51
|
Sztatelman O, Kopeć K, Pędziwiatr M, Trojnar M, Worch R, Wielgus-Kutrowska B, Jemioła-Rzemińska M, Bzowska A, Grzyb J. Heterodimerizing helices as tools for nanoscale control of the organization of protein-protein and protein-quantum dots. Biochimie 2019; 167:93-105. [PMID: 31560933 DOI: 10.1016/j.biochi.2019.09.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 09/19/2019] [Indexed: 01/11/2023]
Abstract
In this study, we tested the possibility of creating complexes of two proteins by fusing them with heterodimerizing helices. We used the fluorescent proteins GFP and mCHERRY expressed with a His-tag as our model system. We added heterodimer-forming sequences at the C- or N- termini of the proteins, opposite to the His-tag position. Heterodimerization was tested for both helices at the C-terminus or at the N- terminus and C-terminus. We observed complex formation with a nanomolar dissociation constant in both cases that was higher by one order of magnitude than the Kds measured for helices alone. The binding of two C-terminal helices was accompanied by an increased enthalpy change. The binding between helices could be stabilized by introducing an additional turn of the helix with cysteine, which was capable of forming disulphide bridges. Covalently linked proteins were obtained using this strategy and observed using fluorescence cross-correlation spectroscopy. Finally, we demonstrated the formation of complexes of protein dimers and quantum dots.
Collapse
Affiliation(s)
- Olga Sztatelman
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, Pawińskiego 5a, PL02106, Warsaw, Poland
| | - Katarzyna Kopeć
- Institute of Physics Polish Academy of Sciences, Aleja Lotników 32/46, PL02668, Warsaw, Poland
| | - Marta Pędziwiatr
- Institute of Physics Polish Academy of Sciences, Aleja Lotników 32/46, PL02668, Warsaw, Poland
| | - Martyna Trojnar
- Department of Biophysics, Faculty of Biotechnology, University of Wroclaw, F. Joliot-Curie Str. 14a, PL50383, Wrocław, Poland
| | - Remigiusz Worch
- Institute of Physics Polish Academy of Sciences, Aleja Lotników 32/46, PL02668, Warsaw, Poland
| | - Beata Wielgus-Kutrowska
- Division of Biophysics, Institute of Experimental Physics, University of Warsaw, Pasteura 5, PL02093, Warsaw, Poland
| | - Małgorzata Jemioła-Rzemińska
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, PL30387, Krakow, Poland; Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, PL30387, Krakow, Poland
| | - Agnieszka Bzowska
- Division of Biophysics, Institute of Experimental Physics, University of Warsaw, Pasteura 5, PL02093, Warsaw, Poland
| | - Joanna Grzyb
- Department of Biophysics, Faculty of Biotechnology, University of Wroclaw, F. Joliot-Curie Str. 14a, PL50383, Wrocław, Poland.
| |
Collapse
|
52
|
Synthetic Protein Scaffolding at Biological Membranes. Trends Biotechnol 2019; 38:432-446. [PMID: 31718802 DOI: 10.1016/j.tibtech.2019.10.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 10/18/2019] [Accepted: 10/21/2019] [Indexed: 02/07/2023]
Abstract
Protein scaffolding is a natural phenomenon whereby proteins colocalize into macromolecular complexes via specific protein-protein interactions. In the case of metabolic enzymes, protein scaffolding drives metabolic flux through specific pathways by colocalizing enzyme active sites. Synthetic protein scaffolding is increasingly used as a mechanism to improve product specificity and yields in metabolic engineering projects. To date, synthetic scaffolding has focused primarily on soluble enzyme systems, but many metabolic pathways for high-value secondary metabolites depend on membrane-bound enzymes. The compositional diversity of biological membranes and general challenges associated with modifying membrane proteins complicate scaffolding with membrane-requiring enzymes. Several recent studies have introduced new approaches to protein scaffolding at membrane surfaces, with notable success in improving product yields from specific metabolic pathways.
Collapse
|
53
|
Ellis GA, Klein WP, Lasarte-Aragonés G, Thakur M, Walper SA, Medintz IL. Artificial Multienzyme Scaffolds: Pursuing in Vitro Substrate Channeling with an Overview of Current Progress. ACS Catal 2019. [DOI: 10.1021/acscatal.9b02413] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Gregory A. Ellis
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - William P. Klein
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
- National Research Council, Washington, D.C. 20001, United States
| | - Guillermo Lasarte-Aragonés
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
- College of Science, George Mason University, Fairfax, Virginia 22030, United States
| | - Meghna Thakur
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
- College of Science, George Mason University, Fairfax, Virginia 22030, United States
| | - Scott A. Walper
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Igor L. Medintz
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| |
Collapse
|
54
|
Towards functional de novo designed proteins. Curr Opin Chem Biol 2019; 52:102-111. [DOI: 10.1016/j.cbpa.2019.06.011] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 04/25/2019] [Accepted: 06/06/2019] [Indexed: 12/31/2022]
|
55
|
Jin J, Baker EG, Wood CW, Bath J, Woolfson DN, Turberfield AJ. Peptide Assembly Directed and Quantified Using Megadalton DNA Nanostructures. ACS NANO 2019; 13:9927-9935. [PMID: 31381314 PMCID: PMC6764022 DOI: 10.1021/acsnano.9b04251] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 08/05/2019] [Indexed: 05/02/2023]
Abstract
In nature, co-assembly of polypeptides, nucleic acids, and polysaccharides is used to create functional supramolecular structures. Here, we show that DNA nanostructures can be used to template interactions between peptides and to enable the quantification of multivalent interactions that would otherwise not be observable. Our functional building blocks are peptide-oligonucleotide conjugates comprising de novo designed dimeric coiled-coil peptides covalently linked to oligonucleotide tags. These conjugates are incorporated in megadalton DNA origami nanostructures and direct nanostructure association through peptide-peptide interactions. Free and bound nanostructures can be counted directly from electron micrographs, allowing estimation of the dissociation constants of the peptides linking them. Results for a single peptide-peptide interaction are consistent with the measured solution-phase free energy; DNA nanostructures displaying multiple peptides allow the effects of polyvalency to be probed. This use of DNA nanostructures as identifiers allows the binding strengths of homo- and heterodimeric peptide combinations to be measured in a single experiment and gives access to dissociation constants that are too low to be quantified by conventional techniques. The work also demonstrates that hybrid biomolecules can be programmed to achieve spatial organization of complex synthetic biomolecular assemblies.
