Rampant Exchange of the Structure and Function of Extramembrane Domains between Membrane and Water Soluble Proteins
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{"title"=>"Rampant Exchange of the Structure and Function of Extramembrane Domains between Membrane and Water Soluble Proteins", "type"=>"journal", "authors"=>[{"first_name"=>"Hyun Jun", "last_name"=>"Nam", "scopus_author_id"=>"35272908100"}, {"first_name"=>"Seong Kyu", "last_name"=>"Han", "scopus_author_id"=>"8046096000"}, {"first_name"=>"James U.", "last_name"=>"Bowie", "scopus_author_id"=>"7102792896"}, {"first_name"=>"Sanguk", "last_name"=>"Kim", "scopus_author_id"=>"7601602471"}], "year"=>2013, "source"=>"PLoS Computational Biology", "identifiers"=>{"pmid"=>"23555228", "doi"=>"10.1371/journal.pcbi.1002997", "sgr"=>"84875976437", "isbn"=>"1553-7358 (Electronic)\\r1553-734X (Linking)", "scopus"=>"2-s2.0-84875976437", "issn"=>"1553734X", "pui"=>"368694317"}, "id"=>"061658b7-de8c-3801-9e14-c9f07444bdc7", "abstract"=>"Of the membrane proteins of known structure, we found that a remarkable 67% of the water soluble domains are structurally similar to water soluble proteins of known structure. Moreover, 41% of known water soluble protein structures share a domain with an already known membrane protein structure. We also found that functional residues are frequently conserved between extramembrane domains of membrane and soluble proteins that share structural similarity. These results suggest membrane and soluble proteins readily exchange domains and their attendant functionalities. The exchanges between membrane and soluble proteins are particularly frequent in eukaryotes, indicating that this is an important mechanism for increasing functional complexity. The high level of structural overlap between the two classes of proteins provides an opportunity to employ the extensive information on soluble proteins to illuminate membrane protein structure and function, for which much less is known. To this end, we employed structure guided sequence alignment to elucidate the functions of membrane proteins in the human genome. Our results bridge the gap of fold space between membrane and water soluble proteins and provide a resource for the prediction of membrane protein function. A database of predicted structural and functional relationships for proteins in the human genome is provided at sbi.postech.ac.kr/emdmp.", "link"=>"http://www.mendeley.com/research/rampant-exchange-structure-function-extramembrane-domains-between-membrane-water-soluble-proteins", "reader_count"=>24, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>1, "Researcher"=>3, "Student > Ph. D. Student"=>12, "Student > Master"=>4, "Student > Bachelor"=>2, "Student > Doctoral Student"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>1, "Researcher"=>3, "Student > Ph. D. Student"=>12, "Student > Master"=>4, "Student > Bachelor"=>2, "Student > Doctoral Student"=>1}, "reader_count_by_subject_area"=>{"Engineering"=>3, "Unspecified"=>1, "Biochemistry, Genetics and Molecular Biology"=>5, "Agricultural and Biological Sciences"=>13, "Physics and Astronomy"=>1, "Chemistry"=>1}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>3}, "Chemistry"=>{"Chemistry"=>1}, "Physics and Astronomy"=>{"Physics and Astronomy"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>13}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>5}, "Unspecified"=>{"Unspecified"=>1}}, "reader_count_by_country"=>{"Korea (South)"=>1, "Denmark"=>1, "Spain"=>1}, "group_count"=>1}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/993748"], "description"=>"<p>(A) Fraction of structurally similar pairs of membrane and soluble proteins. (B) Distribution of RMSD, aligned length, and alignment confidence score according to sequence identities between membrane and soluble proteins.</p>", "links"=>[], "tags"=>["alignments", "membrane", "soluble"], "article_id"=>657094, "categories"=>["Biological Sciences"], "users"=>["Hyun-Jun Nam", "Seong Kyu Han", "James U. Bowie", "Sanguk Kim"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1002997.g001", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Analyses_of_the_structural_alignments_between_membrane_and_soluble_proteins_/657094", "title"=>"Analyses of the structural alignments between membrane and soluble proteins.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-03-22 04:44:45"}
  • {"files"=>["https://ndownloader.figshare.com/files/993749"], "description"=>"<p>(A) All alpha, all beta, alpha+beta and alpha/beta classes from SCOP databases were represented. The RMSD, sequence identity, and aligned lengths of each pair are noted in parentheses. (B) Protein classes of similar structure pairs between membrane and soluble proteins.</p>", "links"=>[], "tags"=>["aligned", "pairs", "membrane", "soluble"], "article_id"=>657095, "categories"=>["Biological Sciences"], "users"=>["Hyun-Jun Nam", "Seong Kyu Han", "James U. Bowie", "Sanguk Kim"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1002997.g002", "stats"=>{"downloads"=>1, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Structurally_aligned_pairs_of_membrane_and_soluble_proteins_/657095", "title"=>"Structurally aligned pairs of membrane and soluble proteins.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-03-22 04:45:08"}
