A Structural Model for Apolipoprotein C-II Amyloid Fibrils: Experimental Characterization and Molecular Dynamics Simulations
The self-assembly of specific proteins to form insoluble amyloid fibrils is a characteristic feature of a number of age-related and debilitating diseases. Lipid-free human apolipoprotein C-II (apoC-II) forms characteristic amyloid fibrils and is one of several apolipoproteins that accumulate in amyl...
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| Published in | Journal of molecular biology Vol. 405; no. 5; pp. 1246 - 1266 |
|---|---|
| Main Authors | , , , , , , , , , , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
England
Elsevier Ltd
04.02.2011
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| Subjects | |
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| Abstract | The self-assembly of specific proteins to form insoluble amyloid fibrils is a characteristic feature of a number of age-related and debilitating diseases. Lipid-free human apolipoprotein C-II (apoC-II) forms characteristic amyloid fibrils and is one of several apolipoproteins that accumulate in amyloid deposits located within atherosclerotic plaques. X-ray diffraction analysis of aligned apoC-II fibrils indicated a simple cross-β-structure composed of two parallel β-sheets. Examination of apoC-II fibrils using transmission electron microscopy, scanning transmission electron microscopy, and atomic force microscopy indicated that the fibrils are flat ribbons composed of one apoC-II molecule per 4.7-Å rise of the cross-β-structure. Cross-linking results using single-cysteine substitution mutants are consistent with a parallel in-register structural model for apoC-II fibrils. Fluorescence resonance energy transfer analysis of apoC-II fibrils labeled with specific fluorophores provided distance constraints for selected donor–acceptor pairs located within the fibrils. These findings were used to develop a simple ‘letter-G-like’ β-strand–loop–β-strand model for apoC-II fibrils. Fully solvated all-atom molecular dynamics (MD) simulations showed that the model contained a stable cross-β-core with a flexible connecting loop devoid of persistent secondary structure. The time course of the MD simulations revealed that charge clusters in the fibril rearrange to minimize the effects of same-charge interactions inherent in parallel in-register models. Our structural model for apoC-II fibrils suggests that apoC-II monomers fold and self-assemble to form a stable cross-β-scaffold containing relatively unstructured connecting loops.
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► ApoC-II forms amyloid fibrils with one apoC-II for every rise of the cross-β-structure. ► There are two in-register parallel β-sheets stabilized by an internal ion pair. ► Each apoC-II molecule is stacked in a ‘letter-G-like’ configuration. ► MD simulations reveal a stable core and a flexible connecting loop. |
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| AbstractList | The self-assembly of specific proteins to form insoluble amyloid fibrils is a characteristic feature of a number of age-related and debilitating diseases. Lipid-free human apolipoprotein C-II (apoC-II) forms characteristic amyloid fibrils and is one of several apolipoproteins that accumulate in amyloid deposits located within atherosclerotic plaques. X-ray diffraction analysis of aligned apoC-II fibrils indicated a simple cross- beta -structure composed of two parallel beta -sheets. Examination of apoC-II fibrils using transmission electron microscopy, scanning transmission electron microscopy, and atomic force microscopy indicated that the fibrils are flat ribbons composed of one apoC-II molecule per 4.7-Aa rise of the cross- beta -structure. Cross-linking results using single-cysteine substitution mutants are consistent with a parallel in-register structural model for apoC-II fibrils. Fluorescence resonance energy transfer analysis of apoC-II fibrils labeled with specific fluorophores provided distance constraints for selected donor-acceptor pairs located within the fibrils. These findings were used to develop a simple 'letter-G-like' beta -strand-loop- beta -strand model for apoC-II fibrils. Fully solvated all-atom molecular dynamics (MD) simulations showed that the model contained a stable cross- beta -core with a flexible connecting loop devoid of persistent secondary