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Aina A, Hsueh SCC, Gibbs E, Peng X, Cashman NR, Plotkin SS. De Novo Design of a β-Helix Tau Protein Scaffold: An Oligomer-Selective Vaccine Immunogen Candidate for Alzheimer's Disease. ACS Chem Neurosci 2023; 14:2603-2617. [PMID: 37458595 DOI: 10.1021/acschemneuro.3c00007] [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: 08/03/2023] Open
Abstract
Tau pathology is associated with many neurodegenerative disorders, including Alzheimer's disease (AD), where the spatio-temporal pattern of tau neurofibrillary tangles strongly correlates with disease progression, which motivates therapeutics selective for misfolded tau. Here, we introduce a new avidity-enhanced, multi-epitope approach for protein-misfolding immunogen design, which is predicted to mimic the conformational state of an exposed epitope in toxic tau oligomers. A predicted oligomer-selective tau epitope 343KLDFK347 was scaffolded by designing a β-helix structure that incorporated multiple instances of the 16-residue tau fragment 339VKSEKLDFKDRVQSKI354. Large-scale conformational ensemble analyses involving Jensen-Shannon Divergence and the embedding depth D showed that the multi-epitope scaffolding approach, employed in designing the β-helix scaffold, was predicted to better discriminate toxic tau oligomers than other "monovalent" strategies utilizing a single instance of an epitope for vaccine immunogen design. Using Rosetta, 10,000 sequences were designed and screened for the linker portions of the β-helix scaffold, along with a C-terminal stabilizing α-helix that interacts with the linkers, to optimize the folded structure and stability of the scaffold. Structures were ranked by energy, and the lowest 1% (82 unique sequences) were verified using AlphaFold. Several selection criteria involving AlphaFold are implemented to obtain a lead-designed sequence. The structure was further predicted to have free energetic stability by using Hamiltonian replica exchange molecular dynamics (MD) simulations. The synthesized β-helix scaffold showed direct binding in surface plasmon resonance (SPR) experiments to several antibodies that were raised to the structured epitope using a designed cyclic peptide. Moreover, the strength of binding of these antibodies to in vitro tau oligomers correlated with the strength of binding to the β-helix construct, suggesting that the construct presents an oligomer-like conformation and may thus constitute an effective oligomer-selective immunogen.
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Affiliation(s)
- Adekunle Aina
- Department of Physics and Astronomy, The University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
| | - Shawn C C Hsueh
- Department of Physics and Astronomy, The University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
| | - Ebrima Gibbs
- Djavad Mowafaghian Centre for Brain Health, The University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
| | - Xubiao Peng
- Department of Physics and Astronomy, The University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
| | - Neil R Cashman
- Djavad Mowafaghian Centre for Brain Health, The University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
| | - Steven S Plotkin
- Department of Physics and Astronomy, The University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
- Genome Science and Technology Program, The University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
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Hsueh SCC, Aina A, Roman AY, Cashman NR, Peng X, Plotkin SS. Optimizing Epitope Conformational Ensembles Using α-Synuclein Cyclic Peptide "Glycindel" Scaffolds: A Customized Immunogen Method for Generating Oligomer-Selective Antibodies for Parkinson's Disease. ACS Chem Neurosci 2022; 13:2261-2280. [PMID: 35840132 DOI: 10.1021/acschemneuro.1c00567] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Effectively presenting epitopes on immunogens, in order to raise conformationally selective antibodies through active immunization, is a central problem in treating protein misfolding diseases, particularly neurodegenerative diseases such as Alzheimer's disease or Parkinson's disease. We seek to selectively target conformations enriched in toxic, oligomeric propagating species while sparing the healthy forms of the protein that are often more abundant. To this end, we computationally modeled scaffolded epitopes in cyclic peptides by inserting/deleting a variable number of flanking glycines ("glycindels") to best mimic a misfolding-specific conformation of an epitope of α-synuclein enriched in the oligomer ensemble, as characterized by a region most readily disordered and solvent-exposed in a stressed, partially denatured protofibril. We screen and rank the cyclic peptide scaffolds of α-synuclein in silico based on their ensemble overlap properties with the fibril, oligomer-model and isolated monomer ensembles. We present experimental data of seeded aggregation that support nucleation rates consistent with computationally predicted cyclic peptide conformational similarity. We also introduce a method for screening against structured off-pathway targets in the human proteome by selecting scaffolds with minimal conformational similarity between their epitope and the same solvent-exposed primary sequence in structured human proteins. Different cyclic peptide scaffolds with variable numbers of glycines are predicted computationally to have markedly different conformational ensembles. Ensemble comparison and overlap were quantified by the Jensen-Shannon divergence and a new measure introduced here, the embedding depth, which determines the extent to which a given ensemble is subsumed by another ensemble and which may be a more useful measure in developing immunogens that confer conformational selectivity to an antibody.
