p15PAF Is an Intrinsically Disordered Protein with Nonrandom Structural Preferences at Sites of Interaction with Other Proteins
We present to our knowledge the first structural characterization of the proliferating-cell-nuclear-antigen-associated factor p15PAF, showing that it is monomeric and intrinsically disordered in solution but has nonrandom conformational preferences at sites of protein-protein interactions. p15PAF is...
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| Published in | Biophysical journal Vol. 106; no. 4; pp. 865 - 874 |
|---|---|
| Main Authors | , , , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
United States
Elsevier Inc
18.02.2014
The Biophysical Society |
| Subjects | |
| Online Access | Get full text |
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| Abstract | We present to our knowledge the first structural characterization of the proliferating-cell-nuclear-antigen-associated factor p15PAF, showing that it is monomeric and intrinsically disordered in solution but has nonrandom conformational preferences at sites of protein-protein interactions. p15PAF is a 12 kDa nuclear protein that acts as a regulator of DNA repair during DNA replication. The p15PAF gene is overexpressed in several types of human cancer. The nearly complete NMR backbone assignment of p15PAF allowed us to measure 86 N-HN residual dipolar couplings. Our residual dipolar coupling analysis reveals nonrandom conformational preferences in distinct regions, including the proliferating-cell-nuclear-antigen-interacting protein motif (PIP-box) and the KEN-box (recognized by the ubiquitin ligase that targets p15PAF for degradation). In accordance with these findings, analysis of the 15N R2 relaxation rates shows a relatively reduced mobility for the residues in these regions. The agreement between the experimental small angle x-ray scattering curve of p15PAF and that computed from a statistical coil ensemble corrected for the presence of local secondary structural elements further validates our structural model for p15PAF. The coincidence of these transiently structured regions with protein-protein interaction and posttranslational modification sites suggests a possible role for these structures as molecular recognition elements for p15PAF. |
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| AbstractList | We present to our knowledge the first structural characterization of the proliferating-cell-nuclear-antigen-associated factor p15(PAF), showing that it is monomeric and intrinsically disordered in solution but has nonrandom conformational preferences at sites of protein-protein interactions. p15(PAF) is a 12 kDa nuclear protein that acts as a regulator of DNA repair during DNA replication. The p15(PAF) gene is overexpressed in several types of human cancer. The nearly complete NMR backbone assignment of p15(PAF) allowed us to measure 86 N-H(N) residual dipolar couplings. Our residual dipolar coupling analysis reveals nonrandom conformational preferences in distinct regions, including the proliferating-cell-nuclear-antigen-interacting protein motif (PIP-box) and the KEN-box (recognized by the ubiquitin ligase that targets p15(PAF) for degradation). In accordance with these findings, analysis of the (15)N R2 relaxation rates shows a relatively reduced mobility for the residues in these regions. The agreement between the experimental small angle x-ray scattering curve of p15(PAF) and that computed from a statistical coil ensemble corrected for the presence of local secondary structural elements further validates our structural model for p15(PAF). The coincidence of these transiently structured regions with protein-protein interaction and posttranslational modification sites suggests a possible role for these structures as molecular recognition elements for p15(PAF). We present to our knowledge the first structural characterization of the proliferating-cell-nuclear-antigen-associated factor p15 PAF , showing that it is monomeric and intrinsically disordered in solution but has nonrandom conformational preferences at sites of protein-protein interactions. p15 PAF is a 12 kDa nuclear protein that acts as a regulator of DNA repair during DNA replication. The p15 PAF gene is overexpressed in several types of human cancer. The nearly complete NMR backbone assignment of p15 PAF allowed us to measure 86 N-H N residual dipolar couplings. Our residual dipolar coupling analysis reveals nonrandom conformational preferences in distinct regions, including the proliferating-cell-nuclear-antigen-interacting protein motif (PIP-box) and the KEN-box (recognized by the ubiquitin ligase that targets p15 PAF for degradation). In accordance with these findings, analysis of the 15 N R 2 relaxation rates shows a relatively reduced mobility for the residues in these regions. The agreement between the experimental