1
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Smith A, Naudin EA, Edgell CL, Baker EG, Mylemans B, FitzPatrick L, Herman A, Rice HM, Andrews DM, Tigue N, Woolfson DN, Savery NJ. Design and Selection of Heterodimerizing Helical Hairpins for Synthetic Biology. ACS Synth Biol 2023; 12:1845-1858. [PMID: 37224449 PMCID: PMC10278171 DOI: 10.1021/acssynbio.3c00231] [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: 04/14/2023] [Indexed: 05/26/2023]
Abstract
Synthetic biology applications would benefit from protein modules of reduced complexity that function orthogonally to cellular components. As many subcellular processes depend on peptide-protein or protein-protein interactions, de novo designed polypeptides that can bring together other proteins controllably are particularly useful. Thanks to established sequence-to-structure relationships, helical bundles provide good starting points for such designs. Typically, however, such designs are tested in vitro and function in cells is not guaranteed. Here, we describe the design, characterization, and application of de novo helical hairpins that heterodimerize to form 4-helix bundles in cells. Starting from a rationally designed homodimer, we construct a library of helical hairpins and identify complementary pairs using bimolecular fluorescence complementation in E. coli. We characterize some of the pairs using biophysics and X-ray crystallography to confirm heterodimeric 4-helix bundles. Finally, we demonstrate the function of an exemplar pair in regulating transcription in both E. coli and mammalian cells.
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Affiliation(s)
- Abigail
J. Smith
- School
of Biochemistry, University of Bristol, Bristol BS8 1TD, U.K.
| | - Elise A. Naudin
- School
of Chemistry, University of Bristol, Bristol BS8 1TS, U.K.
| | - Caitlin L. Edgell
- School
of Biochemistry, University of Bristol, Bristol BS8 1TD, U.K.
- School
of Chemistry, University of Bristol, Bristol BS8 1TS, U.K.
| | - Emily G. Baker
- School
of Biochemistry, University of Bristol, Bristol BS8 1TD, U.K.
- School
of Chemistry, University of Bristol, Bristol BS8 1TS, U.K.
| | - Bram Mylemans
- School
of Chemistry, University of Bristol, Bristol BS8 1TS, U.K.
| | | | - Andrew Herman
- Flow
Cytometry Facility, School of Cellular and Molecular Medicine, University of Bristol, Bristol BS8 1TD, U.K.
| | - Helen M. Rice
- Flow
Cytometry Facility, School of Cellular and Molecular Medicine, University of Bristol, Bristol BS8 1TD, U.K.
| | | | - Natalie Tigue
- BioPharmaceuticals
R&D, AstraZeneca, Cambridge CB4 0WG, U.K.
| | - Derek N. Woolfson
- School
of Biochemistry, University of Bristol, Bristol BS8 1TD, U.K.
- School
of Chemistry, University of Bristol, Bristol BS8 1TS, U.K.
| | - Nigel J. Savery
- School
of Biochemistry, University of Bristol, Bristol BS8 1TD, U.K.
- BrisEngBio,
School of Chemistry, University of Bristol, Bristol BS8 1TS, U.K.
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2
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Merljak E, Malovrh B, Jerala R. Segmentation strategy of de novo designed four-helical bundles expands protein oligomerization modalities for cell regulation. Nat Commun 2023; 14:1995. [PMID: 37031229 PMCID: PMC10082849 DOI: 10.1038/s41467-023-37765-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 03/30/2023] [Indexed: 04/10/2023] Open
Abstract
Protein-protein interactions govern most biological processes. New protein assemblies can be introduced through the fusion of selected proteins with di/oligomerization domains, which interact specifically with their partners but not with other cellular proteins. While four-helical bundle proteins (4HB) have typically been assembled from two segments, each comprising two helices, here we show that they can be efficiently segmented in various ways, expanding the number of combinations generated from a single 4HB. We implement a segmentation strategy of 4HB to design two-, three-, or four-chain combinations for the recruitment of multiple protein components. Different segmentations provide new insight into the role of individual helices for 4HB assembly. We evaluate 4HB segmentations for potential use in mammalian cells for the reconstitution of a protein reporter, transcriptional activation, and inducible 4HB assembly. Furthermore, the implementation of trimerization is demonstrated as a modular chimeric antigen receptor for the recognition of multiple cancer antigens.
