{"id":"https://openalex.org/W4288700708","doi":"https://doi.org/10.1073/pnas.2204131119","title":"Evolution and folding of repeat proteins","display_name":"Evolution and folding of repeat proteins","publication_year":2022,"publication_date":"2022-07-29","ids":{"openalex":"https://openalex.org/W4288700708","doi":"https://doi.org/10.1073/pnas.2204131119","pmid":"https://pubmed.ncbi.nlm.nih.gov/35905321","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/9351489"},"language":"en","primary_location":{"id":"doi:10.1073/pnas.2204131119","doi":"https://doi.org/10.1073/pnas.2204131119","is_oa":true,"landing_page_url":"https://doi.org/10.1073/pnas.2204131119","pdf_url":null,"source":{"id":"https://openalex.org/S125754415","display_name":"Proceedings of the National Academy of Sciences","issn_l":"0027-8424","issn":["0027-8424","1091-6490"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-class-a","anvur-scientific","cwts-core","dongbi-a","doyens","erih-plus","jufo-3","ki-jl-3","medline","norway-2","poland-200","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320052","host_organization_name":"National Academy of Sciences","host_organization_lineage":["https://openalex.org/P4310320052"],"host_organization_lineage_names":["National Academy of Sciences"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the National Academy of Sciences","raw_type":"journal-article"},"volume":null,"type":"article","indexed_in":["arxiv","crossref","datacite","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://doi.org/10.1073/pnas.2204131119","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5035085585","display_name":"Ezequiel Alejandro Galpern","orcid":"https://orcid.org/0000-0001-9516-3985","observed_orcids":["https://orcid.org/0000-0001-9516-3985"]},"institutions":[{"id":"https://openalex.org/I151201029","display_name":"Consejo Nacional de Investigaciones Cient\u00edficas y T\u00e9cnicas","ror":"https://ror.org/03cqe8w59","country_code":"AR","type":"government","lineage":["https://openalex.org/I151201029","https://openalex.org/I4210123736","https://openalex.org/I4387155568"]},{"id":"https://openalex.org/I24354313","display_name":"Universidad de Buenos Aires","ror":"https://ror.org/0081fs513","country_code":"AR","type":"education","lineage":["https://openalex.org/I24354313"]}],"countries":["AR"],"is_corresponding":false,"raw_author_name":"Ezequiel A. Galpern","raw_affiliation_strings":["Consejo Nacional de Investigaciones Cient\u00edficas y T\u00e9cnicas\u2013Universidad de Buenos Aires, Instituto de Qu\u00edmica Biol\u00f3gica de la Facultad de Ciencias Exactas y Naturales, C1428EGA Buenos Aires, Argentina","Protein Physiology Lab, Facultad de Ciencias Exactas y Naturales, Departamento de Qu\u00edmica Biol\u00f3gica, Universidad de Buenos Aires, C1428EGA Buenos Aires, Argentina"],"raw_orcid":"https://orcid.org/0000-0001-9516-3985","affiliations":[{"raw_affiliation_string":"Consejo Nacional de Investigaciones Cient\u00edficas y T\u00e9cnicas\u2013Universidad de Buenos Aires, Instituto de Qu\u00edmica Biol\u00f3gica de la Facultad de Ciencias Exactas y Naturales, C1428EGA Buenos Aires, Argentina","institution_ids":["https://openalex.org/I151201029","https://openalex.org/I24354313"]},{"raw_affiliation_string":"Protein Physiology Lab, Facultad de Ciencias Exactas y Naturales, Departamento de Qu\u00edmica Biol\u00f3gica, Universidad de Buenos Aires, C1428EGA Buenos Aires, Argentina","institution_ids":["https://openalex.org/I24354313"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023018956","display_name":"Jacopo Marchi","orcid":"https://orcid.org/0000-0003-1192-1203","observed_orcids":["https://orcid.org/0000-0003-1192-1203"]},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I204730241","display_name":"Universit\u00e9 