small angle x-ray scattering curve of p15 PAF and that computed from a statistical coil ensemble corrected for the presence of local secondary structural elements further validates our structural model for p15 PAF . The coincidence of these transiently structured regions with protein-protein interaction and posttranslational modification sites suggests a possible role for these structures as molecular recognition elements for p15 PAF . We present to our knowledge the first structural characterization of the proliferating-cell-nuclear-antigen-associated factor p15PAF, showing that it is monomeric and intrinsically disordered in solution but has nonrandom conformational preferences at sites of protein-protein interactions. p15PAF is a 12 kDa nuclear protein that acts as a regulator of DNA repair during DNA replication. The p15PAF gene is overexpressed in several types of human cancer. The nearly complete NMR backbone assignment of p15PAF allowed us to measure 86 N-HN residual dipolar couplings. Our residual dipolar coupling analysis reveals nonrandom conformational preferences in distinct regions, including the proliferating-cell-nuclear-antigen-interacting protein motif (PIP-box) and the KEN-box (recognized by the ubiquitin ligase that targets p15PAF for degradation). In accordance with these findings, analysis of the 15N R2 relaxation rates shows a relatively reduced mobility for the residues in these regions. The agreement between the experimental small angle x-ray scattering curve of p15PAF and that computed from a statistical coil ensemble corrected for the presence of local secondary structural elements further validates our structural model for p15PAF. The coincidence of these transiently structured regions with protein-protein interaction and posttranslational modification sites suggests a possible role for these structures as molecular recognition elements for p15PAF. We present to our knowledge the first structural characterization of the proliferating-cell-nuclear-antigen-associated factor p15(PAF), showing that it is monomeric and intrinsically disordered in solution but has nonrandom conformational preferences at sites of protein-protein interactions. p15(PAF) is a 12 kDa nuclear protein that acts as a regulator of DNA repair during DNA replication. The p15(PAF) gene is overexpressed in several types of human cancer. The nearly complete NMR backbone assignment of p15(PAF) allowed us to measure 86 N-H(N) residual dipolar couplings. Our residual dipolar coupling analysis reveals nonrandom conformational preferences in distinct regions, including the proliferating-cell-nuclear-antigen-interacting protein motif (PIP-box) and the KEN-box (recognized by the ubiquitin ligase that targets p15(PAF) for degradation). In accordance with these findings, analysis of the (15)N R2 relaxation rates shows a relatively reduced mobility for the residues in these regions. The agreement between the experimental small angle x-ray scattering curve of p15(PAF) and that computed from a statistical coil ensemble corrected for the presence of local secondary structural elements further validates our structural model for p15(PAF). The coincidence of these transiently structured regions with protein-protein interaction and posttranslational modification sites suggests a possible role for these structures as molecular recognition elements for p15(PAF).We present to our knowledge the first structural characterization of the proliferating-cell-nuclear-antigen-associated factor p15(PAF), showing that it is monomeric and intrinsically disordered in solution but has nonrandom conformational preferences at sites of protein-protein interactions. p15(PAF) is a 12 kDa nuclear protein that acts as a regulator of DNA repair during DNA replication. The p15(PAF) gene is overexpressed in several types of human cancer. The nearly complete NMR backbone assignment of p15(PAF) allowed us to measure 86 N-H(N) residual dipolar couplings. Our residual dipolar coupling analysis reveals nonrandom conformational preferences in distinct regions, including the proliferating-cell-nuclear-antigen-interacting protein motif (PIP-box) and the KEN-box (recognized by the ubiquitin ligase that targets p15(PAF) for degradation). In accordance with these findings, analysis of the (15)N R2 relaxation rates shows a relatively reduced mobility for the residues in these regions. The agreement between the experimental small angle x-ray scattering curve of p15(PAF) and that computed from a statistical coil ensemble corrected for the presence of local secondary structural elements further validates our structural model for p15(PAF). The coincidence of these transiently structured regions with protein-protein interaction and posttranslational modification sites suggests a possible role for these structures as molecular recognition elements for p15(PAF). |
