1
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Dear AJ, Teng X, Ball SR, Lewin J, Horne RI, Clow D, Stevenson A, Harper N, Yahya K, Yang X, Brewerton SC, Thomson J, Michaels TCT, Linse S, Knowles TPJ, Habchi J, Meisl G. Molecular mechanism of α-synuclein aggregation on lipid membranes revealed. Chem Sci 2024; 15:7229-7242. [PMID: 38756798 PMCID: PMC11095391 DOI: 10.1039/d3sc05661a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 03/14/2024] [Indexed: 05/18/2024] Open
Abstract
The central hallmark of Parkinson's disease pathology is the aggregation of the α-synuclein protein, which, in its healthy form, is associated with lipid membranes. Purified monomeric α-synuclein is relatively stable in vitro, but its aggregation can be triggered by the presence of lipid vesicles. Despite this central importance of lipids in the context of α-synuclein aggregation, their detailed mechanistic role in this process has not been established to date. Here, we use chemical kinetics to develop a mechanistic model that is able to globally describe the aggregation behaviour of α-synuclein in the presence of DMPS lipid vesicles, across a range of lipid and protein concentrations. Through the application of our kinetic model to experimental data, we find that the reaction is a co-aggregation process involving both protein and lipids and that lipids promote aggregation as much by enabling fibril elongation as by enabling their initial formation. Moreover, we find that the primary nucleation of lipid-protein co-aggregates takes place not on the surface of lipid vesicles in bulk solution but at the air-water and/or plate interfaces, where lipids and proteins are likely adsorbed. Our model forms the basis for mechanistic insights, also in other lipid-protein co-aggregation systems, which will be crucial in the rational design of drugs that inhibit aggregate formation and act at the key points in the α-synuclein aggregation cascade.
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Affiliation(s)
- Alexander J Dear
- WaveBreak Therapeutics Ltd, Chemistry of Health Lensfield Road Cambridge CB2 1EW UK
| | - Xiangyu Teng
- WaveBreak Therapeutics Ltd, Chemistry of Health Lensfield Road Cambridge CB2 1EW UK
| | - Sarah R Ball
- WaveBreak Therapeutics Ltd, Chemistry of Health Lensfield Road Cambridge CB2 1EW UK
| | - Joshua Lewin
- WaveBreak Therapeutics Ltd, Chemistry of Health Lensfield Road Cambridge CB2 1EW UK
| | - Robert I Horne
- WaveBreak Therapeutics Ltd, Chemistry of Health Lensfield Road Cambridge CB2 1EW UK
| | - Daniel Clow
- WaveBreak Therapeutics Ltd, Chemistry of Health Lensfield Road Cambridge CB2 1EW UK
| | - Alisdair Stevenson
- Department of Biology, Institute of Biochemistry, ETH Zurich Otto Stern Weg 3 8093 Zurich Switzerland
- Bringing Materials to Life Initiative, ETH Zurich Switzerland
| | - Natasha Harper
- WaveBreak Therapeutics Ltd, Chemistry of Health Lensfield Road Cambridge CB2 1EW UK
| | - Kim Yahya
- WaveBreak Therapeutics Ltd, Chemistry of Health Lensfield Road Cambridge CB2 1EW UK
| | - Xiaoting Yang
- WaveBreak Therapeutics Ltd, Chemistry of Health Lensfield Road Cambridge CB2 1EW UK
| | - Suzanne C Brewerton
- WaveBreak Therapeutics Ltd, Chemistry of Health Lensfield Road Cambridge CB2 1EW UK
| | - John Thomson
- WaveBreak Therapeutics Ltd, Chemistry of Health Lensfield Road Cambridge CB2 1EW UK
| | - Thomas C T Michaels
- Department of Biology, Institute of Biochemistry, ETH Zurich Otto Stern Weg 3 8093 Zurich Switzerland
- Bringing Materials to Life Initiative, ETH Zurich Switzerland
| | - Sara Linse
- WaveBreak Therapeutics Ltd, Chemistry of Health Lensfield Road Cambridge CB2 1EW UK
- Biochemistry and Structural Biology, Lund University Lund Sweden
| | - Tuomas P J Knowles
- Yusuf Hamied Department of Chemistry, University of Cambridge Cambridge UK
- Cavendish Laboratory, University of Cambridge Cambridge UK
| | - Johnny Habchi
- WaveBreak Therapeutics Ltd, Chemistry of Health Lensfield Road Cambridge CB2 1EW UK
| | - Georg Meisl
- WaveBreak Therapeutics Ltd, Chemistry of Health Lensfield Road Cambridge CB2 1EW UK
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2
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Dada ST, Toprakcioglu Z, Cali MP, Röntgen A, Hardenberg MC, Morris OM, Mrugalla LK, Knowles TPJ, Vendruscolo M. Pharmacological inhibition of α-synuclein aggregation within liquid condensates. Nat Commun 2024; 15:3835. [PMID: 38714700 PMCID: PMC11076612 DOI: 10.1038/s41467-024-47585-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 04/03/2024] [Indexed: 05/10/2024] Open
Abstract
Aggregated forms of α-synuclein constitute the major component of Lewy bodies, the proteinaceous aggregates characteristic of Parkinson's disease. Emerging evidence suggests that α-synuclein aggregation may occur within liquid condensates formed through phase separation. This mechanism of aggregation creates new challenges and opportunities for drug discovery for Parkinson's disease, which is otherwise still incurable. Here we show that the condensation-driven aggregation pathway of α-synuclein can be inhibited using small molecules. We report that the aminosterol claramine stabilizes α-synuclein condensates and inhibits α-synuclein aggregation within the condensates both in vitro and in a Caenorhabditis elegans model of Parkinson's disease. By using a chemical kinetics approach, we show that the mechanism of action of claramine is to inhibit primary nucleation within the condensates. These results illustrate a possible therapeutic route based on the inhibition of protein aggregation within condensates, a phenomenon likely to be relevant in other neurodegenerative disorders.
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Affiliation(s)
- Samuel T Dada
- Department of Chemistry, Centre for Misfolding Disease, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Zenon Toprakcioglu
- Department of Chemistry, Centre for Misfolding Disease, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Mariana P Cali
- Department of Chemistry, Centre for Misfolding Disease, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Alexander Röntgen
- Department of Chemistry, Centre for Misfolding Disease, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Maarten C Hardenberg
- Department of Chemistry, Centre for Misfolding Disease, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Owen M Morris
- Department of Chemistry, Centre for Misfolding Disease, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Lena K Mrugalla
- Department of Chemistry, Centre for Misfolding Disease, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Tuomas P J Knowles
- Department of Chemistry, Centre for Misfolding Disease, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Michele Vendruscolo
- Department of Chemistry, Centre for Misfolding Disease, University of Cambridge, Cambridge, CB2 1EW, UK.
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3
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Horne RI, Andrzejewska EA, Alam P, Brotzakis ZF, Srivastava A, Aubert A, Nowinska M, Gregory RC, Staats R, Possenti A, Chia S, Sormanni P, Ghetti B, Caughey B, Knowles TPJ, Vendruscolo M. Discovery of potent inhibitors of α-synuclein aggregation using structure-based iterative learning. Nat Chem Biol 2024; 20:634-645. [PMID: 38632492 PMCID: PMC11062903 DOI: 10.1038/s41589-024-01580-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 02/12/2024] [Indexed: 04/19/2024]
Abstract
Machine learning methods hold the promise to reduce the costs and the failure rates of conventional drug discovery pipelines. This issue is especially pressing for neurodegenerative diseases, where the development of disease-modifying drugs has been particularly challenging. To address this problem, we describe here a machine learning approach to identify small molecule inhibitors of α-synuclein aggregation, a process implicated in Parkinson's disease and other synucleinopathies. Because the proliferation of α-synuclein aggregates takes place through autocatalytic secondary nucleation, we aim to identify compounds that bind the catalytic sites on the surface of the aggregates. To achieve this goal, we use structure-based machine learning in an iterative manner to first identify and then progressively optimize secondary nucleation inhibitors. Our results demonstrate that this approach leads to the facile identification of compounds two orders of magnitude more potent than previously reported ones.
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Affiliation(s)
- Robert I Horne
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Ewa A Andrzejewska
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Parvez Alam
- Laboratory of Neurological Infections and Immunity, Rocky Mountain Laboratories, National Institute for Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Z Faidon Brotzakis
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Ankit Srivastava
- Laboratory of Neurological Infections and Immunity, Rocky Mountain Laboratories, National Institute for Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Alice Aubert
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Magdalena Nowinska
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Rebecca C Gregory
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Roxine Staats
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Andrea Possenti
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Sean Chia
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Pietro Sormanni
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Bernardino Ghetti
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Byron Caughey
- Laboratory of Neurological Infections and Immunity, Rocky Mountain Laboratories, National Institute for Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Tuomas P J Knowles
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Michele Vendruscolo
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK.
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4
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Dear AJ, Garcia GA, Meisl G, Collins GA, Knowles TPJ, Goldberg AL. Maximum entropy determination of mammalian proteome dynamics. Proc Natl Acad Sci U S A 2024; 121:e2313107121. [PMID: 38652742 PMCID: PMC11067036 DOI: 10.1073/pnas.2313107121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 03/04/2024] [Indexed: 04/25/2024] Open
Abstract
Full understanding of proteostasis and energy utilization in cells will require knowledge of the fraction of cell proteins being degraded with different half-lives and their rates of synthesis. We therefore developed a method to determine such information that combines mathematical analysis of protein degradation kinetics obtained in pulse-chase experiments with Bayesian data fitting using the maximum entropy principle. This approach will enable rapid analyses of whole-cell protein dynamics in different cell types, physiological states, and neurodegenerative disease. Using it, we obtained surprising insights about protein stabilities in cultured cells normally and upon activation of proteolysis by mTOR inhibition and increasing cAMP or cGMP. It revealed that >90% of protein content in dividing mammalian cell lines is long-lived, with half-lives of 24 to 200 h, and therefore comprises much of the proteins in daughter cells. The well-studied short-lived proteins (half-lives < 10 h) together comprise <2% of cell protein mass, but surprisingly account for 10 to 20% of measurable newly synthesized protein mass. Evolution thus appears to have minimized intracellular proteolysis except to rapidly eliminate misfolded and regulatory proteins.
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Affiliation(s)
- Alexander J. Dear
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA02115
- Department of Chemistry, University of Cambridge, CambridgeCB2 1EW, United Kingdom
| | - Gonzalo A. Garcia
- Department of Chemistry, University of Cambridge, CambridgeCB2 1EW, United Kingdom
| | - Georg Meisl
- Department of Chemistry, University of Cambridge, CambridgeCB2 1EW, United Kingdom
| | - Galen A. Collins
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA02115
- Department of Biochemistry, Molecular Biology, Entomology & Plant Pathology, Mississippi State University, Starkville, MS39762
| | - Tuomas P. J. Knowles
- Department of Chemistry, University of Cambridge, CambridgeCB2 1EW, United Kingdom
- Cavendish Laboratory, Department of Physics, University of Cambridge, CambridgeCB3 0HE, United Kingdom
| | - Alfred L. Goldberg
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA02115
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5
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Wiita EG, Toprakcioglu Z, Jayaram AK, Knowles TPJ. Selenium-silk microgels as antifungal and antibacterial agents. Nanoscale Horiz 2024; 9:609-619. [PMID: 38288551 PMCID: PMC10962633 DOI: 10.1039/d3nh00385j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 11/29/2023] [Indexed: 03/26/2024]
Abstract
Antimicrobial resistance is a leading threat to global health. Alternative therapeutics to combat the rise in drug-resistant strains of bacteria and fungi are thus needed, but the development of new classes of small molecule therapeutics has remained challenging. Here, we explore an orthogonal approach and address this issue by synthesising micro-scale, protein colloidal particles that possess potent antimicrobial properties. We describe an approach for forming silk-based microgels that contain selenium nanoparticles embedded within the protein scaffold. We demonstrate that these materials have both antibacterial and antifungal properties while, crucially, also remaining highly biocompatible with mammalian cell lines. By combing the nanoparticles with silk, the protein microgel is able to fulfill two critical functions; it protects the mammalian cells from the cytotoxic effects of the bare nanoparticles, while simultaneously serving as a carrier for microbial eradication. Furthermore, since the antimicrobial activity originates from physical contact, bacteria and fungi are unlikely to develop resistance to our hybrid biomaterials, which remains a critical issue with current antibiotic and antifungal treatments. Therefore, taken together, these results provide the basis for innovative antimicrobial materials that can target drug-resistant microbial infections.
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Affiliation(s)
- Elizabeth G Wiita
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lenseld Road, Cambridge CB2 1EW, UK.
| | - Zenon Toprakcioglu
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lenseld Road, Cambridge CB2 1EW, UK.
| | - Akhila K Jayaram
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lenseld Road, Cambridge CB2 1EW, UK.
- Cavendish Laboratory, Department of Physics, University of Cambridge, J J Thomson Avenue, Cambridge CB3 0HE, UK
| | - Tuomas P J Knowles
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lenseld Road, Cambridge CB2 1EW, UK.
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6
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Qian D, Ausserwoger H, Sneideris T, Farag M, Pappu RV, Knowles TPJ. Dominance Analysis: A formalism to uncover dominant energetic contributions to biomolecular condensate formation in multicomponent systems. bioRxiv 2024:2023.06.12.544666. [PMID: 38562796 PMCID: PMC10983860 DOI: 10.1101/2023.06.12.544666] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Phase separation in aqueous solutions of macromolecules is thought to underlie the generation of biomolecular condensates in cells. Condensates are membraneless bodies, representing dense, macromolecule-rich phases that coexist with the dilute, macromolecule-deficient phase. In cells, condensates comprise hundreds of different macromolecular and small molecule solutes. Do all components contribute equally or very differently to the driving forces for phase separation? Currently, we lack a coherent formalism to answer this question, a gap we remedy in this work through the introduction of a formalism we term energy dominance analysis. This approach rests on model-free analysis of shapes of the dilute arms of phase boundaries, slopes of tie lines, and changes to dilute phase concentrations in response to perturbations of concentrations of different solutes. We present the formalism that underlies dominance analysis, and establish its accuracy and flexibility by deploying it to analyse phase spaces probed in silico, in vitro , and in cellulo .
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7
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Chia S, Cataldi RL, Ruggeri FS, Limbocker R, Condado-Morales I, Pisani K, Possenti A, Linse S, Knowles TPJ, Habchi J, Mannini B, Vendruscolo M. A Relationship between the Structures and Neurotoxic Effects of Aβ Oligomers Stabilized by Different Metal Ions. ACS Chem Neurosci 2024; 15:1125-1134. [PMID: 38416693 PMCID: PMC10958495 DOI: 10.1021/acschemneuro.3c00718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 02/06/2024] [Accepted: 02/06/2024] [Indexed: 03/01/2024] Open
Abstract
Oligomeric assemblies of the amyloid β peptide (Aβ) have been investigated for over two decades as possible neurotoxic agents in Alzheimer's disease. However, due to their heterogeneous and transient nature, it is not yet fully established which of the structural features of these oligomers may generate cellular damage. Here, we study distinct oligomer species formed by Aβ40 (the 40-residue form of Aβ) in the presence of four different metal ions (Al3+, Cu2+, Fe2+, and Zn2+) and show that they differ in their structure and toxicity in human neuroblastoma cells. We then describe a correlation between the size of the oligomers and their neurotoxic activity, which provides a type of structure-toxicity relationship for these Aβ40 oligomer species. These results provide insight into the possible role of metal ions in Alzheimer's disease by the stabilization of Aβ oligomers.
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Affiliation(s)
- Sean Chia
- Centre
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K.
| | - Rodrigo Lessa Cataldi
- Centre
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K.
| | - Francesco Simone Ruggeri
- Centre
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K.
| | - Ryan Limbocker
- Centre
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K.
| | - Itzel Condado-Morales
- Centre
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K.
| | - Katarina Pisani
- Centre
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K.
| | - Andrea Possenti
- Centre
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K.
| | - Sara Linse
- Department
of Biochemistry & Structural Biology, Center for Molecular Protein
Science, Lund University, PO box 124, 221 00 Lund, Sweden
| | - Tuomas P. J. Knowles
- Centre
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K.
