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Kandola T, Venkatesan S, Zhang J, Lerbakken BT, Von Schulze A, Blanck JF, Wu J, Unruh JR, Berry P, Lange JJ, Box AC, Cook M, Sagui C, Halfmann R. Pathologic polyglutamine aggregation begins with a self-poisoning polymer crystal. eLife 2023; 12:RP86939. [PMID: 37921648 PMCID: PMC10624427 DOI: 10.7554/elife.86939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2023] Open
Abstract
A long-standing goal of amyloid research has been to characterize the structural basis of the rate-determining nucleating event. However, the ephemeral nature of nucleation has made this goal unachievable with existing biochemistry, structural biology, and computational approaches. Here, we addressed that limitation for polyglutamine (polyQ), a polypeptide sequence that causes Huntington's and other amyloid-associated neurodegenerative diseases when its length exceeds a characteristic threshold. To identify essential features of the polyQ amyloid nucleus, we used a direct intracellular reporter of self-association to quantify frequencies of amyloid appearance as a function of concentration, conformational templates, and rational polyQ sequence permutations. We found that nucleation of pathologically expanded polyQ involves segments of three glutamine (Q) residues at every other position. We demonstrate using molecular simulations that this pattern encodes a four-stranded steric zipper with interdigitated Q side chains. Once formed, the zipper poisoned its own growth by engaging naive polypeptides on orthogonal faces, in a fashion characteristic of polymer crystals with intramolecular nuclei. We further show that self-poisoning can be exploited to block amyloid formation, by genetically oligomerizing polyQ prior to nucleation. By uncovering the physical nature of the rate-limiting event for polyQ aggregation in cells, our findings elucidate the molecular etiology of polyQ diseases.
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Affiliation(s)
- Tej Kandola
- Stowers Institute for Medical ResearchKansas CityUnited States
- The Open UniversityMilton KeynesUnited Kingdom
| | | | - Jiahui Zhang
- Department of Physics, North Carolina State UniversityRaleighUnited States
| | | | | | | | - Jianzheng Wu
- Stowers Institute for Medical ResearchKansas CityUnited States
- Department of Biochemistry and Molecular Biology, University of Kansas Medical CenterKansas CityUnited States
| | - Jay R Unruh
- Stowers Institute for Medical ResearchKansas CityUnited States
| | - Paula Berry
- Stowers Institute for Medical ResearchKansas CityUnited States
| | - Jeffrey J Lange
- Stowers Institute for Medical ResearchKansas CityUnited States
| | - Andrew C Box
- Stowers Institute for Medical ResearchKansas CityUnited States
| | - Malcolm Cook
- Stowers Institute for Medical ResearchKansas CityUnited States
| | - Celeste Sagui
- Department of Physics, North Carolina State UniversityRaleighUnited States
| | - Randal Halfmann
- Stowers Institute for Medical ResearchKansas CityUnited States
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Kandola T, Venkatesan S, Zhang J, Lerbakken B, Schulze AV, Blanck JF, Wu J, Unruh J, Berry P, Lange JJ, Box A, Cook M, Sagui C, Halfmann R. Pathologic polyglutamine aggregation begins with a self-poisoning polymer crystal. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.20.533418. [PMID: 36993401 PMCID: PMC10055281 DOI: 10.1101/2023.03.20.533418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
A long-standing goal of amyloid research has been to characterize the structural basis of the rate-determining nucleating event. However, the ephemeral nature of nucleation has made this goal unachievable with existing biochemistry, structural biology, and computational approaches. Here, we addressed that limitation for polyglutamine (polyQ), a polypeptide sequence that causes Huntington's and other amyloid-associated neurodegenerative diseases when its length exceeds a characteristic threshold. To identify essential features of the polyQ amyloid nucleus, we used a direct intracellular reporter of self-association to quantify frequencies of amyloid appearance as a function of concentration, conformational templates, and rational polyQ sequence permutations. We found that nucleation of pathologically expanded polyQ involves segments of three glutamine (Q) residues at every other position. We demonstrate using molecular simulations that this pattern encodes a four-stranded steric zipper with interdigitated Q side chains. Once formed, the zipper poisoned its own growth by engaging naive polypeptides on orthogonal faces, in a fashion characteristic of polymer crystals with intramolecular nuclei. We further show that self-poisoning can be exploited to block amyloid formation, by genetically oligomerizing polyQ prior to nucleation. By uncovering the physical nature of the rate-limiting event for polyQ aggregation in cells, our findings elucidate the molecular etiology of polyQ diseases.
