The Experts below are selected from a list of 312 Experts worldwide ranked by ideXlab platform
Hidekazu Hiroaki - One of the best experts on this subject based on the ideXlab platform.
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ideal intrinsically disordered proteins with extensive annotations and literature
Nucleic Acids Research, 2012Co-Authors: Satoshi Fukuchi, Shigetaka Sakamoto, Yukiko Nobe, Takayuki Amemiya, Ryotaro Koike, Kazuo Hosoda, Seiko D Murakami, Hidekazu HiroakiAbstract:ABSTRACTIDEAL, Intrinsically Disordered proteins withExtensive Annotations and Literature (http://www.ideal.force.cs.is.nagoya-u.ac.jp/IDEAL/), is a collec-tion of knowledge on experimentally verified intrin-sically disordered proteins. IDEAL contains manualannotations by curators on intrinsically disorderedregions, interaction regions to other molecules,post-translational modification sites, references andstructural domain assignments. In particular, IDEALexplicitly describes protean segments that can betransformed from a disordered state to an orderedstate. Since in most cases they can act as molecularrecognition elements upon binding of partner pro-teins, IDEAL provides a data resource for functionalregions of intrinsically disordered proteins. Theinformation in IDEAL is provided on a user-friendlygraphical view and in a computer-friendly XMLformat.INTRODUCTIONThe discovery of intrinsically disordered proteins (IDPs)hasbroughtaboutaparadigmchangeinstructuralbiology(1,2). Although proteins were believed to adopt unique 3Dstructures to function, IDPs do not, by themselves, assumeany stable 3D structure under physiological conditions,andyet they participate incrucial biological processes suchas signal transduction and transcription control (3–5).Some proteins contain long intrinsically disorderedregions (IDRs) while others are fully disordered. Incontrast to the long studied 3D structures of proteins, in-vestigations on IDPs started only about 10 years ago and,as yet, knowledge of IDPs is not well collected andintegrated. Although the first database of IDPs, Disprot(6), has more than 600 well-annotated entries, this numberis much smaller than the over 70 thousands entries in theProtein Data Bank (PDB) (7). Considering that theprotein 3D structural databases such as PDB, SCOP(Structural Classification of Proteins) (8) and CATH (9),have played important roles in deepening our understand-ing of the nature of protein structures and functions, thedevelopment of IDP databases are essential to theprogress of IDP research.We have developed a database, IDEAL (IDPs withExtensive Annotations and Literature) in which experi-mentally verified IDRs are collected. In the database con-struction process, we paid special attention to thefunctional regions in IDRs, for example, regions thatinteract with other molecules and post-translational modi-fication sites. In particular, we have extensively curatedIDRs that adopt unique 3D structures when they bindto other molecules by the ‘coupled folding and binding’process (10–16). We have called these IDRs the Proteansegments (ProS). The information in IDEAL is providedon a user-friendly web-interface and in computer-friendlyXML files.CONTENTS OF IDEALSummary of the annotation processWe used the UniProt amino acid sequence (17) as the ref-erence, and marked structural and functional featuresalong the sequences. A unique serial identifier, IID(IDEAL Identification), was assigned to each protein inIDEAL, starting with IID0001 for human proteins,IID5001 for other eukaryotic proteins and IID9001 forall other proteins including virus proteins. Ordered anddisordered regions were annotated as follows: First,ordered regions were obtained from the structuralregions atomically detailed in the PDB. Then, disordered
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IDEAL: Intrinsically Disordered proteins with Extensive Annotations and Literature.
Nucleic acids research, 2011Co-Authors: Satoshi Fukuchi, Shigetaka Sakamoto, Yukiko Nobe, Takayuki Amemiya, Ryotaro Koike, Kazuo Hosoda, Seiko D Murakami, Hidekazu HiroakiAbstract:IDEAL, Intrinsically Disordered proteins with Extensive Annotations and Literature (http://www.ideal.force.cs.is.nagoya-u.ac.jp/IDEAL/), is a collection of knowledge on experimentally verified intrinsically disordered proteins. IDEAL contains manual annotations by curators on intrinsically disordered regions, interaction regions to other molecules, post-translational modification sites, references and structural domain assignments. In particular, IDEAL explicitly describes protean segments that can be transformed from a disordered state to an ordered state. Since in most cases they can act as molecular recognition elements upon binding of partner proteins, IDEAL provides a data resource for functional regions of intrinsically disordered proteins. The information in IDEAL is provided on a user-friendly graphical view and in a computer-friendly XML format.