Collapse
Affiliation(s)
- Juan Jin
- Department
of Physics, Clarendon Laboratory, University
of Oxford, Parks Road, Oxford OX1
3PU, United Kingdom
| | - Emily G. Baker
- School
of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, United Kingdom
| | - Christopher W. Wood
- School
of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, United Kingdom
| | - Jonathan Bath
- Department
of Physics, Clarendon Laboratory, University
of Oxford, Parks Road, Oxford OX1
3PU, United Kingdom
| | - Derek N. Woolfson
- School
of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, United Kingdom
- School
of Biochemistry, Medical Sciences Building, University of Bristol, University Walk, Bristol BS8 1TD, United Kingdom
- Bristol
BioDesign Institute, BrisSynBio, University
of Bristol Research Centre in Synthetic Biology, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, United Kingdom
| | - Andrew J. Turberfield
- Department
of Physics, Clarendon Laboratory, University
of Oxford, Parks Road, Oxford OX1
3PU, United Kingdom
| |
Collapse
|
56
|
Hussey BJ, McMillen DR. Programmable T7-based synthetic transcription factors. Nucleic Acids Res 2019; 46:9842-9854. [PMID: 30169636 PMCID: PMC6182181 DOI: 10.1093/nar/gky785] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 08/21/2018] [Indexed: 12/31/2022] Open
Abstract
Despite recent progress on synthetic transcription factor generation in eukaryotes, there remains a need for high-activity bacterial versions of these systems. In synthetic biology applications, it is useful for transcription factors to have two key features: they should be orthogonal (influencing only their own targets, with minimal off-target effects), and programmable (able to be directed to a wide range of user-specified transcriptional start sites). The RNA polymerase of the bacteriophage T7 has a number of appealing properties for synthetic biological designs: it can produce high transcription rates; it is a compact, single-subunit polymerase that has been functionally expressed in a variety of organisms; and its viral origin reduces the connection between its activity and that of its host's transcriptional machinery. We have created a system where a T7 RNA polymerase is recruited to transcriptional start sites by DNA binding proteins, either directly or bridged through protein–protein interactions, yielding a modular and programmable system for strong transcriptional activation of multiple orthogonal synthetic transcription factor variants in Escherichia coli. To our knowledge this is the first exogenous, programmable activator system in bacteria.
Collapse
Affiliation(s)
- Brendan J Hussey
- Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario L5L 1C6, Canada.,Cell and Systems Biology, University of Toronto Mississauga, Mississauga, Ontario L5L 1C6, Canada.,Impact Centre, University of Toronto, Toronto, Ontario M5S 1A7, Canada
| | - David R McMillen
- Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario L5L 1C6, Canada.,Cell and Systems Biology, University of Toronto Mississauga, Mississauga, Ontario L5L 1C6, Canada.,Impact Centre, University of Toronto, Toronto, Ontario M5S 1A7, Canada
| |
Collapse
|
57
|
Rawlings AE, Somner LA, Fitzpatrick-Milton M, Roebuck TP, Gwyn C, Liravi P, Seville V, Neal TJ, Mykhaylyk OO, Baldwin SA, Staniland SS. Artificial coiled coil biomineralisation protein for the synthesis of magnetic nanoparticles. Nat Commun 2019; 10:2873. [PMID: 31253765 PMCID: PMC6599041 DOI: 10.1038/s41467-019-10578-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 05/21/2019] [Indexed: 01/08/2023] Open
Abstract
Green synthesis of precise inorganic nanomaterials is a major challenge. Magnetotactic bacteria biomineralise magnetite nanoparticles (MNPs) within membrane vesicles (magnetosomes), which are embedded with dedicated proteins that control nanocrystal formation. Some such proteins are used in vitro to control MNP formation in green synthesis; however, these membrane proteins self-aggregate, making their production and use in vitro challenging and difficult to scale. Here, we provide an alternative solution by displaying active loops from biomineralisation proteins Mms13 and MmsF on stem-loop coiled-coil scaffold proteins (Mms13cc/MmsFcc). These artificial biomineralisation proteins form soluble, stable alpha-helical hairpin monomers, and MmsFcc successfully controls the formation of MNP when added to magnetite synthesis, regulating synthesis comparably to native MmsF. This study demonstrates how displaying active loops from membrane proteins on coiled-coil scaffolds removes membrane protein solubility issues, while retains activity, enabling a generic approach to readily-expressible, versatile, artificial membrane proteins for more accessible study and exploitation. Proteins have been used in the synthesis of magnetic nanoparticles but issues with aggregation limit this application. Here, the authors report on the synthesis of coiled proteins that display the active loop of the natural proteins to avoid aggregation and investigate the application in nanoparticle synthesis.