- Department
of Physics, Cavendish Laboratory, Cambridge CB3 0HE, U.K.
| | - Johnny Habchi
- Centre
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K.
| | - Benedetta Mannini
- Centre
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K.
| | - Michele Vendruscolo
- Centre
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K.
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8
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Sahtoe DD, Andrzejewska EA, Han HL, Rennella E, Schneider MM, Meisl G, Ahlrichs M, Decarreau J, Nguyen H, Kang A, Levine P, Lamb M, Li X, Bera AK, Kay LE, Knowles TPJ, Baker D. Design of amyloidogenic peptide traps. Nat Chem Biol 2024:10.1038/s41589-024-01578-5. [PMID: 38503834 DOI: 10.1038/s41589-024-01578-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 02/09/2024] [Indexed: 03/21/2024]
Abstract
Segments of proteins with high β-strand propensity can self-associate to form amyloid fibrils implicated in many diseases. We describe a general approach to bind such segments in β-strand and β-hairpin conformations using de novo designed scaffolds that contain deep peptide-binding clefts. The designs bind their cognate peptides in vitro with nanomolar affinities. The crystal structure of a designed protein-peptide complex is close to the design model, and NMR characterization reveals how the peptide-binding cleft is protected in the apo state. We use the approach to design binders to the amyloid-forming proteins transthyretin, tau, serum amyloid A1 and amyloid β1-42 (Aβ42). The Aβ binders block the assembly of Aβ fibrils as effectively as the most potent of the clinically tested antibodies to date and protect cells from toxic Aβ42 species.
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Affiliation(s)
- Danny D Sahtoe
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
- Institute for Protein Design, University of Washington, Seattle, WA, USA.
- HHMI, University of Washington, Seattle, WA, USA.
- Hubrecht Institute, Utrecht, the Netherlands.
| | - Ewa A Andrzejewska
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Hannah L Han
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Enrico Rennella
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | | | - Georg Meisl
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Maggie Ahlrichs
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Justin Decarreau
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Hannah Nguyen
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Alex Kang
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Paul Levine
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Mila Lamb
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Xinting Li
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Asim K Bera
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Lewis E Kay
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
| | - Tuomas P J Knowles
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
- Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
- Institute for Protein Design, University of Washington, Seattle, WA, USA.
- HHMI, University of Washington, Seattle, WA, USA.
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9
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Kosmidis Papadimitriou A, Chong SW, Shen Y, Lee OS, Knowles TPJ, Grover LM, Vigolo D. Fabrication of gradient hydrogels using a thermophoretic approach in microfluidics. Biofabrication 2024; 16:025023. [PMID: 38377611 DOI: 10.1088/1758-5090/ad2b05] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 02/20/2024] [Indexed: 02/22/2024]
Abstract
The extracellular matrix presents spatially varying physical cues that can influence cell behavior in many processes. Physical gradients within hydrogels that mimic the heterogenous mechanical microenvironment are useful to study the impact of these cues on cellular responses. Therefore, simple and reliable techniques to create such gradient hydrogels are highly desirable. This work demonstrates the fabrication of stiffness gradient Gellan gum (GG) hydrogels by applying a temperature gradient across a microchannel containing hydrogel precursor solution. Thermophoretic migration of components within the precursor solution generates a concentration gradient that mirrors the temperature gradient profile, which translates into mechanical gradients upon crosslinking. Using this technique, GG hydrogels with stiffness gradients ranging from 20 to 90 kPa over 600µm are created, covering the elastic moduli typical of moderately hard to hard tissues. MC3T3 osteoblast cells are then cultured on these gradient substrates, which exhibit preferential migration and enhanced osteogenic potential toward the stiffest region on the gradient. Overall, the thermophoretic approach provides a non-toxic and effective method to create hydrogels with defined mechanical gradients at the micron scale suitable forin vitrobiological studies and potentially tissue engineering applications.
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Affiliation(s)
| | - Shin Wei Chong
- The University of Sydney, School of Biomedical Engineering, Sydney, NSW 2006, Australia
- The University of Sydney Nano Institute, University of Sydney, Sydney, NSW 2006, Australia
| | - Yi Shen
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
- The University of Sydney, School of Chemical and Biomolecular Engineering, Sydney, NSW 2006, Australia
- The University of Sydney Nano Institute, University of Sydney, Sydney, NSW 2006, Australia
| | - Oisin Stefan Lee
- The University of Sydney, School of Biomedical Engineering, Sydney, NSW 2006, Australia
| | - Tuomas P J Knowles
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Liam M Grover
- School of Chemical Engineering, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Daniele Vigolo
- School of Chemical Engineering, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
- The University of Sydney, School of Biomedical Engineering, Sydney, NSW 2006, Australia
- The University of Sydney Nano Institute, University of Sydney, Sydney, NSW 2006, Australia
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10
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Bernardim B, Conde J, Hakala T, Becher JB, Canzano M, Vasco AV, Knowles TPJ, Cameron J, Bernardes GJL. Cathepsin B Processing Is Required for the In Vivo Efficacy of Albumin-Drug Conjugates. Bioconjug Chem 2024; 35:132-139. [PMID: 38345213 PMCID: PMC10885003 DOI: 10.1021/acs.bioconjchem.3c00478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 01/26/2024] [Accepted: 01/30/2024] [Indexed: 02/22/2024]
Abstract
Targeted drug delivery approaches that selectively and preferentially deliver therapeutic agents to specific tissues are of great interest for safer and more effective pharmaceutical treatments. We investigated whether cathepsin B cleavage of a valine-citrulline [VC(S)]-containing linker is required for the release of monomethyl auristatin E (MMAE) from albumin-drug conjugates. In this study, we used an engineered version of human serum albumin, Veltis High Binder II (HBII), which has enhanced binding to the neonatal Fc (fragment crystallizable) receptor (FcRn) to improve drug release upon binding and FcRn-mediated recycling. The linker-payload was conjugated to cysteine 34 of albumin using a carbonylacrylic (caa) reagent which produced homogeneous and plasma stable conjugates that retained FcRn binding. Two caa-linker-MMAE reagents were synthesized─one with a cleavable [VC(S)] linker and one with a noncleavable [VC(R)] linker─to question whether protease-mediated cleavage is needed for MMAE release. Our findings demonstrate that cathepsin B is required to achieve efficient and selective antitumor activity. The conjugates equipped with the cleavable [VC(S)] linker had potent antitumor activity in vivo facilitated by the release of free MMAE upon FcRn binding and internalization. In addition to the pronounced antitumor activity of the albumin conjugates in vivo, we also demonstrated their preferable tumor biodistribution and biocompatibility with no associated toxicity or side effects. These results suggest that the use of engineered albumins with high FcRn binding combined with protease cleavable linkers is an efficient strategy to target delivery of drugs to solid tumors.
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Affiliation(s)
- Barbara Bernardim
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, CB2 1EW Cambridge, United Kingdom
| | - João Conde
- Instituto
de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028 Lisboa, Portugal
| | - Tuuli Hakala
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, CB2 1EW Cambridge, United Kingdom
| | - Julie B. Becher
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, CB2 1EW Cambridge, United Kingdom
| | - Mary Canzano
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, CB2 1EW Cambridge, United Kingdom
| | - Aldrin V. Vasco
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, CB2 1EW Cambridge, United Kingdom
| | - Tuomas P. J. Knowles
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, CB2 1EW Cambridge, United Kingdom
| | - Jason Cameron
- Albumedix
Ltd, Mabel Street, Nottingham NG2 3ED, United Kingdom
| | - Gonçalo J. L. Bernardes
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, CB2 1EW Cambridge, United Kingdom
- Instituto
de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028 Lisboa, Portugal
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11
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Curk S, Krausser J, Meisl G, Frenkel D, Linse S, Michaels TCT, Knowles TPJ, Šarić A. Self-replication of A β42 aggregates occurs on small and isolated fibril sites. Proc Natl Acad Sci U S A 2024; 121:e2220075121. [PMID: 38335256 PMCID: PMC10873593 DOI: 10.1073/pnas.2220075121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 11/17/2023] [Indexed: 02/12/2024] Open
Abstract
Self-replication of amyloid fibrils via secondary nucleation is an intriguing physicochemical phenomenon in which existing fibrils catalyze the formation of their own copies. The molecular events behind this fibril surface-mediated process remain largely inaccessible to current structural and imaging techniques. Using statistical mechanics, computer modeling, and chemical kinetics, we show that the catalytic structure of the fibril surface can be inferred from the aggregation behavior in the presence and absence of a fibril-binding inhibitor. We apply our approach to the case of Alzheimer's A[Formula: see text] amyloid fibrils formed in the presence of proSP-C Brichos inhibitors. We find that self-replication of A[Formula: see text] fibrils occurs on small catalytic sites on the fibril surface, which are far apart from each other, and each of which can be covered by a single Brichos inhibitor.
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Affiliation(s)
- Samo Curk
- Institute of Science and Technology Austria, Klosterneuburg3400, Austria
- Department of Physics and Astronomy, Laboratory for Molecular Cell Biology, University College London, LondonWC1E 6BT, United Kingdom
| | - Johannes Krausser
- Department of Physics and Astronomy, Laboratory for Molecular Cell Biology, University College London, LondonWC1E 6BT, United Kingdom
| | - Georg Meisl
- Yusuf Hamied Department of Chemistry, University of Cambridge, CambridgeCB2 1EW, United Kingdom
| | - Daan Frenkel
- Yusuf Hamied Department of Chemistry, University of Cambridge, CambridgeCB2 1EW, United Kingdom
| | - Sara Linse
- Department of Biochemistry and Structural Biology, Lund University, Lund22100, Sweden
| | - Thomas C. T. Michaels
- Department of Physics and Astronomy, Laboratory for Molecular Cell Biology, University College London, LondonWC1E 6BT, United Kingdom
- Department of Biology, Institute of Biochemistry, ETH Zürich, Zürich8093, Switzerland
| | - Tuomas P. J. Knowles
- Yusuf Hamied Department of Chemistry, University of Cambridge, CambridgeCB2 1EW, United Kingdom
| | - Anđela Šarić
- Institute of Science and Technology Austria, Klosterneuburg3400, Austria
- Department of Physics and Astronomy, Laboratory for Molecular Cell Biology, University College London, LondonWC1E 6BT, United Kingdom
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12
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Miller A, Chia S, Klimont E, Knowles TPJ, Vendruscolo M, Ruggeri FS. Maturation-dependent changes in the size, structure and seeding capacity of Aβ42 amyloid fibrils. Commun Biol 2024; 7:153. [PMID: 38321144 PMCID: PMC10847148 DOI: 10.1038/s42003-024-05858-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 01/26/2024] [Indexed: 02/08/2024] Open
Abstract
Many proteins self-assemble to form amyloid fibrils, which are highly organized structures stabilized by a characteristic cross-β network of hydrogen bonds. This process underlies a variety of human diseases and can be exploited to develop versatile functional biomaterials. Thus, protein self-assembly has been widely studied to shed light on the properties of fibrils and their intermediates. A still open question in the field concerns the microscopic processes that underlie the long-time behaviour and properties of amyloid fibrillar assemblies. Here, we use atomic force microscopy with angstrom-sensitivity to observe that amyloid fibrils undergo a maturation process, associated with an increase in both fibril length and thickness, leading to a decrease of their density, and to a change in their cross-β sheet content. These changes affect the ability of the fibrils to catalyse the formation of new aggregates. The identification of these changes helps us understand the fibril maturation processes, facilitate the targeting of amyloid fibrils in drug discovery, and offer insight into the development of biocompatible and sustainable protein-based materials.
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Affiliation(s)
- Alyssa Miller
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Sean Chia
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Ewa Klimont
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Tuomas P J Knowles
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
- Cavendish Laboratory, University of Cambridge, Cambridge, CB3 0HE, UK.
| | - Michele Vendruscolo
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
| | - Francesco Simone Ruggeri
- Laboratory of Organic Chemistry, Wageningen University & Research, Stippeneng 4, Wageningen, 6703 WE, the Netherlands.
- Physical Chemistry and Soft Matter, Wageningen University & Research, Wageningen University, Stippeneng 4, Wageningen, 6703 WE, the Netherlands.
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13
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Priddey A, Chen-Xu MXH, Cooper DJ, MacMillan S, Meisl G, Xu CK, Hosmillo M, Goodfellow IG, Kollyfas R, Doffinger R, Bradley JR, Mohorianu II, Jones R, Knowles TPJ, Smith R, Kosmoliaptsis V. Microfluidic antibody profiling after repeated SARS-CoV-2 vaccination links antibody affinity and concentration to impaired immunity and variant escape in patients on anti-CD20 therapy. Front Immunol 2024; 14:1296148. [PMID: 38259440 PMCID: PMC10800570 DOI: 10.3389/fimmu.2023.1296148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 12/06/2023] [Indexed: 01/24/2024] Open
Abstract
Background Patients with autoimmune/inflammatory conditions on anti-CD20 therapies, such as rituximab, have suboptimal humoral responses to vaccination and are vulnerable to poorer clinical outcomes following SARS-CoV-2 infection. We aimed to examine how the fundamental parameters of antibody responses, namely, affinity and concentration, shape the quality of humoral immunity after vaccination in these patients. Methods We performed in-depth antibody characterisation in sera collected 4 to 6 weeks after each of three vaccine doses to wild-type (WT) SARS-CoV-2 in rituximab-treated primary vasculitis patients (n = 14) using Luminex and pseudovirus neutralisation assays, whereas we used a novel microfluidic-based immunoassay to quantify polyclonal antibody affinity and concentration against both WT and Omicron (B.1.1.529) variants. We performed comparative antibody profiling at equivalent timepoints in healthy individuals after three antigenic exposures to WT SARS-CoV-2 (one infection and two vaccinations; n = 15) and in convalescent patients after WT SARS-CoV-2 infection (n = 30). Results Rituximab-treated patients had lower antibody levels and neutralisation titres against both WT and Omicron SARS-CoV-2 variants compared to healthy individuals. Neutralisation capacity was weaker against Omicron versus WT both in rituximab-treated patients and in healthy individuals. In the rituximab cohort, this was driven by lower antibody affinity against Omicron versus WT [median (range) KD: 21.6 (9.7-38.8) nM vs. 4.6 (2.3-44.8) nM, p = 0.0004]. By contrast, healthy individuals with hybrid immunity produced a broader antibody response, a subset of which recognised Omicron with higher affinity than antibodies in rituximab-treated patients [median (range) KD: 1.05 (0.45-1.84) nM vs. 20.25 (13.2-38.8) nM, p = 0.0002], underpinning the stronger serum neutralisation capacity against Omicron in the former group. Rituximab-treated patients had similar anti-WT antibody levels and neutralisation titres to unvaccinated convalescent individuals, despite two more exposures to SARS-CoV-2 antigen. Temporal profiling of the antibody response showed evidence of affinity maturation in healthy convalescent patients after a single SARS-CoV-2 infection, which was not observed in rituximab-treated patients, despite repeated vaccination. Discussion Our results enrich previous observations of impaired humoral immune responses to SARS-CoV-2 in rituximab-treated patients and highlight the significance of quantitative assessment of serum antibody affinity and concentration in monitoring anti-viral immunity, viral escape, and the evolution of the humoral response.