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IDEAL: Intrinsically Disordered proteins with Extensive Annotations and Literature.
Nucleic acids research, 2011Co-Authors: Satoshi Fukuchi, Shigetaka Sakamoto, Yukiko Nobe, Takayuki Amemiya, Ryotaro Koike, Kazuo Hosoda, Seiko D Murakami, Hidekazu HiroakiAbstract:IDEAL, Intrinsically Disordered proteins with Extensive Annotations and Literature (http://www.ideal.force.cs.is.nagoya-u.ac.jp/IDEAL/), is a collection of knowledge on experimentally verified intrinsically disordered proteins. IDEAL contains manual annotations by curators on intrinsically disordered regions, interaction regions to other molecules, post-translational modification sites, references and structural domain assignments. In particular, IDEAL explicitly describes protean segments that can be transformed from a disordered state to an ordered state. Since in most cases they can act as molecular recognition elements upon binding of partner proteins, IDEAL provides a data resource for functional regions of intrinsically disordered proteins. The information in IDEAL is provided on a user-friendly graphical view and in a computer-friendly XML format.
Franziska Endriß - One of the best experts on this subject based on the ideXlab platform.
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Energy-coupled outer membrane transport proteins and regulatory proteins
BioMetals, 2007Co-Authors: Volkmar Braun, Franziska EndrißAbstract:FhuA and FecA are two examples of energy-coupled outer membrane import proteins of gram-negative bacteria. FhuA transports iron complexed by the siderophore ferrichrome and serves as a receptor for phages, a toxic bacterial peptide, and a toxic protein. FecA transports diferric dicitrate and regulates transcription of an operon encoding five ferric citrate (Fec) transport genes. Properties of FhuA mutants selected according to the FhuA crystal structure are described. FhuA mutants in the TonB box, the hatch, and the β-barrel are rather robust. TonB box mutants in FhuA FecA, FepA, Cir, and BtuB are compared; some mutations are suppressed by mutations in TonB. Mutant studies have not revealed a ferrichrome diffusion pathway, and tolerance to mutations in the region linking the TonB box to the hatch does not disclose a mechanism for how energy transfer from the cytoplasmic membrane to FhuA changes the conformation of FhuA such that bound substrates are released, the pore is opened, and substrates enter the periplasm, or how surface loops change their conformation such that TonB-dependent phages bind irreversibly and release their DNA into the cells. The FhuA and FecA crystal structures do not disclose the mechanism of these proteins, but they provide important information for specific functional studies. FecA is also a regulatory protein that transduces a signal from the cell surface into the cytoplasm. The interacting subdomains of the proteins in the FecA → FecR → FecI → RNA polymerase signal transduction pathway resulting in fecABCDE transcription have been determined. Energy-coupled transporters transport not only iron and vitamin B_12, but also other substrates of very low abundance such as sugars across the outer membrane; transcription regulation of the transport genes may occur similarly to that of the Fec transport genes.
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Energy-coupled outer membrane transport proteins and regulatory proteins.