Paris Cit\u00e9","ror":"https://ror.org/05f82e368","country_code":"FR","type":"education","lineage":["https://openalex.org/I204730241"]},{"id":"https://openalex.org/I2746051580","display_name":"Universit\u00e9 Paris Sciences et Lettres","ror":"https://ror.org/013cjyk83","country_code":"FR","type":"education","lineage":["https://openalex.org/I2746051580"]},{"id":"https://openalex.org/I39804081","display_name":"Sorbonne Universit\u00e9","ror":"https://ror.org/02en5vm52","country_code":"FR","type":"education","lineage":["https://openalex.org/I39804081"]},{"id":"https://openalex.org/I4210129651","display_name":"Laboratoire de Physique de l'Ecole Normale Sup\u00e9rieure","ror":"https://ror.org/03a26mh11","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I204730241","https://openalex.org/I2746051580","https://openalex.org/I2800004676","https://openalex.org/I29607241","https://openalex.org/I39804081","https://openalex.org/I4210129651"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Jacopo Marchi","raw_affiliation_strings":["Laboratoire de Physique de l\u2019\u00c9cole Normale Sup\u00e9rieure, CNRS, Paris Sciences et Lettres University, Sorbonne Universit\u00e9, and Universit\u00e9 de Paris-Cit\u00e9, 75005 Paris, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratoire de Physique de l\u2019\u00c9cole Normale Sup\u00e9rieure, CNRS, Paris Sciences et Lettres University, Sorbonne Universit\u00e9, and Universit\u00e9 de Paris-Cit\u00e9, 75005 Paris, France","institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I204730241","https://openalex.org/I2746051580","https://openalex.org/I39804081","https://openalex.org/I4210129651"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064369206","display_name":"Thierry Mora","orcid":"https://orcid.org/0000-0002-5456-9361","observed_orcids":["https://orcid.org/0000-0002-5456-9361"]},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I204730241","display_name":"Universit\u00e9 Paris Cit\u00e9","ror":"https://ror.org/05f82e368","country_code":"FR","type":"education","lineage":["https://openalex.org/I204730241"]},{"id":"https://openalex.org/I2746051580","display_name":"Universit\u00e9 Paris Sciences et Lettres","ror":"https://ror.org/013cjyk83","country_code":"FR","type":"education","lineage":["https://openalex.org/I2746051580"]},{"id":"https://openalex.org/I39804081","display_name":"Sorbonne Universit\u00e9","ror":"https://ror.org/02en5vm52","country_code":"FR","type":"education","lineage":["https://openalex.org/I39804081"]},{"id":"https://openalex.org/I4210129651","display_name":"Laboratoire de Physique de l'Ecole Normale Sup\u00e9rieure","ror":"https://ror.org/03a26mh11","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I204730241","https://openalex.org/I2746051580","https://openalex.org/I2800004676","https://openalex.org/I29607241","https://openalex.org/I39804081","https://openalex.org/I4210129651"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Thierry Mora","raw_affiliation_strings":["Laboratoire de Physique de l\u2019\u00c9cole Normale Sup\u00e9rieure, CNRS, Paris Sciences et Lettres University, Sorbonne Universit\u00e9, and Universit\u00e9 de Paris-Cit\u00e9, 75005 Paris, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratoire de Physique de l\u2019\u00c9cole Normale Sup\u00e9rieure, CNRS, Paris Sciences et Lettres University, Sorbonne Universit\u00e9, and Universit\u00e9 de Paris-Cit\u00e9, 75005 Paris, France","institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I204730241","https://openalex.org/I2746051580","https://openalex.org/I39804081","https://openalex.org/I4210129651"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016850339","display_name":"Aleksandra