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Affiliation(s)
- Ashley Priddey
- Department of Surgery, University of Cambridge, Addenbrooke’s Hospital, Cambridge, United Kingdom
| | - Michael Xin Hua Chen-Xu
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, United Kingdom
- Department of Medicine, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Daniel James Cooper
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, United Kingdom
- Department of Medicine, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Serena MacMillan
- Department of Surgery, University of Cambridge, Addenbrooke’s Hospital, Cambridge, United Kingdom
| | - Georg Meisl
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Catherine K. Xu
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Myra Hosmillo
- Department of Pathology, Division of Virology, University of Cambridge, Cambridge, United Kingdom
| | - Ian G. Goodfellow
- Department of Pathology, Division of Virology, University of Cambridge, Cambridge, United Kingdom
| | - Rafael Kollyfas
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, United Kingdom
| | - Rainer Doffinger
- Department of Clinical Biochemistry and Immunology, Addenbrooke’s Hospital, Cambridge, United Kingdom
| | - John R. Bradley
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, United Kingdom
- Department of Medicine, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Irina I. Mohorianu
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, United Kingdom
| | - Rachel Jones
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, United Kingdom
- Department of Medicine, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Tuomas P. J. Knowles
- Department of Medicine, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
- Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, United Kingdom
| | - Rona Smith
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, United Kingdom
- Department of Medicine, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Vasilis Kosmoliaptsis
- Department of Surgery, University of Cambridge, Addenbrooke’s Hospital, Cambridge, United Kingdom
- NIHR Blood and Transplant Research Unit in Organ Donation and Transplantation at the University of Cambridge and the NIHR Cambridge Biomedical Research Centre, Cambridge, United Kingdom
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14
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Herling TW, Invernizzi G, Ausserwöger H, Bjelke JR, Egebjerg T, Lund S, Lorenzen N, Knowles TPJ. Nonspecificity fingerprints for clinical-stage antibodies in solution. Proc Natl Acad Sci U S A 2023; 120:e2306700120. [PMID: 38109540 PMCID: PMC10756282 DOI: 10.1073/pnas.2306700120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 11/06/2023] [Indexed: 12/20/2023] Open
Abstract
Monoclonal antibodies (mAbs) have successfully been developed for the treatment of a wide range of diseases. The clinical success of mAbs does not solely rely on optimal potency and safety but also require good biophysical properties to ensure a high developability potential. In particular, nonspecific interactions are a key developability parameter to monitor during discovery and development. Despite an increased focus on the detection of nonspecific interactions, their underlying physicochemical origins remain poorly understood. Here, we employ solution-based microfluidic technologies to characterize a set of clinical-stage mAbs and their interactions with commonly used nonspecificity ligands to generate nonspecificity fingerprints, providing quantitative data on the underlying physical chemistry. Furthermore, the solution-based analysis enables us to measure binding affinities directly, and we evaluate the contribution of avidity in nonspecific binding by mAbs. We find that avidity can increase the apparent affinity by two orders of magnitude. Notably, we find that a subset of these highly developed mAbs show nonspecific electrostatic interactions, even at physiological pH and ionic strength, and that they can form microscale particles with charge-complementary polymers. The group of mAb constructs flagged here for nonspecificity are among the worst performers in independent reports of surface and column-based screens. The solution measurements improve on the state-of-the-art by providing a stand-alone result for individual mAbs without the need to benchmark against cohort data. Based on our findings, we propose a quantitative solution-based nonspecificity score, which can be integrated in the development workflow for biological therapeutics and more widely in protein engineering.
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Affiliation(s)
- Therese W. Herling
- Yusuf Hamied Department of Chemistry, University of Cambridge, CambridgeCB2 1EW, United Kingdom
| | | | - Hannes Ausserwöger
- Yusuf Hamied Department of Chemistry, University of Cambridge, CambridgeCB2 1EW, United Kingdom
| | - Jais Rose Bjelke
- Global Research Technologies, Novo Nordisk A/S, Måløv2760, Denmark
| | - Thomas Egebjerg
- Global Research Technologies, Novo Nordisk A/S, Måløv2760, Denmark
| | - Søren Lund
- Global Research Technologies, Novo Nordisk A/S, Måløv2760, Denmark
| | - Nikolai Lorenzen
- Global Research Technologies, Novo Nordisk A/S, Måløv2760, Denmark
| | - Tuomas P. J. Knowles
- Yusuf Hamied Department of Chemistry, University of Cambridge, CambridgeCB2 1EW, United Kingdom
- Department of Physics, University of Cambridge, CambridgeCB3 0HE, United Kingdom
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15
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Sneideris T, Erkamp NA, Ausserwöger H, Saar KL, Welsh TJ, Qian D, Katsuya-Gaviria K, Johncock MLLY, Krainer G, Borodavka A, Knowles TPJ. Targeting nucleic acid phase transitions as a mechanism of action for antimicrobial peptides. Nat Commun 2023; 14:7170. [PMID: 37935659 PMCID: PMC10630377 DOI: 10.1038/s41467-023-42374-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 10/10/2023] [Indexed: 11/09/2023] Open
Abstract
Antimicrobial peptides (AMPs), which combat bacterial infections by disrupting the bacterial cell membrane or interacting with intracellular targets, are naturally produced by a number of different organisms, and are increasingly also explored as therapeutics. However, the mechanisms by which AMPs act on intracellular targets are not well understood. Using machine learning-based sequence analysis, we identified a significant number of AMPs that have a strong tendency to form liquid-like condensates in the presence of nucleic acids through phase separation. We demonstrate that this phase separation propensity is linked to the effectiveness of the AMPs in inhibiting transcription and translation in vitro, as well as their ability to compact nucleic acids and form clusters with bacterial nucleic acids in bacterial cells. These results suggest that the AMP-driven compaction of nucleic acids and modulation of their phase transitions constitute a previously unrecognised mechanism by which AMPs exert their antibacterial effects. The development of antimicrobials that target nucleic acid phase transitions may become an attractive route to finding effective and long-lasting antibiotics.
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Affiliation(s)
- Tomas Sneideris
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UK
| | - Nadia A Erkamp
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UK
| | - Hannes Ausserwöger
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UK
| | - Kadi L Saar
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UK
| | - Timothy J Welsh
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UK
| | - Daoyuan Qian
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UK
| | - Kai Katsuya-Gaviria
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, UK
| | - Margaret L L Y Johncock
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UK
| | - Georg Krainer
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UK
| | - Alexander Borodavka
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, UK.
| | - Tuomas P J Knowles
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UK.
- Cavendish Laboratory, Department of Physics, University of Cambridge, J J Thomson Ave, Cambridge, UK.
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16
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Simatos D, Jacobs IE, Dobryden I, Nguyen M, Savva A, Venkateshvaran D, Nikolka M, Charmet J, Spalek LJ, Gicevičius M, Zhang Y, Schweicher G, Howe DJ, Ursel S, Armitage J, Dimov IB, Kraft U, Zhang W, Alsufyani M, McCulloch I, Owens RM, Claesson PM, Knowles TPJ, Sirringhaus H. Effects of Processing-Induced Contamination on Organic Electronic Devices. Small Methods 2023; 7:e2300476. [PMID: 37661594 DOI: 10.1002/smtd.202300476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 06/28/2023] [Indexed: 09/05/2023]
Abstract
Organic semiconductors are a family of pi-conjugated compounds used in many applications, such as displays, bioelectronics, and thermoelectrics. However, their susceptibility to processing-induced contamination is not well understood. Here, it is shown that many organic electronic devices reported so far may have been unintentionally contaminated, thus affecting their performance, water uptake, and thin film properties. Nuclear magnetic resonance spectroscopy is used to detect and quantify contaminants originating from the glovebox atmosphere and common laboratory consumables used during device fabrication. Importantly, this in-depth understanding of the sources of contamination allows the establishment of clean fabrication protocols, and the fabrication of organic field effect transistors (OFETs) with improved performance and stability. This study highlights the role of unintentional contaminants in organic electronic devices, and demonstrates that certain stringent processing conditions need to be met to avoid scientific misinterpretation, ensure device reproducibility, and facilitate performance stability. The experimental procedures and conditions used herein are typical of those used by many groups in the field of solution-processed organic semiconductors. Therefore, the insights gained into the effects of contamination are likely to be broadly applicable to studies, not just of OFETs, but also of other devices based on these materials.
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Affiliation(s)
- Dimitrios Simatos
- Optoelectronics Group, Cavendish Laboratory, University of Cambridge, Cambridge, CB3 0HE, UK
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Ian E Jacobs
- Optoelectronics Group, Cavendish Laboratory, University of Cambridge, Cambridge, CB3 0HE, UK
| | - Illia Dobryden
- RISE Research Institutes of Sweden, Division of Bioeconomy and Health, Department of Material and Surface Design, RISE Research Institutes of Sweden, 11486, Stockholm, Sweden
| | - Małgorzata Nguyen
- Optoelectronics Group, Cavendish Laboratory, University of Cambridge, Cambridge, CB3 0HE, UK
| | - Achilleas Savva
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, CB3 OAS, UK
| | - Deepak Venkateshvaran
- Optoelectronics Group, Cavendish Laboratory, University of Cambridge, Cambridge, CB3 0HE, UK
| | - Mark Nikolka
- Optoelectronics Group, Cavendish Laboratory, University of Cambridge, Cambridge, CB3 0HE, UK
| | - Jérôme Charmet
- School of Engineering-HE-Arc Ingénierie, HES-SO University of Applied Sciences Western Switzerland, 2000, Neuchâtel, Switzerland
| | - Leszek J Spalek
- Optoelectronics Group, Cavendish Laboratory, University of Cambridge, Cambridge, CB3 0HE, UK
| | - Mindaugas Gicevičius
- Optoelectronics Group, Cavendish Laboratory, University of Cambridge, Cambridge, CB3 0HE, UK
| | - Youcheng Zhang
- Optoelectronics Group, Cavendish Laboratory, University of Cambridge, Cambridge, CB3 0HE, UK
| | - Guillaume Schweicher
- Laboratoire de Chimie des Polymères, Faculté des Sciences, Université Libre de Bruxelles (ULB), 1050, Bruxelles, Belgium
| | - Duncan J Howe
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Sarah Ursel
- Optoelectronics Group, Cavendish Laboratory, University of Cambridge, Cambridge, CB3 0HE, UK
| | - John Armitage
- Optoelectronics Group, Cavendish Laboratory, University of Cambridge, Cambridge, CB3 0HE, UK
| | - Ivan B Dimov
- Electrical Engineering Division, Department of Engineering, University of Cambridge, Cambridge, CB3 0FA, UK
| | - Ulrike Kraft
- Department of Molecular Electronics, Max Planck Institute for Polymer Research, 55128, Mainz, Germany
| | - Weimin Zhang
- Physical Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Maryam Alsufyani
- Department of Chemistry, University of Oxford, Oxford, OX1 3TA, UK
| | - Iain McCulloch
- Physical Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
- Department of Chemistry, University of Oxford, Oxford, OX1 3TA, UK
| | - Róisín M Owens
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, CB3 OAS, UK
| | - Per M Claesson
- KTH Royal Institute of Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Chemistry, Division of Surface and Corrosion Science, 10044, Stockholm, Sweden
| | - Tuomas P J Knowles
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Henning Sirringhaus
- Optoelectronics Group, Cavendish Laboratory, University of Cambridge, Cambridge, CB3 0HE, UK
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17
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Hastings N, Yu Y, Huang B, Middya S, Inaoka M, Erkamp NA, Mason RJ, Carnicer‐Lombarte A, Rahman S, Knowles TPJ, Bance M, Malliaras GG, Kotter MRN. Electrophysiological In Vitro Study of Long-Range Signal Transmission by Astrocytic Networks. Adv Sci (Weinh) 2023; 10:e2301756. [PMID: 37485646 PMCID: PMC10582426 DOI: 10.1002/advs.202301756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 07/09/2023] [Indexed: 07/25/2023]
Abstract
Astrocytes are diverse brain cells that form large networks communicating via gap junctions and chemical transmitters. Despite recent advances, the functions of astrocytic networks in information processing in the brain are not fully understood. In culture, brain slices, and in vivo, astrocytes, and neurons grow in tight association, making it challenging to establish whether signals that spread within astrocytic networks communicate with neuronal groups at distant sites, or whether astrocytes solely respond to their local environments. A multi-electrode array (MEA)-based device called AstroMEA is designed to separate neuronal and astrocytic networks, thus allowing to study the transfer of chemical and/or electrical signals transmitted via astrocytic networks capable of changing neuronal electrical behavior. AstroMEA demonstrates that cortical astrocytic networks can induce a significant upregulation in the firing frequency of neurons in response to a theta-burst charge-balanced biphasic current stimulation (5 pulses of 100 Hz × 10 with 200 ms intervals, 2 s total duration) of a separate neuronal-astrocytic group in the absence of direct neuronal contact. This result corroborates the view of astrocytic networks as a parallel mechanism of signal transmission in the brain that is separate from the neuronal connectome. Translationally, it highlights the importance of astrocytic network protection as a treatment target.
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Affiliation(s)
- Nataly Hastings
- Department of Clinical NeurosciencesUniversity of CambridgeCambridgeCB2 0QQUK
- Wellcome‐MRC Cambridge Stem Cell InstituteUniversity of CambridgeCambridgeCB2 0AWUK
- Electrical Engineering DivisionDepartment of EngineeringUniversity of CambridgeCambridgeCB3 0FAUK
| | - Yi‐Lin Yu
- Department of Clinical NeurosciencesUniversity of CambridgeCambridgeCB2 0QQUK
- Department of Neurological SurgeryTri‐Service General HospitalNational Defence Medical CentreTaipei, Neihu District11490Taiwan
| | - Botian Huang
- Department of Clinical NeurosciencesUniversity of CambridgeCambridgeCB2 0QQUK
| | - Sagnik Middya
- Electrical Engineering DivisionDepartment of EngineeringUniversity of CambridgeCambridgeCB3 0FAUK
| | - Misaki Inaoka
- Electrical Engineering DivisionDepartment of EngineeringUniversity of CambridgeCambridgeCB3 0FAUK
| | - Nadia A. Erkamp
- Yusuf Hamied Department of ChemistryCentre for Misfolding DiseasesUniversity of CambridgeLensfield RoadCambridgeCB2 1EWUK
| | - Roger J. Mason
- Department of Clinical NeurosciencesUniversity of CambridgeCambridgeCB2 0QQUK
| | | | - Saifur Rahman
- Department of Clinical NeurosciencesUniversity of CambridgeCambridgeCB2 0QQUK
- Wellcome‐MRC Cambridge Stem Cell InstituteUniversity of CambridgeCambridgeCB2 0AWUK
| | - Tuomas P. J. Knowles
- Yusuf Hamied Department of ChemistryCentre for Misfolding DiseasesUniversity of CambridgeLensfield RoadCambridgeCB2 1EWUK
- Cavendish LaboratoryDepartment of PhysicsUniversity of CambridgeJ J Thomson AveCambridgeCB3 0HEUK
| | - Manohar Bance
- Department of Clinical NeurosciencesUniversity of CambridgeCambridgeCB2 0QQUK
| | - George G. Malliaras
- Electrical Engineering DivisionDepartment of EngineeringUniversity of CambridgeCambridgeCB3 0FAUK
| | - Mark R. N. Kotter
- Department of Clinical NeurosciencesUniversity of CambridgeCambridgeCB2 0QQUK
- Wellcome‐MRC Cambridge Stem Cell InstituteUniversity of CambridgeCambridgeCB2 0AWUK
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18
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Kar M, Vogel LT, Chauhan G, Ausserwöger H, Welsh TJ, Kamath AR, Knowles TPJ, Hyman AA, Seidel CAM, Pappu RV. Glutamate helps unmask the differences in driving forces for phase separation versus clustering of FET family proteins in sub-saturated solutions. Res Sq 2023:rs.3.rs-3252197. [PMID: 37790538 PMCID: PMC10543311 DOI: 10.21203/rs.3.rs-3252197/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Multivalent proteins undergo coupled segregative and associative phase transitions. Phase separation, a segregative transition, is driven by macromolecular solubility, and this leads to coexisting phases above system-specific saturation concentrations. Percolation is a continuous transition that is driven by multivalent associations among cohesive motifs. Contributions from percolation are highlighted by the formation of heterogeneous distributions of clusters in sub-saturated solutions, as was recently reported for Fused in sarcoma (FUS) and FET family proteins. Here, we show that clustering and phase separation are defined by a separation of length- and energy-scales. This is unmasked when glutamate is the primary solution anion. Glutamate is preferentially excluded from protein sites, and this enhances molecular associations. Differences between glutamate and chloride are manifest at ultra-low protein concentrations. These differences are amplified as concentrations increase, and they saturate as the micron-scale is approached. Therefore, condensate formation in supersaturated solutions and clustering in sub-saturated are governed by distinct energy and length scales. Glutamate, unlike chloride, is the dominant intracellular anion, and the separation of scales, which is masked in chloride, is unmasked in glutamate. Our work highlights how components of cellular milieus and sequence-encoded interactions contribute to amplifying distinct contributions from associative versus segregative phase transitions.
