{"id":{"repo_id":"uiuc","oai_identifier":"oai:www.ideals.illinois.edu:2142/89192"},"canonical_url":"https://search.dev.ndltd.org/etd/uiuc/oai:www.ideals.illinois.edu:2142/89192","repository":{"repo_id":"uiuc","name":"University of Illinois - Urbana-Champaign","base_url":"https://www.ideals.illinois.edu/oai-pmh"},"display":{"title":"The early history and emergence of molecular functions and modular scale-free network behavior","abstract":"The formation of protein structural domains requires that biochemical functions, defined by conserved amino acid sequence motifs, be embedded into a structural scaffold. Here we trace domain history onto a bipartite network of elementary functional loop (EFL) sequences and domain structures defined at the fold superfamily (FSF) level of Structural Classification of Proteins (SCOP). The resulting ‘elementary functionome’ network and its EFL and FSF graph projections unfold evolutionary ‘waterfalls’ describing emergence of primordial functions. Waterfalls reveal how ancient EFLs are shared by FSF structures in two initial waves of functional innovation that involve founder ‘p-loop’ and ‘winged helix’ domain structures. They also uncover a dynamics of modular motif embedding in domain structures that is ongoing, which transfers ‘preferential’ cooption properties of ancient EFLs to emerging FSFs. Remarkably, we find that the emergence of molecular functions induces hierarchical modularity and power law behavior in network evolution as the networks of motifs and structures expand metabolic pathways and translation.","abstract_html":"The formation of protein structural domains requires that biochemical functions, defined by conserved amino acid sequence motifs, be embedded into a structural scaffold. Here we trace domain history onto a bipartite network of elementary functional loop (EFL) sequences and domain structures defined at the fold superfamily (FSF) level of Structural Classification of Proteins (SCOP). The resulting ‘elementary functionome’ network and its EFL and FSF graph projections unfold evolutionary ‘waterfalls’ describing emergence of primordial functions. Waterfalls reveal how ancient EFLs are shared by FSF structures in two initial waves of functional innovation that involve founder ‘p-loop’ and ‘winged helix’ domain structures. They also uncover a dynamics of modular motif embedding in domain structures that is ongoing, which transfers ‘preferential’ cooption properties of ancient EFLs to emerging FSFs. Remarkably, we find that the emergence of molecular functions induces hierarchical modularity and power law behavior in network evolution as the networks of motifs and structures expand metabolic pathways and translation.","abstract_has_math":false,"creators":["Aziz, Muhammad Fayez"],"institution":"University of Illinois at Urbana-Champaign","degree_name":"M.S.","degree_level":"Thesis","degree_discipline":"Bioinformatics","degree_department":null,"school":null,"contributors":["Caetano-Anollés, Gustavo","Rodriguez-Zas, Sandra Luisa","Bhalerao, Kaustubh","Ma, Jian"],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2016,"date_issued":"2016-03-02T21:06:23Z","date_published":"2016-03-02T21:06:23Z","updated_at":"2026-07-22T22:26:32Z","subjects":["Protein domains","Elementary loop sequences","Bipartite network","Network projections","Evolutionary timeline","Molecular functions","Scale-free dynamics","Modularity"],"languages":["en"],"rights":["Copyright 2015 Muhammad Fayez Aziz. Materials in this document (all chapters, including the abstract) are reprinted, with permission, from Aziz MF, Caetano-Anollés K and Caetano-Anollés G, 2015, “The early history and emergence of molecular functions and modular scale-free network behavior,” manuscript submitted"],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"http://hdl.handle.net/2142/89192","outbound_label":"Handle","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Caetano-Anollés, Gustavo","Rodriguez-Zas, Sandra Luisa","Bhalerao, Kaustubh","Ma, Jian"]},{"key":"dc:creator","label":"Author","values":["Aziz, Muhammad Fayez"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date","label":"Dc Date","values":["2016-03-02T21:06:23Z","2018-03-03T10:15:34Z","2015-12-03","2015-12"]},{"key":"dc:type","label":"Dc Type","values":["text"]},{"key":"thesis:degree_discipline","label":"Discipline","values":["Bioinformatics"]},{"key":"thesis:degree_level","label":"Degree Level","values":["Thesis"]},{"key":"thesis:degree_name","label":"Degree Name","values":["M.S."]},{"key":"thesis:institution_name","label":"Thesis Institution Name","values":["University of Illinois at Urbana-Champaign"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["Protein domains","Elementary loop sequences","Bipartite network","Network projections","Evolutionary timeline","Molecular functions","Scale-free dynamics","Modularity"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language","label":"Dc Language","values":["en"]},{"key":"dc:rights","label":"Dc Rights","values":["Copyright 2015 Muhammad Fayez Aziz. Materials in this document (all chapters, including the abstract) are reprinted, with permission, from Aziz MF, Caetano-Anollés K and Caetano-Anollés G, 2015, “The early history and emergence of molecular functions and modular scale-free network behavior,” manuscript submitted"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["http://hdl.handle.net/2142/89192"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description","label":"Description","values":["The