{"id":{"repo_id":"iupui","oai_identifier":"oai:scholarworks.indianapolis.iu.edu:1805/2261"},"canonical_url":"https://search.dev.ndltd.org/etd/iupui/oai:scholarworks.indianapolis.iu.edu:1805/2261","repository":{"repo_id":"iupui","name":"IUPUI","base_url":"https://scholarworks.indianapolis.iu.edu/server/oai/request"},"display":{"title":"Intrinsic Disorder and Protein Evolution: Amino Acid Composition of Proteins in Last Universal Ancestor","abstract":"All twenty amino acids did not appear simultaneously in nature. Instead some of them appeared early, while others were added into the genetic code later. The amino acids that were formed by Miller (1953) are suggested to have appeared early in evolutionary history, and the amino acids associated with codon capture developed late in the course of evolution. The chronological order of appearance of the amino acids proposed by Trifonov (2000) was G/A, V/D, P, S, E/L, T, R, N, K, Q, I, C, H, F, M, Y, W. According to Romero et al. (1997) amino acids G, D, E, P and S are disorder-promoting residues and C, F, W and Y are order-promoting residues this means that the early or the ancient amino acids were disorder promoting and the order promoting residues came late into the genetic code. These observations led to the hypothesis that the first proteins, which were comprised of the early amino acids only, were disordered, and, furthermore, that the appearance of the late amino acids and the appearance of the structural proteins were concurrent. Software developed by Brooks et al. (2004) to find the amino acid composition of the LUA (Last Universal Ancestor) was used to test this hypothesis. For this work, the Clusters of Orhtologous Groups of proteins (65 COGs) were split into enzymes and non-enzymes. It was found that intrinsic disorder was abundant in both the groups of proteins, with non enzymes being much more disorder than enzymes. Further analysis was done to check for the frequency of the modern amino acids C, F, W, and Y in the Protein data bank (PDB) and Swissprot.","abstract_html":"All twenty amino acids did not appear simultaneously in nature. Instead some of them appeared early, while others were added into the genetic code later. The amino acids that were formed by Miller (1953) are suggested to have appeared early in evolutionary history, and the amino acids associated with codon capture developed late in the course of evolution. The chronological order of appearance of the amino acids proposed by Trifonov (2000) was G/A, V/D, P, S, E/L, T, R, N, K, Q, I, C, H, F, M, Y, W. According to Romero et al. (1997) amino acids G, D, E, P and S are disorder-promoting residues and C, F, W and Y are order-promoting residues this means that the early or the ancient amino acids were disorder promoting and the order promoting residues came late into the genetic code. These observations led to the hypothesis that the first proteins, which were comprised of the early amino acids only, were disordered, and, furthermore, that the appearance of the late amino acids and the appearance of the structural proteins were concurrent. Software developed by Brooks et al. (2004) to find the amino acid composition of the LUA (Last Universal Ancestor) was used to test this hypothesis. For this work, the Clusters of Orhtologous Groups of proteins (65 COGs) were split into enzymes and non-enzymes. It was found that intrinsic disorder was abundant in both the groups of proteins, with non enzymes being much more disorder than enzymes. Further analysis was done to check for the frequency of the modern amino acids C, F, W, and Y in the Protein data bank (PDB) and Swissprot.","abstract_has_math":false,"creators":["Karne, Sai Harish Babu"],"institution":null,"degree_name":null,"degree_level":null,"degree_discipline":null,"degree_department":null,"school":null,"contributors":[],"advisors":["Romero, Pedro"],"committee_chairs":[],"committee_members":[],"year":null,"date_issued":"","date_published":null,"updated_at":"2026-07-24T02:40:57Z","subjects":["Amino Acid Composition","Protein Evolution","Intrinsic Disorder"],"languages":["en"],"rights":[],"rights_urls":[],"identifier_entries":[{"key":"dc:identifier.uri","label":"Identifier URI","values":["http://dx.doi.org/10.7912/C2/863"],"render_values":[{"text":"http://dx.doi.org/10.7912/C2/863","href":"http://dx.doi.org/10.7912/C2/863","code":true}]}]},"links":{"outbound_url":"https://hdl.handle.net/1805/2261","outbound_label":"Handle","outbound_source":"dc:identifier.uri"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor.advisor","label":"Advisor","values":["Romero, Pedro"]},{"key":"dc:creator","label":"Author","values":["Karne, Sai Harish