1
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Rizuan A, Shenoy J, Mohanty P, dos Passos PMS, Mercado Ortiz JF, Bai L, Viswanathan R, Wang SH, Johnson V, Mamede LD, Ayala YM, Ghirlando R, Mittal J, Fawzi NL. Structural details of helix-mediated TDP-43 C-terminal domain multimerization. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.05.602258. [PMID: 39005345 PMCID: PMC11245101 DOI: 10.1101/2024.07.05.602258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
The primarily disordered C-terminal domain (CTD) of TAR DNA binding protein-43 (TDP-43), a key nuclear protein in RNA metabolism, forms neuronal inclusions in several neurodegenerative diseases. A conserved region (CR, spanning residues 319-341) in CTD forms transient helix-helix contacts important for its higher-order oligomerization and function that are disrupted by ALS-associated mutations. However, the structural details of CR assembly and the explanation for several ALS-associated variants' impact on phase separation and function remain unclear due to challenges in analyzing the dynamic association of TDP-43 CTD using traditional structural biology approaches. By employing an integrative approach, combining biophysical experiments, biochemical assays, AlphaFold2-Multimer (AF2-Multimer), and atomistic simulations, we generated structural models of helical oligomerization of TDP-43 CR. Using NMR, we first established that the native state of TDP-43 CR under physiological conditions is α-helical. Next, alanine scanning mutagenesis revealed that while hydrophobic residues in the CR are important for CR assembly, phase separation and TDP-43 nuclear retention function, polar residues down regulate these processes. Finally, pairing AF2-Multimer modeling with AAMD simulations indicated that dynamic, oligomeric assemblies of TDP-43 that are stabilized by a methionine-rich core with specific contributions from a tryptophan/leucine pair. In conclusion, our results advance the structural understanding of the mechanisms driving TDP-43 function and provide a window into the initial stages of its conversion into pathogenic aggregates.
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Affiliation(s)
- Azamat Rizuan
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843
| | - Jayakrishna Shenoy
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI 02912
| | - Priyesh Mohanty
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843
| | - Patricia M. S. dos Passos
- Edward Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri
| | - José F. Mercado Ortiz
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI 02912
| | - Leanna Bai
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI 02912
| | - Renjith Viswanathan
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI 02912
| | - Szu-Huan Wang
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI 02912
| | - Victoria Johnson
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI 02912
| | - Lohany D. Mamede
- Edward Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri
| | - Yuna M. Ayala
- Edward Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri
| | - Rodolfo Ghirlando
- Laboratory of Molecular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Jeetain Mittal
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843
- Department of Chemistry, Texas A&M University, College Station, TX 77843
- Interdisciplinary Graduate Program in Genetics and Genomics, Texas A&M University, College Station, TX 77843
| | - Nicolas L. Fawzi
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI 02912
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2
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Hilditch AT, Romanyuk A, Cross SJ, Obexer R, McManus JJ, Woolfson DN. Assembling membraneless organelles from de novo designed proteins. Nat Chem 2024; 16:89-97. [PMID: 37710047 PMCID: PMC10774119 DOI: 10.1038/s41557-023-01321-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 08/09/2023] [Indexed: 09/16/2023]
Abstract
Recent advances in de novo protein design have delivered a diversity of discrete de novo protein structures and complexes. A new challenge for the field is to use these designs directly in cells to intervene in biological processes and augment natural systems. The bottom-up design of self-assembled objects such as microcompartments and membraneless organelles is one such challenge. Here we describe the design of genetically encoded polypeptides that form membraneless organelles in Escherichia coli. To do this, we combine de novo α-helical sequences, intrinsically disordered linkers and client proteins in single-polypeptide constructs. We tailor the properties of the helical regions to shift protein assembly from arrested assemblies to dynamic condensates. The designs are characterized in cells and in vitro using biophysical methods and soft-matter physics. Finally, we use the designed polypeptide to co-compartmentalize a functional enzyme pair in E. coli, improving product formation close to the theoretical limit.
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Affiliation(s)
- Alexander T Hilditch
- School of Chemistry, University of Bristol, Bristol, UK
- School of Biochemistry, University of Bristol, Bristol, UK
- Max Planck-Bristol Centre for Minimal Biology, University of Bristol, Bristol, UK
| | - Andrey Romanyuk
- School of Chemistry, University of Bristol, Bristol, UK
- Max Planck-Bristol Centre for Minimal Biology, University of Bristol, Bristol, UK
| | - Stephen J Cross
- Wolfson Bioimaging Facility, University of Bristol, Bristol, UK
| | - Richard Obexer
- School of Chemistry, University of Bristol, Bristol, UK.