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Affiliation(s)
- Shawn C C Hsueh
- Department of Physics and Astronomy, The University of British Columbia, Vancouver, BC V6T 1Z1, Canada
| | - Adekunle Aina
- Department of Physics and Astronomy, The University of British Columbia, Vancouver, BC V6T 1Z1, Canada
| | - Andrei Yu Roman
- Djavad Mowafaghian Centre for Brain Health, The University of British Columbia, Vancouver, BC V6T 2B5, Canada
| | - Neil R Cashman
- Djavad Mowafaghian Centre for Brain Health, The University of British Columbia, Vancouver, BC V6T 2B5, Canada
| | - Xubiao Peng
- Department of Physics and Astronomy, The University of British Columbia, Vancouver, BC V6T 1Z1, Canada
| | - Steven S Plotkin
- Department of Physics and Astronomy, The University of British Columbia, Vancouver, BC V6T 1Z1, Canada.,Genome Science and Technology Program, The University of British Columbia, Vancouver, BC V6T 1Z1, Canada
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Nam J, Kwon S, Yu YG, Seo HB, Lee JS, Lee WB, Kim Y, Seo M. Folding of Sequence-Controlled Graft Copolymers to Subdomain-Defined Single-Chain Nanoparticles. Macromolecules 2021. [DOI: 10.1021/acs.macromol.1c01674] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Jiyun Nam
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Sangwoo Kwon
- School of Chemical and Biological Engineering, Institute of Chemical Processes, Seoul National University, Seoul 08826, Republic of Korea
| | - Yong-Guen Yu
- School of Materials Science and Engineering, Gwangju Institute of Science and Technology, 123 Cheomdangwagi-ro, Buk-gu, Gwangju 61005, Republic of Korea
| | - Ho-Bin Seo
- School of Materials Science and Engineering, Gwangju Institute of Science and Technology, 123 Cheomdangwagi-ro, Buk-gu, Gwangju 61005, Republic of Korea
| | - Jae-Suk Lee
- School of Materials Science and Engineering, Gwangju Institute of Science and Technology, 123 Cheomdangwagi-ro, Buk-gu, Gwangju 61005, Republic of Korea
| | - Won Bo Lee
- School of Chemical and Biological Engineering, Institute of Chemical Processes, Seoul National University, Seoul 08826, Republic of Korea
| | - YongJoo Kim
- School of Advanced Materials Engineering, Kookmin University, Seoul 02707, Republic of Korea
| | - Myungeun Seo
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
- KAIST Institute for the Nanocentury, KAIST, Daejeon 34141, Republic of Korea
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Rovigatti L, Gnan N, Ninarello A, Zaccarelli E. Connecting Elasticity and Effective Interactions of Neutral Microgels: The Validity of the Hertzian Model. Macromolecules 2019. [DOI: 10.1021/acs.macromol.9b00099] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Lorenzo Rovigatti
- Dipartimento di Fisica, Sapienza Università di Roma, Piazzale A. Moro 2, 00185 Roma, Italy
- CNR-ISC, Uos Sapienza, Piazzale A. Moro 2, 00185 Roma, Italy
| | - Nicoletta Gnan
- Dipartimento di Fisica, Sapienza Università di Roma, Piazzale A. Moro 2, 00185 Roma, Italy
- CNR-ISC, Uos Sapienza, Piazzale A. Moro 2, 00185 Roma, Italy
| | - Andrea Ninarello
- Dipartimento di Fisica, Sapienza Università di Roma, Piazzale A. Moro 2, 00185 Roma, Italy
- CNR-ISC, Uos Sapienza, Piazzale A. Moro 2, 00185 Roma, Italy
| | - Emanuela Zaccarelli
- Dipartimento di Fisica, Sapienza Università di Roma, Piazzale A. Moro 2, 00185 Roma, Italy
- CNR-ISC, Uos Sapienza, Piazzale A. Moro 2, 00185 Roma, Italy
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CAVALLI M, GRIFFA M, BRESSI S, PARTL M, TEBALDI G, POULIKAKOS L. Multiscale imaging and characterization of the effect of mixing temperature on asphalt concrete containing recycled components. J Microsc 2016; 264:22-33. [DOI: 10.1111/jmi.12412] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Revised: 02/22/2016] [Accepted: 03/25/2016] [Indexed: 11/27/2022]
Affiliation(s)
- M.C. CAVALLI
- Empa; Swiss Federal Laboratories for Materials Science and Technology; Dübendorf Switzerland
| | - M. GRIFFA
- Empa; Swiss Federal Laboratories for Materials Science and Technology; Dübendorf Switzerland
| | - S. BRESSI
- École polytechnique fédérale de Lausanne; EPFL; Lausanne Switzerland
| | - M.N. PARTL
- Empa; Swiss Federal Laboratories for Materials Science and Technology; Dübendorf Switzerland
| | - G. TEBALDI
- Department of Civil and Environmental Engineering and Architecture; University of Parma; Parma Italy
- Department of Civil & Coastal Engineering; University of Florida - E.S.S.I.E; Florida U.S.A