Biometals : an international journal on the role of metal ions in biology biochemistry and medicine, 2007Co-Authors: Volkmar Braun, Franziska EndrißAbstract:FhuA and FecA are two examples of energy-coupled outer membrane import proteins of gram-negative bacteria. FhuA transports iron complexed by the siderophore ferrichrome and serves as a receptor for phages, a toxic bacterial peptide, and a toxic protein. FecA transports diferric dicitrate and regulates transcription of an operon encoding five ferric citrate (Fec) transport genes. Properties of FhuA mutants selected according to the FhuA crystal structure are described. FhuA mutants in the TonB box, the hatch, and the beta-barrel are rather robust. TonB box mutants in FhuA FecA, FepA, Cir, and BtuB are compared; some mutations are suppressed by mutations in TonB. Mutant studies have not revealed a ferrichrome diffusion pathway, and tolerance to mutations in the region linking the TonB box to the hatch does not disclose a mechanism for how energy transfer from the cytoplasmic membrane to FhuA changes the conformation of FhuA such that bound substrates are released, the pore is opened, and substrates enter the periplasm, or how surface loops change their conformation such that TonB-dependent phages bind irreversibly and release their DNA into the cells. The FhuA and FecA crystal structures do not disclose the mechanism of these proteins, but they provide important information for specific functional studies. FecA is also a regulatory protein that transduces a signal from the cell surface into the cytoplasm. The interacting subdomains of the proteins in the FecA --> FecR --> FecI --> RNA polymerase signal transduction pathway resulting in fecABCDE transcription have been determined. Energy-coupled transporters transport not only iron and vitamin B12, but also other substrates of very low abundance such as sugars across the outer membrane; transcription regulation of the transport genes may occur similarly to that of the Fec transport genes.
Satoshi Fukuchi - One of the best experts on this subject based on the ideXlab platform.
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ideal intrinsically disordered proteins with extensive annotations and literature
Nucleic Acids Research, 2012Co-Authors: Satoshi Fukuchi, Shigetaka Sakamoto, Yukiko Nobe, Takayuki Amemiya, Ryotaro Koike, Kazuo Hosoda, Seiko D Murakami, Hidekazu HiroakiAbstract:ABSTRACTIDEAL, Intrinsically Disordered proteins withExtensive Annotations and Literature (http://www.ideal.force.cs.is.nagoya-u.ac.jp/IDEAL/), is a collec-tion of knowledge on experimentally verified intrin-sically disordered proteins. IDEAL contains manualannotations by curators on intrinsically disorderedregions, interaction regions to other molecules,post-translational modification sites, references andstructural domain assignments. In particular, IDEALexplicitly describes protean segments that can betransformed from a disordered state to an orderedstate. Since in most cases they can act as molecularrecognition elements upon binding of partner pro-teins, IDEAL provides a data resource for functionalregions of intrinsically disordered proteins. Theinformation in IDEAL is provided on a user-friendlygraphical view and in a computer-friendly XMLformat.INTRODUCTIONThe discovery of intrinsically disordered proteins (IDPs)hasbroughtaboutaparadigmchangeinstructuralbiology(1,2). Although proteins were believed to adopt unique 3Dstructures to function, IDPs do not, by themselves, assumeany stable 3D structure under physiological conditions,andyet they participate incrucial biological processes suchas signal transduction and transcription control (3–5).Some proteins contain long intrinsically disorderedregions (IDRs) while others are fully disordered. Incontrast to the long studied 3D structures of proteins, in-vestigations on IDPs started only about 10 years ago and,as yet, knowledge of IDPs is not well collected andintegrated. Although the first database of IDPs, Disprot(6), has more than 600 well-annotated entries, this numberis much smaller than the over 70 thousands entries in theProtein Data Bank (PDB) (7). Considering that theprotein 3D structural databases such as PDB, SCOP(Structural Classification of Proteins) (8) and CATH (9),have played important roles in deepening our understand-ing of the nature of protein structures and functions, thedevelopment of IDP databases are essential to theprogress of IDP research.We have developed a database, IDEAL (IDPs withExtensive Annotations and Literature) in which experi-mentally verified IDRs are collected. In the database con-struction process, we paid special attention to thefunctional regions in IDRs, for example, regions thatinteract with other molecules and post-translational modi-fication sites. In particular, we have extensively curatedIDRs that adopt unique 3D structures when they bindto other molecules by the ‘coupled folding and binding’process (10–16). We have called these IDRs the Proteansegments (ProS). The information in IDEAL is providedon a user-friendly web-interface and in computer-friendlyXML files.CONTENTS OF IDEALSummary of the annotation processWe used the UniProt amino acid sequence (17) as the ref-erence, and marked structural and functional featuresalong the sequences. A unique serial identifier, IID(IDEAL Identification), was assigned to each protein inIDEAL, starting with IID0001 for human proteins,IID5001 for other eukaryotic proteins and IID9001 forall other proteins including virus proteins. Ordered anddisordered regions were annotated as follows: First,ordered regions were obtained from the structuralregions atomically detailed in the PDB. Then, disordered
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IDEAL: Intrinsically Disordered proteins with Extensive Annotations and Literature.