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Affiliation(s)
- Mrityunjoy Kar
- Max Planck Institute of Cell Biology and Genetics, 01307, Dresden, Germany
| | - Laura T. Vogel
- Department of Molecular Physical Chemistry, Heinrich Heine University, 40225, Düsseldorf, Germany
| | - Gaurav Chauhan
- Department of Biomedical Engineering and Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Hannes Ausserwöger
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, CB2 1EW, Cambridge, UK
| | - Timothy J. Welsh
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, CB2 1EW, Cambridge, UK
| | - Anjana R. Kamath
- Max Planck Institute of Cell Biology and Genetics, 01307, Dresden, Germany
| | - Tuomas P. J. Knowles
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, CB2 1EW, Cambridge, UK
| | - Anthony A. Hyman
- Max Planck Institute of Cell Biology and Genetics, 01307, Dresden, Germany
| | - Claus A. M. Seidel
- Department of Molecular Physical Chemistry, Heinrich Heine University, 40225, Düsseldorf, Germany
| | - Rohit V. Pappu
- Department of Biomedical Engineering and Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO 63130, USA
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19
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Rebelo M, Tang C, Coelho AR, Labão-Almeida C, Schneider MM, Tatalick L, Ruivo P, de Miranda MP, Gomes A, Carvalho T, Walker MJ, Ausserwoeger H, Pedro Simas J, Veldhoen M, Knowles TPJ, Silva DA, Shoultz D, Bernardes GJL. De Novo Human Angiotensin-Converting Enzyme 2 Decoy NL-CVX1 Protects Mice From Severe Disease After Severe Acute Respiratory Syndrome Coronavirus 2 Infection. J Infect Dis 2023; 228:723-733. [PMID: 37279654 PMCID: PMC10503951 DOI: 10.1093/infdis/jiad135] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 05/27/2023] [Indexed: 06/08/2023] Open
Abstract
The emergence of novel variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) underscores the need to investigate alternative approaches to prevent infection and treat patients with coronavirus disease 2019. Here, we report the preclinical efficacy of NL-CVX1, a de novo decoy that blocks virus entry into cells by binding with nanomolar affinity and high specificity to the receptor-binding domain of the SARS-CoV-2 spike protein. Using a transgenic mouse model of SARS-CoV-2 infection, we showed that a single prophylactic intranasal dose of NL-CVX1 conferred complete protection from severe disease following SARS-CoV-2 infection. Multiple therapeutic administrations of NL-CVX1 also protected mice from succumbing to infection. Finally, we showed that infected mice treated with NL-CVX1 developed both anti-SARS-CoV-2 antibodies and memory T cells and were protected against reinfection a month after treatment. Overall, these observations suggest NL-CVX1 is a promising therapeutic candidate for preventing and treating severe SARS-CoV-2 infections.
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Affiliation(s)
- Maria Rebelo
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Cong Tang
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Ana R Coelho
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Carlos Labão-Almeida
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Matthias M Schneider
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | | | - Pedro Ruivo
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Marta Pires de Miranda
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Andreia Gomes
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Tânia Carvalho
- Histopathology Unit, Champalimaud Research, Lisboa, Portugal
| | | | - Hannes Ausserwoeger
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - J Pedro Simas
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
- Católica Biomedical Research and Católica Medical School, Universidade Católica Portuguesa, Lisboa, Portugal
| | - Marc Veldhoen
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Tuomas P J Knowles
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | | | | | - Gonçalo J L Bernardes
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
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20
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Shen Y, Chen A, Wang W, Shen Y, Ruggeri FS, Aime S, Wang Z, Qamar S, Espinosa JR, Garaizar A, St George-Hyslop P, Collepardo-Guevara R, Weitz DA, Vigolo D, Knowles TPJ. The liquid-to-solid transition of FUS is promoted by the condensate surface. Proc Natl Acad Sci U S A 2023; 120:e2301366120. [PMID: 37549257 PMCID: PMC10438845 DOI: 10.1073/pnas.2301366120] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 06/20/2023] [Indexed: 08/09/2023] Open
Abstract
A wide range of macromolecules can undergo phase separation, forming biomolecular condensates in living cells. These membraneless organelles are typically highly dynamic, formed reversibly, and carry out essential functions in biological systems. Crucially, however, a further liquid-to-solid transition of the condensates can lead to irreversible pathological aggregation and cellular dysfunction associated with the onset and development of neurodegenerative diseases. Despite the importance of this liquid-to-solid transition of proteins, the mechanism by which it is initiated in normally functional condensates is unknown. Here we show, by measuring the changes in structure, dynamics, and mechanics in time and space, that single-component FUS condensates do not uniformly convert to a solid gel, but rather that liquid and gel phases coexist simultaneously within the same condensate, resulting in highly inhomogeneous structures. Furthermore, our results show that this transition originates at the interface between the condensate and the dilute continuous phase, and once initiated, the gelation process propagates toward the center of the condensate. To probe such spatially inhomogeneous rheology during condensate aging, we use a combination of established micropipette aspiration experiments together with two optical techniques, spatial dynamic mapping and reflective confocal dynamic speckle microscopy. These results reveal the importance of the spatiotemporal dimension of the liquid-to-solid transition and highlight the interface of biomolecular condensates as a critical element in driving pathological protein aggregation.
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Affiliation(s)
- Yi Shen
- Yusuf Hamied Department of Chemistry, University of Cambridge, CambridgeCB2 1EW, United Kingdom
- School of Chemical and Biomolecular Engineering, The University of Sydney, Sydney, NSW2006, Australia
- The University of Sydney Nano Institute, The University of Sydney, Sydney, NSW2006, Australia
| | - Anqi Chen
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA02138
| | - Wenyun Wang
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA02138
| | - Yinan Shen
- Department of Physics, Harvard University, Cambridge, MA02138
| | - Francesco Simone Ruggeri
- Yusuf Hamied Department of Chemistry, University of Cambridge, CambridgeCB2 1EW, United Kingdom
- Laboratory of Organic Chemistry, Wageningen University, 6708 WE Wageningen, the Netherlands
- Physical Chemistry and Soft Matter, Wageningen University, 6708 WE Wageningen, the Netherlands
| | - Stefano Aime
- Molecular, Macromolecular Chemistry, and Materials, École Supérieure de Physique et de Chimie Industrielles Paris, CNRS, Paris Sciences & Lettres University, Paris75005, France
| | - Zizhao Wang
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA02138
| | - Seema Qamar
- Cambridge Institute for Medical Research, Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, CambridgeCB2 0XY, United Kingdom
| | - Jorge R. Espinosa
- Cavendish Laboratory, University of Cambridge, CambridgeCB3 0HE, United Kingdom
| | - Adiran Garaizar
- Cavendish Laboratory, University of Cambridge, CambridgeCB3 0HE, United Kingdom
| | - Peter St George-Hyslop
- Cambridge Institute for Medical Research, Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, CambridgeCB2 0XY, United Kingdom
- Department of Medicine (Neurology), Tanz Temerty Faculty of Medicine, University of Toronto, Toronto, ONM5T 0S8, Canada
- University Health Network, Toronto, ONM5T 0S8, Canada
- Taub Institute For Research on Alzheimer’s Disease and the Aging Brain, Department of Neurology, Columbia University Irvine Medical Center, New York, NY10032
| | - Rosana Collepardo-Guevara
- Yusuf Hamied Department of Chemistry, University of Cambridge, CambridgeCB2 1EW, United Kingdom
- Cavendish Laboratory, University of Cambridge, CambridgeCB3 0HE, United Kingdom
- Department of Genetics, University of Cambridge, CambridgeCB2 3EH, United Kingdom
| | - David A. Weitz
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA02138
- Department of Physics, Harvard University, Cambridge, MA02138
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA02115
| | - Daniele Vigolo
- The University of Sydney Nano Institute, The University of Sydney, Sydney, NSW2006, Australia
- School of Biomedical Engineering, The University of Sydney, Sydney, NSW2006, Australia
| | - Tuomas P. J. Knowles
- Yusuf Hamied Department of Chemistry, University of Cambridge, CambridgeCB2 1EW, United Kingdom
- Cavendish Laboratory, University of Cambridge, CambridgeCB3 0HE, United Kingdom
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21
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Kar M, Vogel LT, Chauhan G, Ausserwöger H, Welsh TJ, Kamath AR, Knowles TPJ, Hyman AA, Seidel CAM, Pappu RV. Glutamate helps unmask the differences in driving forces for phase separation versus clustering of FET family proteins in sub-saturated solutions. bioRxiv 2023:2023.08.11.552963. [PMID: 37609232 PMCID: PMC10441405 DOI: 10.1101/2023.08.11.552963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Multivalent proteins undergo coupled segregative and associative phase transitions. Phase separation, a segregative transition, is driven by macromolecular solubility, and this leads to coexisting phases above system-specific saturation concentrations. Percolation is a continuous transition that is driven by multivalent associations among cohesive motifs. Contributions from percolation are highlighted by the formation of heterogeneous distributions of clusters in sub-saturated solutions, as was recently reported for Fused in sarcoma (FUS) and FET family proteins. Here, we show that clustering and phase separation are defined by a separation of length- and energy-scales. This is unmasked when glutamate is the primary solution anion. Glutamate is preferentially excluded from protein sites, and this enhances molecular associations. Differences between glutamate and chloride are manifest at ultra-low protein concentrations. These differences are amplified as concentrations increase, and they saturate as the micron-scale is approached. Therefore, condensate formation in supersaturated solutions and clustering in sub-saturated are governed by distinct energy and length scales. Glutamate, unlike chloride, is the dominant intracellular anion, and the separation of scales, which is masked in chloride, is unmasked in glutamate. Our work highlights how components of cellular milieus and sequence-encoded interactions contribute to amplifying distinct contributions from associative versus segregative phase transitions.
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22
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Saar KL, Qian D, Good LL, Morgunov AS, Collepardo-Guevara R, Best RB, Knowles TPJ. Theoretical and Data-Driven Approaches for Biomolecular Condensates. Chem Rev 2023; 123:8988-9009. [PMID: 37171907 PMCID: PMC10375482 DOI: 10.1021/acs.chemrev.2c00586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Indexed: 05/14/2023]
Abstract
Biomolecular condensation processes are increasingly recognized as a fundamental mechanism that living cells use to organize biomolecules in time and space. These processes can lead to the formation of membraneless organelles that enable cells to perform distinct biochemical processes in controlled local environments, thereby supplying them with an additional degree of spatial control relative to that achieved by membrane-bound organelles. This fundamental importance of biomolecular condensation has motivated a quest to discover and understand the molecular mechanisms and determinants that drive and control this process. Within this molecular viewpoint, computational methods can provide a unique angle to studying biomolecular condensation processes by contributing the resolution and scale that are challenging to reach with experimental techniques alone. In this Review, we focus on three types of dry-lab approaches: theoretical methods, physics-driven simulations and data-driven machine learning methods. We review recent progress in using these tools for probing biomolecular condensation across all three fields and outline the key advantages and limitations of each of the approaches. We further discuss some of the key outstanding challenges that we foresee the community addressing next in order to develop a more complete picture of the molecular driving forces behind biomolecular condensation processes and their biological roles in health and disease.
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Affiliation(s)
- Kadi L. Saar
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Cambridge CB2 1EW, United Kingdom
- Transition
Bio Ltd., Cambridge, United Kingdom
| | - Daoyuan Qian
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Lydia L. Good
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Cambridge CB2 1EW, United Kingdom
- Laboratory
of Chemical Physics, National Institute of Diabetes and Digestive
and Kidney Diseases, National Institutes
of Health, Bethesda, Maryland 20892, United States
| | - Alexey S. Morgunov
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Rosana Collepardo-Guevara
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Cambridge CB2 1EW, United Kingdom
- Department
of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
| | - Robert B. Best
- Laboratory
of Chemical Physics, National Institute of Diabetes and Digestive
and Kidney Diseases, National Institutes
of Health, Bethesda, Maryland 20892, United States
| | - Tuomas P. J. Knowles
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Cambridge CB2 1EW, United Kingdom
- Cavendish
Laboratory, Department of Physics, University
of Cambridge, Cambridge CB3 0HE, United Kingdom
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23
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Morse DB, Michalowski AM, Ceribelli M, De Jonghe J, Vias M, Riley D, Davies-Hill T, Voss T, Pittaluga S, Muus C, Liu J, Boyle S, Weitz DA, Brenton JD, Buenrostro JD, Knowles TPJ, Thomas CJ. Positional influence on cellular transcriptional identity revealed through spatially segmented single-cell transcriptomics. Cell Syst 2023; 14:464-481.e7. [PMID: 37348462 PMCID: PMC10424188 DOI: 10.1016/j.cels.2023.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 01/22/2023] [Accepted: 05/17/2023] [Indexed: 06/24/2023]
Abstract
Single-cell RNA sequencing (scRNA-seq) is a powerful technique for describing cell states. Identifying the spatial arrangement of these states in tissues remains challenging, with the existing methods requiring niche methodologies and expertise. Here, we describe segmentation by exogenous perfusion (SEEP), a rapid and integrated method to link surface proximity and environment accessibility to transcriptional identity within three-dimensional (3D) disease models. The method utilizes the steady-state diffusion kinetics of a fluorescent dye to establish a gradient along the radial axis of disease models. Classification of sample layers based on dye accessibility enables dissociated and sorted cells to be characterized by transcriptomic and regional identities. Using SEEP, we analyze spheroid, organoid, and in vivo tumor models of high-grade serous ovarian cancer (HGSOC). The results validate long-standing beliefs about the relationship between cell state and position while revealing new concepts regarding how spatially unique microenvironments influence the identity of individual cells within tumors.
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Affiliation(s)
- David B Morse
- Cavendish Laboratory, Department of Physics, University of Cambridge, J J Thomson Ave, Cambridge, UK; Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, USA; John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Aleksandra M Michalowski
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Michele Ceribelli
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, USA
| | | | - Maria Vias
- Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge, UK
| | - Deanna Riley
- Laboratory of Pathology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Theresa Davies-Hill
- Laboratory of Pathology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ty Voss
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, USA
| | - Stefania Pittaluga
- Laboratory of Pathology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Christoph Muus
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jiamin Liu
- Advanced Imaging and Microscopy Resource, National Institutes of Health Clinical Center, Bethesda, MD, USA
| | - Samantha Boyle
- Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge, UK
| | - David A Weitz
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA; Department of Physics, Harvard University, Cambridge, MA, USA
| | - James D Brenton
- Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge, UK
| | - Jason D Buenrostro
- Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Tuomas P J Knowles
- Cavendish Laboratory, Department of Physics, University of Cambridge, J J Thomson Ave, Cambridge, UK; Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UK.
| | - Craig J Thomas
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, USA; Lymphoid Malignancies Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
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24
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Zhang Q, Toprakcioglu Z, Jayaram AK, Guo G, Wang X, Knowles TPJ. Formation of Protein Nanoparticles in Microdroplet Flow Reactors. ACS Nano 2023. [PMID: 37306477 DOI: 10.1021/acsnano.3c00107] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Nanoparticles are increasingly being used for biological applications, such as drug delivery and gene transfection. Different biological and bioinspired building blocks have been used for generating such particles, including lipids and synthetic polymers. Proteins are an attractive class of material for such applications due to their excellent biocompatibility, low immunogenicity, and self-assembly characteristics. Stable, controllable, and homogeneous formation of protein nanoparticles, which is key to successfully delivering cargo intracellularly, has been challenging to achieve using conventional methods. In order to address this issue, we employed droplet microfluidics and utilized the characteristic of rapid and continuous mixing within microdroplets in order to produce highly monodisperse protein nanoparticles. We exploit the naturally occurring vortex flows within microdroplets to prevent nanoparticle aggregation following nucleation, resulting in systematic control over the particle size and monodispersity. Through combination of simulation and experiment, we find that the internal vortex velocity within microdroplets determines the uniformity of the protein nanoparticles, and by varying parameters such as protein concentration and flow rates, we are able to finely tune nanoparticle dimensional properties. Finally, we show that our nanoparticles are highly biocompatible with HEK-293 cells, and through confocal microscopy, we determine that the nanoparticles fully enter into the cell with almost all cells containing them. Due to the high throughput of the method of production and the level of control afforded, we believe that the approach described in this study for generating monodisperse protein-based nanoparticles has the potential for intracellular drug delivery or for gene transfection in the future.