structure. The time course of the MD simulations revealed that charge clusters in the fibril rearrange to minimize the effects of same-charge interactions inherent in parallel in-register models. Our structural model for apoC-II fibrils suggests that apoC-II monomers fold and self-assemble to form a stable cross- beta -scaffold containing relatively unstructured connecting loops. The self-assembly of specific proteins to form insoluble amyloid fibrils is a characteristic feature of a number of age-related and debilitating diseases. Lipid-free human apolipoprotein C-II (apoC-II) forms characteristic amyloid fibrils and is one of several apolipoproteins that accumulate in amyloid deposits located within atherosclerotic plaques. X-ray diffraction analysis of aligned apoC-II fibrils indicated a simple cross-β-structure composed of two parallel β-sheets. Examination of apoC-II fibrils using transmission electron microscopy, scanning transmission electron microscopy, and atomic force microscopy indicated that the fibrils are flat ribbons composed of one apoC-II molecule per 4.7-Å rise of the cross-β-structure. Cross-linking results using single-cysteine substitution mutants are consistent with a parallel in-register structural model for apoC-II fibrils. Fluorescence resonance energy transfer analysis of apoC-II fibrils labeled with specific fluorophores provided distance constraints for selected donor-acceptor pairs located within the fibrils. These findings were used to develop a simple 'letter-G-like' β-strand-loop-β-strand model for apoC-II fibrils. Fully solvated all-atom molecular dynamics (MD) simulations showed that the model contained a stable cross-β-core with a flexible connecting loop devoid of persistent secondary structure. The time course of the MD simulations revealed that charge clusters in the fibril rearrange to minimize the effects of same-charge interactions inherent in parallel in-register models. Our structural model for apoC-II fibrils suggests that apoC-II monomers fold and self-assemble to form a stable cross-β-scaffold containing relatively unstructured connecting loops. The self-assembly of specific proteins to form insoluble amyloid fibrils is a characteristic feature of a number of age-related and debilitating diseases. Lipid-free human apolipoprotein C-II (apoC-II) forms characteristic amyloid fibrils and is one of several apolipoproteins that accumulate in amyloid deposits located within atherosclerotic plaques. X-ray diffraction analysis of aligned apoC-II fibrils indicated a simple cross-β-structure composed of two parallel β-sheets. Examination of apoC-II fibrils using transmission electron microscopy, scanning transmission electron microscopy, and atomic force microscopy indicated that the fibrils are flat ribbons composed of one apoC-II molecule per 4.7-Å rise of the cross-β-structure. Cross-linking results using single-cysteine substitution mutants are consistent with a parallel in-register structural model for apoC-II fibrils. Fluorescence resonance energy transfer analysis of apoC-II fibrils labeled with specific fluorophores provided distance constraints for selected donor–acceptor pairs located within the fibrils. These findings were used to develop a simple ‘letter-G-like’ β-strand–loop–β-strand model for apoC-II fibrils. Fully solvated all-atom molecular dynamics (MD) simulations showed that the model contained a stable cross-β-core with a flexible connecting loop devoid of persistent secondary structure. The time course of the MD simulations revealed that charge clusters in the fibril rearrange to minimize the effects of same-charge interactions inherent in parallel in-register models. Our structural model for apoC-II fibrils suggests that apoC-II monomers fold and self-assemble to form a stable cross-β-scaffold containing relatively unstructured connecting loops. [Display omitted] ► ApoC-II forms amyloid fibrils with one apoC-II for every rise of the cross-β-structure. ► There are two in-register parallel β-sheets stabilized by an internal ion pair. ► Each apoC-II molecule is stacked in a ‘letter-G-like’ configuration. ► MD simulations reveal a stable core and a flexible connecting loop. |
| Author | Todorova, Nevena Müller, Shirley A. Binger, Katrina J. Thomson, Neil H. Yarovsky, Irene Pham, Chi L.L. Radford, Sheena E. Engel, Andreas Teoh, Chai Lean Hung, Andrew Howlett, Geoffrey J. Smith, Trevor A. Lincoln, Craig N. Gooley, Paul R. Lam, Yuen Han Lees, Emma Griffin, Michael D.W. |