M. Walczak","orcid":"https://orcid.org/0000-0002-2686-5702","observed_orcids":["https://orcid.org/0000-0002-2686-5702"]},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I204730241","display_name":"Universit\u00e9 Paris Cit\u00e9","ror":"https://ror.org/05f82e368","country_code":"FR","type":"education","lineage":["https://openalex.org/I204730241"]},{"id":"https://openalex.org/I2746051580","display_name":"Universit\u00e9 Paris Sciences et Lettres","ror":"https://ror.org/013cjyk83","country_code":"FR","type":"education","lineage":["https://openalex.org/I2746051580"]},{"id":"https://openalex.org/I39804081","display_name":"Sorbonne Universit\u00e9","ror":"https://ror.org/02en5vm52","country_code":"FR","type":"education","lineage":["https://openalex.org/I39804081"]},{"id":"https://openalex.org/I4210129651","display_name":"Laboratoire de Physique de l'Ecole Normale Sup\u00e9rieure","ror":"https://ror.org/03a26mh11","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I204730241","https://openalex.org/I2746051580","https://openalex.org/I2800004676","https://openalex.org/I29607241","https://openalex.org/I39804081","https://openalex.org/I4210129651"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Aleksandra M. Walczak","raw_affiliation_strings":["Laboratoire de Physique de l\u2019\u00c9cole Normale Sup\u00e9rieure, CNRS, Paris Sciences et Lettres University, Sorbonne Universit\u00e9, and Universit\u00e9 de Paris-Cit\u00e9, 75005 Paris, France"],"raw_orcid":"https://orcid.org/0000-0002-2686-5702","affiliations":[{"raw_affiliation_string":"Laboratoire de Physique de l\u2019\u00c9cole Normale Sup\u00e9rieure, CNRS, Paris Sciences et Lettres University, Sorbonne Universit\u00e9, and Universit\u00e9 de Paris-Cit\u00e9, 75005 Paris, France","institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I204730241","https://openalex.org/I2746051580","https://openalex.org/I39804081","https://openalex.org/I4210129651"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5026249041","display_name":"Diego Ulises Ferreiro","orcid":"https://orcid.org/0000-0002-7869-4247","observed_orcids":["https://orcid.org/0000-0002-7869-4247"]},"institutions":[{"id":"https://openalex.org/I151201029","display_name":"Consejo Nacional de Investigaciones Cient\u00edficas y T\u00e9cnicas","ror":"https://ror.org/03cqe8w59","country_code":"AR","type":"government","lineage":["https://openalex.org/I151201029","https://openalex.org/I4210123736","https://openalex.org/I4387155568"]},{"id":"https://openalex.org/I24354313","display_name":"Universidad de Buenos Aires","ror":"https://ror.org/0081fs513","country_code":"AR","type":"education","lineage":["https://openalex.org/I24354313"]}],"countries":["AR"],"is_corresponding":true,"raw_author_name":"Diego U. Ferreiro","raw_affiliation_strings":["Consejo Nacional de Investigaciones Cient\u00edficas y T\u00e9cnicas\u2013Universidad de Buenos Aires, Instituto de Qu\u00edmica Biol\u00f3gica de la Facultad de Ciencias Exactas y Naturales, C1428EGA Buenos Aires, Argentina","Protein Physiology Lab, Facultad de Ciencias Exactas y Naturales, Departamento de Qu\u00edmica Biol\u00f3gica, Universidad de Buenos Aires, C1428EGA Buenos Aires, Argentina"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Consejo Nacional de Investigaciones Cient\u00edficas y T\u00e9cnicas\u2013Universidad de Buenos Aires, Instituto de Qu\u00edmica Biol\u00f3gica de la Facultad de Ciencias Exactas y Naturales, C1428EGA Buenos Aires, Argentina","institution_ids":["https://openalex.org/I151201029","https://openalex.org/I24354313"]},{"raw_affiliation_string":"Protein Physiology Lab, Facultad de