Nucleic acids research, 2011Co-Authors: Satoshi Fukuchi, Shigetaka Sakamoto, Yukiko Nobe, Takayuki Amemiya, Ryotaro Koike, Kazuo Hosoda, Seiko D Murakami, Hidekazu HiroakiAbstract:IDEAL, Intrinsically Disordered proteins with Extensive Annotations and Literature (http://www.ideal.force.cs.is.nagoya-u.ac.jp/IDEAL/), is a collection of knowledge on experimentally verified intrinsically disordered proteins. IDEAL contains manual annotations by curators on intrinsically disordered regions, interaction regions to other molecules, post-translational modification sites, references and structural domain assignments. In particular, IDEAL explicitly describes protean segments that can be transformed from a disordered state to an ordered state. Since in most cases they can act as molecular recognition elements upon binding of partner proteins, IDEAL provides a data resource for functional regions of intrinsically disordered proteins. The information in IDEAL is provided on a user-friendly graphical view and in a computer-friendly XML format.
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IDEAL: Intrinsically Disordered proteins with Extensive Annotations and Literature.
Nucleic acids research, 2011Co-Authors: Satoshi Fukuchi, Shigetaka Sakamoto, Yukiko Nobe, Takayuki Amemiya, Ryotaro Koike, Kazuo Hosoda, Seiko D Murakami, Hidekazu HiroakiAbstract:IDEAL, Intrinsically Disordered proteins with Extensive Annotations and Literature (http://www.ideal.force.cs.is.nagoya-u.ac.jp/IDEAL/), is a collection of knowledge on experimentally verified intrinsically disordered proteins. IDEAL contains manual annotations by curators on intrinsically disordered regions, interaction regions to other molecules, post-translational modification sites, references and structural domain assignments. In particular, IDEAL explicitly describes protean segments that can be transformed from a disordered state to an ordered state. Since in most cases they can act as molecular recognition elements upon binding of partner proteins, IDEAL provides a data resource for functional regions of intrinsically disordered proteins. The information in IDEAL is provided on a user-friendly graphical view and in a computer-friendly XML format.
Takayuki Amemiya - One of the best experts on this subject based on the ideXlab platform.
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interface property responsible for effective interactions of protean segments intrinsically disordered regions that undergo disorder to order transitions upon binding
Biochemical and Biophysical Research Communications, 2016Co-Authors: Divya Shaji, Takayuki Amemiya, Ryotaro Koike, Motonori OtaAbstract:Proteins that lack a well-defined conformation under native conditions are referred to as intrinsically disordered proteins. When interacting with partner proteins, short regions in disordered proteins can undergo disorder-to-order transitions upon binding; these regions are called protean segments (ProSs). It has been indicated that interactions of ProSs are effective: the number of contacts per residue of ProS interface is large. To reveal the properties of ProS interface that are responsible for the interaction efficiency, we classified the interface into core, rim and support, and analyzed them based on the relative accessible surface area (rASA). Despite the effective interactions, the ProS interface is mainly composed of rim residues, rather than core. The ProS rim is more effective than the rim of heterodimers, because the average rASAs of ProS rim, which is significantly large in the monomeric state, provides a large area to be used for the interactions. The amino acid composition of ProSs correlated well with those of heterodimers in both the core and rim. Therefore, the composition cannot explain why the rASAs of the ProS rim are large in the monomeric state. The balance between a small core and a large rim, and the large solvent exposure of the rim in the monomeric state, are the key to the disorder-to-order transition and the effective interactions of ProSs.