formation of protein structural domains requires that biochemical functions, defined by conserved amino acid sequence motifs, be embedded into a structural scaffold. Here we trace domain history onto a bipartite network of elementary functional loop (EFL) sequences and domain structures defined at the fold superfamily (FSF) level of Structural Classification of Proteins (SCOP). The resulting ‘elementary functionome’ network and its EFL and FSF graph projections unfold evolutionary ‘waterfalls’ describing emergence of primordial functions. Waterfalls reveal how ancient EFLs are shared by FSF structures in two initial waves of functional innovation that involve founder ‘p-loop’ and ‘winged helix’ domain structures. They also uncover a dynamics of modular motif embedding in domain structures that is ongoing, which transfers ‘preferential’ cooption properties of ancient EFLs to emerging FSFs. Remarkably, we find that the emergence of molecular functions induces hierarchical modularity and power law behavior in network evolution as the networks of motifs and structures expand metabolic pathways and translation.","Submission published under a 24 month embargo labeled 'Closed Access', the embargo will last until 2017-12-01","The student, Muhammad Fayez Aziz, accepted the attached license on 2015-11-07 at 12:19.","The student, Muhammad Fayez Aziz, submitted this Thesis for approval on 2015-11-07 at 12:53.","This Thesis was approved for publication on 2015-12-03 at 13:19.","DSpace SAF Submission Ingestion Package generated from Vireo submission #8765 on 2016-03-02 at 14:12:51","Made available in DSpace on 2016-03-02T21:06:23Z (GMT). No. of bitstreams: 4 AZIZ-THESIS-2015.pdf: 1948525 bytes, checksum: 146fe25a75d8b90cbad3f82494e81c69 (MD5) Video 1 EFL_FSFHeatmapNG_age.mp4: 20022592 bytes, checksum: db610b39e30c4dbbde6bc50a84dd194a (MD5) Video 2 EFL_FSFDendrogramNG_age.mp4: 34865615 bytes, checksum: 5728703240f5c1459f70fb871da92cda (MD5) LICENSE.txt: 4216 bytes, checksum: 5e4fd493fc3ec0328150552390bc9a50 (MD5) Previous issue date: 2015-12-03","Embargo set by: Seth Robbins for item 91395 Lift date: 2018-03-02T21:07:27Z Reason: Author requested closed access (OA after 2yrs) in Vireo ETD system","Limited Restriction Lifted for Item 91395 on 2018-03-03T10:15:34Z."]},{"key":"dc:format","label":"Dc Format","values":["application/pdf"]},{"key":"dc:title","label":"Title","values":["The early history and emergence of molecular functions and modular scale-free network behavior"]}]}],"canonical_facts":{"dc:contributor":["Caetano-Anollés, Gustavo","Rodriguez-Zas, Sandra Luisa","Bhalerao, Kaustubh","Ma, Jian"],"dc:creator":["Aziz, Muhammad Fayez"],"dc:date":["2016-03-02T21:06:23Z","2018-03-03T10:15:34Z","2015-12-03","2015-12"],"dc:description":["The formation of protein structural domains requires that biochemical functions, defined by conserved amino acid sequence motifs, be embedded into a structural scaffold. Here we trace domain history onto a bipartite network of elementary functional loop (EFL) sequences and domain structures defined at the fold superfamily (FSF) level of Structural Classification of Proteins (SCOP). The resulting ‘elementary functionome’ network and its EFL and FSF graph projections unfold evolutionary ‘waterfalls’ describing emergence of primordial functions. Waterfalls reveal how ancient EFLs are shared by FSF structures in two initial waves of functional innovation that involve founder ‘p-loop’ and ‘winged helix’ domain structures. They also uncover a dynamics of modular motif embedding in domain structures that is ongoing, which transfers ‘preferential’ cooption properties of ancient EFLs to emerging FSFs. 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No. of bitstreams: 4 AZIZ-THESIS-2015.pdf: 1948525 bytes, checksum: 146fe25a75d8b90cbad3f82494e81c69 (MD5) Video 1 EFL_FSFHeatmapNG_age.mp4: 20022592 bytes, checksum: db610b39e30c4dbbde6bc50a84dd194a (MD5) Video 2 EFL_FSFDendrogramNG_age.mp4: 34865615 bytes, checksum: 5728703240f5c1459f70fb871da92cda (MD5) LICENSE.txt: 4216 bytes, checksum: 5e4fd493fc3ec0328150552390bc9a50 (MD5) Previous issue date: 2015-12-03","Embargo set by: Seth Robbins for item 91395 Lift date: 2018-03-02T21:07:27Z Reason: Author requested closed access (OA after 2yrs) in Vireo ETD system","Limited Restriction Lifted for Item 91395 on 2018-03-03T10:15:34Z."],"dc:format":["application/pdf"],"dc:identifier":["http://hdl.handle.net/2142/89192"],"dc:language":["en"],"dc:rights":["Copyright 2015 Muhammad Fayez Aziz. Materials in this document (all chapters, including the abstract) are reprinted, with permission, from Aziz MF, Caetano-Anollés K and Caetano-Anollés G, 2015, “The early history and emergence of molecular functions and modular scale-free network behavior,” manuscript submitted"],"dc:subject":["Protein domains","Elementary loop sequences","Bipartite network","Network projections","Evolutionary timeline","Molecular functions","Scale-free dynamics","Modularity"],"dc:title":["The early history and emergence of molecular functions and modular scale-free network behavior"],"dc:type":["text"],"thesis:degree_discipline":["Bioinformatics"],"thesis:degree_level":["Thesis"],"thesis:degree_name":["M.S."],"thesis:institution_name":["University of Illinois at Urbana-Champaign"]},"updated_at":"2026-07-22T22:26:32Z"}