Ciencias Exactas y Naturales, Departamento de Qu\u00edmica Biol\u00f3gica, Universidad de Buenos Aires, C1428EGA Buenos Aires, Argentina","institution_ids":["https://openalex.org/I24354313"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5026249041"],"corresponding_institution_ids":["https://openalex.org/I151201029","https://openalex.org/I24354313"],"apc_list":null,"apc_paid":null,"fwci":1.7955,"has_fulltext":true,"cited_by_count":23,"citation_normalized_percentile":{"value":0.85981833,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"119","issue":"31","first_page":"e2204131119","last_page":"e2204131119"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9970999956130981,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9970999956130981,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.0012000000569969416,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11764","display_name":"Evolution and Genetic Dynamics","score":0.0003000000142492354,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/repeat-proteins","display_name":"repeat proteins","score":0.9879999756813049},{"id":"https://openalex.org/keywords/protein-folding","display_name":"protein folding","score":0.9240000247955322},{"id":"https://openalex.org/keywords/ankyrin-repeats","display_name":"ankyrin repeats","score":0.8130000233650208},{"id":"https://openalex.org/keywords/protein-evolution","display_name":"protein evolution","score":0.6140000224113464},{"id":"https://openalex.org/keywords/ising-model","display_name":"Ising model","score":0.8870000243186951},{"id":"https://openalex.org/keywords/folding-intermediates","display_name":"folding intermediates","score":0.5849999785423279},{"id":"https://openalex.org/keywords/cooperative-folding","display_name":"cooperative folding","score":0.699999988079071},{"id":"https://openalex.org/keywords/sequence-similarity","display_name":"sequence similarity","score":0.4059999883174896},{"id":"https://openalex.org/keywords/protein-stability","display_name":"protein stability","score":0.3490000069141388}],"concepts":[{"id":"https://openalex.org/C204328495","wikidata":"https://www.wikidata.org/wiki/Q847556","display_name":"Protein folding","level":2,"score":0.6015304327011108},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5325884819030762},{"id":"https://openalex.org/C2776545253","wikidata":"https://www.wikidata.org/wiki/Q5464292","display_name":"Folding (DSP implementation)","level":2,"score":0.45577147603034973},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.41140320897102356},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.34705761075019836},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.33318257331848145},{"id":"https://openalex.org/C95444343","wikidata":"https://www.wikidata.org/wiki/Q7141","display_name":"Cell biology","level":1,"score":0.24446836113929749},{"id":"https://openalex.org/C119599485","wikidata":"https://www.wikidata.org/wiki/Q43035","display_name":"Electrical engineering","level":1,"score":0.0},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017089","descriptor_name":"Ankyrin Repeat","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017510","descriptor_name":"Protein Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":6,"locations":[{"id":"doi:10.1073/pnas.2204131119","doi":"https://doi.org/10.1073/pnas.2204131119","is_oa":true,"landing_page_url":"https://doi.org/10.1073/pnas.2204131119","pdf_url":null,"source":{"id":"https://openalex.org/S125754415","display_name":"Proceedings of the National Academy of Sciences","issn_l":"0027-8424","issn":["0027-8424","1091-6490"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-class-a","anvur-scientific","cwts-core","dongbi-a","doyens","erih-plus","jufo-3","ki-jl-3","medline","norway-2","poland-200","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320052","host_organization_name":"National