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ideal intrinsically disordered proteins with extensive annotations and literature
Nucleic Acids Research, 2012Co-Authors: Satoshi Fukuchi, Shigetaka Sakamoto, Yukiko Nobe, Takayuki Amemiya, Ryotaro Koike, Kazuo Hosoda, Seiko D Murakami, Hidekazu HiroakiAbstract:ABSTRACTIDEAL, Intrinsically Disordered proteins withExtensive Annotations and Literature (http://www.ideal.force.cs.is.nagoya-u.ac.jp/IDEAL/), is a collec-tion of knowledge on experimentally verified intrin-sically disordered proteins. IDEAL contains manualannotations by curators on intrinsically disorderedregions, interaction regions to other molecules,post-translational modification sites, references andstructural domain assignments. In particular, IDEALexplicitly describes protean segments that can betransformed from a disordered state to an orderedstate. Since in most cases they can act as molecularrecognition elements upon binding of partner pro-teins, IDEAL provides a data resource for functionalregions of intrinsically disordered proteins. Theinformation in IDEAL is provided on a user-friendlygraphical view and in a computer-friendly XMLformat.INTRODUCTIONThe discovery of intrinsically disordered proteins (IDPs)hasbroughtaboutaparadigmchangeinstructuralbiology(1,2). Although proteins were believed to adopt unique 3Dstructures to function, IDPs do not, by themselves, assumeany stable 3D structure under physiological conditions,andyet they participate incrucial biological processes suchas signal transduction and transcription control (3–5).Some proteins contain long intrinsically disorderedregions (IDRs) while others are fully disordered. Incontrast to the long studied 3D structures of proteins, in-vestigations on IDPs started only about 10 years ago and,as yet, knowledge of IDPs is not well collected andintegrated. Although the first database of IDPs, Disprot(6), has more than 600 well-annotated entries, this numberis much smaller than the over 70 thousands entries in theProtein Data Bank (PDB) (7). Considering that theprotein 3D structural databases such as PDB, SCOP(Structural Classification of Proteins) (8) and CATH (9),have played important roles in deepening our understand-ing of the nature of protein structures and functions, thedevelopment of IDP databases are essential to theprogress of IDP research.We have developed a database, IDEAL (IDPs withExtensive Annotations and Literature) in which experi-mentally verified IDRs are collected. In the database con-struction process, we paid special attention to thefunctional regions in IDRs, for example, regions thatinteract with other molecules and post-translational modi-fication sites. In particular, we have extensively curatedIDRs that adopt unique 3D structures when they bindto other molecules by the ‘coupled folding and binding’process (10–16). We have called these IDRs the Proteansegments (ProS). The information in IDEAL is providedon a user-friendly web-interface and in computer-friendlyXML files.CONTENTS OF IDEALSummary of the annotation processWe used the UniProt amino acid sequence (17) as the ref-erence, and marked structural and functional featuresalong the sequences. A unique serial identifier, IID(IDEAL Identification), was assigned to each protein inIDEAL, starting with IID0001 for human proteins,IID5001 for other eukaryotic proteins and IID9001 forall other proteins including virus proteins. Ordered anddisordered regions were annotated as follows: First,ordered regions were obtained from the structuralregions atomically detailed in the PDB. Then, disordered
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IDEAL: Intrinsically Disordered proteins with Extensive Annotations and Literature.
Nucleic acids research, 2011Co-Authors: Satoshi Fukuchi, Shigetaka Sakamoto, Yukiko Nobe, Takayuki Amemiya, Ryotaro Koike, Kazuo Hosoda, Seiko D Murakami, Hidekazu HiroakiAbstract:IDEAL, Intrinsically Disordered proteins with Extensive Annotations and Literature (http://www.ideal.force.cs.is.nagoya-u.ac.jp/IDEAL/), is a collection of knowledge on experimentally verified intrinsically disordered proteins. IDEAL contains manual annotations by curators on intrinsically disordered regions, interaction regions to other molecules, post-translational modification sites, references and structural domain assignments. In particular, IDEAL explicitly describes protean segments that can be transformed from a disordered state to an ordered state. Since in most cases they can act as molecular recognition elements upon binding of partner proteins, IDEAL provides a data resource for functional regions of intrinsically disordered proteins. The information in IDEAL is provided on a user-friendly graphical view and in a computer-friendly XML format.