Collapse
Affiliation(s)
- Andrea E Rawlings
- Department of Chemistry, University of Sheffield, Sheffield, S3 7HF, UK.,School of Physics and Astronomy, University of Leeds, Leeds, LS2 9JT, UK
| | - Lori A Somner
- Department of Chemistry, University of Sheffield, Sheffield, S3 7HF, UK
| | | | - Thomas P Roebuck
- Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Christopher Gwyn
- School of Physics and Astronomy, University of Leeds, Leeds, LS2 9JT, UK
| | - Panah Liravi
- Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Victoria Seville
- Department of Chemistry, University of Sheffield, Sheffield, S3 7HF, UK
| | - Thomas J Neal
- Department of Chemistry, University of Sheffield, Sheffield, S3 7HF, UK
| | | | - Stephen A Baldwin
- Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Sarah S Staniland
- Department of Chemistry, University of Sheffield, Sheffield, S3 7HF, UK. .,School of Physics and Astronomy, University of Leeds, Leeds, LS2 9JT, UK.
| |
Collapse
|
58
|
Bio-engineering of bacterial microcompartments: a mini review. Biochem Soc Trans 2019; 47:765-777. [DOI: 10.1042/bst20170564] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 05/09/2019] [Accepted: 05/22/2019] [Indexed: 12/30/2022]
Abstract
AbstractBacterial microcompartments (BMCs) are protein-bound prokaryotic organelles, discovered in cyanobacteria more than 60 years ago. Functionally similar to eukaryotic cellular organelles, BMCs compartment metabolic activities in the cytoplasm, foremost to increase local enzyme concentration and prevent toxic intermediates from damaging the cytosolic content. Advanced knowledge of the functional and structural properties of multiple types of BMCs, particularly over the last 10 years, have highlighted design principles of microcompartments. This has prompted new research into their potential to function as programmable synthetic nano-bioreactors and novel bio-materials with biotechnological and medical applications. Moreover, due to the involvement of microcompartments in bacterial pathogenesis and human health, BMCs have begun to gain attention as potential novel drug targets. This mini-review gives an overview of important synthetic biology developments in the bioengineering of BMCs and a perspective on future directions in the field.
Collapse
|
59
|
Smith AJ, Thomas F, Shoemark D, Woolfson DN, Savery NJ. Guiding Biomolecular Interactions in Cells Using de Novo Protein-Protein Interfaces. ACS Synth Biol 2019; 8:1284-1293. [PMID: 31059644 DOI: 10.1021/acssynbio.8b00501] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
An improved ability to direct and control biomolecular interactions in living cells would have an impact on synthetic biology. A key issue is the need to introduce interacting components that act orthogonally to endogenous proteomes and interactomes. Here, we show that low-complexity, de novo designed protein-protein interaction (PPI) domains can substitute for natural PPIs and guide engineered protein-DNA interactions in Escherichia coli. Specifically, we use de novo homo- and heterodimeric coiled coils to reconstitute a cytoplasmic split adenylate cyclase, recruit RNA polymerase to a promoter and activate gene expression, and oligomerize both natural and designed DNA-binding domains to repress transcription. Moreover, the stabilities of the heterodimeric coiled coils can be modulated by rational design and, thus, adjust the levels of gene activation and repression in vivo. These experiments demonstrate the possibilities for using designed proteins and interactions to control biomolecular systems such as enzyme cascades and circuits in cells.
Collapse
Affiliation(s)
- Abigail J. Smith
- School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk, Bristol BS8 1TD, U.K
- BrisSynBio, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, U.K
| | - Franziska Thomas
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K
| | - Deborah Shoemark
- School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk, Bristol BS8 1TD, U.K
- BrisSynBio, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, U.K
| | - Derek N. Woolfson
- School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk, Bristol BS8 1TD, U.K
- BrisSynBio, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, U.K
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K
| | - Nigel J. Savery
- School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk, Bristol BS8 1TD, U.K
- BrisSynBio, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, U.K
| |
Collapse
|
60
|
Rhys GG, Wood CW, Beesley JL, Zaccai NR, Burton AJ, Brady RL, Thomson AR, Woolfson DN. Navigating the Structural Landscape of De Novo α-Helical Bundles. J Am Chem Soc 2019; 141:8787-8797. [PMID: 31066556 DOI: 10.1021/jacs.8b13354] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The association of amphipathic α helices in water leads to α-helical-bundle protein structures. However, the driving force for this-the hydrophobic effect-is not specific and does not define the number or the orientation of helices in the associated state. Rather, this is achieved through deeper sequence-to-structure relationships, which are increasingly being discerned. For example, for one structurally extreme but nevertheless ubiquitous class of bundle-the α-helical coiled coils-relationships have been established that discriminate between all-parallel dimers, trimers, and tetramers. Association states above this are known, as are antiparallel and mixed arrangements of the helices. However, these alternative states are less well understood. Here, we describe a synthetic-peptide system that switches between parallel hexamers and various up-down-up-down tetramers in response to single-amino-acid changes and solution conditions. The main accessible states of each peptide variant are characterized fully in solution and, in most cases, to high resolution with X-ray crystal structures. Analysis and inspection of these structures helps rationalize the different states formed. This navigation of the structural landscape of α-helical coiled coils above the dimers and trimers that dominate in nature has allowed us to design rationally a well-defined and hyperstable antiparallel coiled-coil tetramer (apCC-Tet). This robust de novo protein provides another scaffold for further structural and functional designs in protein engineering and synthetic biology.