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Affiliation(s)
- Qi Zhang
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
- Center of Excellence for Environmental Safety and Biological Effects, Beijing Key Laboratory for Green Catalysis and Separation, Department of Chemistry, Beijing University of Technology, Beijing 100124, People's Republic of China
| | - Zenon Toprakcioglu
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Akhila K Jayaram
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
- Cavendish Laboratory, Department of Physics, University of Cambridge, J J Thomson Avenue, Cambridge CB3 OHE, U.K
| | - Guangsheng Guo
- Center of Excellence for Environmental Safety and Biological Effects, Beijing Key Laboratory for Green Catalysis and Separation, Department of Chemistry, Beijing University of Technology, Beijing 100124, People's Republic of China
| | - Xiayan Wang
- Center of Excellence for Environmental Safety and Biological Effects, Beijing Key Laboratory for Green Catalysis and Separation, Department of Chemistry, Beijing University of Technology, Beijing 100124, People's Republic of China
| | - Tuomas P J Knowles
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
- Cavendish Laboratory, Department of Physics, University of Cambridge, J J Thomson Avenue, Cambridge CB3 OHE, U.K
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25
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Miller A, Wei J, Meehan S, Dobson CM, Welland ME, Klenerman D, Vendruscolo M, Ruggeri FS, Knowles TPJ. Formation of amyloid loops in brain tissues is controlled by the flexibility of protofibril chains. Proc Natl Acad Sci U S A 2023; 120:e2216234120. [PMID: 37186840 DOI: 10.1073/pnas.2216234120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023] Open
Abstract
Neurodegenerative diseases, such as Alzheimer's disease (AD), are associated with protein misfolding and aggregation into amyloid fibrils. Increasing evidence suggests that soluble, low-molecular-weight aggregates play a key role in disease-associated toxicity. Within this population of aggregates, closed-loop pore-like structures have been observed for a variety of amyloid systems, and their presence in brain tissues is associated with high levels of neuropathology. However, their mechanism of formation and relationship with mature fibrils have largely remained challenging to elucidate. Here, we use atomic force microscopy and statistical theory of biopolymers to characterize amyloid ring structures derived from the brains of AD patients. We analyze the bending fluctuations of protofibrils and show that the process of loop formation is governed by the mechanical properties of their chains. We conclude that ex vivo protofibril chains possess greater flexibility than that imparted by hydrogen-bonded networks characteristic of mature amyloid fibrils, such that they are able to form end-to-end connections. These results explain the diversity in the structures formed from protein aggregation and shed light on the links between early forms of flexible ring-forming aggregates and their role in disease.
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Affiliation(s)
- Alyssa Miller
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Jiapeng Wei
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Sarah Meehan
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Christopher M Dobson
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Mark E Welland
- Nanoscience Centre, Department of Engineering, University of Cambridge, Cambridge CB3 0FF, United Kingdom
| | - David Klenerman
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Michele Vendruscolo
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Francesco Simone Ruggeri
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
- Laboratory of Organic Chemistry, Department of Agrotechnology and Food Sciences, Wageningen University & Research, Wageningen 6703 WE, the Netherlands
- Physical Chemistry, Department of Agrotechnology and Food Sciences, Wageningen University & Research, Wageningen 6703 WE, the Netherlands
| | - Tuomas P J Knowles
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
- Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge CB3 0HE, United Kingdom
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26
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Schneider MM, Scheidt T, Priddey AJ, Xu CK, Hu M, Meisl G, Devenish SRA, Dobson CM, Kosmoliaptsis V, Knowles TPJ. Microfluidic antibody affinity profiling of alloantibody-HLA interactions in human serum. Biosens Bioelectron 2023; 228:115196. [PMID: 36921387 DOI: 10.1016/j.bios.2023.115196] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 02/17/2023] [Accepted: 03/03/2023] [Indexed: 03/07/2023]
Abstract
Antibody profiling is a fundamental component of understanding the humoral response in a wide range of disease areas. Most currently used approaches operate by capturing antibodies onto functionalised surfaces. Such measurements of surface binding are governed by an overall antibody titre, while the two fundamental molecular parameters, antibody affinity and antibody concentration, are challenging to determine individually from such approaches. Here, by applying microfluidic diffusional sizing (MDS), we show how we can overcome this challenge and demonstrate reliable quantification of alloantibody binding affinity and concentration of alloantibodies binding to Human Leukocyte Antigens (HLA), an extensively used clinical biomarker in organ transplantation, both in buffer and in crude human serum. Capitalising on the ability to vary both serum and HLA concentrations during MDS, we show that both affinity and concentration of HLA-specific antibodies can be determined directly in serum when neither of these parameters is known. Finally, we provide proof of principle in clinical transplant patient sera that our assay enables differentiation of alloantibody reactivity against HLA proteins of highly similar structure, providing information not attainable through currently available techniques. These results outline a path towards detection and in-depth profiling of humoral immunity and may enable further insights into the clinical relevance of antibody reactivity in clinical transplantation and beyond.
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Affiliation(s)
- Matthias M Schneider
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Tom Scheidt
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Ashley J Priddey
- Department of Surgery, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge, CB2 0QQ, UK
| | - Catherine K Xu
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Mengsha Hu
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Georg Meisl
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Sean R A Devenish
- Fluidic Analytics, Unit A, The Paddocks Business Centre, Cherry Hinton Rd, Cambridge, CB1 8DH, UK
| | - Christopher M Dobson
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Vasilis Kosmoliaptsis
- Department of Surgery, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge, CB2 0QQ, UK; NIHR Blood and Transplant Research Unit in Organ Donation and Transplantation, University of Cambridge, Hills Road, Cambridge, CB2 0QQ, UK; NIHR Cambridge Biomedical Research Centre, Hills Road, Cambridge, CB2 0QQ, UK.
| | - Tuomas P J Knowles
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK; Cavendish Laboratory, Department of Physics, University of Cambridge, JJ Thomson Ave, Cambridge, CB3 0HE, UK.
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27
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Ausserwöger H, Krainer G, Welsh TJ, Thorsteinson N, de Csilléry E, Sneideris T, Schneider MM, Egebjerg T, Invernizzi G, Herling TW, Lorenzen N, Knowles TPJ. Surface patches induce nonspecific binding and phase separation of antibodies. Proc Natl Acad Sci U S A 2023; 120:e2210332120. [PMID: 37011217 PMCID: PMC10104583 DOI: 10.1073/pnas.2210332120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 02/06/2023] [Indexed: 04/05/2023] Open
Abstract
Nonspecific interactions are a key challenge in the successful development of therapeutic antibodies. The tendency for nonspecific binding of antibodies is often difficult to reduce by rational design, and instead, it is necessary to rely on comprehensive screening campaigns. To address this issue, we performed a systematic analysis of the impact of surface patch properties on antibody nonspecificity using a designer antibody library as a model system and single-stranded DNA as a nonspecificity ligand. Using an in-solution microfluidic approach, we find that the antibodies tested bind to single-stranded DNA with affinities as high as KD = 1 µM. We show that DNA binding is driven primarily by a hydrophobic patch in the complementarity-determining regions. By quantifying the surface patches across the library, the nonspecific binding affinity is shown to correlate with a trade-off between the hydrophobic and total charged patch areas. Moreover, we show that a change in formulation conditions at low ionic strengths leads to DNA-induced antibody phase separation as a manifestation of nonspecific binding at low micromolar antibody concentrations. We highlight that phase separation is driven by a cooperative electrostatic network assembly mechanism of antibodies with DNA, which correlates with a balance between positive and negative charged patches. Importantly, our study demonstrates that both nonspecific binding and phase separation are controlled by the size of the surface patches. Taken together, these findings highlight the importance of surface patches and their role in conferring antibody nonspecificity and its macroscopic manifestation in phase separation.
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Affiliation(s)
- Hannes Ausserwöger
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, CambridgeCB2 1EW, United Kingdom
| | - Georg Krainer
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, CambridgeCB2 1EW, United Kingdom
| | - Timothy J. Welsh
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, CambridgeCB2 1EW, United Kingdom
| | - Nels Thorsteinson
- Research and Development, Chemical Computing Group, Montreal, QuebecH3A 2R7, Canada
| | - Ella de Csilléry
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, CambridgeCB2 1EW, United Kingdom
| | - Tomas Sneideris
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, CambridgeCB2 1EW, United Kingdom
| | - Matthias M. Schneider
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, CambridgeCB2 1EW, United Kingdom
| | - Thomas Egebjerg
- Global Research Technologies, Novo Nordisk A/S2760Måløv, Denmark
| | | | - Therese W. Herling
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, CambridgeCB2 1EW, United Kingdom
| | - Nikolai Lorenzen
- Global Research Technologies, Novo Nordisk A/S2760Måløv, Denmark
| | - Tuomas P. J. Knowles
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, CambridgeCB2 1EW, United Kingdom
- Department of Physics, Cavendish Laboratory, University of Cambridge, CambridgeCB3 0HE, United Kingdom
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28
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Nixon-Abell J, Ruggeri FS, Qamar S, Herling TW, Czekalska MA, Shen Y, Wang G, King C, Fernandopulle MS, Sneideris T, Watson JL, Pillai VVS, Meadows W, Henderson JW, Chambers JE, Wagstaff JL, Williams SH, Coyle H, Lu Y, Zhang S, Marciniak SJ, Freund SMV, Derivery E, Ward ME, Vendruscolo M, Knowles TPJ, St George-Hyslop P. ANXA11 biomolecular condensates facilitate protein-lipid phase coupling on lysosomal membranes. bioRxiv 2023:2023.03.22.533832. [PMID: 36993242 PMCID: PMC10055329 DOI: 10.1101/2023.03.22.533832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Phase transitions of cellular proteins and lipids play a key role in governing the organisation and coordination of intracellular biology. The frequent juxtaposition of proteinaceous biomolecular condensates to cellular membranes raises the intriguing prospect that phase transitions in proteins and lipids could be co-regulated. Here we investigate this possibility in the ribonucleoprotein (RNP) granule-ANXA11-lysosome ensemble, where ANXA11 tethers RNP granule condensates to lysosomal membranes to enable their co-trafficking. We show that changes to the protein phase state within this system, driven by the low complexity ANXA11 N-terminus, induce a coupled phase state change in the lipids of the underlying membrane. We identify the ANXA11 interacting proteins ALG2 and CALC as potent regulators of ANXA11-based phase coupling and demonstrate their influence on the nanomechanical properties of the ANXA11-lysosome ensemble and its capacity to engage RNP granules. The phenomenon of protein-lipid phase coupling we observe within this system offers an important template to understand the numerous other examples across the cell whereby biomolecular condensates closely juxtapose cell membranes. GRAPHICAL ABSTRACT
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29
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Emmenegger M, Worth R, Fiedler S, Devenish SRA, Knowles TPJ, Aguzzi A. Protocol to determine antibody affinity and concentration in complex solutions using microfluidic antibody affinity profiling. STAR Protoc 2023; 4:102095. [PMID: 36853663 PMCID: PMC9925161 DOI: 10.1016/j.xpro.2023.102095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 12/24/2022] [Accepted: 01/18/2023] [Indexed: 02/17/2023] Open
Abstract
Conventional methods of measuring affinity are limited by artificial immobilization, large sample volumes, and homogeneous solutions. This protocol describes microfluidic antibody affinity profiling on complex human samples in solution to obtain a fingerprint reflecting both affinity and active concentration of the target protein. To illustrate the protocol, we analyze the antibody response in SARS-CoV-2 omicron-naïve samples against different SARS-CoV-2 variants of concern. However, the protocol and the technology are amenable to a broad spectrum of biomedical questions. For complete details on the use and execution of this protocol, please refer to Emmenegger et al. (2022),1 Schneider et al. (2022),2 and Fiedler et al. (2022).3.
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Affiliation(s)
- Marc Emmenegger
- Institute of Neuropathology, University of Zurich, 8091 Zurich, Switzerland.
| | - Roland Worth
- Fluidic Analytics, Unit A, The Paddocks Business Centre, Cherry Hinton Road, Cambridge CB1 8DH, UK
| | - Sebastian Fiedler
- Fluidic Analytics, Unit A, The Paddocks Business Centre, Cherry Hinton Road, Cambridge CB1 8DH, UK
| | - Sean R A Devenish
- Fluidic Analytics, Unit A, The Paddocks Business Centre, Cherry Hinton Road, Cambridge CB1 8DH, UK
| | - Tuomas P J Knowles
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK; Cavendish Laboratory, Department of Physics, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, UK
| | - Adriano Aguzzi
- Institute of Neuropathology, University of Zurich, 8091 Zurich, Switzerland.
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30
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Erkamp NA, Oeller M, Sneideris T, Ausserwoger H, Levin A, Welsh TJ, Qi R, Qian D, Lorenzen N, Zhu H, Sormanni P, Vendruscolo M, Knowles TPJ. Multidimensional Protein Solubility Optimization with an Ultrahigh-Throughput Microfluidic Platform. Anal Chem 2023; 95:5362-5368. [PMID: 36930285 PMCID: PMC10061369 DOI: 10.1021/acs.analchem.2c05495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
Protein-based biologics are highly suitable for drug development as they exhibit low toxicity and high specificity for their targets. However, for therapeutic applications, biologics must often be formulated to elevated concentrations, making insufficient solubility a critical bottleneck in the drug development pipeline. Here, we report an ultrahigh-throughput microfluidic platform for protein solubility screening. In comparison with previous methods, this microfluidic platform can make, incubate, and measure samples in a few minutes, uses just 20 μg of protein (>10-fold improvement), and yields 10,000 data points (1000-fold improvement). This allows quantitative comparison of formulation excipients, such as sodium chloride, polysorbate, histidine, arginine, and sucrose. Additionally, we can measure how solubility is affected by the combinatorial effect of multiple additives, find a suitable pH for the formulation, and measure the impact of mutations on solubility, thus enabling the screening of large libraries. By reducing material and time costs, this approach makes detailed multidimensional solubility optimization experiments possible, streamlining drug development and increasing our understanding of biotherapeutic solubility and the effects of excipients.
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Affiliation(s)
- Nadia A Erkamp
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Marc Oeller
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Tomas Sneideris
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Hannes Ausserwoger
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Aviad Levin
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Timothy J Welsh
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Runzhang Qi
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Daoyuan Qian
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Nikolai Lorenzen
- Biophysics and Injectable Formulation, Global Research Technology, Novo Nordisk A/S, 2760 Maaloev, Denmark
| | - Hongjia Zhu
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Pietro Sormanni
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Michele Vendruscolo
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Tuomas P J Knowles
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
- Cavendish Laboratory, Department of Physics, University of Cambridge, J J Thomson Ave, Cambridge CB3 0HE, U.K
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31
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Kamada A, Toprakcioglu Z, Knowles TPJ. Kinetic Analysis Reveals the Role of Secondary Nucleation in Regenerated Silk Fibroin Self-Assembly. Biomacromolecules 2023; 24:1709-1716. [PMID: 36926854 PMCID: PMC10091410 DOI: 10.1021/acs.biomac.2c01479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
Silk proteins obtained from the Bombyx mori silkworm have been extensively studied due to their remarkable mechanical properties. One of the major structural components of this complex material is silk fibroin, which can be isolated and processed further in vitro to form artificial functional materials. Due to the excellent biocompatibility and rich self-assembly behavior, there has been sustained interest in such materials formed through the assembly of regenerated silk fibroin feedstocks. The molecular mechanisms by which the soluble regenerated fibroin molecules self-assemble into protein nanofibrils remain, however, largely unknown. Here, we use the framework of chemical kinetics to connect macroscopic measurements of regenerated silk fibroin self-assembly to the underlying microscopic mechanisms. Our results reveal that the aggregation of regenerated silk fibroin is dominated by a nonclassical secondary nucleation processes, where the formation of new fibrils is catalyzed by the existing aggregates in an autocatalytic manner. Such secondary nucleation pathways were originally discovered in the context of polymerization of disease-associated proteins, but the present results demonstrate that this pathway can also occur in functional assembly. Furthermore, our results show that shear flow induces the formation of nuclei, which subsequently accelerate the process of aggregation through an autocatalytic amplification driven by the secondary nucleation pathway. Taken together, these results allow us to identify the parameters governing the kinetics of regenerated silk fibroin self-assembly and expand our current understanding of the spinning of bioinspired protein-based fibers, which have a wide range of applications in materials science.
