Disentangling polydispersity in the PCNA−p15PAF complex, a disordered, transient and multivalent macromolecular assembly

The intrinsically disordered p15PAF regulates DNA replication and repair when interacting with the Proliferating Cell Nuclear Antigen (PCNA) sliding clamp. As many interactions between disordered proteins and globular partners involved in signaling and regulation, the complex between p15PAF and trim...

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Published inNucleic acids research Vol. 45; no. 3; pp. 1501 - 1515
Main Authors Cordeiro, Tiago N., Chen, Po-chia, De Biasio, Alfredo, Sibille, Nathalie, Blanco, Francisco J., Hub, Jochen S., Crehuet, Ramon, Bernadó, Pau
Format Journal Article
LanguageEnglish
Published England Oxford University Press 17.02.2017
Subjects
Biochemistry, Molecular Biology
Biological Physics
Carrier Proteins - chemistry
Chemical Sciences
Humans
Intrinsically Disordered Proteins - chemistry
Life Sciences
Molecular Dynamics Simulation
Multiprotein Complexes - chemistry
Nuclear Magnetic Resonance, Biomolecular
Physics
Proliferating Cell Nuclear Antigen - chemistry
Protein Structure, Quaternary
Recombinant Proteins - chemistry
Scattering, Small Angle
Structural Biology
X-Ray Diffraction
Online AccessGet full text
ISSN0305-1048
1362-4962
DOI10.1093/nar/gkw1183