Collapse
Affiliation(s)
- Guto G Rhys
- School of Chemistry , University of Bristol , Cantock's Close , Bristol BS8 1TS , United Kingdom
| | - Christopher W Wood
- School of Chemistry , University of Bristol , Cantock's Close , Bristol BS8 1TS , United Kingdom
| | - Joseph L Beesley
- School of Chemistry , University of Bristol , Cantock's Close , Bristol BS8 1TS , United Kingdom
| | - Nathan R Zaccai
- School of Biochemistry , University of Bristol , Medical Sciences Building, University Walk , Bristol BS8 1TD , United Kingdom
| | - Antony J Burton
- School of Chemistry , University of Bristol , Cantock's Close , Bristol BS8 1TS , United Kingdom
- Frick Chemistry Laboratory , Princeton University , Princeton , New Jersey 08544 , United States
| | - R Leo Brady
- School of Biochemistry , University of Bristol , Medical Sciences Building, University Walk , Bristol BS8 1TD , United Kingdom
| | - Andrew R Thomson
- School of Chemistry , University of Bristol , Cantock's Close , Bristol BS8 1TS , United Kingdom
- School of Chemistry , University of Glasgow , Glasgow G12 8QQ , United Kingdom
| | - Derek N Woolfson
- School of Chemistry , University of Bristol , Cantock's Close , Bristol BS8 1TS , United Kingdom
- School of Biochemistry , University of Bristol , Medical Sciences Building, University Walk , Bristol BS8 1TD , United Kingdom
- BrisSynBio , University of Bristol , Life Sciences Building, Tyndall Avenue , Bristol BS8 1TQ , United Kingdom
| |
Collapse
|
61
|
Trang VH, Zhang X, Yumul RC, Zeng W, Stone IJ, Wo SW, Dominguez MM, Cochran JH, Simmons JK, Ryan MC, Lyon RP, Senter PD, Levengood MR. A coiled-coil masking domain for selective activation of therapeutic antibodies. Nat Biotechnol 2019; 37:761-765. [PMID: 31133742 DOI: 10.1038/s41587-019-0135-x] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 04/16/2019] [Indexed: 11/09/2022]
Abstract
The use of monoclonal antibodies in cancer therapy is limited by their cross-reactivity to healthy tissue. Tumor targeting has been improved by generating masked antibodies that are selectively activated in the tumor microenvironment, but each such antibody necessitates a custom design. Here, we present a generalizable approach for masking the binding domains of antibodies with a heterodimeric coiled-coil domain that sterically occludes the complementarity-determining regions. On exposure to tumor-associated proteases, such as matrix metalloproteinases 2 and 9, the coiled-coil peptides are cleaved and antigen binding is restored. We test multiple coiled-coil formats and show that the optimized masking domain is broadly applicable to antibodies of interest. Our approach prevents anti-CD3-associated cytokine release in mice and substantially improves circulation half-life by protecting the antibody from an antigen sink. When applied to antibody-drug conjugates, our masked antibodies are preferentially unmasked at the tumor site and have increased anti-tumor efficacy compared with unmasked antibodies in mouse models of cancer.
Collapse
Affiliation(s)
- Vivian H Trang
- Department of Protein Sciences, Seattle Genetics Inc., Bothell, WA, USA
| | - Xinqun Zhang
- Department of Protein Sciences, Seattle Genetics Inc., Bothell, WA, USA
| | - Roma C Yumul
- Department of Nonclinical Science, Seattle Genetics Inc., Bothell, WA, USA
| | - Weiping Zeng
- Department of Nonclinical Science, Seattle Genetics Inc., Bothell, WA, USA
| | - Ivan J Stone
- Department of Nonclinical Science, Seattle Genetics Inc., Bothell, WA, USA
| | - Serena W Wo
- Department of Protein Sciences, Seattle Genetics Inc., Bothell, WA, USA
| | | | - Julia H Cochran
- Department of Protein Sciences, Seattle Genetics Inc., Bothell, WA, USA
| | - Jessica K Simmons
- Department of Nonclinical Science, Seattle Genetics Inc., Bothell, WA, USA
| | - Maureen C Ryan
- Department of Antibody Discovery, Seattle Genetics Inc., Bothell, WA, USA
| | - Robert P Lyon
- Department of Protein Sciences, Seattle Genetics Inc., Bothell, WA, USA
| | - Peter D Senter
- Department of Chemistry, Seattle Genetics Inc., Bothell, WA, USA
| | | |
Collapse
|
62
|
Beesley JL, Woolfson DN. The de novo design of α-helical peptides for supramolecular self-assembly. Curr Opin Biotechnol 2019; 58:175-182. [PMID: 31039508 DOI: 10.1016/j.copbio.2019.03.017] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 03/25/2019] [Indexed: 12/14/2022]
Abstract
One approach to designing de novo proteinaceous assemblies and materials is to develop simple, standardised building blocks and then to combine these symmetrically to construct more-complex higher-order structures. This has been done extensively using β-structured peptides to produce peptide fibres and hydrogels. Here, we focus on building with de novo α-helical peptides. Because of their self-contained, well-defined structures and clear sequence-to-structure relationships, α helices are highly programmable making them robust building blocks for biomolecular construction. The progress made with this approach over the past two decades is astonishing and has led to a variety of de novo assemblies, including discrete nanoscale objects, and fibrous, nanotube, sheet and colloidal materials. This body of work provides an exceptionally strong foundation for advancing the field beyond in vitro design and into in vivo applications including what we call protein design in cells.