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Affiliation(s)
- Ayaka Kamada
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Zenon Toprakcioglu
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Tuomas P J Knowles
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.,Cavendish Laboratory, University of Cambridge, Cambridge CB3 0FE, U.K
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32
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Jacquat RB, Krainer G, Peter QAE, Babar AN, Vanderpoorten O, Xu CK, Welsh TJ, Kaminski CF, Keyser UF, Baumberg JJ, Knowles TPJ. Single-Molecule Sizing through Nanocavity Confinement. Nano Lett 2023; 23:1629-1636. [PMID: 36826991 PMCID: PMC9999452 DOI: 10.1021/acs.nanolett.1c04830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 02/16/2023] [Indexed: 06/18/2023]
Abstract
An approach relying on nanocavity confinement is developed in this paper for the sizing of nanoscale particles and single biomolecules in solution. The approach, termed nanocavity diffusional sizing (NDS), measures particle residence times within nanofluidic cavities to determine their hydrodynamic radii. Using theoretical modeling and simulations, we show that the residence time of particles within nanocavities above a critical time scale depends on the diffusion coefficient of the particle, which allows the estimation of the particle's size. We demonstrate this approach experimentally through the measurement of particle residence times within nanofluidic cavities using single-molecule confocal microscopy. Our data show that the residence times scale linearly with the sizes of nanoscale colloids, protein aggregates, and single DNA oligonucleotides. NDS thus constitutes a new single molecule optofluidic approach that allows rapid and quantitative sizing of nanoscale particles for potential applications in nanobiotechnology, biophysics, and clinical diagnostics.
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Affiliation(s)
- Raphaël
P. B. Jacquat
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge, CB2 1EW, United Kingdom
- Cavendish
Laboratory, Department of Physics, University
of Cambridge, J. J. Thomson
Avenue, Cambridge CB3 0HE, United Kingdom
| | - Georg Krainer
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge, CB2 1EW, United Kingdom
| | - Quentin A. E. Peter
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge, CB2 1EW, United Kingdom
| | - Ali Nawaz Babar
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge, CB2 1EW, United Kingdom
| | - Oliver Vanderpoorten
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge, CB2 1EW, United Kingdom
- Department
of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, United Kingdom
- Department
of Physics and Technology, UiT The Arctic
University of Norway, Technology Building, Klokkargårdsbakken 35, 9019 Tromsø, Norway
| | - Catherine K. Xu
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge, CB2 1EW, United Kingdom
| | - Timothy J. Welsh
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge, CB2 1EW, United Kingdom
| | - Clemens F. Kaminski
- Department
of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, United Kingdom
| | - Ulrich F. Keyser
- Cavendish
Laboratory, Department of Physics, University
of Cambridge, J. J. Thomson
Avenue, Cambridge CB3 0HE, United Kingdom
| | - Jeremy J. Baumberg
- Cavendish
Laboratory, Department of Physics, University
of Cambridge, J. J. Thomson
Avenue, Cambridge CB3 0HE, United Kingdom
| | - Tuomas P. J. Knowles
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge, CB2 1EW, United Kingdom
- Cavendish
Laboratory, Department of Physics, University
of Cambridge, J. J. Thomson
Avenue, Cambridge CB3 0HE, United Kingdom
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33
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Toprakcioglu Z, Wiita EG, Jayaram AK, Gregory RC, Knowles TPJ. Selenium Silk Nanostructured Films with Antifungal and Antibacterial Activity. ACS Appl Mater Interfaces 2023; 15:10452-10463. [PMID: 36802477 PMCID: PMC9982822 DOI: 10.1021/acsami.2c21013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 02/08/2023] [Indexed: 06/18/2023]
Abstract
The rapid emergence of drug-resistant bacteria and fungi poses a threat for healthcare worldwide. The development of novel effective small molecule therapeutic strategies in this space has remained challenging. Therefore, one orthogonal approach is to explore biomaterials with physical modes of action that have the potential to generate antimicrobial activity and, in some cases, even prevent antimicrobial resistance. Here, to this effect, we describe an approach for forming silk-based films that contain embedded selenium nanoparticles. We show that these materials exhibit both antibacterial and antifungal properties while crucially also remaining highly biocompatible and noncytotoxic toward mammalian cells. By incorporating the nanoparticles into silk films, the protein scaffold acts in a 2-fold manner; it protects the mammalian cells from the cytotoxic effects of the bare nanoparticles, while also providing a template for bacterial and fungal eradication. A range of hybrid inorganic/organic films were produced and an optimum concentration was found, which allowed for both high bacterial and fungal death while also exhibiting low mammalian cell cytotoxicity. Such films can thus pave the way for next-generation antimicrobial materials for applications such as wound healing and as agents against topical infections, with the added benefit that bacteria and fungi are unlikely to develop antimicrobial resistance to these hybrid materials.
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Affiliation(s)
- Zenon Toprakcioglu
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Elizabeth G. Wiita
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Akhila K. Jayaram
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
- Cavendish
Laboratory, Department of Physics, University
of Cambridge, J J Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Rebecca C. Gregory
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Tuomas P. J. Knowles
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
- Cavendish
Laboratory, Department of Physics, University
of Cambridge, J J Thomson Avenue, Cambridge CB3 0HE, United Kingdom
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34
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Qian D, Michaels TCT, Knowles TPJ. Approximate analytical solution to the Flory-Huggins model. Biophys J 2023; 122:207a. [PMID: 36783004 DOI: 10.1016/j.bpj.2022.11.1243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023] Open
Affiliation(s)
- Daoyuan Qian
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | | | - Tuomas P J Knowles
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
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35
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Erkamp NA, Sneideris T, Ausserwöger H, Qian D, Qamar S, Nixon-Abell J, St George-Hyslop P, Schmit JD, Weitz DA, Knowles TPJ. Spatially non-uniform condensates emerge from dynamically arrested phase separation. Nat Commun 2023; 14:684. [PMID: 36755024 PMCID: PMC9908939 DOI: 10.1038/s41467-023-36059-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 01/13/2023] [Indexed: 02/10/2023] Open
Abstract
The formation of biomolecular condensates through phase separation from proteins and nucleic acids is emerging as a spatial organisational principle used broadly by living cells. Many such biomolecular condensates are not, however, homogeneous fluids, but possess an internal structure consisting of distinct sub-compartments with different compositions. Notably, condensates can contain compartments that are depleted in the biopolymers that make up the condensate. Here, we show that such double-emulsion condensates emerge via dynamically arrested phase transitions. The combination of a change in composition coupled with a slow response to this change can lead to the nucleation of biopolymer-poor droplets within the polymer-rich condensate phase. Our findings demonstrate that condensates with a complex internal architecture can arise from kinetic, rather than purely thermodynamic driving forces, and provide more generally an avenue to understand and control the internal structure of condensates in vitro and in vivo.
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Affiliation(s)
- Nadia A Erkamp
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Tomas Sneideris
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Hannes Ausserwöger
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Daoyuan Qian
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Seema Qamar
- Cambridge Institute for Medical Research, Department of Clinical Neurosciences, University of Cambridge, Cambridge, CB2 0XY, UK
| | - Jonathon Nixon-Abell
- Cambridge Institute for Medical Research, Department of Clinical Neurosciences, University of Cambridge, Cambridge, CB2 0XY, UK
| | - Peter St George-Hyslop
- Cambridge Institute for Medical Research, Department of Clinical Neurosciences, University of Cambridge, Cambridge, CB2 0XY, UK
- Department of Medicine (Division of Neurology), University of Toronto and University Health Network, Toronto, Ontario, M5S 3H2, Canada
- Department of Neurology, Columbia University, 630 West 168th St, New York, NY, 10032, USA
| | - Jeremy D Schmit
- Department of Physics, Kansas State University, Manhattan, KS, 66506, USA
| | - David A Weitz
- Department of Physics, Harvard University, 17 Oxford Street, Cambridge, MA, 02138, USA
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, 02138, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA, 02138, USA
| | - Tuomas P J Knowles
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
- Cavendish Laboratory, Department of Physics, University of Cambridge, J J Thomson Ave, Cambridge, CB3 0HE, UK.
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36
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Krainer G, Saar KL, Arter WE, Welsh TJ, Czekalska MA, Jacquat RPB, Peter Q, Traberg WC, Pujari A, Jayaram AK, Challa P, Taylor CG, van der Linden LM, Franzmann T, Owens RM, Alberti S, Klenerman D, Knowles TPJ. Direct digital sensing of protein biomarkers in solution. Nat Commun 2023; 14:653. [PMID: 36746944 PMCID: PMC9902533 DOI: 10.1038/s41467-023-35792-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 01/03/2023] [Indexed: 02/08/2023] Open
Abstract
The detection of proteins is of central importance to biomolecular analysis and diagnostics. Typical immunosensing assays rely on surface-capture of target molecules, but this constraint can limit specificity, sensitivity, and the ability to obtain information beyond simple concentration measurements. Here we present a surface-free, single-molecule microfluidic sensing platform for direct digital protein biomarker detection in solution, termed digital immunosensor assay (DigitISA). DigitISA is based on microchip electrophoretic separation combined with single-molecule detection and enables absolute number/concentration quantification of proteins in a single, solution-phase step. Applying DigitISA to a range of targets including amyloid aggregates, exosomes, and biomolecular condensates, we demonstrate that the assay provides information beyond stoichiometric interactions, and enables characterization of immunochemistry, binding affinity, and protein biomarker abundance. Taken together, our results suggest a experimental paradigm for the sensing of protein biomarkers, which enables analyses of targets that are challenging to address using conventional immunosensing approaches.
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Affiliation(s)
- Georg Krainer
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Kadi L Saar
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - William E Arter
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Timothy J Welsh
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Magdalena A Czekalska
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.,Fluidic Analytics Limited, Unit A The Paddocks Business Centre, Cherry Hinton Road, Cambridge, CB1 8DH, UK
| | - Raphaël P B Jacquat
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Quentin Peter
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Walther C Traberg
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge, CB3 0AS, UK
| | - Arvind Pujari
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.,Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge, CB3 0AS, UK
| | - Akhila K Jayaram
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Pavankumar Challa
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Christopher G Taylor
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Lize-Mari van der Linden
- Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden, Tatzberg 47/49, Dresden, Germany
| | - Titus Franzmann
- Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden, Tatzberg 47/49, Dresden, Germany
| | - Roisin M Owens
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge, CB3 0AS, UK
| | - Simon Alberti
- Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden, Tatzberg 47/49, Dresden, Germany
| | - David Klenerman
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Tuomas P J Knowles
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK. .,Cavendish Laboratory, Department of Physics, University of Cambridge, J J Thomson Ave, Cambridge, CB3 0HE, UK.
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37
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Ou Y, Cao S, Zhang Y, Zhu H, Guo C, Yan W, Xin F, Dong W, Zhang Y, Narita M, Yu Z, Knowles TPJ. Bioprinting microporous functional living materials from protein-based core-shell microgels. Nat Commun 2023; 14:322. [PMID: 36658120 PMCID: PMC9852579 DOI: 10.1038/s41467-022-35140-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 11/21/2022] [Indexed: 01/20/2023] Open
Abstract
Living materials bring together material science and biology to allow the engineering and augmenting of living systems with novel functionalities. Bioprinting promises accurate control over the formation of such complex materials through programmable deposition of cells in soft materials, but current approaches had limited success in fine-tuning cell microenvironments while generating robust macroscopic morphologies. Here, we address this challenge through the use of core-shell microgel ink to decouple cell microenvironments from the structural shell for further processing. Cells are microfluidically immobilized in the viscous core that can promote the formation of both microbial populations and mammalian cellular spheroids, followed by interparticle annealing to give covalently stabilized functional scaffolds with controlled microporosity. The results show that the core-shell strategy mitigates cell leakage while affording a favorable environment for cell culture. Furthermore, we demonstrate that different microbial consortia can be printed into scaffolds for a range of applications. By compartmentalizing microbial consortia in separate microgels, the collective bioprocessing capability of the scaffold is significantly enhanced, shedding light on strategies to augment living materials with bioprocessing capabilities.
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Affiliation(s)
- Yangteng Ou
- State Key Laboratory of Materials-oriented Chemical Engineering, College of Chemical Engineering, Nanjing Tech University, 30 Puzhu South Road, Nanjing, 211816, P. R. China
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
- Cambridge University-Nanjing Centre of Technology and Innovation, 126 Dingshan Street, Nanjing, 210046, P. R. China
| | - Shixiang Cao
- State Key Laboratory of Materials-oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, 30 Puzhu South Road, Nanjing, 211816, P. R. China
| | - Yang Zhang
- State Key Laboratory of Materials-oriented Chemical Engineering, College of Chemical Engineering, Nanjing Tech University, 30 Puzhu South Road, Nanjing, 211816, P. R. China
| | - Hongjia Zhu
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Chengzhi Guo
- State Key Laboratory of Materials-oriented Chemical Engineering, College of Chemical Engineering, Nanjing Tech University, 30 Puzhu South Road, Nanjing, 211816, P. R. China
- Department of Chemical Engineering, University College London, Torrington Place, London, WC1E 7JE, UK
| | - Wei Yan
- State Key Laboratory of Materials-oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, 30 Puzhu South Road, Nanjing, 211816, P. R. China
| | - Fengxue Xin
- State Key Laboratory of Materials-oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, 30 Puzhu South Road, Nanjing, 211816, P. R. China
| | - Weiliang Dong
- State Key Laboratory of Materials-oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, 30 Puzhu South Road, Nanjing, 211816, P. R. China
| | - Yanli Zhang
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Masashi Narita
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
| | - Ziyi Yu
- State Key Laboratory of Materials-oriented Chemical Engineering, College of Chemical Engineering, Nanjing Tech University, 30 Puzhu South Road, Nanjing, 211816, P. R. China.
| | - Tuomas P J Knowles
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
- Cavendish Laboratory, University of Cambridge, J J Thomson Avenue, Cambridge, CB3 0HE, UK.
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38
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Ball S, Adamson JSP, Sullivan MA, Zimmermann MR, Lo V, Sanz-Hernandez M, Jiang X, Kwan AH, McKenzie ADJ, Werry EL, Knowles TPJ, Kassiou M, Meisl G, Todd MH, Rutledge PJ, Sunde M. Perphenazine-Macrocycle Conjugates Rapidly Sequester the Aβ42 Monomer and Prevent Formation of Toxic Oligomers and Amyloid. ACS Chem Neurosci 2023; 14:87-98. [PMID: 36542544 PMCID: PMC9818246 DOI: 10.1021/acschemneuro.2c00498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Accepted: 11/28/2022] [Indexed: 12/24/2022] Open
Abstract
Alzheimer's disease is imposing a growing social and economic burden worldwide, and effective therapies are urgently required. One possible approach to modulation of the disease outcome is to use small molecules to limit the conversion of monomeric amyloid (Aβ42) to cytotoxic amyloid oligomers and fibrils. We have synthesized modulators of amyloid assembly that are unlike others studied to date: these compounds act primarily by sequestering the Aβ42 monomer. We provide kinetic and nuclear magnetic resonance data showing that these perphenazine conjugates divert the Aβ42 monomer into amorphous aggregates that are not cytotoxic. Rapid monomer sequestration by the compounds reduces fibril assembly, even in the presence of pre-formed fibrillar seeds. The compounds are therefore also able to disrupt monomer-dependent secondary nucleation, the autocatalytic process that generates the majority of toxic oligomers. The inhibitors have a modular design that is easily varied, aiding future exploration and use of these tools to probe the impact of distinct Aβ42 species populated during amyloid assembly.