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IDEAL: Intrinsically Disordered proteins with Extensive Annotations and Literature.
Nucleic acids research, 2011Co-Authors: Satoshi Fukuchi, Shigetaka Sakamoto, Yukiko Nobe, Takayuki Amemiya, Ryotaro Koike, Kazuo Hosoda, Seiko D Murakami, Hidekazu HiroakiAbstract:IDEAL, Intrinsically Disordered proteins with Extensive Annotations and Literature (http://www.ideal.force.cs.is.nagoya-u.ac.jp/IDEAL/), is a collection of knowledge on experimentally verified intrinsically disordered proteins. IDEAL contains manual annotations by curators on intrinsically disordered regions, interaction regions to other molecules, post-translational modification sites, references and structural domain assignments. In particular, IDEAL explicitly describes protean segments that can be transformed from a disordered state to an ordered state. Since in most cases they can act as molecular recognition elements upon binding of partner proteins, IDEAL provides a data resource for functional regions of intrinsically disordered proteins. The information in IDEAL is provided on a user-friendly graphical view and in a computer-friendly XML format.
Ryotaro Koike - One of the best experts on this subject based on the ideXlab platform.
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interface property responsible for effective interactions of protean segments intrinsically disordered regions that undergo disorder to order transitions upon binding
Biochemical and Biophysical Research Communications, 2016Co-Authors: Divya Shaji, Takayuki Amemiya, Ryotaro Koike, Motonori OtaAbstract:Proteins that lack a well-defined conformation under native conditions are referred to as intrinsically disordered proteins. When interacting with partner proteins, short regions in disordered proteins can undergo disorder-to-order transitions upon binding; these regions are called protean segments (ProSs). It has been indicated that interactions of ProSs are effective: the number of contacts per residue of ProS interface is large. To reveal the properties of ProS interface that are responsible for the interaction efficiency, we classified the interface into core, rim and support, and analyzed them based on the relative accessible surface area (rASA). Despite the effective interactions, the ProS interface is mainly composed of rim residues, rather than core. The ProS rim is more effective than the rim of heterodimers, because the average rASAs of ProS rim, which is significantly large in the monomeric state, provides a large area to be used for the interactions. The amino acid composition of ProSs correlated well with those of heterodimers in both the core and rim. Therefore, the composition cannot explain why the rASAs of the ProS rim are large in the monomeric state. The balance between a small core and a large rim, and the large solvent exposure of the rim in the monomeric state, are the key to the disorder-to-order transition and the effective interactions of ProSs.
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ideal intrinsically disordered proteins with extensive annotations and literature
Nucleic Acids Research, 2012Co-Authors: Satoshi Fukuchi, Shigetaka Sakamoto, Yukiko Nobe, Takayuki Amemiya, Ryotaro Koike, Kazuo Hosoda, Seiko D Murakami, Hidekazu HiroakiAbstract:ABSTRACTIDEAL, Intrinsically Disordered proteins withExtensive Annotations and Literature (http://www.ideal.force.cs.is.nagoya-u.ac.jp/IDEAL/), is a collec-tion of knowledge on experimentally verified intrin-sically disordered proteins. IDEAL contains manualannotations by curators on intrinsically disorderedregions, interaction regions to other molecules,post-translational modification sites, references andstructural domain assignments. In particular, IDEALexplicitly describes protean segments that can betransformed from a disordered state to an orderedstate. Since in most cases they can act as molecularrecognition elements upon binding of partner pro-teins, IDEAL provides a data resource for functionalregions of intrinsically disordered proteins. Theinformation in IDEAL is provided on a user-friendlygraphical view and in a computer-friendly XMLformat.INTRODUCTIONThe discovery of intrinsically disordered proteins (IDPs)hasbroughtaboutaparadigmchangeinstructuralbiology(1,2). Although proteins were believed to adopt unique 3Dstructures to function, IDPs do not, by themselves, assumeany stable 3D structure under physiological conditions,andyet