Collapse
Affiliation(s)
- Joseph L Beesley
- 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; School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk, Bristol BS8 1TD, UK; BrisSynBio, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK.
| |
Collapse
|
63
|
Ormaza G, Rodríguez JA, Ibáñez de Opakua A, Merino N, Villate M, Gorroño I, Rábano M, Palmero I, Vilaseca M, Kypta R, Vivanco MDM, Rojas AL, Blanco FJ. The Tumor Suppressor ING5 Is a Dimeric, Bivalent Recognition Molecule of the Histone H3K4me3 Mark. J Mol Biol 2019; 431:2298-2319. [PMID: 31026448 DOI: 10.1016/j.jmb.2019.04.018] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 04/10/2019] [Accepted: 04/10/2019] [Indexed: 10/26/2022]
Abstract
The INhibitor of Growth (ING) family of tumor suppressors regulates the transcriptional state of chromatin by recruiting remodeling complexes to sites with histone H3 trimethylated at lysine 4 (H3K4me3). This modification is recognized by the plant homeodomain (PHD) present at the C-terminus of the five ING proteins. ING5 facilitates histone H3 acetylation by the HBO1 complex, and also H4 acetylation by the MOZ/MORF complex. We show that ING5 forms homodimers through its N-terminal domain, which folds independently into an elongated coiled-coil structure. The central region of ING5, which contains the nuclear localization sequence, is flexible and disordered, but it binds dsDNA with micromolar affinity. NMR analysis of the full-length protein reveals that the two PHD fingers of the dimer are chemically equivalent and independent of the rest of the molecule, and they bind H3K4me3 in the same way as the isolated PHD. We have observed that ING5 can form heterodimers with the highly homologous ING4, and that two of three primary tumor-associated mutants in the N-terminal domain strongly destabilize the coiled-coil structure. They also affect cell proliferation and cell cycle phase distribution, suggesting a driver role in cancer progression.
Collapse
Affiliation(s)
- Georgina Ormaza
- CIC bioGUNE, Parque Tecnológico de Bizkaia, 48160 Derio, Spain
| | | | | | - Nekane Merino
- CIC bioGUNE, Parque Tecnológico de Bizkaia, 48160 Derio, Spain
| | - Maider Villate
- CIC bioGUNE, Parque Tecnológico de Bizkaia, 48160 Derio, Spain
| | - Irantzu Gorroño
- CIC bioGUNE, Parque Tecnológico de Bizkaia, 48160 Derio, Spain
| | - Miriam Rábano
- CIC bioGUNE, Parque Tecnológico de Bizkaia, 48160 Derio, Spain
| | - Ignacio Palmero
- Instituto de Investigaciones Biomédicas "Alberto Sols", CSIC-UAM, 28029 Madrid, Spain
| | - Marta Vilaseca
- Institute for Research in Biomedicine, 08028 Barcelona, Spain
| | - Robert Kypta
- CIC bioGUNE, Parque Tecnológico de Bizkaia, 48160 Derio, Spain; Department of Surgery and Cancer, Imperial College London, London, W12 0NN, UK
| | | | - Adriana L Rojas
- CIC bioGUNE, Parque Tecnológico de Bizkaia, 48160 Derio, Spain
| | - Francisco J Blanco
- CIC bioGUNE, Parque Tecnológico de Bizkaia, 48160 Derio, Spain; IKERBASQUE, Basque Foundation for Science, 48011 Bilbao, Spain.
| |
Collapse
|
64
|
Khairil Anuar INA, Banerjee A, Keeble AH, Carella A, Nikov GI, Howarth M. Spy&Go purification of SpyTag-proteins using pseudo-SpyCatcher to access an oligomerization toolbox. Nat Commun 2019; 10:1734. [PMID: 30988307 PMCID: PMC6465384 DOI: 10.1038/s41467-019-09678-w] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 03/22/2019] [Indexed: 12/14/2022] Open
Abstract
Peptide tags are a key resource, introducing minimal change while enabling a consistent process to purify diverse proteins. However, peptide tags often provide minimal benefit post-purification. We previously designed SpyTag, forming an irreversible bond with its protein partner SpyCatcher. SpyTag provides an easy route to anchor, bridge or multimerize proteins. Here we establish Spy&Go, enabling protein purification using SpyTag. Through rational engineering we generated SpyDock, which captures SpyTag-fusions and allows efficient elution. Spy&Go enabled sensitive purification of SpyTag-fusions from Escherichia coli, giving superior purity than His-tag/nickel-nitrilotriacetic acid. Spy&Go allowed purification of mammalian-expressed, N-terminal, C-terminal or internal SpyTag. As an oligomerization toolbox, we established a panel of SpyCatcher-linked coiled coils, so SpyTag-fusions can be dimerized, trimerized, tetramerized, pentamerized, hexamerized or heptamerized. Assembling oligomers for Death Receptor 5 stimulation, we probed multivalency effects on cancer cell death. Spy&Go, combined with simple oligomerization, should have broad application for exploring multivalency in signaling.