Babu"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date.accessioned","label":"Dc Date Accessioned","values":["2010-09-29T18:52:40Z"]},{"key":"dc:date.available","label":"Dc Date Available","values":["2010-09-29T18:52:40Z"]},{"key":"dc:type","label":"Dc Type","values":["Thesis"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["Amino Acid Composition","Protein Evolution","Intrinsic Disorder"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language.iso","label":"Language (ISO)","values":["en"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier.uri","label":"Identifier URI","values":["https://hdl.handle.net/1805/2261","http://dx.doi.org/10.7912/C2/863"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description.abstract","label":"Abstract","values":["All twenty amino acids did not appear simultaneously in nature. Instead some of them appeared early, while others were added into the genetic code later. The amino acids that were formed by Miller (1953) are suggested to have appeared early in evolutionary history, and the amino acids associated with codon capture developed late in the course of evolution. The chronological order of appearance of the amino acids proposed by Trifonov (2000) was G/A, V/D, P, S, E/L, T, R, N, K, Q, I, C, H, F, M, Y, W. According to Romero et al. (1997) amino acids G, D, E, P and S are disorder-promoting residues and C, F, W and Y are order-promoting residues this means that the early or the ancient amino acids were disorder promoting and the order promoting residues came late into the genetic code. These observations led to the hypothesis that the first proteins, which were comprised of the early amino acids only, were disordered, and, furthermore, that the appearance of the late amino acids and the appearance of the structural proteins were concurrent. Software developed by Brooks et al. (2004) to find the amino acid composition of the LUA (Last Universal Ancestor) was used to test this hypothesis. For this work, the Clusters of Orhtologous Groups of proteins (65 COGs) were split into enzymes and non-enzymes. It was found that intrinsic disorder was abundant in both the groups of proteins, with non enzymes being much more disorder than enzymes. Further analysis was done to check for the frequency of the modern amino acids C, F, W, and Y in the Protein data bank (PDB) and Swissprot."]},{"key":"dc:title","label":"Title","values":["Intrinsic Disorder and Protein Evolution: Amino Acid Composition of Proteins in Last Universal Ancestor"]}]}],"canonical_facts":{"dc:contributor.advisor":["Romero, Pedro"],"dc:creator":["Karne, Sai Harish Babu"],"dc:date.accessioned":["2010-09-29T18:52:40Z"],"dc:date.available":["2010-09-29T18:52:40Z"],"dc:description.abstract":["All twenty amino acids did not appear simultaneously in nature. Instead some of them appeared early, while others were added into the genetic code later. The amino acids that were formed by Miller (1953) are suggested to have appeared early in evolutionary history, and the amino acids associated with codon capture developed late in the course of evolution. The chronological order of appearance of the amino acids proposed by Trifonov (2000) was G/A, V/D, P, S, E/L, T, R, N, K, Q, I, C, H, F, M, Y, W. According to Romero et al. (1997) amino acids G, D, E, P and S are disorder-promoting residues and C, F, W and Y are order-promoting residues this means that the early or the ancient amino acids were disorder promoting and the order promoting residues came late into the genetic code. These observations led to the hypothesis that the first proteins, which were comprised of the early amino acids only, were disordered, and, furthermore, that the appearance of the late amino acids and the appearance of the structural proteins were concurrent. Software developed by Brooks et al. (2004) to find the amino acid composition of the LUA (Last Universal Ancestor) was used to test this hypothesis. For this work, the Clusters of Orhtologous Groups of proteins (65 COGs) were split into enzymes and non-enzymes. It was found that intrinsic disorder was abundant in both the groups of proteins, with non enzymes being much more disorder than enzymes. Further analysis was done to check for the frequency of the modern amino acids C, F, W, and Y in the Protein data bank (PDB) and Swissprot."],"dc:identifier.uri":["https://hdl.handle.net/1805/2261","http://dx.doi.org/10.7912/C2/863"],"dc:language.iso":["en"],"dc:subject":["Amino Acid Composition","Protein Evolution","Intrinsic Disorder"],"dc:title":["Intrinsic Disorder and Protein Evolution: Amino Acid Composition of Proteins in Last Universal Ancestor"],"dc:type":["Thesis"]},"updated_at":"2026-07-24T02:40:57Z"}