| Author | Ibáñez de Opakua, Alain Villate, Maider Blanco, Francisco J. Sibille, Nathalie Bernadó, Pau Cordeiro, Tiago N. Merino, Nekane De Biasio, Alfredo Lelli, Moreno Diercks, Tammo |
| AuthorAffiliation | Centre de Biochimie Structurale, Institut National de la Santé et de la Recherche Médicale (INSERM) U1054, Centre National de la Recherche Scientifique (CNRS) UMR 5048, Université Montpellier 1 and 2, Montpellier, France Centre de Résonance Magnétique Nucléaire à Très Hauts Champs, Institut de Sciences Analytiques (CNRS/Ecole Normale Supérieure de Lyon/Université Claude Bernard Lyon 1), Villeurbanne, France IKERBASQUE, Basque Foundation for Science, Bilbao, Spain Structural Biology Unit, Center for Cooperative Research in Biosciences (CIC bioGUNE), Derio, Spain |
| AuthorAffiliation_xml | – name: Centre de Résonance Magnétique Nucléaire à Très Hauts Champs, Institut de Sciences Analytiques (CNRS/Ecole Normale Supérieure de Lyon/Université Claude Bernard Lyon 1), Villeurbanne, France – name: Centre de Biochimie Structurale, Institut National de la Santé et de la Recherche Médicale (INSERM) U1054, Centre National de la Recherche Scientifique (CNRS) UMR 5048, Université Montpellier 1 and 2, Montpellier, France – name: IKERBASQUE, Basque Foundation for Science, Bilbao, Spain – name: Structural Biology Unit, Center for Cooperative Research in Biosciences (CIC bioGUNE), Derio, Spain |
| Author_xml | – sequence: 1 givenname: Alfredo surname: De Biasio fullname: De Biasio, Alfredo organization: Structural Biology Unit, Center for Cooperative Research in Biosciences (CIC bioGUNE), Derio, Spain – sequence: 2 givenname: Alain surname: Ibáñez de Opakua fullname: Ibáñez de Opakua, Alain organization: Structural Biology Unit, Center for Cooperative Research in Biosciences (CIC bioGUNE), Derio, Spain – sequence: 3 givenname: Tiago N. surname: Cordeiro fullname: Cordeiro, Tiago N. organization: Centre de Biochimie Structurale, Institut National de la Santé et de la Recherche Médicale (INSERM) U1054, Centre National de la Recherche Scientifique (CNRS) UMR 5048, Université Montpellier 1 and 2, Montpellier, France – sequence: 4 givenname: Maider surname: Villate fullname: Villate, Maider organization: Structural Biology Unit, Center for Cooperative Research in Biosciences (CIC bioGUNE), Derio, Spain – sequence: 5 givenname: Nekane surname: Merino fullname: Merino, Nekane organization: Structural Biology Unit, Center for Cooperative Research in Biosciences (CIC bioGUNE), Derio, Spain – sequence: 6 givenname: Nathalie surname: Sibille fullname: Sibille, Nathalie organization: Centre de Biochimie Structurale, Institut National de la Santé et de la Recherche Médicale (INSERM) U1054, Centre National de la Recherche Scientifique (CNRS) UMR 5048, Université Montpellier 1 and 2, Montpellier, France – sequence: 7 givenname: Moreno surname: Lelli fullname: Lelli, Moreno organization: Centre de Résonance Magnétique Nucléaire à Très Hauts Champs, Institut de Sciences Analytiques (CNRS/Ecole Normale Supérieure de Lyon/Université Claude Bernard Lyon 1), Villeurbanne, France – sequence: 8 givenname: Tammo surname: Diercks fullname: Diercks, Tammo organization: Structural Biology Unit, Center for Cooperative Research in Biosciences (CIC bioGUNE), Derio, Spain – sequence: 9 givenname: Pau surname: Bernadó fullname: Bernadó, Pau organization: Centre de Biochimie Structurale, Institut National de la Santé et de la Recherche Médicale (INSERM) U1054, Centre National de la Recherche Scientifique (CNRS) UMR 5048, Université Montpellier 1 and 2, Montpellier, France – sequence: 10 givenname: Francisco J. surname: Blanco fullname: Blanco, Francisco J. email: fblanco@cicbiogune.es organization: Structural Biology Unit, Center for Cooperative Research in Biosciences (CIC bioGUNE), Derio, Spain |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/24559989$$D View this record in MEDLINE/PubMed |
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| Snippet | We present to our knowledge the first structural characterization of the proliferating-cell-nuclear-antigen-associated factor p15PAF, showing that it is... We present to our knowledge the first structural characterization of the proliferating-cell-nuclear-antigen-associated factor p15(PAF), showing that it is... We present to our knowledge the first structural characterization of the proliferating-cell-nuclear-antigen-associated factor p15 PAF , showing that it is... |
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| SubjectTerms | Amino Acid Sequence Binding Sites Carrier Proteins - chemistry Carrier Proteins - metabolism Humans Molecular Sequence Data Protein Binding Proteins and Nucleic Acids |
| Title | p15PAF Is an Intrinsically Disordered Protein with Nonrandom Structural Preferences at Sites of Interaction with Other Proteins |
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