Collapse
Affiliation(s)
| | - Anusuya Banerjee
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Anthony H Keeble
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Alberto Carella
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Georgi I Nikov
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Mark Howarth
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK.
| |
Collapse
|
65
|
Tunn I, Harrington MJ, Blank KG. Bioinspired Histidine⁻Zn 2+ Coordination for Tuning the Mechanical Properties of Self-Healing Coiled Coil Cross-Linked Hydrogels. Biomimetics (Basel) 2019; 4:biomimetics4010025. [PMID: 31105210 PMCID: PMC6477626 DOI: 10.3390/biomimetics4010025] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Revised: 03/06/2019] [Accepted: 03/06/2019] [Indexed: 12/22/2022] Open
Abstract
Natural biopolymeric materials often possess properties superior to their individual components. In mussel byssus, reversible histidine (His)–metal coordination is a key feature, which mediates higher-order self-assembly as well as self-healing. The byssus structure, thus, serves as an excellent natural blueprint for the development of self-healing biomimetic materials with reversibly tunable mechanical properties. Inspired by byssal threads, we bioengineered His–metal coordination sites into a heterodimeric coiled coil (CC). These CC-forming peptides serve as a noncovalent cross-link for poly(ethylene glycol)-based hydrogels and participate in the formation of higher-order assemblies via intermolecular His–metal coordination as a second cross-linking mode. Raman and circular dichroism spectroscopy revealed the presence of α-helical, Zn2+ cross-linked aggregates. Using rheology, we demonstrate that the hydrogel is self-healing and that the addition of Zn2+ reversibly switches the hydrogel properties from viscoelastic to elastic. Importantly, using different Zn2+:His ratios allows for tuning the hydrogel relaxation time over nearly three orders of magnitude. This tunability is attributed to the progressive transformation of single CC cross-links into Zn2+ cross-linked aggregates; a process that is fully reversible upon addition of the metal chelator ethylenediaminetetraacetic acid. These findings reveal that His–metal coordination can be used as a versatile cross-linking mechanism for tuning the viscoelastic properties of biomimetic hydrogels.
Collapse
Affiliation(s)
- Isabell Tunn
- Mechano(bio)chemistry, Max Planck Institute of Colloids and Interfaces, Science Park Potsdam-Golm, 14424 Potsdam, Germany.
| | - Matthew J Harrington
- Department of Biomaterials, Max Planck Institute of Colloids and Interfaces, Science Park Potsdam-Golm, 14424 Potsdam, Germany.
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal, QC H3A 0B8, Canada.
| | - Kerstin G Blank
- Mechano(bio)chemistry, Max Planck Institute of Colloids and Interfaces, Science Park Potsdam-Golm, 14424 Potsdam, Germany.
| |
Collapse
|
66
|
Skyttner C, Selegård R, Larsson J, Aronsson C, Enander K, Aili D. Sequence and length optimization of membrane active coiled coils for triggered liposome release. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2019; 1861:449-456. [DOI: 10.1016/j.bbamem.2018.11.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 10/20/2018] [Accepted: 11/08/2018] [Indexed: 12/26/2022]
|
67
|
López-García P, Goktas M, Bergues-Pupo AE, Koksch B, Varón Silva D, Blank KG. Structural determinants of coiled coil mechanics. Phys Chem Chem Phys 2019; 21:9145-9149. [PMID: 31016294 DOI: 10.1039/c9cp00665f] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The natural abundance of coiled coil (CC) motifs in the cytoskeleton and the extracellular matrix suggests that CCs play a crucial role in the bidirectional mechanobiochemical signaling between cells and the matrix. Their functional importance and structural simplicity has allowed the development of numerous applications, such as protein-origami structures, drug delivery systems and biomaterials. With the goal of establishing CCs as nanomechanical building blocks, we investigated the importance of helix propensity and hydrophobic core packing on the mechanical stability of 4-heptad CC heterodimers. Using single-molecule force spectroscopy, we show that both parameters determine the force-induced dissociation in shear loading geometry; however, with different effects on the energy landscape. Decreasing the helix propensity lowers the transition barrier height, leading to a concomitant decrease in the distance to the transition state. In contrast, a less tightly packed hydrophobic core increases the distance to the transition state. We propose that this originates from a larger side chain dynamics, possible water intrusion at the interface as well as differences in solvation of the hydrophobic amino acids at the transition state. In conclusion, the different contributions of helix propensity and hydrophobic core packing need to be considered when tuning the mechanical properties of CCs for applications.
Collapse
Affiliation(s)
- Patricia López-García
- Max Planck Institute of Colloids and Interfaces, Mechano(bio)chemistry, Science-Park Potsdam Golm, 14424 Potsdam, Germany.