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Affiliation(s)
- Estera Merljak
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
- Interdisciplinary Doctoral Programme of Biomedicine, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Benjamin Malovrh
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Roman Jerala
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia.
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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: 17] [Impact Index Per Article: 17.0] [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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Lee B, Wang T. A Modular Scaffold for Controlling Transcriptional Activation via Homomeric Protein-Protein Interactions. ACS Synth Biol 2022; 11:3198-3206. [PMID: 36215660 DOI: 10.1021/acssynbio.2c00501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Protein-protein interactions (PPIs) have been extensively utilized in synthetic biology to construct artificial gene networks. However, synthetic regulation of gene expression by PPIs in E. coli has largely relied upon repressors, and existing PPI-controlled transcriptional activators have generally been employed with heterodimeric interactions. Here we report a highly modular, PPI-dependent transcriptional activator, cCadC, that was designed to be compatible with homomeric interactions. We describe the process of engineering cCadC from a transmembrane protein into a soluble cytosolic regulator. We then show that gene transcription by cCadC can be controlled by homomeric PPIs and furthermore discriminates between dimeric and higher-order interactions. Finally, we demonstrate that cCadC activity can be placed under small molecule regulation using chemically induced dimerization or ligand dependent stabilization. This work should greatly expand the scope of PPIs that can be employed in artificial gene circuits in E. coli and complements the existing repertoire of tools for transcriptional regulation in synthetic biology.
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Affiliation(s)
- ByungUk Lee
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Tina Wang
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
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5
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Marchand A, Van Hall-Beauvais AK, Correia BE. Computational design of novel protein–protein interactions – An overview on methodological approaches and applications. Curr Opin Struct Biol 2022; 74:102370. [DOI: 10.1016/j.sbi.2022.102370] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 02/21/2022] [Accepted: 02/28/2022] [Indexed: 11/27/2022]
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6
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Sahtoe DD, Praetorius F, Courbet A, Hsia Y, Wicky BI, Edman NI, Miller LM, Timmermans BJR, Decarreau J, Morris HM, Kang A, Bera AK, Baker D. Reconfigurable asymmetric protein assemblies through implicit negative design. Science 2022; 375:eabj7662. [PMID: 35050655 PMCID: PMC9881579 DOI: 10.1126/science.abj7662] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Asymmetric multiprotein complexes that undergo subunit exchange play central roles in biology but present a challenge for design because the components must not only contain interfaces that enable reversible association but also be stable and well behaved in isolation. We use implicit negative design to generate β sheet-mediated heterodimers that can be assembled into a wide variety of complexes. The designs are stable, folded, and soluble in isolation and rapidly assemble upon mixing, and crystal structures are close to the computational models. We construct linearly arranged hetero-oligomers with up to six different components, branched hetero-oligomers, closed C4-symmetric two-component rings, and hetero-oligomers assembled on a cyclic homo-oligomeric central hub and demonstrate that such complexes can readily reconfigure through subunit exchange. Our approach provides a general route to designing asymmetric reconfigurable protein systems.