- Max Planck-Bristol Centre for Minimal Biology, University of Bristol, Bristol, UK.
- Department of Chemistry, Manchester Institute of Biotechnology, University of Manchester, Manchester, UK.
| | - Jennifer J McManus
- HH Wills Physics Laboratory, School of Physics, University of Bristol, Bristol, UK.
- Bristol BioDesign Institute, School of Chemistry, University of Bristol, Bristol, UK.
| | - Derek N Woolfson
- School of Chemistry, University of Bristol, Bristol, UK.
- School of Biochemistry, University of Bristol, Bristol, UK.
- Max Planck-Bristol Centre for Minimal Biology, University of Bristol, Bristol, UK.
- Bristol BioDesign Institute, School of Chemistry, University of Bristol, Bristol, UK.
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3
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Woolfson DN. Understanding a protein fold: the physics, chemistry, and biology of α-helical coiled coils. J Biol Chem 2023; 299:104579. [PMID: 36871758 PMCID: PMC10124910 DOI: 10.1016/j.jbc.2023.104579] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 02/25/2023] [Accepted: 02/27/2023] [Indexed: 03/07/2023] Open
Abstract
Protein science is being transformed by powerful computational methods for structure prediction and design: AlphaFold2 can predict many natural protein structures from sequence, and other AI methods are enabling the de novo design of new structures. This raises a question: how much do we understand the underlying sequence-to-structure/function relationships being captured by these methods? This perspective presents our current understanding of one class of protein assembly, the α-helical coiled coils. At first sight, these are straightforward: sequence repeats of hydrophobic (h) and polar (p) residues, (hpphppp)n, direct the folding and assembly of amphipathic α helices into bundles. However, many different bundles are possible: they can have two or more helices (different oligomers); the helices can have parallel, antiparallel or mixed arrangements (different topologies); and the helical sequences can be the same (homomers) or different (heteromers). Thus, sequence-to-structure relationships must be present within the hpphppp repeats to distinguish these states. I discuss the current understanding of this problem at three levels: First, physics gives a parametric framework to generate the many possible coiled-coil backbone structures. Second, chemistry provides a means to explore and deliver sequence-to-structure relationships. Third, biology shows how coiled coils are adapted and functionalized in nature, inspiring applications of coiled coils in synthetic biology. I argue that the chemistry is largely understood; the physics is partly solved, though the considerable challenge of predicting even relative stabilities of different coiled-coil states remains; but there is much more to explore in the biology and synthetic biology of coiled coils.
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Affiliation(s)
- Derek N Woolfson
- School of Chemistry, University of Bristol, Bristol, United Kingdom; School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk, Bristol, United Kingdom; BrisEngBio, School of Chemistry, University of Bristol, Bristol, United Kingdom; Max Planck-Bristol Centre for Minimal Biology, University of Bristol, Bristol, United Kingdom.
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4
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Rhys GG, Cross JA, Dawson WM, Thompson HF, Shanmugaratnam S, Savery NJ, Dodding MP, Höcker B, Woolfson DN. De novo designed peptides for cellular delivery and subcellular localisation. Nat Chem Biol 2022; 18:999-1004. [PMID: 35836017 DOI: 10.1038/s41589-022-01076-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 06/03/2022] [Indexed: 12/14/2022]
Abstract
Increasingly, it is possible to design peptide and protein assemblies de novo from first principles or computationally. This approach provides new routes to functional synthetic polypeptides, including designs to target and bind proteins of interest. Much of this work has been developed in vitro. Therefore, a challenge is to deliver de novo polypeptides efficiently to sites of action within cells. Here we describe the design, characterisation, intracellular delivery, and subcellular localisation of a de novo synthetic peptide system. This system comprises a dual-function basic peptide, programmed both for cell penetration and target binding, and a complementary acidic peptide that can be fused to proteins of interest and introduced into cells using synthetic DNA. The designs are characterised in vitro using biophysical methods and X-ray crystallography. The utility of the system for delivery into mammalian cells and subcellular targeting is demonstrated by marking organelles and actively engaging functional protein complexes.
