{"id":{"repo_id":"umkc","oai_identifier":"oai:mospace.umsystem.edu:10355/61496"},"canonical_url":"https://search.dev.ndltd.org/etd/umkc/oai:mospace.umsystem.edu:10355/61496","repository":{"repo_id":"umkc","name":"University of Missouri - Kansas City","base_url":"https://mospace.umsystem.edu/oai/request"},"display":{"title":"Hyper-Plastic Structural Evolution Of The PEX Domain - A Model Of Evolutionary Exaptation And Neofunctionalization At The Molecular Level","abstract":"With the advent of sophisticated genetic, biophysical and in silico technology an enormous amount of information is being generated regarding the structural, biochemical and physiological aspects of proteins. Tertiary protein structural domains are assumed to be features of proteins whose bio-historical relationships can be traceable over relevant evolutionary space. The phylogenetics of protein domains, including their genesis, duplication, combination, selectively derived loss and potential horizontal capture to derive novel functional rearrangements, are of great interest to molecular evolutionists. Evolutionary and bioinformatic analyses of a considerable collection of variable protein primary, secondary, tertiary, quaternary and biochemical structures has established the principle that, from a functional perspective, many, if not most, proteins are evolutionarily dependent on the functional capacity of readily defined and identifiable, globular components defined as \"domains\". Therefore, it is reasonable to infer that specific secondary and tertiary folds, or arrangements, represent functional phenotypic characters that can be analyzed to provide insights into the evolutionary history of any given protein domain. The evolution of proteins, at the domain level, has a significant impact on the overall functionality of metabolic pathways in general. Therefore, insights into the evolutionary trajectories of protein domains have the potential to inform the understanding of every aspect in which any given protein has a role of functional significance including, but certainly not limited to basic metabolic equilibrium, potential physical compromise at the phenotypic level, and deeper insights into corruptions that often lead to metabolic dysfunction and potential progression to full blown disease states. The prime focus of this study is to investigate the evolutionary relationships of proteins, across all Kingdoms of life, that contain within their tertiary phenotypic structure the 4-bladed β-propeller domain (the \"Hemopexin\" or \"PEX\" domain), towards illuminating the biophysical and biochemical significance of this specific domain's impact on protein functionality. While the phylogenetic relationships of entire proteins that have PEX domains is relatively straight forward, the mutational accumulation in gene sequences that lead to the tertiary structure of the PEX domain itself seems to have partially, if not entirely, obscured the evolutionary history at the domain level. The phylogenetic analyses presented here allow for several novel conclusions. First, this research demonstrates that a derived primary amino acid sequence in mammalian Hemopexin proteins (the JEN-14 epitope) represents a functional synapomorphy at the molecular level. Secondly, that there is substantial evidence for horizontal gene transfer of PEX domain proteins into specific Fungi. Additionally, there are no proteins containing a PEX domain in Kingdom Archaea. Lastly, it argues that the PEX domain itself represents an evolutionary “spandrel” (sensu Gould and Lewontin) with specifically derived functions existing around a core, preserved structural architecture.","abstract_html":"With the advent of sophisticated genetic, biophysical and in silico technology an enormous amount of information is being generated regarding the structural, biochemical and physiological aspects of proteins. Tertiary protein structural domains are assumed to be features of proteins whose bio-historical relationships can be traceable over relevant evolutionary space. The phylogenetics of protein domains, including their genesis, duplication, combination, selectively derived loss and potential horizontal capture to derive novel functional rearrangements, are of great interest to molecular evolutionists. Evolutionary and bioinformatic analyses of a considerable collection of variable protein primary, secondary, tertiary, quaternary and biochemical structures has established the principle that, from a functional perspective, many, if not most, proteins are evolutionarily dependent on the functional capacity of readily defined and identifiable, globular components defined as "domains". Therefore, it is reasonable to infer that specific secondary and tertiary folds, or arrangements, represent functional phenotypic characters that can be analyzed to provide insights into the evolutionary history of any given protein domain. The evolution of proteins, at the domain level, has a significant impact on the overall functionality of metabolic pathways in general. Therefore, insights into the evolutionary trajectories of protein domains have the potential to inform the understanding of every aspect in which any given protein has a role of functional significance including, but certainly not limited to basic metabolic equilibrium, potential physical compromise at the phenotypic level, and deeper insights into corruptions that often lead to metabolic dysfunction and potential progression to full blown disease states. The prime focus of this study is to investigate the evolutionary relationships of proteins, across all