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Affiliation(s)
- Danny D. Sahtoe
- Department of Biochemistry, University of Washington, Seattle, WA 98195,Institute for Protein Design, University of Washington, Seattle, WA 98195,HHMI, University of Washington, Seattle, WA 98195
| | - Florian Praetorius
- Department of Biochemistry, University of Washington, Seattle, WA 98195,Institute for Protein Design, University of Washington, Seattle, WA 98195
| | - Alexis Courbet
- Department of Biochemistry, University of Washington, Seattle, WA 98195,Institute for Protein Design, University of Washington, Seattle, WA 98195,HHMI, University of Washington, Seattle, WA 98195
| | - Yang Hsia
- Department of Biochemistry, University of Washington, Seattle, WA 98195,Institute for Protein Design, University of Washington, Seattle, WA 98195
| | - Basile I.M. Wicky
- Department of Biochemistry, University of Washington, Seattle, WA 98195,Institute for Protein Design, University of Washington, Seattle, WA 98195
| | - Natasha I. Edman
- Department of Biochemistry, University of Washington, Seattle, WA 98195,Institute for Protein Design, University of Washington, Seattle, WA 98195,Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA, USA.,Medical Scientist Training Program, University of Washington, Seattle, WA, USA
| | - Lauren M. Miller
- Department of Biochemistry, University of Washington, Seattle, WA 98195,Institute for Protein Design, University of Washington, Seattle, WA 98195
| | - Bart J. R. Timmermans
- Department of Biochemistry, University of Washington, Seattle, WA 98195,Institute for Protein Design, University of Washington, Seattle, WA 98195
| | - Justin Decarreau
- Department of Biochemistry, University of Washington, Seattle, WA 98195,Institute for Protein Design, University of Washington, Seattle, WA 98195
| | - Hana M. Morris
- Department of Biochemistry, University of Washington, Seattle, WA 98195,Institute for Protein Design, University of Washington, Seattle, WA 98195
| | - Alex Kang
- Department of Biochemistry, University of Washington, Seattle, WA 98195,Institute for Protein Design, University of Washington, Seattle, WA 98195
| | - Asim K. Bera
- Department of Biochemistry, University of Washington, Seattle, WA 98195,Institute for Protein Design, University of Washington, Seattle, WA 98195
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA 98195,Institute for Protein Design, University of Washington, Seattle, WA 98195,HHMI, University of Washington, Seattle, WA 98195,Corresponding author.
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7
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Naudin EA, Albanese KI, Smith AJ, Mylemans B, Baker EG, Weiner OD, Andrews DM, Tigue N, Savery NJ, Woolfson DN. From peptides to proteins: coiled-coil tetramers to single-chain 4-helix bundles. Chem Sci 2022; 13:11330-11340. [PMID: 36320580 PMCID: PMC9533478 DOI: 10.1039/d2sc04479j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 08/24/2022] [Indexed: 11/21/2022] Open
Abstract
The design of completely synthetic proteins from first principles—de novo protein design—is challenging. This is because, despite recent advances in computational protein–structure prediction and design, we do not understand fully the sequence-to-structure relationships for protein folding, assembly, and stabilization. Antiparallel 4-helix bundles are amongst the most studied scaffolds for de novo protein design. We set out to re-examine this target, and to determine clear sequence-to-structure relationships, or design rules, for the structure. Our aim was to determine a common and robust sequence background for designing multiple de novo 4-helix bundles. In turn, this could be used in chemical and synthetic biology to direct protein–protein interactions and as scaffolds for functional protein design. Our approach starts by analyzing known antiparallel 4-helix coiled-coil structures to deduce design rules. In terms of the heptad repeat, abcdefg—i.e., the sequence signature of many helical bundles—the key features that we identify are: a = Leu, d = Ile, e = Ala, g = Gln, and the use of complementary charged residues at b and c. Next, we implement these rules in the rational design of synthetic peptides to form antiparallel homo- and heterotetramers. Finally, we use the sequence of the homotetramer to derive in one step a single-chain 4-helix-bundle protein for recombinant production in E. coli. All of the assembled designs are confirmed in aqueous solution using biophysical methods, and ultimately by determining high-resolution X-ray crystal structures. Our route from peptides to proteins provides an understanding of the role of each residue in each design. Rules for designing 4-helix bundles are defined, tested, and used to generate de novo peptide assemblies and a single-chain protein.![]()
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Affiliation(s)
- Elise A. Naudin
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK
| | - Katherine I. Albanese
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK
- Max Planck-Bristol Centre for Minimal Biology, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK
| | - Abigail J. Smith
- School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk, Bristol BS8 1TD, UK
| | - Bram Mylemans
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK
- Max Planck-Bristol Centre for Minimal Biology, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK
| | - Emily G. Baker
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK
- School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk, Bristol BS8 1TD, UK
| | - Orion D. Weiner
- Cardiovascular Research Institute, Department of Biochemistry and Biophysics, University of California, 555 Mission Bay Blvd. South, San Francisco, CA 94158, USA
| | - David M. Andrews
- Oncology R&D, AstraZeneca, Cambridge Science Park, Darwin Building, Cambridge CB4 0WG, UK
| | - Natalie Tigue
- BioPharmaceuticals R&D, AstraZeneca, Granta Park, Cambridge CB21 6GH, UK
| | - Nigel J. Savery
- School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk, Bristol BS8 1TD, UK
- BrisEngBio, School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK
| | - Derek N. Woolfson
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK
- Max Planck-Bristol Centre for Minimal Biology, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK
- School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk, Bristol BS8 1TD, UK
- BrisEngBio, School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK
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8
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Neitz H, Paul NB, Häge FR, Lindner C, Graebner R, Kovermann M, Thomas F. Identification of novel functional mini-receptors by combinatorial screening of split-WW domains. Chem Sci 2022; 13:9079-9090. [PMID: 36091217 PMCID: PMC9365081 DOI: 10.1039/d2sc01078j] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 07/14/2022] [Indexed: 11/21/2022] Open
Abstract
A combinatorial approach toward novel functional WW domains based on coiled-coil-mediated reconstitution of split WW domains is presented. As such, an ATP-binding WW domain was found from a 4-by-6 library of N- and C-terminal WW domain fragments.
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Affiliation(s)
- Hermann Neitz
- Institute of Organic Chemistry, University of Würzburg, Am Hubland, Würzburg 97074, Germany
| | - Niels Benjamin Paul
- Institute of Organic and Biomolecular Chemistry, University of Göttingen, Tammannstr. 2, Göttingen 37077, Germany
| | - Florian R. Häge
- Institute of Organic Chemistry, Heidelberg University, Im Neuenheimer Feld 270, Heidelberg 69120, Germany
- Centre for Advanced Materials, Heidelberg University, Im Neuenheimer Feld 225, Heidelberg 69120, Germany
| | - Christina Lindner
- Institute of Organic Chemistry, Heidelberg University, Im Neuenheimer Feld 270, Heidelberg 69120, Germany
- Centre for Advanced Materials, Heidelberg University, Im Neuenheimer Feld 225, Heidelberg 69120, Germany
| | - Roman Graebner
- Institute of Organic Chemistry, Heidelberg University, Im Neuenheimer Feld 270, Heidelberg 69120, Germany
- Centre for Advanced Materials, Heidelberg University, Im Neuenheimer Feld 225, Heidelberg 69120, Germany
| | - Michael Kovermann
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, Konstanz 78457, Germany
| | - Franziska Thomas
- Institute of Organic Chemistry, Heidelberg University, Im Neuenheimer Feld 270, Heidelberg 69120, Germany
- Centre for Advanced Materials, Heidelberg University, Im Neuenheimer Feld 225, Heidelberg 69120, Germany
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9
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Synthetic Protein Circuits and Devices Based on Reversible Protein-Protein Interactions: An Overview. Life (Basel) 2021; 11:life11111171. [PMID: 34833047 PMCID: PMC8623019 DOI: 10.3390/life11111171] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/25/2021] [Accepted: 10/26/2021] [Indexed: 12/30/2022] Open
Abstract
Protein-protein interactions (PPIs) contribute to regulate many aspects of cell physiology and metabolism. Protein domains involved in PPIs are important building blocks for engineering genetic circuits through synthetic biology. These domains can be obtained from known proteins and rationally engineered to produce orthogonal scaffolds, or computationally designed de novo thanks to recent advances in structural biology and molecular dynamics prediction. Such circuits based on PPIs (or protein circuits) appear of particular interest, as they can directly affect transcriptional outputs, as well as induce behavioral/adaptational changes in cell metabolism, without the need for further protein synthesis. This last example was highlighted in recent works to enable the production of fast-responding circuits which can be exploited for biosensing and diagnostics. Notably, PPIs can also be engineered to develop new drugs able to bind specific intra- and extra-cellular targets. In this review, we summarize recent findings in the field of protein circuit design, with particular focus on the use of peptides as scaffolds to engineer these circuits.