  • {"files"=>["https://ndownloader.figshare.com/files/993752"], "description"=>"<p>(A) Phylogenetic distribution of soluble proteins that share similar structure with membrane proteins. Phylogenetic distribution was sorted by sequence identity of membrane and soluble proteins. For three groups divided by sequence identity between membrane and soluble proteins (low: 0–20%, medium: 20–40% and high: 40–80%), the fraction of eukaryotic and prokaryotic orthologues was represented. (B) Functional enrichment of membrane and soluble protein structure pairs. Three groups divided by their sequence identity were analyzed for enrichment of gene ontology. Circles of each functional term were colored by their <i>P</i>-value. The fraction of proteins which are included in each functional term is proportional to the diameter of the circles.</p>", "links"=>[], "tags"=>["enrichment", "pairs", "membrane", "soluble"], "article_id"=>657098, "categories"=>["Biological Sciences"], "users"=>["Hyun-Jun Nam", "Seong Kyu Han", "James U. Bowie", "Sanguk Kim"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1002997.g003", "stats"=>{"downloads"=>2, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogenetic_and_function_enrichment_analysis_of_the_structure_pairs_of_membrane_and_soluble_proteins_/657098", "title"=>"Phylogenetic and function enrichment analysis of the structure pairs of membrane and soluble proteins.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-03-22 04:45:41"}
  • {"files"=>["https://ndownloader.figshare.com/files/993753"], "description"=>"<p>(A) Nicotinic acetylcholine receptor and acetylcholine-binding protein. (B) Chloride intracellular channel protein and glutathione S-transferase. (C) Fraction of domain annotation found in membrane and soluble proteins.</p>", "links"=>[], "tags"=>["domains", "membrane", "soluble"], "article_id"=>657099, "categories"=>["Biological Sciences"], "users"=>["Hyun-Jun Nam", "Seong Kyu Han", "James U. Bowie", "Sanguk Kim"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1002997.g004", "stats"=>{"downloads"=>1, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Shared_domains_between_membrane_and_soluble_proteins_/657099", "title"=>"Shared domains between membrane and soluble proteins.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-03-22 04:46:01"}
  • {"files"=>["https://ndownloader.figshare.com/files/993755"], "description"=>"<p>(A) Conserved catalytic sites between structurally aligned membrane and soluble protein domains. (B) Alignment of envelope structure-factor and phophotyrosyl phosphase. Catalytic sites are depicted on the structural alignment. (C) Alignment of penicillin-binding protein and OXA-10 beta-lactamase.</p>", "links"=>[], "tags"=>["residues", "conserved", "membrane", "soluble"], "article_id"=>657100, "categories"=>["Biological Sciences"], "users"=>["Hyun-Jun Nam", "Seong Kyu Han", "James U. Bowie", "Sanguk Kim"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1002997.g005", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Functional_residues_conserved_between_membrane_and_soluble_proteins_/657100", "title"=>"Functional residues conserved between membrane and soluble proteins.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-03-22 04:46:17"}
  • {"files"=>["https://ndownloader.figshare.com/files/993756"], "description"=>"<p>(a) Distribution of the ssea scores of the positive set (similar structures) and the negative set (dissimilar structures) of membrane and soluble proteins. (b) SSEA score to filter the positives and the negatives was set to 50. (c) Fraction of membrane protein sequences that have structural homology with soluble protein structures.</p>", "links"=>[], "tags"=>["dissimilar", "pairs", "membrane", "soluble"], "article_id"=>657101, "categories"=>["Biological Sciences"], "users"=>["Hyun-Jun Nam", "Seong Kyu Han", "James U. Bowie", "Sanguk Kim"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1002997.g006", "stats"=>{"downloads"=>1, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Training_process_of_secondary_structure_element_score_to_separate_similar_and_dissimilar_structure_pairs_between_membrane_and_soluble_proteins_/657101", "title"=>"Training process of secondary structure element score to separate similar and dissimilar structure pairs between membrane and soluble proteins.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-03-22 04:46:30"}
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Relative Metric

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