Academy of Sciences","host_organization_lineage":["https://openalex.org/P4310320052"],"host_organization_lineage_names":["National Academy of Sciences"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the National Academy of Sciences","raw_type":"journal-article"},{"id":"pmh:oai:pubmedcentral.nih.gov:9351489","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9351489","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proc Natl Acad Sci U S A","raw_type":"Text"},{"id":"pmid:35905321","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35905321","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the National Academy of Sciences of the United States of America","raw_type":"Journal Article"},{"id":"pmh:oai:arXiv.org:2202.12223","doi":null,"is_oa":true,"landing_page_url":"http://arxiv.org/abs/2202.12223","pdf_url":"https://arxiv.org/pdf/2202.12223","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},{"id":"pmh:oai:HAL:hal-03854601v1","doi":null,"is_oa":true,"landing_page_url":"https://hal.science/hal-03854601","pdf_url":"https://hal.science/hal-03854601v1/document","source":{"id":"https://openalex.org/S4306402512","display_name":"HAL","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I4405252976","host_organization_name":"Centre pour la Communication Scientifique Directe","host_organization_lineage":["https://openalex.org/I4405252976"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Proceedings of the National Academy of Sciences of the United States of America, 2022, 119 (31), pp.e2204131119. ⟨10.1073/pnas.2204131119⟩","raw_type":"info:eu-repo/semantics/article"},{"id":"doi:10.48550/arxiv.2202.12223","doi":"https://doi.org/10.48550/arxiv.2202.12223","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2202.12223","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article-journal"}],"best_oa_location":{"id":"doi:10.1073/pnas.2204131119","doi":"https://doi.org/10.1073/pnas.2204131119","is_oa":true,"landing_page_url":"https://doi.org/10.1073/pnas.2204131119","pdf_url":null,"source":{"id":"https://openalex.org/S125754415","display_name":"Proceedings of the National Academy of Sciences","issn_l":"0027-8424","issn":["0027-8424","1091-6490"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-class-a","anvur-scientific","cwts-core","dongbi-a","doyens","erih-plus","jufo-3","ki-jl-3","medline","norway-2","poland-200","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320052","host_organization_name":"National Academy of Sciences","host_organization_lineage":["https://openalex.org/P4310320052"],"host_organization_lineage_names":["National Academy of Sciences"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the National Academy of Sciences","raw_type":"journal-article"},"sustainable_development_goals":[],"sustainable_development_goals_aurora":[{"display_name":"Affordable and clean energy","score":0.8100000023841858,"id":"https://metadata.un.org/sdg/7"}],"study_designs":[],"awards":[{"id":"https://openalex.org/G871666106","display_name":"LIFE IS ELECTRIC. THE ELECTRONIC CIRCUITRY IS CATALYZED BY A SMALL SUBSET OF PROTEINS THAT FUNCTION AS SOPHISTICATED NANOMACHINES. CURRENTLY  VERY LITTLE IS KNOWN ABOUT THE ORIGIN OF PROTEINS ON EARTH AND THEIR EVOLUTION IN EARLY MICROBIAL LIFE. TO FILL THIS KNOWLEDGE GAP  THE ENIGMA RESEARCH PROGRAM WILL CARRY OUT EXPERIMENTAL  BIOINFORMATIC  DATA-DRIVEN ABDUCTIVE STUDIES TO EXPLORE THE ORIGIN OF CATALYSIS  THE EVOLUTION OF PROTEIN STRUCTURES IN MICROBIAL ANCESTORS  AND THE CO-EVOLUTION OF PROTEINS AND THE GEOSPHERE THROUGH