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10
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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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11
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Plaper T, Aupič J, Dekleva P, Lapenta F, Keber MM, Jerala R, Benčina M. Coiled-coil heterodimers with increased stability for cellular regulation and sensing SARS-CoV-2 spike protein-mediated cell fusion. Sci Rep 2021; 11:9136. [PMID: 33911109 PMCID: PMC8080620 DOI: 10.1038/s41598-021-88315-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 04/12/2021] [Indexed: 12/19/2022] Open
Abstract
Coiled-coil (CC) dimer-forming peptides are attractive designable modules for mediating protein association. Highly stable CCs are desired for biological activity regulation and assay. Here, we report the design and versatile applications of orthogonal CC dimer-forming peptides with a dissociation constant in the low nanomolar range. In vitro stability and specificity was confirmed in mammalian cells by enzyme reconstitution, transcriptional activation using a combination of DNA-binding and a transcriptional activation domain, and cellular-enzyme-activity regulation based on externally-added peptides. In addition to cellular regulation, coiled-coil-mediated reporter reconstitution was used for the detection of cell fusion mediated by the interaction between the spike protein of pandemic SARS-CoV2 and the ACE2 receptor. This assay can be used to investigate the mechanism of viral spike protein-mediated fusion or screening for viral inhibitors under biosafety level 1 conditions.
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Affiliation(s)
- Tjaša Plaper
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, 1001, Ljubljana, Slovenia.,Interfaculty Doctoral Study of Biomedicine, University of Ljubljana, Ljubljana, Slovenia
| | - Jana Aupič
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, 1001, Ljubljana, Slovenia
| | - Petra Dekleva
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, 1001, Ljubljana, Slovenia
| | - Fabio Lapenta
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, 1001, Ljubljana, Slovenia.,EN-FIST Centre of Excellence, Trg Osvobodilne Fronte 13, 1000, Ljubljana, Slovenia
| | - Mateja Manček Keber
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, 1001, Ljubljana, Slovenia.,EN-FIST Centre of Excellence, Trg Osvobodilne Fronte 13, 1000, Ljubljana, Slovenia
| | - Roman Jerala
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, 1001, Ljubljana, Slovenia. .,EN-FIST Centre of Excellence, Trg Osvobodilne Fronte 13, 1000, Ljubljana, Slovenia.
| | - Mojca Benčina
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, 1001, Ljubljana, Slovenia. .,EN-FIST Centre of Excellence, Trg Osvobodilne Fronte 13, 1000, Ljubljana, Slovenia.
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12
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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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13
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De novo design of a reversible phosphorylation-dependent switch for membrane targeting. Nat Commun 2021; 12:1472. [PMID: 33674566 PMCID: PMC7935970 DOI: 10.1038/s41467-021-21622-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 02/03/2021] [Indexed: 02/06/2023] Open
Abstract
Modules that switch protein-protein interactions on and off are essential to develop synthetic biology; for example, to construct orthogonal signaling pathways, to control artificial protein structures dynamically, and for protein localization in cells or protocells. In nature, the E. coli MinCDE system couples nucleotide-dependent switching of MinD dimerization to membrane targeting to trigger spatiotemporal pattern formation. Here we present a de novo peptide-based molecular switch that toggles reversibly between monomer and dimer in response to phosphorylation and dephosphorylation. In combination with other modules, we construct fusion proteins that couple switching to lipid-membrane targeting by: (i) tethering a ‘cargo’ molecule reversibly to a permanent membrane ‘anchor’; and (ii) creating a ‘membrane-avidity switch’ that mimics the MinD system but operates by reversible phosphorylation. These minimal, de novo molecular switches have potential applications for introducing dynamic processes into designed and engineered proteins to augment functions in living cells and add functionality to protocells. The ability to dynamically control protein-protein interactions and localization of proteins is critical in synthetic biological systems. Here the authors develop a peptide-based molecular switch that regulates dimer formation and lipid membrane targeting via reversible phosphorylation.
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