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Affiliation(s)
- Guto G Rhys
- Department of Biochemistry, University of Bayreuth, Bayreuth, Germany
| | - Jessica A Cross
- School of Chemistry, University of Bristol, Bristol, UK.,School of Biochemistry, University of Bristol, Bristol, UK
| | | | - Harry F Thompson
- School of Chemistry, University of Bristol, Bristol, UK.,School of Biochemistry, University of Bristol, Bristol, UK
| | | | - Nigel J Savery
- School of Biochemistry, University of Bristol, Bristol, UK.,BrisSynBio, University of Bristol, Bristol, UK
| | - Mark P Dodding
- School of Biochemistry, University of Bristol, Bristol, UK
| | - Birte Höcker
- Department of Biochemistry, University of Bayreuth, Bayreuth, Germany.
| | - Derek N Woolfson
- School of Chemistry, University of Bristol, Bristol, UK. .,School of Biochemistry, University of Bristol, Bristol, UK. .,BrisSynBio, University of Bristol, Bristol, UK.
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5
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Warren JP, Miles DE, Kapur N, Wilcox RK, Beales PA. Hydrodynamic Mixing Tunes the Stiffness of Proteoglycan-Mimicking Physical Hydrogels. Adv Healthc Mater 2021; 10:e2001998. [PMID: 33943034 DOI: 10.1002/adhm.202001998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 02/23/2021] [Indexed: 11/09/2022]
Abstract
Self-assembling hydrogels are promising materials for regenerative medicine and tissue engineering. However, designing hydrogels that replicate the 3-4 order of magnitude variation in soft tissue mechanics remains a major challenge. Here hybrid hydrogels are investigated formed from short self-assembling β-fibril peptides, and the glycosaminoglycan chondroitin sulfate (CS), chosen to replicate physical aspects of proteoglycans, specifically natural aggrecan, which provides structural mechanics to soft tissues. Varying the peptide:CS compositional ratio (1:2, 1:10, or 1:20) can tune the mechanics of the gel by one to two orders of magnitude. In addition, it is demonstrated that at any fixed composition, the gel shear modulus can be tuned over approximately two orders of magnitude through varying the initial vortex mixing time. This tuneability arises due to changes in the mesoscale structure of the gel network (fibril width, length, and connectivity), giving rise to both shear-thickening and shear-thinning behavior. The resulting hydrogels range in shear elastic moduli from 0.14 to 220 kPa, mimicking the mechanical variability in a range of soft tissues. The high degree of discrete tuneability of composition and mechanics in these hydrogels makes them particularly promising for matching the chemical and mechanical requirements of different applications in tissue engineering and regenerative medicine.
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Affiliation(s)
- James P. Warren
- School of Chemistry University of Leeds Leeds LS2 9JT UK
- School of Mechanical Engineering University of Leeds Leeds LS2 9JT UK
- Institute of Medical and Biological Engineering University of Leeds Leeds LS2 9JT UK
| | - Danielle E. Miles
- School of Chemistry University of Leeds Leeds LS2 9JT UK
- School of Mechanical Engineering University of Leeds Leeds LS2 9JT UK
- Institute of Medical and Biological Engineering University of Leeds Leeds LS2 9JT UK
| | - Nikil Kapur
- School of Mechanical Engineering University of Leeds Leeds LS2 9JT UK
| | - Ruth K. Wilcox
- School of Mechanical Engineering University of Leeds Leeds LS2 9JT UK
- Institute of Medical and Biological Engineering University of Leeds Leeds LS2 9JT UK
| | - Paul A. Beales
- School of Chemistry University of Leeds Leeds LS2 9JT UK
- Astbury Centre for Structural Biology University of Leeds Leeds LS2 9JT UK
- Bragg Centre for Materials Research University of Leeds Leeds LS2 9JT UK
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6
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ElGamacy M, Hernandez Alvarez B. Expanding the versatility of natural and de novo designed coiled coils and helical bundles. Curr Opin Struct Biol 2021; 68:224-234. [PMID: 33964630 DOI: 10.1016/j.sbi.2021.03.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 03/23/2021] [Accepted: 03/23/2021] [Indexed: 10/21/2022]
Abstract
Natural helical bundles (HBs) constitute a ubiquitous class of protein folds built of two or more longitudinally arranged α-helices. They adopt topologies that include symmetric, highly regular assemblies all the way to asymmetric, loosely packed domains. The diverse functional spectrum of HBs ranges from structural scaffolds to complex and dynamic effectors as molecular motors, signaling and sensing molecules, enzymes, and molecular switches. Symmetric HBs, particularly coiled coils, offer simple model systems providing an ideal entry point for protein folding and design studies. Herein, we review recent progress unveiling new structural features and functional mechanisms in natural HBs and cover staggering advances in the de novo design of HBs, giving rise to exotic structures and the creation of novel functions.
