6446d0c6a3b", "abstract"=>"Olfactomedin (OLF) domains are found within extracellular, multidomain proteins in numerous tissues of multicellular organisms. Even though these proteins have been implicated in human disorders ranging from cancers to attention deficit disorder to glaucoma, little is known about their structure(s) and function(s). Here we biophysically, biochemically, and structurally characterize OLF domains from H. sapiens olfactomedin-1 (npoh-OLF, also called noelin, pancortin, OLFM1, and hOlfA), and M. musculus gliomedin (glio-OLF, also called collomin, collmin, and CRG-L2), and compare them with available structures of myocilin (myoc-OLF) recently reported by us and R. norvegicus glio-OLF and M. musculus latrophilin-3 (lat3-OLF) by others. Although the five-bladed β-propeller architecture remains unchanged, numerous physicochemical characteristics differ among these OLF domains. First, npoh-OLF and glio-OLF exhibit prominent, yet distinct, positive surface charges and copurify with polynucleotides. Second, whereas npoh-OLF and myoc-OLF exhibit thermal stabilities typical of human proteins near 55°C, and most myoc-OLF variants are destabilized and highly prone to aggregation, glio-OLF is nearly 20°C more stable and significantly more resistant to chemical denaturation. Phylogenetically, glio-OLF is most similar to primitive OLFs, and structurally, glio-OLF is missing distinguishing features seen in OLFs such as the disulfide bond formed by N- and C- terminal cysteines, the sequestered Ca2+ ion within the propeller central hydrophilic cavity, and a key loop-stabilizing cation-π interaction on the top face of npoh-OLF and myoc-OLF. While deciphering the explicit biological functions, ligands, and binding partners for OLF domains will likely continue to be a challenging long-term experimental pursuit, we used structural insights gained here to generate a new antibody selective for myoc-OLF over npoh-OLF and glio-OLF as a first step in overcoming the impasse in detailed functional characterization of these biomedically important protein domains.", "link"=>"http://www.mendeley.com/research/molecular-details-olfactomedin-domains-provide-pathway-structurefunction-studies", "reader_count"=>10, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>1, "Researcher"=>1, "Student > Ph. D. Student"=>2, "Student > Master"=>2, "Student > Bachelor"=>3}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>1, "Researcher"=>1, "Student > Ph. D. Student"=>2, "Student > Master"=>2, "Student > Bachelor"=>3}, "reader_count_by_subject_area"=>{"Unspecified"=>2, "Biochemistry, Genetics and Molecular Biology"=>1, "Agricultural and Biological Sciences"=>6, "Medicine and Dentistry"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>6}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>1}, "Unspecified"=>{"Unspecified"=>2}}, "reader_count_by_country"=>{"United States"=>1}, "group_count"=>0}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/2154707"], "description"=>"<p>(a) Electrostatic surfaces of npoh-OLF and glio-OLF at top and bottom faces. (b) Electrostatic surfaces of myoc-OLF (PDB code 4WXU) and lat3-OLF (PDB code 5AFB). Surface potentials are colored negative (red, -5 kT/e<sup>-</sup>) to positive (blue, + 5 kT/e<sup>-</sup>). (c) Extraction analysis reveals small nucleotide stretches bound to npoh-OLF. (d) Low affinity binding of npoh-OLF to heparin column; no binding occurs with buffers at physiological ionic strength. (e) Commercial antibodies, anti-npoh-OLF and anti-myocilin (H130), lack specificity and detect npoh-OLF, myoc-OLF, and glio-OLF compared to custom myocilin antibody prepared in this study.</p>", "links"=>[], "tags"=>["OLFM", "OLF domains", "attention deficit disorder", "protein"], "article_id"=>1467597, "categories"=>["Uncategorised"], "users"=>["Shannon E. Hill", "Rebecca K. Donegan", "Elaine Nguyen", "Tanay M. Desai", "Raquel L. Lieberman"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0130888.g004", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Electrostatic_surface_representations_and_biochemical_analysis_of_nucleotide_and_heparin_binding_for_npoh_OLF_/1467597", "title"=>"Electrostatic surface representations and biochemical analysis of nucleotide and heparin binding for npoh-OLF.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-06-29 03:33:06"}