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Affiliation(s)
- Sarah
R. Ball
- School
of Medical Sciences, The University of Sydney, Sydney, New South Wales2006, Australia
| | - Julius S. P. Adamson
- School
of Chemistry, The University of Sydney, Sydney, New South Wales2006, Australia
| | - Michael A. Sullivan
- School
of Medical Sciences, The University of Sydney, Sydney, New South Wales2006, Australia
| | - Manuela R. Zimmermann
- Centre
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, CambridgeCB2 1EW, U.K.
| | - Victor Lo
- School
of Medical Sciences, The University of Sydney, Sydney, New South Wales2006, Australia
| | | | - Xiaofan Jiang
- School
of Chemistry, The University of Sydney, Sydney, New South Wales2006, Australia
| | - Ann H. Kwan
- School
of Life and Environmental Sciences, The
University of Sydney, Sydney, New South Wales2006, Australia
| | - André D. J. McKenzie
- School
of Chemistry, The University of Sydney, Sydney, New South Wales2006, Australia
| | - Eryn L. Werry
- School
of Chemistry, The University of Sydney, Sydney, New South Wales2006, Australia
- Brain and
Mind Centre, The University of Sydney, Sydney, New South Wales2006, Australia
| | - Tuomas P. J. Knowles
- Centre
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, CambridgeCB2 1EW, U.K.
- Cavendish
Laboratory, University of Cambridge, CambridgeCB3 0HE, U.K.
| | - Michael Kassiou
- School
of Chemistry, The University of Sydney, Sydney, New South Wales2006, Australia
| | - Georg Meisl
- Centre
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, CambridgeCB2 1EW, U.K.
| | - Matthew H. Todd
- School
of Pharmacy, University College London, LondonWC1N 1AX, U.K.
| | - Peter J. Rutledge
- School
of Chemistry, The University of Sydney, Sydney, New South Wales2006, Australia
| | - Margaret Sunde
- School
of Medical Sciences, The University of Sydney, Sydney, New South Wales2006, Australia
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39
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Zhu H, Narita M, Joseph JA, Krainer G, Arter WE, Olan I, Saar KL, Ermann N, Espinosa JR, Shen Y, Kuri MA, Qi R, Welsh TJ, Collepardo‐Guevara R, Narita M, Knowles TPJ. The Chromatin Regulator HMGA1a Undergoes Phase Separation in the Nucleus. Chembiochem 2023; 24:e202200450. [PMID: 36336658 PMCID: PMC10098602 DOI: 10.1002/cbic.202200450] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 10/20/2022] [Indexed: 11/09/2022]
Abstract
The protein high mobility group A1 (HMGA1) is an important regulator of chromatin organization and function. However, the mechanisms by which it exerts its biological function are not fully understood. Here, we report that the HMGA isoform, HMGA1a, nucleates into foci that display liquid-like properties in the nucleus, and that the protein readily undergoes phase separation to form liquid condensates in vitro. By bringing together machine-leaning modelling, cellular and biophysical experiments and multiscale simulations, we demonstrate that phase separation of HMGA1a is promoted by protein-DNA interactions, and has the potential to be modulated by post-transcriptional effects such as phosphorylation. We further show that the intrinsically disordered C-terminal tail of HMGA1a significantly contributes to its phase separation through electrostatic interactions via AT hooks 2 and 3. Our work sheds light on HMGA1 phase separation as an emergent biophysical factor in regulating chromatin structure.
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Affiliation(s)
- Hongjia Zhu
- Centre for Misfolding DiseasesYusuf Hamied Department of ChemistryUniversity of CambridgeCambridgeUK
| | - Masako Narita
- Cancer Research UK Cambridge InstituteLi Ka Shing CentreUniversity of CambridgeCambridgeUK
| | - Jerelle A. Joseph
- Department of GeneticsUniversity of CambridgeCambridgeUK
- Cavendish LaboratoryDepartment of PhysicsUniversity of CambridgeJJ Thomson AvenueCambridgeUK
- Yusuf Hamied Department of ChemistryUniversity of CambridgeCambridgeUK
| | - Georg Krainer
- Centre for Misfolding DiseasesYusuf Hamied Department of ChemistryUniversity of CambridgeCambridgeUK
| | - William E. Arter
- Centre for Misfolding DiseasesYusuf Hamied Department of ChemistryUniversity of CambridgeCambridgeUK
- Transition Bio Ltd., Maxwell CentreJJ Thomson AvenueCambridgeUK
| | - Ioana Olan
- Cancer Research UK Cambridge InstituteLi Ka Shing CentreUniversity of CambridgeCambridgeUK
| | - Kadi L. Saar
- Centre for Misfolding DiseasesYusuf Hamied Department of ChemistryUniversity of CambridgeCambridgeUK
- Transition Bio Ltd., Maxwell CentreJJ Thomson AvenueCambridgeUK
| | - Niklas Ermann
- Transition Bio Ltd., Maxwell CentreJJ Thomson AvenueCambridgeUK
| | - Jorge R. Espinosa
- Cavendish LaboratoryDepartment of PhysicsUniversity of CambridgeJJ Thomson AvenueCambridgeUK
| | - Yi Shen
- School of Chemical and Biomolecular EngineeringThe University of SydneySydneyAustralia
| | - Masami Ando Kuri
- Cancer Research UK Cambridge InstituteLi Ka Shing CentreUniversity of CambridgeCambridgeUK
| | - Runzhang Qi
- Centre for Misfolding DiseasesYusuf Hamied Department of ChemistryUniversity of CambridgeCambridgeUK
| | - Timothy J. Welsh
- Centre for Misfolding DiseasesYusuf Hamied Department of ChemistryUniversity of CambridgeCambridgeUK
| | - Rosana Collepardo‐Guevara
- Department of GeneticsUniversity of CambridgeCambridgeUK
- Cavendish LaboratoryDepartment of PhysicsUniversity of CambridgeJJ Thomson AvenueCambridgeUK
- Yusuf Hamied Department of ChemistryUniversity of CambridgeCambridgeUK
| | - Masashi Narita
- Cancer Research UK Cambridge InstituteLi Ka Shing CentreUniversity of CambridgeCambridgeUK
| | - Tuomas P. J. Knowles
- Centre for Misfolding DiseasesYusuf Hamied Department of ChemistryUniversity of CambridgeCambridgeUK
- Cavendish LaboratoryDepartment of PhysicsUniversity of CambridgeJJ Thomson AvenueCambridgeUK
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40
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Chia S, Faidon Brotzakis Z, Horne RI, Possenti A, Mannini B, Cataldi R, Nowinska M, Staats R, Linse S, Knowles TPJ, Habchi J, Vendruscolo M. Structure-Based Discovery of Small-Molecule Inhibitors of the Autocatalytic Proliferation of α-Synuclein Aggregates. Mol Pharm 2023; 20:183-193. [PMID: 36374974 PMCID: PMC9811465 DOI: 10.1021/acs.molpharmaceut.2c00548] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The presence of amyloid fibrils of α-synuclein is closely associated with Parkinson's disease and related synucleinopathies. It is still very challenging, however, to systematically discover small molecules that prevent the formation of these aberrant aggregates. Here, we describe a structure-based approach to identify small molecules that specifically inhibit the surface-catalyzed secondary nucleation step in the aggregation of α-synuclein by binding to the surface of the amyloid fibrils. The resulting small molecules are screened using a range of kinetic and thermodynamic assays for their ability to bind α-synuclein fibrils and prevent the further generation of α-synuclein oligomers. This study demonstrates that the combination of structure-based and kinetic-based drug discovery methods can lead to the identification of small molecules that selectively inhibit the autocatalytic proliferation of α-synuclein aggregates.
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Affiliation(s)
- Sean Chia
- Centre
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, CambridgeCB2 1EW, U.K.
| | - Z. Faidon Brotzakis
- Centre
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, CambridgeCB2 1EW, U.K.
| | - Robert I. Horne
- Centre
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, CambridgeCB2 1EW, U.K.
| | - Andrea Possenti
- Centre
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, CambridgeCB2 1EW, U.K.
| | - Benedetta Mannini
- Centre
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, CambridgeCB2 1EW, U.K.
| | - Rodrigo Cataldi
- Centre
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, CambridgeCB2 1EW, U.K.
| | - Magdalena Nowinska
- Centre
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, CambridgeCB2 1EW, U.K.
| | - Roxine Staats
- Centre
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, CambridgeCB2 1EW, U.K.
| | - Sara Linse
- Department
of Biochemistry & Structural Biology, Center for Molecular Protein
Science, Lund University, 221 00Lund, Sweden
| | - Tuomas P. J. Knowles
- Centre
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, CambridgeCB2 1EW, U.K.,Department
of Physics, Cavendish Laboratory, CambridgeCB3 0HE, U.K.
| | - Johnny Habchi
- Centre
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, CambridgeCB2 1EW, U.K.
| | - Michele Vendruscolo
- Centre
for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, CambridgeCB2 1EW, U.K.,
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41
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Baumann K, Šneiderienė G, Sanguanini M, Schneider M, Rimon O, González Díaz A, Greer H, Thacker D, Linse S, Knowles TPJ, Vendruscolo M. A Kinetic Map of the Influence of Biomimetic Lipid Model Membranes on Aβ 42 Aggregation. ACS Chem Neurosci 2022; 14:323-329. [PMID: 36574473 PMCID: PMC9853501 DOI: 10.1021/acschemneuro.2c00765] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The aggregation of the amyloid β (Aβ) peptide is one of the molecular hallmarks of Alzheimer's disease (AD). Although Aβ deposits have mostly been observed extracellularly, various studies have also reported the presence of intracellular Aβ assemblies. Because these intracellular Aβ aggregates might play a role in the onset and progression of AD, it is important to investigate their possible origins at different locations of the cell along the secretory pathway of the amyloid precursor protein, from which Aβ is derived by proteolytic cleavage. Senile plaques found in AD are largely composed of the 42-residue form of Aβ (Aβ42). Intracellularly, Aβ42 is produced in the endoplasmatic reticulum (ER) and Golgi apparatus. Since lipid bilayers have been shown to promote the aggregation of Aβ, in this study, we measure the effects of the lipid membrane composition on the in vitro aggregation kinetics of Aβ42. By using large unilamellar vesicles to model cellular membranes at different locations, including the inner and outer leaflets of the plasma membrane, late endosomes, the ER, and the Golgi apparatus, we show that Aβ42 aggregation is inhibited by the ER and Golgi model membranes. These results provide a preliminary map of the possible effects of the membrane composition in different cellular locations on Aβ aggregation and suggest the presence of an evolutionary optimization of the lipid composition to prevent the intracellular aggregation of Aβ.
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Affiliation(s)
- Kevin
N. Baumann
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, CambridgeCB2 1EW, U.K.
| | - Greta Šneiderienė
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, CambridgeCB2 1EW, U.K.
| | - Michele Sanguanini
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, CambridgeCB2 1EW, U.K.
| | - Matthias Schneider
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, CambridgeCB2 1EW, U.K.
| | - Oded Rimon
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, CambridgeCB2 1EW, U.K.
| | - Alicia González Díaz
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, CambridgeCB2 1EW, U.K.
| | - Heather Greer
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, CambridgeCB2 1EW, U.K.
| | - Dev Thacker
- Department
of Biochemistry and Structural Biology, Lund University, LundSE22100, Sweden
| | - Sara Linse
- Department
of Biochemistry and Structural Biology, Lund University, LundSE22100, Sweden
| | - Tuomas P. J. Knowles
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, CambridgeCB2 1EW, U.K.,Cavendish
Laboratory, University of Cambridge, CambridgeCB3 0HE, U.K.
| | - Michele Vendruscolo
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, CambridgeCB2 1EW, U.K.,
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42
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Erkamp NA, Qi R, Welsh TJ, Knowles TPJ. Microfluidics for multiscale studies of biomolecular condensates. Lab Chip 2022; 23:9-24. [PMID: 36269080 PMCID: PMC9764808 DOI: 10.1039/d2lc00622g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 09/04/2022] [Indexed: 05/12/2023]
Abstract
Membraneless organelles formed through condensation of biomolecules in living cells have become the focus of sustained efforts to elucidate their mechanisms of formation and function. These condensates perform a range of vital functions in cells and are closely connected to key processes in functional and aberrant biology. Since these systems occupy a size scale intermediate between single proteins and conventional protein complexes on the one hand, and cellular length scales on the other hand, they have proved challenging to probe using conventional approaches from either protein science or cell biology. Additionally, condensate can form, solidify and perform functions on various time-scales. From a physical point of view, biomolecular condensates are colloidal soft matter systems, and microfluidic approaches, which originated in soft condensed matter research, have successfully been used to study biomolecular condensates. This review explores how microfluidics have aided condensate research into the thermodynamics, kinetics and other properties of condensates, by offering high-throughput and novel experimental setups.
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Affiliation(s)
- Nadia A Erkamp
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
| | - Runzhang Qi
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
| | - Timothy J Welsh
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
| | - Tuomas P J Knowles
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
- Cavendish Laboratory, Department of Physics, University of Cambridge, J J Thomson Ave, Cambridge, CB3 0HE, UK
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43
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Fiedler S, Devenish SRA, Morgunov AS, Ilsley A, Ricci F, Emmenegger M, Kosmoliaptsis V, Theel ES, Mills JR, Sholukh AM, Aguzzi A, Iwasaki A, Lynn AK, Knowles TPJ. Serological fingerprints link antiviral activity of therapeutic antibodies to affinity and concentration. Sci Rep 2022; 12:19791. [PMID: 36396691 PMCID: PMC9672333 DOI: 10.1038/s41598-022-22214-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 10/11/2022] [Indexed: 11/18/2022] Open
Abstract
The effectiveness of therapeutic monoclonal antibodies (mAbs) against variants of the SARS-CoV-2 virus is highly variable. As target recognition of mAbs relies on tight binding affinity, we assessed the affinities of five therapeutic mAbs to the receptor binding domain (RBD) of wild type (A), Delta (B.1.617.2), and Omicron BA.1 SARS-CoV-2 (B.1.1.529.1) spike using microfluidic diffusional sizing (MDS). Four therapeutic mAbs showed strongly reduced affinity to Omicron BA.1 RBD, whereas one (sotrovimab) was less impacted. These affinity reductions correlate with reduced antiviral activities suggesting that affinity could serve as a rapid indicator for activity before time-consuming virus neutralization assays are performed. We also compared the same mAbs to serological fingerprints (affinity and concentration) obtained by MDS of antibodies in sera of 65 convalescent individuals. The affinities of the therapeutic mAbs to wild type and Delta RBD were similar to the serum antibody response, indicating high antiviral activities. For Omicron BA.1 RBD, only sotrovimab retained affinities within the range of the serum antibody response, in agreement with high antiviral activity. These results suggest that serological fingerprints provide a route to evaluating affinity and antiviral activity of mAb drugs and could guide the development of new therapeutics.
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Affiliation(s)
- Sebastian Fiedler
- Fluidic Analytics, Unit A, The Paddocks Business Centre, Cherry Hinton Road, Cambridge, CB1 8DH, UK.
| | - Sean R A Devenish
- Fluidic Analytics, Unit A, The Paddocks Business Centre, Cherry Hinton Road, Cambridge, CB1 8DH, UK
| | - Alexey S Morgunov
- Fluidic Analytics, Unit A, The Paddocks Business Centre, Cherry Hinton Road, Cambridge, CB1 8DH, UK
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Alison Ilsley
- Fluidic Analytics, Unit A, The Paddocks Business Centre, Cherry Hinton Road, Cambridge, CB1 8DH, UK
| | - Francesco Ricci
- Fluidic Analytics, Unit A, The Paddocks Business Centre, Cherry Hinton Road, Cambridge, CB1 8DH, UK
| | - Marc Emmenegger
- Institute of Neuropathology, University of Zurich, 8091, Zurich, Switzerland
| | - Vasilis Kosmoliaptsis
- Department of Surgery, University of Cambridge, Addenbrookes Hospital, Cambridge, CB2 0QQ, UK
- NIHR Blood and Transplant Research Unit in Organ Donation and Transplantation, University of Cambridge, Hills Road, Cambridge, CB2 0QQ, UK
- NIHR Cambridge Biomedical Research Centre, Hills Road, Cambridge, CB2 0QQ, UK
| | - Elitza S Theel
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - John R Mills
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
- Center for MS and Autoimmune Neurology, Mayo Clinic, Rochester, MN, USA
| | - Anton M Sholukh
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Adriano Aguzzi
- Institute of Neuropathology, University of Zurich, 8091, Zurich, Switzerland
| | - Akiko Iwasaki
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, 06519, USA
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06510, USA
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, 06511, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA
| | - Andrew K Lynn
- Fluidic Analytics, Unit A, The Paddocks Business Centre, Cherry Hinton Road, Cambridge, CB1 8DH, UK
| | - Tuomas P J Knowles
- Fluidic Analytics, Unit A, The Paddocks Business Centre, Cherry Hinton Road, Cambridge, CB1 8DH, UK.