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Affiliation(s)
- Tej Kandola
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
- The Open University, Milton Keyes, MK7 6AA, UK
| | | | - Jiahui Zhang
- Department of Physics, North Carolina State University, Raleigh, NC 27695, USA
| | | | - Alex Von Schulze
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Jillian F Blanck
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Jianzheng Wu
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Jay Unruh
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Paula Berry
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Jeffrey J Lange
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Andrew Box
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Malcolm Cook
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Celeste Sagui
- Department of Physics, North Carolina State University, Raleigh, NC 27695, USA
| | - Randal Halfmann
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
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Nacar C. Propensities of Some Amino Acid Pairings in α-Helices Vary with Length. Protein J 2022; 41:551-562. [PMID: 36169766 DOI: 10.1007/s10930-022-10076-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/15/2022] [Indexed: 11/29/2022]
Abstract
The results of secondary structure prediction methods are widely used in applications in biotechnology and bioinformatics. However, the accuracy limit of these methods could be improved up to 92%. One approach to achieve this goal is to harvest information from the primary structure of the peptide. This study aims to contribute to this goal by investigating the variations in propensity of amino acid pairings to α-helices in globular proteins depending on helix length. (n):(n + 4) residue pairings were determined using a comprehensive peptide data set according to backbone hydrogen bond criterion which states that backbone hydrogen bond is the dominant driving force of protein folding. Helix length is limited to 13 to 26 residues. Findings of this study show that propensities of ALA:GLY and GLY:GLU pairings to α-helix in globular protein increase with increasing helix length but of ALA:ALA and ALA:VAL decrease. While the frequencies of ILE:ALA, LEU:ALA, LEU:GLN, LEU:GLU, LEU:LEU, MET:ILE and VAL:LEU pairings remain roughly constant with length, the 25 residue pairings have varying propensities in narrow helix lengths. The remaining pairings have no prominent propensity to α-helices.
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Affiliation(s)
- Cevdet Nacar
- Department of Biophysics, School of Medicine, Marmara University, Istanbul, Turkey.
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Chan NJ, Lentz S, Gurr PA, Tan S, Scheibel T, Qiao GG. Crosslinked Polypeptide Films via RAFT-Mediated Continuous Assembly of Polymers. Angew Chem Int Ed Engl 2022; 61:e202112842. [PMID: 34861079 PMCID: PMC9305155 DOI: 10.1002/anie.202112842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Indexed: 11/08/2022]
Abstract
Polypeptide coatings are a cornerstone in the field of surface modification due to their widespread biological potential. As their properties are dictated by their structural features, subsequent control thereof using unique fabrication strategies is important. Herein, we report a facile method of precisely creating densely crosslinked polypeptide films with unusually high random coil content through continuous assembly polymerization via reversible addition-fragmentation chain transfer (CAP-RAFT). CAP-RAFT was fundamentally investigated using methacrylated poly-l-lysine (PLLMA) and methacrylated poly-l-glutamic acid (PLGMA). Careful technique refinement resulted in films up to 36.1±1.1 nm thick which could be increased to 94.9±8.2 nm after using this strategy multiple times. PLLMA and PLGMA films were found to have 30-50 % random coil conformations. Degradation by enzymes present during wound healing reveals potential for applications in drug delivery and tissue engineering.
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Affiliation(s)
- Nicholas J. Chan
- Polymer Science GroupDepartment of Chemical EngineeringUniversity of MelbourneParkvilleMelbourneVictoria3010Australia
- Lehrstuhl BiomaterialienUniversität BayreuthProf.-Rüdiger-Bormann-Str. 195447BayreuthGermany
| | - Sarah Lentz
- Polymer Science GroupDepartment of Chemical EngineeringUniversity of MelbourneParkvilleMelbourneVictoria3010Australia
- Lehrstuhl BiomaterialienUniversität BayreuthProf.-Rüdiger-Bormann-Str. 195447BayreuthGermany
| | - Paul A. Gurr
- Polymer Science GroupDepartment of Chemical EngineeringUniversity of MelbourneParkvilleMelbourneVictoria3010Australia
| | - Shereen Tan
- Polymer Science GroupDepartment of Chemical EngineeringUniversity of MelbourneParkvilleMelbourneVictoria3010Australia
| | - Thomas Scheibel
- Lehrstuhl BiomaterialienUniversität BayreuthProf.-Rüdiger-Bormann-Str. 195447BayreuthGermany
| | - Greg G. Qiao
- Polymer Science GroupDepartment of Chemical EngineeringUniversity of MelbourneParkvilleMelbourneVictoria3010Australia
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Chan NJ, Lentz S, Gurr PA, Tan S, Scheibel T, Qiao GG. Vernetzte Polypeptide durch RAFT‐vermittelte Polymerisation zum kontinuierlichen Aufbau von Polymerfilmen. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202112842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Nicholas J. Chan
- Polymer Science Group Department of Chemical Engineering University of Melbourne Parkville, Melbourne Victoria 3010 Australien
- Lehrstuhl Biomaterialien Universität Bayreuth Prof.-Rüdiger-Bormann-Str. 1 95447 Bayreuth Deutschland
| | - Sarah Lentz
- Polymer Science Group Department of Chemical Engineering University of Melbourne Parkville, Melbourne Victoria 3010 Australien
- Lehrstuhl Biomaterialien Universität Bayreuth Prof.-Rüdiger-Bormann-Str. 1 95447 Bayreuth Deutschland
| | - Paul A. Gurr
- Polymer Science Group Department of Chemical Engineering University of Melbourne Parkville, Melbourne Victoria 3010 Australien
| | - Shereen Tan
- Polymer Science Group Department of Chemical Engineering University of Melbourne Parkville, Melbourne Victoria 3010 Australien
| | - Thomas Scheibel
- Lehrstuhl Biomaterialien Universität Bayreuth Prof.-Rüdiger-Bormann-Str. 1 95447 Bayreuth Deutschland
| | - Greg G. Qiao
- Polymer Science Group Department of Chemical Engineering University of Melbourne Parkville, Melbourne Victoria 3010 Australien
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