| Author_xml | – sequence: 1 givenname: Chai Lean surname: Teoh fullname: Teoh, Chai Lean organization: Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria 3010, Australia – sequence: 2 givenname: Chi L.L. surname: Pham fullname: Pham, Chi L.L. organization: Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria 3010, Australia – sequence: 3 givenname: Nevena surname: Todorova fullname: Todorova, Nevena organization: Health Innovations Research Institute, School of Applied Sciences, RMIT University, GPO Box 2476V, Melbourne, Victoria 3001, Australia – sequence: 4 givenname: Andrew surname: Hung fullname: Hung, Andrew organization: Health Innovations Research Institute, School of Applied Sciences, RMIT University, GPO Box 2476V, Melbourne, Victoria 3001, Australia – sequence: 5 givenname: Craig N. surname: Lincoln fullname: Lincoln, Craig N. organization: School of Chemistry and ARC Center of Excellence for Coherent X-ray Science, University of Melbourne, Parkville, Victoria 3010, Australia – sequence: 6 givenname: Emma surname: Lees fullname: Lees, Emma organization: Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria 3010, Australia – sequence: 7 givenname: Yuen Han surname: Lam fullname: Lam, Yuen Han organization: Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria 3010, Australia – sequence: 8 givenname: Katrina J. surname: Binger fullname: Binger, Katrina J. organization: Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria 3010, Australia – sequence: 9 givenname: Neil H. surname: Thomson fullname: Thomson, Neil H. organization: The Astbury Center for Structural Molecular Biology and School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, UK – sequence: 10 givenname: Sheena E. surname: Radford fullname: Radford, Sheena E. organization: The Astbury Center for Structural Molecular Biology and Institute of Structural and Molecular Biology, University of Leeds, Leeds LS2 9JT, UK – sequence: 11 givenname: Trevor A. surname: Smith fullname: Smith, Trevor A. organization: School of Chemistry and ARC Center of Excellence for Coherent X-ray Science, University of Melbourne, Parkville, Victoria 3010, Australia – sequence: 12 givenname: Shirley A. surname: Müller fullname: Müller, Shirley A. organization: C-CINA and Maurice E. Müller Institute, Biozentrum, University of Basel, WRO-1058 Mattenstrasse 26, CH-4058 Basel, Switzerland – sequence: 13 givenname: Andreas surname: Engel fullname: Engel, Andreas organization: C-CINA and Maurice E. Müller Institute, Biozentrum, University of Basel, WRO-1058 Mattenstrasse 26, CH-4058 Basel, Switzerland – sequence: 14 givenname: Michael D.W. surname: Griffin fullname: Griffin, Michael D.W. organization: Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria 3010, Australia – sequence: 15 givenname: Irene surname: Yarovsky fullname: Yarovsky, Irene organization: Health Innovations Research Institute, School of Applied Sciences, RMIT University, GPO Box 2476V, Melbourne, Victoria 3001, Australia – sequence: 16 givenname: Paul R. surname: Gooley fullname: Gooley, Paul R. organization: Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria 3010, Australia – sequence: 17 givenname: Geoffrey J. surname: Howlett fullname: Howlett, Geoffrey J. email: ghowlett@unimelb.edu.au organization: Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria 3010, Australia |
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| Keywords | ThT SPC X-ray diffraction fluorescence resonance energy transfer AFM MPL TCSPC cross-β-structure atomic force microscopy 1,5-I-AEDANS STEM MD scanning transmission electron microscopy FRET apoC-II H/D TEM GuHCl |
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| SubjectTerms | Amino Acid Sequence Amyloid - chemistry Amyloid - ultrastructure Apolipoprotein C-II - chemistry atomic force microscopy cross-β-structure fluorescence resonance energy transfer Humans Microscopy, Atomic Force Models, Chemical Molecular Dynamics Simulation Molecular Sequence Data Protein Structure, Secondary scanning transmission electron microscopy Sequence Analysis, Protein X-Ray Diffraction |
| Title | A Structural Model for Apolipoprotein C-II Amyloid Fibrils: Experimental Characterization and Molecular Dynamics Simulations |
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