Kingdoms of life, that contain within their tertiary phenotypic structure the 4-bladed β-propeller domain (the "Hemopexin" or "PEX" domain), towards illuminating the biophysical and biochemical significance of this specific domain's impact on protein functionality. While the phylogenetic relationships of entire proteins that have PEX domains is relatively straight forward, the mutational accumulation in gene sequences that lead to the tertiary structure of the PEX domain itself seems to have partially, if not entirely, obscured the evolutionary history at the domain level. The phylogenetic analyses presented here allow for several novel conclusions. First, this research demonstrates that a derived primary amino acid sequence in mammalian Hemopexin proteins (the JEN-14 epitope) represents a functional synapomorphy at the molecular level. Secondly, that there is substantial evidence for horizontal gene transfer of PEX domain proteins into specific Fungi. Additionally, there are no proteins containing a PEX domain in Kingdom Archaea. Lastly, it argues that the PEX domain itself represents an evolutionary “spandrel” (sensu Gould and Lewontin) with specifically derived functions existing around a core, preserved structural architecture.","abstract_has_math":false,"creators":["Likins, Lee"],"institution":"University of Missouri--Kansas City","degree_name":"Ph.D.","degree_level":"Doctoral","degree_discipline":"Molecular Biology and Biochemistry (UMKC)","degree_department":null,"school":null,"contributors":[],"advisors":["Wyckoff, Gerald J."],"committee_chairs":[],"committee_members":[],"year":2017,"date_issued":"2017","date_published":"2017","updated_at":"2026-07-24T05:17:10Z","subjects":[],"languages":["en_US"],"rights":[],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"https://hdl.handle.net/10355/61496","outbound_label":"Handle","outbound_source":"dc:identifier.uri"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor.advisor","label":"Advisor","values":["Wyckoff, Gerald J."]},{"key":"dc:creator","label":"Author","values":["Likins, Lee"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date.accessioned","label":"Dc Date Accessioned","values":["2017-09-05T13:55:06Z"]},{"key":"dc:date.available","label":"Dc Date Available","values":["2017-09-05T13:55:06Z"]},{"key":"dc:date.issued","label":"Date","values":["2017"]},{"key":"dc:publisher","label":"Institution","values":["University of Missouri--Kansas City"]},{"key":"dc:type","label":"Dc Type","values":["Thesis"]},{"key":"thesis:degree_discipline","label":"Discipline","values":["Molecular Biology and Biochemistry (UMKC)","Cell Biology and Biophysics (UMKC)"]},{"key":"thesis:degree_level","label":"Degree Level","values":["Doctoral"]},{"key":"thesis:degree_name","label":"Degree Name","values":["Ph.D."]},{"key":"thesis:institution_name","label":"Thesis Institution Name","values":["University of Missouri--Kansas City"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language.iso","label":"Language (ISO)","values":["en_US"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier.uri","label":"Identifier URI","values":["https://hdl.handle.net/10355/61496"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description","label":"Description","values":["Title from PDF of title page viewed august 6, 2017","Dissertation advisor: Gerald J. Wyckoff","Vita","Includes bibliographical references (pages 132-150)","Thesis (Ph.D.)--School of Biological Sciences. University of Missouri--Kansas City, 2017"]},{"key":"dc:description.abstract","label":"Abstract","values":["With the advent of sophisticated genetic, biophysical and in silico technology an enormous amount of information is being generated regarding the structural, biochemical and physiological aspects of proteins. Tertiary protein structural domains are assumed to be features of proteins whose bio-historical relationships can be traceable over relevant evolutionary space. The phylogenetics of protein domains, including their genesis, duplication, combination, selectively derived loss and potential horizontal capture to derive novel functional rearrangements, are of great interest to molecular evolutionists. Evolutionary and bioinformatic analyses of a considerable collection of variable protein primary, secondary, tertiary, quaternary and biochemical structures has established the principle that, from a functional perspective, many, if not most, proteins are evolutionarily dependent on the functional capacity of readily defined and identifiable, globular components defined as \"domains\". Therefore, it is reasonable to infer that specific secondary and tertiary folds, or arrangements, represent functional phenotypic characters that can be analyzed to provide insights into the evolutionary history of any given protein domain. The evolution of proteins, at the domain level, has a significant impact on the overall functionality of metabolic pathways in general. Therefore, insights into the evolutionary trajectories of protein domains have the potential to inform the understanding of every aspect in which any given protein has a role of functional significance including, but certainly not limited to basic metabolic equilibrium, potential physical compromise at the phenotypic level, and deeper insights into corruptions that often lead to metabolic dysfunction and potential progression to full blown disease states. The prime focus of this study is to investigate the evolutionary relationships of proteins, across all Kingdoms of life, that contain within their tertiary phenotypic structure the 4-bladed β-propeller domain (the \"Hemopexin\" or \"PEX\" domain), towards illuminating the biophysical and biochemical significance of this specific domain's impact on protein functionality. While the phylogenetic relationships of entire proteins that have PEX domains is relatively straight forward, the mutational accumulation in gene sequences that lead to the tertiary structure of the PEX domain itself seems to have partially, if not entirely, obscured the evolutionary history at the domain level. The phylogenetic analyses presented here allow for several novel conclusions. First, this research demonstrates that a derived primary amino acid sequence in mammalian Hemopexin proteins (the JEN-14 epitope) represents a functional synapomorphy at the molecular level. Secondly, that there is substantial evidence for horizontal gene transfer of PEX domain proteins into specific Fungi. Additionally, there are no proteins containing a PEX domain in Kingdom Archaea. Lastly, it argues that the PEX domain itself represents an evolutionary “spandrel” (sensu Gould and Lewontin) with specifically derived functions existing around a core, preserved structural architecture."]},{"key":"dc:title","label":"Title","values":["Hyper-Plastic Structural Evolution Of The PEX Domain - A Model Of Evolutionary Exaptation And Neofunctionalization At The Molecular Level"]}]}],"canonical_facts":{"dc:contributor.advisor":["Wyckoff, Gerald J."],"dc:creator":["Likins, Lee"],"dc:date.accessioned":["2017-09-05T13:55:06Z"],"dc:date.available":["2017-09-05T13:55:06Z"],"dc:date.issued":["2017"],"dc:description":["Title from PDF of title page viewed august 6, 2017","Dissertation advisor: Gerald J. Wyckoff","Vita","Includes bibliographical references (pages 132-150)","Thesis (Ph.D.)--School of Biological Sciences. University of Missouri--Kansas City, 2017"],"dc:description.abstract":["With the advent of sophisticated genetic, biophysical and in silico technology an enormous amount of information is being generated regarding the structural, biochemical and physiological aspects of proteins. Tertiary protein structural domains are assumed to be features of proteins whose bio-historical relationships can be traceable over relevant evolutionary space. The phylogenetics of protein domains, including their genesis, duplication, combination, selectively derived loss and potential horizontal capture to derive novel functional rearrangements, are of great interest to molecular evolutionists. Evolutionary and bioinformatic analyses of a considerable collection of variable protein primary, secondary, tertiary, quaternary and biochemical structures has established the principle that, from a functional perspective, many, if not most, proteins are evolutionarily dependent on the functional capacity of readily defined and identifiable, globular components defined as \"domains\". Therefore, it is reasonable to infer that specific secondary and tertiary folds, or arrangements, represent functional phenotypic characters that can be analyzed to provide insights into the evolutionary history of any given protein domain. The evolution of proteins, at the domain level, has a significant impact on the overall functionality of metabolic pathways in general. Therefore, insights into the evolutionary trajectories of protein domains have the potential to inform the understanding of every aspect in which any given protein has a role of functional significance including, but certainly not limited to basic metabolic equilibrium, potential physical compromise at the phenotypic level, and deeper insights into corruptions that often lead to metabolic dysfunction and potential progression to full blown disease states. The prime focus of this study is to investigate the evolutionary relationships of proteins, across all Kingdoms of life, that contain within their tertiary phenotypic structure the 4-bladed β-propeller domain (the \"Hemopexin\" or \"PEX\" domain), towards illuminating the biophysical and biochemical significance of this specific domain's impact on protein functionality. While the phylogenetic relationships of entire proteins that have PEX domains is relatively straight forward, the mutational accumulation in gene sequences that lead to the tertiary structure of the PEX domain itself seems to have partially, if not entirely, obscured the evolutionary history at the domain level. The phylogenetic analyses presented here allow for several novel conclusions. First, this research demonstrates that a derived primary amino acid sequence in mammalian Hemopexin proteins (the JEN-14 epitope) represents a functional synapomorphy at the molecular level. Secondly, that there is substantial evidence for horizontal gene transfer of PEX domain proteins into specific Fungi. Additionally, there are no proteins containing a PEX domain in Kingdom Archaea. Lastly, it argues that the PEX domain itself represents an evolutionary “spandrel” (sensu Gould and Lewontin) with specifically derived functions existing around a core, preserved structural architecture."],"dc:identifier.uri":["https://hdl.handle.net/10355/61496"],"dc:language.iso":["en_US"],"dc:publisher":["University of Missouri--Kansas City"],"dc:title":["Hyper-Plastic Structural Evolution Of The PEX Domain - A Model Of Evolutionary Exaptation And Neofunctionalization At The Molecular Level"],"dc:type":["Thesis"],"thesis:degree_discipline":["Molecular Biology and Biochemistry (UMKC)","Cell Biology and Biophysics (UMKC)"],"thesis:degree_level":["Doctoral"],"thesis:degree_name":["Ph.D."],"thesis:institution_name":["University of Missouri--Kansas City"]},"updated_at":"2026-07-24T05:17:10Z"}