| | - L.D. POULIKAKOS
- Empa; Swiss Federal Laboratories for Materials Science and Technology; Dübendorf Switzerland
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Li X, Zhu L, Duan S, Zhao Y, Ågren H. Aggregation-induced chiral symmetry breaking of a naphthalimide–cyanostilbene dyad. Phys Chem Chem Phys 2014; 16:23854-60. [DOI: 10.1039/c4cp04070h] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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Tang X, Koenig PH, Larson RG. Molecular Dynamics Simulations of Sodium Dodecyl Sulfate Micelles in Water—The Effect of the Force Field. J Phys Chem B 2014; 118:3864-80. [DOI: 10.1021/jp410689m] [Citation(s) in RCA: 112] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Xueming Tang
- Department
of Chemical Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Peter H. Koenig
- Computational Chemistry, Modeling and Simulation, The Procter & Gamble Company, 8611 Beckett Road, West Chester, Ohio 45069, United States
| | - Ronald G. Larson
- Department
of Chemical Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
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Farooque TM, Camp CH, Tison CK, Kumar G, Parekh SH, Simon CG. Measuring stem cell dimensionality in tissue scaffolds. Biomaterials 2014; 35:2558-67. [DOI: 10.1016/j.biomaterials.2013.12.092] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Accepted: 12/22/2013] [Indexed: 01/28/2023]
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Crowding in Polymer–Nanoparticle Mixtures. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2014; 307:27-71. [DOI: 10.1016/b978-0-12-800046-5.00003-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
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Das A, Sin BK, Mohazab AR, Plotkin SS. Unfolded protein ensembles, folding trajectories, and refolding rate prediction. J Chem Phys 2013; 139:121925. [DOI: 10.1063/1.4817215] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
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Fytas NG, Theodorakis PE. Molecular dynamics simulations of single-component bottle-brush polymers with flexible backbones under poor solvent conditions. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2013; 25:285105. [PMID: 23765452 DOI: 10.1088/0953-8984/25/28/285105] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Conformations of a single-component bottle-brush polymer with a fully flexible backbone under poor solvent conditions are studied by molecular dynamics simulations, using a coarse-grained bead-spring model with side chains of up to N = 40 effective monomers. By variation of the solvent quality and the grafting density σ with which side chains are grafted onto the flexible backbone, we study for backbone lengths of up to Nb = 100 the crossover from the brush/coil regime to the dense collapsed state. At lower temperatures, where collapsed chains with a constant monomer density are observed, the choice of the above parameters does not play any role and it is the total number of monomers that defines the dimensions of the chains. Furthermore, bottle-brush polymers with longer side chains possess higher spherical symmetry compared to polymers with lower side-chain lengths in contrast to what one may intuitively expect, as the stretching of the side chains is less important than the increase of their length. At higher temperatures, always below the Theta (Θ) temperature, coil-like configurations, similar to a single polymer chain, or brush-like configurations, similar to a homogeneous cylindrical bottle-brush polymer with a rigid backbone, are observed, depending on the choice of the particular parameters N and σ. In the crossover regime between the collapsed state (globule) and the coil/brush regime the acylindricity increases, whereas for temperatures outside of this range, bottle-brush polymers maintain a highly cylindrical symmetry in all configurational states.
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Affiliation(s)
- Nikolaos G Fytas
- Applied Mathematics Research Centre, Coventry University, Coventry CV1 5FB, UK.
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Theodorakis PE, Fytas NG. A study for the static properties of symmetric linear multiblock copolymers under poor solvent conditions. J Chem Phys 2012; 136:094902. [DOI: 10.1063/1.3689303] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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