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
- Cavendish Laboratory, Department of Physics, University of Cambridge, JJ Thomson Ave, Cambridge, CB3 0HE, UK.
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44
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Julian L, Sang JC, Wu Y, Meisl G, Brelstaff JH, Miller A, Cheetham MR, Vendruscolo M, Knowles TPJ, Ruggeri FS, Bryant C, Ros S, Brindle KM, Klenerman D. Characterization of full-length p53 aggregates and their kinetics of formation. Biophys J 2022; 121:4280-4298. [PMID: 36230002 PMCID: PMC9703098 DOI: 10.1016/j.bpj.2022.10.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 09/04/2022] [Accepted: 10/11/2022] [Indexed: 12/14/2022] Open
Abstract
Mutations in the TP53 gene are common in cancer with the R248Q missense mutation conferring an increased propensity to aggregate. Previous p53 aggregation studies showed that, at micromolar concentrations, protein unfolding to produce aggregation-prone species is the rate-determining step. Here we show that, at physiological concentrations, aggregation kinetics of insect cell-derived full-length wild-type p53 and p53R248Q are determined by a nucleation-growth model, rather than formation of aggregation-prone monomeric species. Self-seeding, but not cross-seeding, increases aggregation rate, confirming the aggregation process as rate determining. p53R248Q displays enhanced aggregation propensity due to decreased solubility and increased aggregation rate, forming greater numbers of larger amorphous aggregates that disrupt lipid bilayers and invokes an inflammatory response. These results suggest that p53 aggregation can occur under physiological conditions, a rate enhanced by R248Q mutation, and that aggregates formed can cause membrane damage and inflammation that may influence tumorigenesis.
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Affiliation(s)
- Linda Julian
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom; Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Jason C Sang
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Yunzhao Wu
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Georg Meisl
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Jack H Brelstaff
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, United Kingdom; Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Alyssa Miller
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Matthew R Cheetham
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Michele Vendruscolo
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Tuomas P J Knowles
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Francesco Simone Ruggeri
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Clare Bryant
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom; Department of Veterinary Medicine, University of Cambridge, United Kingdom
| | - Susana Ros
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
| | - Kevin M Brindle
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom.
| | - David Klenerman
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, United Kingdom; UK Dementia Research Institute, University of Cambridge, Cambridge, United Kingdom.
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45
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Ausserwöger H, Schneider MM, Herling TW, Arosio P, Invernizzi G, Knowles TPJ, Lorenzen N. Non-specificity as the sticky problem in therapeutic antibody development. Nat Rev Chem 2022; 6:844-861. [PMID: 37117703 DOI: 10.1038/s41570-022-00438-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/07/2022] [Indexed: 11/16/2022]
Abstract
Antibodies are highly potent therapeutic scaffolds with more than a hundred different products approved on the market. Successful development of antibody-based drugs requires a trade-off between high target specificity and target binding affinity. In order to better understand this problem, we here review non-specific interactions and explore their fundamental physicochemical origins. We discuss the role of surface patches - clusters of surface-exposed amino acid residues with similar physicochemical properties - as inducers of non-specific interactions. These patches collectively drive interactions including dipole-dipole, π-stacking and hydrophobic interactions to complementary moieties. We elucidate links between these supramolecular assembly processes and macroscopic development issues, such as decreased physical stability and poor in vivo half-life. Finally, we highlight challenges and opportunities for optimizing protein binding specificity and minimizing non-specificity for future generations of therapeutics.
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46
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Peter QE, Jacquat RB, Herling TW, Challa PK, Kartanas T, Knowles TPJ. Microscale Diffusiophoresis of Proteins. J Phys Chem B 2022; 126:8913-8920. [PMID: 36306420 PMCID: PMC9661530 DOI: 10.1021/acs.jpcb.2c04029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Living systems are characterized by their spatially highly inhomogeneous nature which is susceptible to modify fundamentally the behavior of biomolecular species, including the proteins that underpin biological functionality in cells. Spatial gradients in chemical potential are known to lead to strong transport effects for colloidal particles, but their effect on molecular scale species such as proteins has remained largely unexplored. Here, we improve on existing diffusiophoresis microfluidic technique to measure protein diffusiophoresis in real space. The measurement of proteins is made possible by two ameliorations. First, a label-free microscope is used to suppress label interference. Second, improvements in numerical methods are developed to meet the particular challenges posed by small molecules. We demonstrate that individual proteins can undergo strong diffusiophoretic motion in salt gradients in a manner which is sufficient to overcome diffusion and which leads to dramatic changes in their spatial organization on the scale of a cell. Moreover, we demonstrate that this phenomenon can be used to control the motion of proteins in microfluidic devices. These results open up a path towards a physical understanding of the role of gradients in living systems in the spatial organization of macromolecules and highlight novel routes towards protein sorting applications on device.
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Affiliation(s)
- Quentin
A. E. Peter
- Department
of Chemistry, University of Cambridge, Lensfield Road, CB2 1EWCambridge, U.K.
| | - Raphaël
P. B. Jacquat
- Cavendish
Laboratory, Department of Physics, University
of Cambridge, JJ Thomson Avenue, CB3 0HECambridge, U.K.
| | - Therese W. Herling
- Department
of Chemistry, University of Cambridge, Lensfield Road, CB2 1EWCambridge, U.K.
| | - Pavan Kumar Challa
- Department
of Chemistry, University of Cambridge, Lensfield Road, CB2 1EWCambridge, U.K.
| | - Tadas Kartanas
- Department
of Chemistry, University of Cambridge, Lensfield Road, CB2 1EWCambridge, U.K.
| | - Tuomas P. J. Knowles
- Department
of Chemistry, University of Cambridge, Lensfield Road, CB2 1EWCambridge, U.K.,
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47
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Mavrakis E, Toprakcioglu Z, Lydakis-Simantiris N, Knowles TPJ, Pergantis SA. A chip-based supersonic microfluidic nebulizer for efficient sample introduction into inductively coupled plasma - Mass spectrometry. Anal Chim Acta 2022; 1229:340342. [PMID: 36156219 DOI: 10.1016/j.aca.2022.340342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 08/29/2022] [Accepted: 08/31/2022] [Indexed: 11/29/2022]
Abstract
As the use of microfluidic chips for handling biological samples is increasing, so is the need for combining them with powerful analytical techniques for metal determination such as inductively-coupled plasma mass spectrometry (ICP-MS). So far, coupling a microfluidic chip to an ICP-MS has been demonstrated mainly through the use of conventional pneumatic micro-flow nebulizers. However, disadvantages associated with the use of such nebulizers entail dead volume issues and liquid suction exerted on the outlet channel of the chip. Herein, we propose that a microfluidic chip, bearing a pneumatic nozzle for liquid nebulization, has the potential to advance metal determination in chip-based ICP-MS. More specifically, we demonstrate for the first time that the coupling of a chip-based supersonic microfluidic nebulizer (chip-μf-Neb) to an ICP-MS can be conveniently achieved through the use of a spray chamber with a laminar flow makeup gas. Operation of the combined system was evaluated at low liquid flow rates across 0.5-20 μL min-1, while nebulization and makeup argon (Ar) gas flow rates were optimized with respect to maximizing indium (In) sensitivity and minimizing oxide formation; a maximum sensitivity of 40000 cps (μg L-1)-1 was achieved at 10 μL min-1. The system was further evaluated for its performance in single-particle analysis, featuring a transport efficiency of 46% for Ag nanoparticles. Finally, the capabilities for conducting single-cell analysis were demonstrated with the detection of 80Se and 75As in individual Chlamydomas reinhardtii cells, which were previously incubated in 20 μM of selenate and 300 μM of arsenate, respectively. Efficient operation at low liquid flow rates along with the absence of self-aspiration render this nebulizer a promising tool for combining the powerful field of microfluidics with metal quantitation by means of ICP-MS.
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Affiliation(s)
- E Mavrakis
- Environmental Chemical Processes Laboratory, Department of Chemistry, University of Crete, Voutes Campus, Heraklion, 70013, Greece
| | - Z Toprakcioglu
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - N Lydakis-Simantiris
- Laboratory of Biological & Biotechnological Applications, Department of Agriculture, Hellenic Mediterranean University, Estavromenos, Heraklion, 71410, Greece; Hellenic Mediterranean University Research Center, Institute of Agri-food and Life Sciences, Heraklion, Crete, Greece
| | - T P J Knowles
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom; Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, United Kingdom.
| | - S A Pergantis
- Environmental Chemical Processes Laboratory, Department of Chemistry, University of Crete, Voutes Campus, Heraklion, 70013, Greece.
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48
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Yang H, Knowles TPJ. Hydrodynamics of Droplet Sorting in Asymmetric Acute Junctions. Micromachines (Basel) 2022; 13:1640. [PMID: 36295993 PMCID: PMC9611150 DOI: 10.3390/mi13101640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 09/16/2022] [Accepted: 09/27/2022] [Indexed: 06/16/2023]
Abstract
Droplet sorting is one of the fundamental manipulations of droplet-based microfluidics. Although many sorting methods have already been proposed, there is still a demand to develop new sorting methods for various applications of droplet-based microfluidics. This work presents numerical investigations on droplet sorting with asymmetric acute junctions. It is found that the asymmetric acute junctions could achieve volume-based sorting and velocity-based sorting. The pressure distributions in the asymmetric junctions are discussed to reveal the physical mechanism behind the droplet sorting. The dependence of the droplet sorting on the droplet volume, velocity, and junction angle is explored. The possibility of the employment of the proposed sorting method in most real experiments is also discussed. This work provides a new, simple, and cost-effective passive strategy to separate droplets in microfluidic channels. Moreover, the proposed acute junctions could be used in combination with other sorting methods, which may boost more opportunities to sort droplets.
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Affiliation(s)
- He Yang
- School of Mechanical Engineering, Hangzhou Dianzi University, No. 2 Street, Qiantang District, Hangzhou 310018, China
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Tuomas P. J. Knowles
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
- Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, UK
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49
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Weiffert T, Meisl G, Curk S, Cukalevski R, Šarić A, Knowles TPJ, Linse S. Influence of denaturants on amyloid β42 aggregation kinetics. Front Neurosci 2022; 16:943355. [PMID: 36203800 PMCID: PMC9531139 DOI: 10.3389/fnins.2022.943355] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 08/08/2022] [Indexed: 11/24/2022] Open
Abstract
Amyloid formation is linked to devastating neurodegenerative diseases, motivating detailed studies of the mechanisms of amyloid formation. For Aβ, the peptide associated with Alzheimer’s disease, the mechanism and rate of aggregation have been established for a range of variants and conditions in vitro and in bodily fluids. A key outstanding question is how the relative stabilities of monomers, fibrils and intermediates affect each step in the fibril formation process. By monitoring the kinetics of aggregation of Aβ42, in the presence of urea or guanidinium hydrochloride (GuHCl), we here determine the rates of the underlying microscopic steps and establish the importance of changes in relative stability induced by the presence of denaturant for each individual step. Denaturants shift the equilibrium towards the unfolded state of each species. We find that a non-ionic denaturant, urea, reduces the overall aggregation rate, and that the effect on nucleation is stronger than the effect on elongation. Urea reduces the rate of secondary nucleation by decreasing the coverage of fibril surfaces and the rate of nucleus formation. It also reduces the rate of primary nucleation, increasing its reaction order. The ionic denaturant, GuHCl, accelerates the aggregation at low denaturant concentrations and decelerates the aggregation at high denaturant concentrations. Below approximately 0.25 M GuHCl, the screening of repulsive electrostatic interactions between peptides by the charged denaturant dominates, leading to an increased aggregation rate. At higher GuHCl concentrations, the electrostatic repulsion is completely screened, and the denaturing effect dominates. The results illustrate how the differential effects of denaturants on stability of monomer, oligomer and fibril translate to differential effects on microscopic steps, with the rate of nucleation being most strongly reduced.
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Affiliation(s)
- Tanja Weiffert
- Department of Biochemistry and Structural Biology, Lund University, Lund, Sweden
| | - Georg Meisl
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Cambridge, United Kingdom
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Samo Curk
- Department of Physics and Astronomy, University College London, London, United Kingdom
| | - Risto Cukalevski
- Department of Biochemistry and Structural Biology, Lund University, Lund, Sweden
| | - Anđela Šarić
- Department of Physics and Astronomy, University College London, London, United Kingdom
| | - Tuomas P. J. Knowles
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Cambridge, United Kingdom
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
- Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, United Kingdom
| | - Sara Linse
- Department of Biochemistry and Structural Biology, Lund University, Lund, Sweden
- *Correspondence: Sara Linse,
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50
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Heck JR, Miele E, Mouthaan RP, Frosz MH, Knowles TPJ, Euser TG. Label-free monitoring of proteins in optofluidic hollow-core photonic crystal fibres. Methods Appl Fluoresc 2022; 10. [PMID: 36084629 DOI: 10.1088/2050-6120/ac9113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 09/09/2022] [Indexed: 11/11/2022]
Abstract
The fluorescent detection of proteins without labels or stains, which affect their behaviour and require additional genetic or chemical preparation, has broad applications to biological research. However, standard approaches require large sample volumes or analyse only a small fraction of the sample. Here we use optofluidic hollow-core photonic crystal fibres to detect and quantify sub-microlitre volumes of unmodified bovine serum albumin (BSA) protein down to 100 nM concentrations. The optofluidic fibre's waveguiding properties are optimised for guidance at the (auto)fluorescence emission wavelength, enabling fluorescence collection from a 10 cm long excitation region, increasing sensitivity. The observed spectra agree with spectra taken from a conventional cuvette-based fluorimeter, corrected for the guidance properties of the fibre. The BSA fluorescence depended linearly on BSA concentration, while only a small hysteresis effect was observed, suggesting limited biofouling of the fibre sensor. Finally, we briefly discuss how this method could be used to study aggregation kinetics. With small sample volumes, the ability to use unlabelled proteins, and continuous flow, the method will be of interest to a broad range of protein-related research.
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Affiliation(s)
- Jan Robert Heck
- Department of Physics, Cambridge University, JJ Thomson Ave, Cambridge, CB3 071, UNITED KINGDOM OF GREAT BRITAIN AND NORTHERN IRELAND
| | - Ermanno Miele
- Department of Physics, Cambridge University, JJ Thomson Ave, Cambridge, Cambridgeshire, CB2 1TN, UNITED KINGDOM OF GREAT BRITAIN AND NORTHERN IRELAND
| | - Ralf P Mouthaan
- Department of Physics, Cambridge University, JJ Thomson Ave, Cambridge, Cambridgeshire, CB2 1TN, UNITED KINGDOM OF GREAT BRITAIN AND NORTHERN IRELAND
| | - Michael H Frosz
- Max Planck Institute for the Science of Light, Max-Planck-Institut fuer die Physik des Lichts, Staudtstr. 2, Erlangen, 91058, GERMANY
| | - Tuomas P J Knowles
- Department of Physics, Cambridge University, JJ Thomson Ave, Cambridge, Cambridgeshire, CB2 1TN, UNITED KINGDOM OF GREAT BRITAIN AND NORTHERN IRELAND
| | - Tijmen G Euser
- Department of Physics, Cambridge University, JJ Thomson Ave, Cambridge, Cambridgeshire, CB2 1TN, UNITED KINGDOM OF GREAT BRITAIN AND NORTHERN IRELAND
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