  • {"files"=>["https://ndownloader.figshare.com/files/2154703"], "description"=>"<p>(a) Metal binding sites in npoh-OLF. (b) Metal binding sites in myoc-OLF (PDB code 4WXU). (c) Metal binding sites in lat3-OLF (PDB code 5AFB). (d) Metal binding site in <i>M</i>. <i>musculus</i> glio-OLF. Lower panels show interacting distances ≤ 2.7 Å. For (a), (d), 2F<sub>o</sub>-F<sub>c</sub> electron density is contoured at 1σ. (e) Quin-2 fluorescence (in a.f.u., arbitrary fluorescence units) due to Ca<sup>2+</sup> binding under native and denaturing conditions. Denaturing concentrations were 1.4 M GdHCl for npoh-OLF, and 5 M GdHCl for glio-OLF. (f) Chemical unfolding curves of npoh-OLF and glio-OLF monitored by the change in maximum intrinsic tryptophan fluorescence using GdHCl (left) and urea (right). Concentration at unfolding midpoint indicated in parentheses.</p>", "links"=>[], "tags"=>["OLFM", "OLF domains", "attention deficit disorder", "protein"], "article_id"=>1467593, "categories"=>["Uncategorised"], "users"=>["Shannon E. Hill", "Rebecca K. Donegan", "Elaine Nguyen", "Tanay M. Desai", "Raquel L. Lieberman"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0130888.g002", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_metal_ion_binding_sites_for_four_OLFs_and_biophysical_analysis_for_npoh_OLF_and_glio_OLF_/1467593", "title"=>"Comparison of metal ion binding sites for four OLFs and biophysical analysis for npoh-OLF and glio-OLF.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-06-29 03:33:06"}
  • {"files"=>["https://ndownloader.figshare.com/files/2154702"], "description"=>"<p>(a) Overlay of npoh-OLF and glio-OLF in two orientations with strands and blades labeled (r.m.s.d. over Cα atoms is 1.456 Å). (b) Disulfide bond in npoh-OLF (left) and corresponding cation-π interaction in glio-OLF (right). (c) Overview of molecular clasp region highlighting Pro, Tyr residues discussed in text; polar contacts < 3.5 Å are depicted as black dashes (left). Crystal contact of npoh-OLF involving residues from the molecular clasp and an outer strand of blade A from an adjacent symmetry-related molecule (right).</p>", "links"=>[], "tags"=>["OLFM", "OLF domains", "attention deficit disorder", "protein"], "article_id"=>1467592, "categories"=>["Uncategorised"], "users"=>["Shannon E. Hill", "Rebecca K. Donegan", "Elaine Nguyen", "Tanay M. Desai", "Raquel L. Lieberman"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0130888.g001", "stats"=>{"downloads"=>0, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Structural_features_of_npoh_OLF_yellow_and_glio_OLF_purple_/1467592", "title"=>"Structural features of npoh-OLF (yellow) and glio-OLF (purple).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-06-29 03:33:06"}
  • {"files"=>["https://ndownloader.figshare.com/files/2154709"], "description"=>"<p><sup>a</sup>T<sub>m</sub> measured in 10 mM Hepes, 200 mM NaCl pH 7.5 (Buffer A) with or without 0.75 mg/mL of GAG. For myoc-OLF, T<sub>m</sub> is ~53°C in Buffer A [<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0130888#pone.0130888.ref061\" target=\"_blank\">61</a>].</p><p>Analysis of Thermal Stabilization of OLF domains.</p>", "links"=>[], "tags"=>["OLFM", "OLF domains", "attention deficit disorder", "protein"], "article_id"=>1467599, "categories"=>["Uncategorised"], "users"=>["Shannon E. Hill", "Rebecca K. Donegan", "Elaine Nguyen", "Tanay M. Desai", "Raquel L. Lieberman"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0130888.t002", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Analysis_of_Thermal_Stabilization_of_OLF_domains_/1467599", "title"=>"Analysis of Thermal Stabilization of OLF domains.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-06-29 03:33:06"}
  • {"files"=>["https://ndownloader.figshare.com/files/2154710", "https://ndownloader.figshare.com/files/2154711"], "description"=>"<div><p>Olfactomedin (OLF) domains are found within extracellular, multidomain proteins in numerous tissues of multicellular organisms. Even though these proteins have been implicated in human disorders ranging from cancers to attention deficit disorder to glaucoma, little is known about their structure(s) and function(s). Here we biophysically, biochemically, and structurally characterize OLF domains from <i>H</i>. <i>sapiens</i> olfactomedin-1 (npoh-OLF, also called noelin, pancortin, OLFM1, and hOlfA), and <i>M</i>. <i>musculus</i> gliomedin (glio-OLF, also called collomin, collmin, and CRG-L2), and compare them with available structures of myocilin (myoc-OLF) recently reported by us and <i>R</i>. <i>norvegicus</i> glio-OLF and <i>M</i>. <i>musculus</i> latrophilin-3 (lat3-OLF) by others. Although the five-bladed β-propeller architecture remains unchanged, numerous physicochemical characteristics differ among these OLF domains. First, npoh-OLF and glio-OLF exhibit prominent, yet distinct, positive surface charges and copurify with polynucleotides. Second, whereas npoh-OLF and myoc-OLF exhibit thermal stabilities typical of human proteins near 55°C, and most myoc-OLF variants are destabilized and highly prone to aggregation, glio-OLF is nearly 20°C more stable and significantly more resistant to chemical denaturation. Phylogenetically, glio-OLF is most similar to primitive OLFs, and structurally, glio-OLF is missing distinguishing features seen in OLFs such as the disulfide bond formed by N- and C- terminal cysteines, the sequestered Ca<sup>2+</sup> ion within the propeller central hydrophilic cavity, and a key loop-stabilizing cation-π interaction on the top face of npoh-OLF and myoc-OLF. While deciphering the explicit biological functions, ligands, and binding partners for OLF domains will likely continue to be a challenging long-term experimental pursuit, we used structural insights gained here to generate a new antibody selective for myoc-OLF over npoh-OLF and glio-OLF as a first step in overcoming the impasse in detailed functional characterization of these biomedically important protein domains.</p></div>", "links"=>[], "tags"=>["OLFM", "OLF domains", "attention deficit disorder", "protein"], "article_id"=>1467600, "categories"=>["Uncategorised"], "users"=>["Shannon E. Hill", "Rebecca K. Donegan", "Elaine Nguyen", "Tanay M. Desai", "Raquel L. Lieberman"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0130888.s001", "https://dx.doi.org/10.1371/journal.pone.0130888.s002"], "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Molecular_Details_of_Olfactomedin_Domains_Provide_Pathway_to_Structure_Function_Studies_/1467600", "title"=>"Molecular Details of Olfactomedin Domains Provide Pathway to Structure-Function Studies", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2015-06-29 03:33:06"}
  • {"files"=>["https://ndownloader.figshare.com/files/2154708"], "description"=>"<p>Crystallographic Data Collection and Refinement Statistics (values in parentheses are for the highest resolution shell).</p>", "links"=>[], "tags"=>["OLFM", "OLF domains", "attention deficit disorder", "protein"], "article_id"=>1467598, "categories"=>["Uncategorised"], "users"=>["Shannon E. Hill", "Rebecca K. Donegan", "Elaine Nguyen", "Tanay M. Desai", "Raquel L. Lieberman"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0130888.t001", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Crystallographic_Data_Collection_and_Refinement_Statistics_values_in_parentheses_are_for_the_highest_resolution_shell_/1467598", "title"=>"Crystallographic Data Collection and Refinement Statistics (values in parentheses are for the highest resolution shell).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-06-29 03:33:06"}
  • {"files"=>["https://ndownloader.figshare.com/files/2154705"], "description"=>"<p>Comparison of (a) myoc-OLF (PDB code 4WXU), (b) npoh-OLF, and (c) <i>M</i>. <i>musculus</i> glio-OLF. Left: surface representation of loop region; right: key side chain interactions presented as sticks in two orientations. (d) Overlay of Lys/Tyr cation-π interaction conserved for myoc-OLF (blue-green), npoh-OLF (yellow), and lat3-OLF (orange) but disrupted for glio-OLF (purple).</p>", "links"=>[], "tags"=>["OLFM", "OLF domains", "attention deficit disorder", "protein"], "article_id"=>1467595, "categories"=>["Uncategorised"], "users"=>["Shannon E. Hill", "Rebecca K. Donegan", "Elaine Nguyen", "Tanay M. Desai", "Raquel L. Lieberman"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0130888.g003", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_top_surface_features_loop_B_10_C_11_and_related_cation_960_interaction_/1467595", "title"=>"Comparison of top surface features, loop B-10/C-11, and related cation-π interaction.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-06-29 03:33:06"}

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