GEOLOGIC TIME. ENIGMA HAS THREE INTEGRATED RESEARCH THEMES FOCUSED ON UNDERSTANDING THE EVOLUTION OF PROTEINS INVOLVED IN ELECTRON TRANSFER AND ENERGY GENERATION. THEME 1 WILL INVESTIGATE THE SYNTHESIS AND FUNCTION OF METALLOPROTEINS IN PREBIOTIC SYSTEMS. EXTANT MICROBIAL PROTEINS WILL BE ANALYZED TO IDENTIFY THE SIMPLEST STRUCTURES THAT CAN PERFORM ELECTRON TRANSFER REACTIONS. USING DE NOVO COMPUTATIONAL PROTEIN DESIGN  SMALL PEPTIDES WILL BE SYNTHESIZED AND CHARACTERIZED TO ELUCIDATE THE EARLIEST BIOCHEMICAL REACTIONS IN THE ORIGIN OF LIFE. THEME 2 WILL EXAMINE THE EMERGENT COMPLEXITY OF METALLOPROTEINS IN MICROBIAL ANCESTORS. NEW COMPUTATIONAL METHODS LINKING PROTEIN STRUCTURE AND PHYLOGENY WILL BE DEVELOPED TO STUDY THE EVOLUTION OF METAL BINDING LIGANDS IN PROTEINS. A STRUCTURAL ALIGNMENT-BASED HOMOLOGY APPROACH WILL BE USED TO IDENTIFY THE OLDEST STRUCTURES IN PROTEINS AND TO TRACE THE EARLY EVOLUTION OF METAL BINDING FOLDS. THEME 3 WILL EXPLORE THE CO-EVOLUTION OF PROTEINS AND THE GEOSPHERE. DEEP-TIME DATA ON THE NATURE AND DISTRIBUTION OF REDOX-SENSITIVE ELEMENTS IN ROCKS AND MINERALS WILL BE INTEGRATED WITH PROTEIN STRUCTURAL DATA IN THE PROTEIN DATA BANK. MINERALOGICAL DATA (E.G. MINERAL COMPOSITION  SOLUBILITY  AND AGE) WILL BE INCORPORATED INTO GEOCHEMICAL MODELS TO CONSTRAIN THE BIOAVAILABILITY OF METALS OVER GEOLOGIC TIME AND METAL BIOAVAILABILITY DURING ARCHEAN AND PROTEROZOIC ERAS WILL USED TO DATE SPECIFIC POSITIONS IN THE EVOLUTIONARY TREE CONSTRUCTED IN THEME 2. THE THREE ENIGMA RESEARCH THEMES ARE DIRECTLY RELEVANT TO THE MAJOR TOPICS  SYNTHESIS AND FUNCTION OF MACROMOLECULES IN THE ORIGIN OF LIFE    EARLY LIFE AND INCREASING COMPLEXITY  AND  CO-EVOLUTION OF LIFE AND THE PHYSICAL ENVIRONMENT  IDENTIFIED IN THE 2015 ASTROBIOLOGY SCIENCE STRATEGY. FURTHERMORE  THE ENIGMA PROGRAM COMPLEMENTS THE NAI CAN 7 TEAMS ON EXPERIMENTAL MICROBIAL GENOMICS (GEORGIA TECH) AND LIFE ON A DYNAMIC EARLY EARTH (UC RIVERSIDE). THE RESULTS OF THE ENIGMA RESEARCH PROGRAM WILL HELP THE NAI ANSWER A CENTRAL QUESTION IN ASTROBIOLOGY: HOW DID PROTEINS EVOLVE TO BECOME THE CATALYSTS OF LIFE ON EARTH?","funder_award_id":"80NSSC18M0093","funder_id":"https://openalex.org/F4320306101","funder_display_name":"National Aeronautics and Space Administration"}],"funders":[{"id":"https://openalex.org/F4320306101","display_name":"National Aeronautics and Space Administration","ror":"https://ror.org/027ka1x80"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":53,"referenced_works":["https://openalex.org/W24553703","https://openalex.org/W1537712541","https://openalex.org/W1861406683","https://openalex.org/W1966159203","https://openalex.org/W1972486808","https://openalex.org/W1978365676","https://openalex.org/W1979762151","https://openalex.org/W1991443411","https://openalex.org/W1992827895","https://openalex.org/W1997828975","https://openalex.org/W1999894788","https://openalex.org/W2008545402","https://openalex.org/W2009644062","https://openalex.org/W2014461019","https://openalex.org/W2024257845","https://openalex.org/W2030100088","https://openalex.org/W2055382743","https://openalex.org/W2060619683","https://openalex.org/W2065884669","https://openalex.org/W2070582998","https://openalex.org/W2084679948","https://openalex.org/W2087786915","https://openalex.org/W2094799958","https://openalex.org/W2105888864","https://openalex.org/W2115858100","https://openalex.org/W2117724788","https://openalex.org/W2126189887","https://openalex.org/W2128925969","https://openalex.org/W2139859483","https://openalex.org/W2141171773","https://openalex.org/W2144729032","https://openalex.org/W2155531787","https://openalex.org/W2161332101","https://openalex.org/W2164148522","https://