they participate incrucial biological processes suchas signal transduction and transcription control (3–5).Some proteins contain long intrinsically disorderedregions (IDRs) while others are fully disordered. Incontrast to the long studied 3D structures of proteins, in-vestigations on IDPs started only about 10 years ago and,as yet, knowledge of IDPs is not well collected andintegrated. Although the first database of IDPs, Disprot(6), has more than 600 well-annotated entries, this numberis much smaller than the over 70 thousands entries in theProtein Data Bank (PDB) (7). Considering that theprotein 3D structural databases such as PDB, SCOP(Structural Classification of Proteins) (8) and CATH (9),have played important roles in deepening our understand-ing of the nature of protein structures and functions, thedevelopment of IDP databases are essential to theprogress of IDP research.We have developed a database, IDEAL (IDPs withExtensive Annotations and Literature) in which experi-mentally verified IDRs are collected. In the database con-struction process, we paid special attention to thefunctional regions in IDRs, for example, regions thatinteract with other molecules and post-translational modi-fication sites. In particular, we have extensively curatedIDRs that adopt unique 3D structures when they bindto other molecules by the ‘coupled folding and binding’process (10–16). We have called these IDRs the Proteansegments (ProS). The information in IDEAL is providedon a user-friendly web-interface and in computer-friendlyXML files.CONTENTS OF IDEALSummary of the annotation processWe used the UniProt amino acid sequence (17) as the ref-erence, and marked structural and functional featuresalong the sequences. A unique serial identifier, IID(IDEAL Identification), was assigned to each protein inIDEAL, starting with IID0001 for human proteins,IID5001 for other eukaryotic proteins and IID9001 forall other proteins including virus proteins. Ordered anddisordered regions were annotated as follows: First,ordered regions were obtained from the structuralregions atomically detailed in the PDB. Then, disordered
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IDEAL: Intrinsically Disordered proteins with Extensive Annotations and Literature.
Nucleic acids research, 2011Co-Authors: Satoshi Fukuchi, Shigetaka Sakamoto, Yukiko Nobe, Takayuki Amemiya, Ryotaro Koike, Kazuo Hosoda, Seiko D Murakami, Hidekazu HiroakiAbstract:IDEAL, Intrinsically Disordered proteins with Extensive Annotations and Literature (http://www.ideal.force.cs.is.nagoya-u.ac.jp/IDEAL/), is a collection of knowledge on experimentally verified intrinsically disordered proteins. IDEAL contains manual annotations by curators on intrinsically disordered regions, interaction regions to other molecules, post-translational modification sites, references and structural domain assignments. In particular, IDEAL explicitly describes protean segments that can be transformed from a disordered state to an ordered state. Since in most cases they can act as molecular recognition elements upon binding of partner proteins, IDEAL provides a data resource for functional regions of intrinsically disordered proteins. The information in IDEAL is provided on a user-friendly graphical view and in a computer-friendly XML format.
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IDEAL: Intrinsically Disordered proteins with Extensive Annotations and Literature.
Nucleic acids research, 2011Co-Authors: Satoshi Fukuchi, Shigetaka Sakamoto, Yukiko Nobe, Takayuki Amemiya, Ryotaro Koike, Kazuo Hosoda, Seiko D Murakami, Hidekazu HiroakiAbstract:IDEAL, Intrinsically Disordered proteins with Extensive Annotations and Literature (http://www.ideal.force.cs.is.nagoya-u.ac.jp/IDEAL/), is a collection of knowledge on experimentally verified intrinsically disordered proteins. IDEAL contains manual annotations by curators on intrinsically disordered regions, interaction regions to other molecules, post-translational modification sites, references and structural domain assignments. In particular, IDEAL explicitly describes protean segments that can be transformed from a disordered state to an ordered state. Since in most cases they can act as molecular recognition elements upon binding of partner proteins, IDEAL provides a data resource for functional regions of intrinsically disordered proteins. The information in IDEAL is provided on a user-friendly graphical view and in a computer-friendly XML format.