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Abstract The intrinsically disordered p15PAF regulates DNA replication and repair when interacting with the Proliferating Cell Nuclear Antigen (PCNA) sliding clamp. As many interactions between disordered proteins and globular partners involved in signaling and regulation, the complex between p15PAF and trimeric PCNA is of low affinity, forming a transient complex that is difficult to characterize at a structural level due to its inherent polydispersity. We have determined the structure, conformational fluctuations, and relative population of the five species that coexist in solution by combining small-angle X-ray scattering (SAXS) with molecular modelling. By using explicit ensemble descriptions for the individual species, built using integrative approaches and molecular dynamics (MD) simulations, we collectively interpreted multiple SAXS profiles as population-weighted thermodynamic mixtures. The analysis demonstrates that the N-terminus of p15PAF penetrates the PCNA ring and emerges on the back face. This observation substantiates the role of p15PAF as a drag regulating PCNA processivity during DNA repair. Our study reveals the power of ensemble-based approaches to decode structural, dynamic, and thermodynamic information from SAXS data. This strategy paves the way for deciphering the structural bases of flexible, transient and multivalent macromolecular assemblies involved in pivotal biological processes.
AbstractList The intrinsically disordered p15PAF regulates DNA replication and repair when interacting with the Proliferating Cell Nuclear Antigen (PCNA) sliding clamp. As many interactions between disordered proteins and globular partners involved in signaling and regulation, the complex between p15PAF and trimeric PCNA is of low affinity, forming a transient complex that is difficult to characterize at a structural level due to its inherent polydispersity. We have determined the structure, conformational fluctuations, and relative population of the five species that coexist in solution by combining small-angle X-ray scattering (SAXS) with molecular modelling. By using explicit ensemble descriptions for the individual species, built using integrative approaches and molecular dynamics (MD) simulations, we collectively interpreted multiple SAXS profiles as population-weighted thermodynamic mixtures. The analysis demonstrates that the N-terminus of p15PAF penetrates the PCNA ring and emerges on the back face. This observation substantiates the role of p15PAF as a drag regulating PCNA processivity during DNA repair. Our study reveals the power of ensemble-based approaches to decode structural, dynamic, and thermodynamic information from SAXS data. This strategy paves the way for deciphering the structural bases of flexible, transient and multivalent macromolecular assemblies involved in pivotal biological processes.
The intrinsically disordered p15 PAF regulates DNA replication and repair when interacting with the Proliferating Cell Nuclear Antigen (PCNA) sliding clamp. As many interactions between disordered proteins and globular partners involved in signaling and regulation, the complex between p15 PAF and trimeric PCNA is of low affinity, forming a transient complex that is difficult to characterize at a structural level due to its inherent polydispersity. We have determined the structure, conformational fluctuations, and relative population of the five species that coexist in solution by combining small-angle X-ray scattering (SAXS) with molecular modelling. By using explicit ensemble descriptions for the individual species, built using integrative approaches and molecular dynamics (MD) simulations, we collectively interpreted multiple SAXS profiles as population-weighted thermodynamic mixtures. The analysis demonstrates that the N-terminus of p15 PAF penetrates the PCNA ring and emerges on the back face. This observation substantiates the role of p15 PAF as a drag regulating PCNA processivity during DNA repair. Our study reveals the power of ensemble-based approaches to decode structural, dynamic, and thermodynamic information from SAXS data. This strategy paves the way for deciphering the structural bases of flexible, transient and multivalent macromolecular assemblies involved in pivotal biological processes.
The intrinsically disordered p15 PAF regulates DNA replication and repair when interacting with the Proliferating Cell Nuclear Antigen (PCNA) sliding clamp. As many interactions between disordered proteins and globular partners involved in signaling and regulation, the complex between p15 PAF and trimeric PCNA is of low affinity, forming a transient complex that is difficult to characterize at a structural level due to its inherent polydispersity. We have determined the structure, conformational fluctuations, and relative population of the five species that coexist in solution by combining small-angle X-ray scattering (SAXS) with molecular modelling. By using explicit ensemble descriptions for the individual species, built using integrative approaches and molecular dynamics (MD) simulations, we collectively interpreted multiple SAXS profiles as population-weighted thermodynamic mixtures. The analysis demonstrates that the N-terminus of p15 PAF penetrates the PCNA ring and emerges on the back face. This observation substantiates the role of p15 PAF as a drag regulating PCNA processivity during DNA repair. Our study reveals the power of ensemble-based approaches to decode structural, dynamic, and thermodynamic information from SAXS data. This strategy paves the way for deciphering the structural bases of flexible, transient and multivalent macromolecular assemblies involved in pivotal biological processes.
Author Hub, Jochen S.
Chen, Po-chia
Sibille, Nathalie
Bernadó, Pau
Cordeiro, Tiago N.
De Biasio, Alfredo
Blanco, Francisco J.
Crehuet, Ramon
AuthorAffiliation 6 Institute of Advanced Chemistry of Catalonia, CSIC, Barcelona 08034, Spain
4 CIC-bioGUNE, Derio, Spain
1 Centre de Biochimie Structurale, INSERM-U1054, CNRS UMR-5048, Université de Montpellier, Montpellier, France
5 IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
2 Institute for Microbiology and Genetics, Georg-August-University Göttingen, Göttingen, Lower Saxony, Germany
3 Elettra-Sincrotrone Trieste S.C.p.A., Trieste 34149, Italy
AuthorAffiliation_xml – name: 5 IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
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– name: 3 Elettra-Sincrotrone Trieste S.C.p.A., Trieste 34149, Italy
– name: 2 Institute for Microbiology and Genetics, Georg-August-University Göttingen, Göttingen, Lower Saxony, Germany
– name: 4 CIC-bioGUNE, Derio, Spain
– name: 6 Institute of Advanced Chemistry of Catalonia, CSIC, Barcelona 08034, Spain
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SSID ssj0014154
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Snippet The intrinsically disordered p15PAF regulates DNA replication and repair when interacting with the Proliferating Cell Nuclear Antigen (PCNA) sliding clamp. As...
The intrinsically disordered p15 PAF regulates DNA replication and repair when interacting with the Proliferating Cell Nuclear Antigen (PCNA) sliding clamp. As...
The intrinsically disordered p15 PAF regulates DNA replication and repair when interacting with the Proliferating Cell Nuclear Antigen (PCNA) sliding clamp. As...
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pubmed
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SourceType Open Access Repository
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Enrichment Source
StartPage 1501
SubjectTerms Biochemistry, Molecular Biology
Biological Physics
Carrier Proteins - chemistry
Chemical Sciences
Humans
Intrinsically Disordered Proteins - chemistry
Life Sciences
Molecular Dynamics Simulation
Multiprotein Complexes - chemistry
Nuclear Magnetic Resonance, Biomolecular
Physics
Proliferating Cell Nuclear Antigen - chemistry
Protein Structure, Quaternary
Recombinant Proteins - chemistry
Scattering, Small Angle
Structural Biology
X-Ray Diffraction
Title Disentangling polydispersity in the PCNA−p15PAF complex, a disordered, transient and multivalent macromolecular assembly
URI https://www.ncbi.nlm.nih.gov/pubmed/28180305
https://www.proquest.com/docview/1866695034
https://hal.science/hal-02348011
https://pubmed.ncbi.nlm.nih.gov/PMC5388412
Volume 45
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