| | | | | | | | | | | |
Collapse
|
68
|
Shoemark DK, Avila Ibarra A, Ross JF, Beesley JL, Bray HE, Mosayebi M, Linden N, Liverpool TB, McIntosh-Smith SN, Woolfson DN, Sessions RB. The dynamical interplay between a megadalton peptide nanocage and solutes probed by microsecond atomistic MD; implications for design. Phys Chem Chem Phys 2019; 21:137-147. [DOI: 10.1039/c8cp06282j] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Better understanding of the dynamics of protein-based supramolecular capsids can be applied to synthetic biology and biotechnology.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Noah Linden
- School of Mathematics
- University Walk
- Bristol
- UK
| | | | | | - Derek N. Woolfson
- School of Biochemistry
- Biomedical Sciences Building
- University Walk
- Bristol
- UK
| | | |
Collapse
|
69
|
Programmable design of orthogonal protein heterodimers. Nature 2018; 565:106-111. [PMID: 30568301 DOI: 10.1038/s41586-018-0802-y] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 11/08/2018] [Indexed: 11/09/2022]
Abstract
Specificity of interactions between two DNA strands, or between protein and DNA, is often achieved by varying bases or side chains coming off the DNA or protein backbone-for example, the bases participating in Watson-Crick pairing in the double helix, or the side chains contacting DNA in TALEN-DNA complexes. By contrast, specificity of protein-protein interactions usually involves backbone shape complementarity1, which is less modular and hence harder to generalize. Coiled-coil heterodimers are an exception, but the restricted geometry of interactions across the heterodimer interface (primarily at the heptad a and d positions2) limits the number of orthogonal pairs that can be created simply by varying side-chain interactions3,4. Here we show that protein-protein interaction specificity can be achieved using extensive and modular side-chain hydrogen-bond networks. We used the Crick generating equations5 to produce millions of four-helix backbones with varying degrees of supercoiling around a central axis, identified those accommodating extensive hydrogen-bond networks, and used Rosetta to connect pairs of helices with short loops and to optimize the remainder of the sequence. Of 97 such designs expressed in Escherichia coli, 65 formed constitutive heterodimers, and the crystal structures of four designs were in close agreement with the computational models and confirmed the designed hydrogen-bond networks. In cells, six heterodimers were fully orthogonal, and in vitro-following mixing of 32 chains from 16 heterodimer designs, denaturation in 5 M guanidine hydrochloride and reannealing-almost all of the interactions observed by native mass spectrometry were between the designed cognate pairs. The ability to design orthogonal protein heterodimers should enable sophisticated protein-based control logic for synthetic biology, and illustrates that nature has not fully explored the possibilities for programmable biomolecular interaction modalities.
Collapse
|
70
|
Tunn I, de Léon AS, Blank KG, Harrington MJ. Tuning coiled coil stability with histidine-metal coordination. NANOSCALE 2018; 10:22725-22729. [PMID: 30500033 DOI: 10.1039/c8nr07259k] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Coiled coils (CCs) have emerged as versatile building blocks for the synthesis of nanostructures, drug delivery systems and biomimetic hydrogels. Bioengineering metal coordination sites into the terminal ends of a synthetic coiled coil (CC), we generate a nanoscale biological building block with tunable stability. The reversible coordination of Ni2+ thermodynamically stabilizes the CC, as shown with circular dichroism spectroscopy. Using atomic force microscopy-based single-molecule force spectroscopy, it is further shown that Ni2+-binding reinforces the CC mechanically, increasing the barrier height for dissociation. When used as a dynamic crosslink in polyethyleneglycol-based hydrogels, the single-molecule stability of the CC is directly transferred to the bulk material and determines its viscoelastic properties. This reversibly tunable CC, thus, highlights an effective strategy for rationally engineering the single-molecule properties of biomolecular building blocks, which can be translated to the emergent properties of biomimetic materials, as well as other CC containing molecular assemblies.
Collapse
Affiliation(s)
- Isabell Tunn
- Max Planck Institute of Colloids and Interfaces, Science Park Potsdam-Golm, 14424 Potsdam, Germany.
| | | | | | | |
Collapse
|
71
|
Bergues-Pupo AE, Blank KG, Lipowsky R, Vila Verde A. Trimeric coiled coils expand the range of strength, toughness and dynamics of coiled coil motifs under shear. Phys Chem Chem Phys 2018; 20:29105-29115. [PMID: 30426982 DOI: 10.1039/c8cp04896g] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Coiled coils are widespread protein motifs in nature, and promising building blocks for bio-inspired nanomaterials and nanoscale force sensors. Detailed structural insight into their mechanical response is required to understand their role in tissues and to design building blocks for applications. We use all-atom molecular dynamics simulations to elucidate the mechanical response of two types of coiled coils under shear: dimers and trimers. The amino acid sequences of both systems are similar, thus enabling universal (vs. system-specific) features to be identified. The trimer is mechanically more stable - it is both stronger and tougher - than the dimer, withstanding higher forces (127 pN vs. 49 pN at v = 10-3 nm ns-1) and dissipating up to five times more energy before rupture. The deformation mechanism of the trimer at all pull speeds is dominated by progressive helix unfolding. In contrast, at the lowest pull speeds, dimers deform by unfolding/refolding-assisted sliding. The additional helix in the trimer thus both determines the stability of the structure and affects the deformation mechanism, preventing helix sliding. The mechanical response of the coiled coils is not only sensitive to the oligomerization state but also to helix stability: preventing helix unfolding doubles the mechanical strength of the trimer, but decreases its toughness to half. Our results show that coiled coil trimers expand the range of coiled coil responses to an applied shear force. Altering the stability of individual helices against deformation emerges as one possible route towards fine-tuning this response, enabling the use of these motifs as nanomechanical building blocks.