openalex.org/W2170869273","https://openalex.org/W2205148961","https://openalex.org/W2258593748","https://openalex.org/W2416642098","https://openalex.org/W2526034046","https://openalex.org/W2607008053","https://openalex.org/W2762365522","https://openalex.org/W2775582576","https://openalex.org/W2792977793","https://openalex.org/W2941849126","https://openalex.org/W3009854264","https://openalex.org/W3037466057","https://openalex.org/W3044778276","https://openalex.org/W3107404305","https://openalex.org/W3129436609","https://openalex.org/W3167891224","https://openalex.org/W3177828909","https://openalex.org/W3200310457","https://openalex.org/W4288700708"],"related_works":["https://openalex.org/W2055382743","https://openalex.org/W61275590","https://openalex.org/W3129436609","https://openalex.org/W1978365676","https://openalex.org/W2008494223","https://openalex.org/W4411678969","https://openalex.org/W2149647521","https://openalex.org/W7099539674","https://openalex.org/W2273837001","https://openalex.org/W2164148522"],"abstract_inverted_index":{"Repeat":[0],"proteins":[1,18,146],"are":[2,102,126,155,161,183,190],"made":[3],"with":[4,77,129,165],"tandem":[5],"copies":[6],"of":[7,60,62,72,82,86,93,114,122,140,142,152,209],"similar":[8],"amino":[9],"acid":[10],"stretches":[11],"that":[12,109,125,149,203],"fold":[13],"into":[14],"elongated":[15],"architectures.":[16],"These":[17,100],"constitute":[19],"excellent":[20],"model":[21,49,66,81,108],"systems":[22],"to":[23,28,38,46,56,88,104],"investigate":[24,57],"how":[25],"evolution":[26],"relates":[27],"structure,":[29],"folding,":[30],"and":[31,53,84,120,147,169,185,197,207],"function.":[32],"Here,":[33],"we":[34,194],"propose":[35],"a":[36,47,70,150],"scheme":[37,76],"map":[39],"evolutionary":[40,91],"information":[41],"at":[42,96],"the":[43,58,67,90,94,97,112,138,181,186,204,210],"sequence":[44,218],"level":[45],"coarse-grained":[48],"for":[50,111,163],"repeat-protein":[51],"folding":[52,59,115,139,153,178,199],"use":[54],"it":[55],"thousands":[61,141],"repeat":[63,145],"proteins.":[64],"We":[65,136,201],"energetics":[68],"by":[69],"combination":[71],"an":[73,78,106],"inverse":[74],"Potts-model":[75],"explicit":[79],"mechanistic":[80],"duplications":[83],"deletions":[85],"repeats":[87],"calculate":[89],"parameters":[92,101],"system":[95],"single-residue":[98],"level.":[99],"used":[103],"inform":[105],"Ising-like":[107],"allows":[110],"generation":[113],"curves,":[116],"apparent":[117],"domain":[118],"emergence,":[119],"occupation":[121],"intermediate":[123],"states":[124],"highly":[127],"compatible":[128],"experimental":[130],"data":[131],"in":[132],"specific":[133],"case":[134],"studies.":[135],"analyzed":[137],"natural":[143],"Ankyrin":[144],"found":[148],"multiplicity":[151],"mechanisms":[154],"possible.":[156],"Fully":[157],"cooperative":[158],"all-or-none":[159],"transitions":[160],"obtained":[162],"arrays":[164,212],"enough":[166],"sequence-similar":[167],"elements":[168,182],"strong":[170],"interactions":[171,187],"between":[172,188],"them,":[173],"while":[174],"noncooperative":[175],"element-by-element":[176],"intermittent":[177],"arose":[179],"if":[180],"dissimilar":[184],"them":[189],"energetically":[191],"weak.":[192],"Additionally,":[193],"characterized":[195],"nucleation-propagation":[196],"multidomain":[198],"mechanisms.":[200],"show":[202],"global":[205],"stability":[206],"cooperativity":[208],"repeating":[211],"can":[213],"be":[214],"predicted":[215],"from":[216],"simple":[217],"scores.":[219]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":9},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":8}],"updated_date":"2026-10-31T12:09:11.096373","created_date":"2022-07-30T00:00:00"}