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Affiliation(s)
- Mohammad ElGamacy
- Systems Biology of Development Group, Friedrich Miescher Laboratory of the Max Planck Society, Max-Planck-Ring 9, Tübingen, 72076, Germany; Division of Translational Oncology, Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, Otfried-Müller-Strasse 10, Tübingen, 72076, Germany; Department of Protein Evolution, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, Tübingen, 72076, Germany
| | - Birte Hernandez Alvarez
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, Tübingen, 72076, Germany.
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7
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Ferrando J, Solomon LA. Recent Progress Using De Novo Design to Study Protein Structure, Design and Binding Interactions. Life (Basel) 2021; 11:life11030225. [PMID: 33802210 PMCID: PMC7999464 DOI: 10.3390/life11030225] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 03/04/2021] [Accepted: 03/05/2021] [Indexed: 12/14/2022] Open
Abstract
De novo protein design is a powerful methodology used to study natural functions in an artificial-protein context. Since its inception, it has been used to reproduce a plethora of reactions and uncover biophysical principles that are often difficult to extract from direct studies of natural proteins. Natural proteins are capable of assuming a variety of different structures and subsequently binding ligands at impressively high levels of both specificity and affinity. Here, we will review recent examples of de novo design studies on binding reactions for small molecules, nucleic acids, and the formation of protein-protein interactions. We will then discuss some new structural advances in the field. Finally, we will discuss some advancements in computational modeling and design approaches and provide an overview of some modern algorithmic tools being used to design these proteins.
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Affiliation(s)
- Juan Ferrando
- Department of Biology, George Mason University, 4400 University Dr, Fairfax, VA 22030, USA;
| | - Lee A. Solomon
- Department of Chemistry and Biochemistry, George Mason University, 10920 George Mason Circle, Manassas, VA 20110, USA
- Correspondence: ; Tel.: +703-993-6418
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8
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Lapenta F, Aupič J, Vezzoli M, Strmšek Ž, Da Vela S, Svergun DI, Carazo JM, Melero R, Jerala R. Self-assembly and regulation of protein cages from pre-organised coiled-coil modules. Nat Commun 2021; 12:939. [PMID: 33574245 PMCID: PMC7878516 DOI: 10.1038/s41467-021-21184-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 01/13/2021] [Indexed: 11/09/2022] Open
Abstract
Coiled-coil protein origami (CCPO) is a modular strategy for the de novo design of polypeptide nanostructures. CCPO folds are defined by the sequential order of concatenated orthogonal coiled-coil (CC) dimer-forming peptides, where a single-chain protein is programmed to fold into a polyhedral cage. Self-assembly of CC-based nanostructures from several chains, similarly as in DNA nanotechnology, could facilitate the design of more complex assemblies and the introduction of functionalities. Here, we show the design of a de novo triangular bipyramid fold comprising 18 CC-forming segments and define the strategy for the two-chain self-assembly of the bipyramidal cage from asymmetric and pseudo-symmetric pre-organised structural modules. In addition, by introducing a protease cleavage site and masking the interfacial CC-forming segments in the two-chain bipyramidal cage, we devise a proteolysis-mediated conformational switch. This strategy could be extended to other modular protein folds, facilitating the construction of dynamic multi-chain CC-based complexes. Coiled-coil protein origami is a strategy for the de novo design of polypeptide nanostructures based on coiled-coil dimer forming peptides, where a single chain protein folds into a polyhedral cage. Here, the authors design a single-chain triangular bipyramid and also demonstrate that the bipyramid can be self-assembled as a heterodimeric complex, comprising pre-defined subunits.
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Affiliation(s)
- Fabio Lapenta
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia.,EN-FIST Centre of Excellence, Ljubljana, Slovenia
| | - Jana Aupič
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Marco Vezzoli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Žiga Strmšek
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
| | | | | | | | - Roberto Melero
- Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Roman Jerala
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia. .,EN-FIST Centre of Excellence, Ljubljana, Slovenia.
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