Collapse
Affiliation(s)
- Ana E Bergues-Pupo
- Max Planck Institute of Colloids and Interfaces, Department of Theory & Bio-Systems, 14424 Potsdam, Germany.
| | | | | | | |
Collapse
|
72
|
VIPER is a genetically encoded peptide tag for fluorescence and electron microscopy. Proc Natl Acad Sci U S A 2018; 115:12961-12966. [PMID: 30518560 DOI: 10.1073/pnas.1808626115] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Many discoveries in cell biology rely on making specific proteins visible within their native cellular environment. There are various genetically encoded tags, such as fluorescent proteins, developed for fluorescence microscopy (FM). However, there are almost no genetically encoded tags that enable cellular proteins to be observed by both FM and electron microscopy (EM). Herein, we describe a technology for labeling proteins with diverse chemical reporters, including bright organic fluorophores for FM and electron-dense nanoparticles for EM. Our technology uses versatile interacting peptide (VIP) tags, a class of genetically encoded tag. We present VIPER, which consists of a coiled-coil heterodimer formed between the genetic tag, CoilE, and a probe-labeled peptide, CoilR. Using confocal FM, we demonstrate that VIPER can be used to highlight subcellular structures or to image receptor-mediated iron uptake. Additionally, we used VIPER to image the iron uptake machinery by correlative light and EM (CLEM). VIPER compared favorably with immunolabeling for imaging proteins by CLEM, and is an enabling technology for protein targets that cannot be immunolabeled. VIPER is a versatile peptide tag that can be used to label and track proteins with diverse chemical reporters observable by both FM and EM instrumentation.
Collapse
|
73
|
Mueller C, Grossmann TN. Coiled-Coil Peptide Beacon: A Tunable Conformational Switch for Protein Detection. Angew Chem Int Ed Engl 2018; 57:17079-17083. [PMID: 30411434 PMCID: PMC6391972 DOI: 10.1002/anie.201811515] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Indexed: 11/12/2022]
Abstract
The understanding of protein folding and assembly is of central importance for the design of proteins and enzymes with novel or improved functions. Minimalistic model systems, such as coiled-coils, provide an excellent platform to improve this understanding and to construct novel molecular devices. Along those lines, we designed a conformational switch that is composed of two coiled-coil forming peptides and a central binding epitope. In the absence of a binding partner, this switch adopts a hairpin-like conformation that opens upon receptor binding. Variation of the coiled-coil length modulates the strength of the intramolecular constraint. The two conformational states of this switch have been linked with characteristic fluorescent properties, which enables the detection of the receptor in real-time.
Collapse
Affiliation(s)
- Carolin Mueller
- VU University Amsterdam, Department of Chemistry & Pharmaceutical Sciences, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
| | - Tom N Grossmann
- VU University Amsterdam, Department of Chemistry & Pharmaceutical Sciences, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
| |
Collapse
|
74
|
Rink WM, Thomas F. De Novo Designed α-Helical Coiled-Coil Peptides as Scaffolds for Chemical Reactions. Chemistry 2018; 25:1665-1677. [DOI: 10.1002/chem.201802849] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Indexed: 01/31/2023]
Affiliation(s)
- W. Mathis Rink
- Institute of Organic and Biomolecular Chemistry; Georg-August-Universität Göttingen; Tammannstraße 2 37077 Göttingen Germany
| | - Franziska Thomas
- Institute of Organic and Biomolecular Chemistry; Georg-August-Universität Göttingen; Tammannstraße 2 37077 Göttingen Germany
- Center for Biostructural Imaging of Neurodegeneration; Von-Siebold-Straße 3a 37075 Göttingen Germany
| |
Collapse
|
75
|
Mueller C, Grossmann TN. Coiled‐Coil Peptide Beacon: A Tunable Conformational Switch for Protein Detection. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201811515] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Carolin Mueller
- VU University Amsterdam Department of Chemistry & Pharmaceutical Sciences De Boelelaan 1108 1081 HZ Amsterdam The Netherlands
| | - Tom N. Grossmann
- VU University Amsterdam Department of Chemistry & Pharmaceutical Sciences De Boelelaan 1108 1081 HZ Amsterdam The Netherlands
| |
Collapse
|
76
|
Tallec G, Loh C, Liberelle B, Garcia-Ac A, Duy SV, Sauvé S, Banquy X, Murschel F, De Crescenzo G. Adequate Reducing Conditions Enable Conjugation of Oxidized Peptides to Polymers by One-Pot Thiol Click Chemistry. Bioconjug Chem 2018; 29:3866-3876. [PMID: 30350572 DOI: 10.1021/acs.bioconjchem.8b00684] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Thiol(-click) chemistry has been extensively investigated to conjugate (bio)molecules to polymers. Handling of cysteine-containing molecules may however be cumbersome, especially in the case of fast-oxidizing coiled-coil-forming peptides. In the present study, we investigated the practicality of a one-pot process to concomitantly reduce and conjugate an oxidized peptide to a polymer. Three thiol-based conjugation chemistries (vinyl sulfone (VS), maleimide, and pyridyldithiol) were assayed along with three reducing agents (tris(2-carboxyethyl)phosphine (TCEP), dithiothreitol, and β-mercaptoethanol). Seven out of the nine possible combinations significantly enhanced the conjugation yield, provided that an adequate concentration of reductant was used. Among them, the coincubation of an oxidized peptide with TCEP and a VS-modified polymer displayed the highest level of conjugation. Our results also provide insights into two topics that currently lack consensus: TCEP is stable in 10 mM phosphate buffered saline and it reacts with thiol-alkylating agents at submillimolar concentrations, and thus should be carefully used in order to avoid interference with thiol-based conjugation reactions.
Collapse
Affiliation(s)
- Gwendoline Tallec
- Department of Chemical Engineering, Groupe de Recherche en Sciences et Technologies Biomédicales (GRSTB), Bio-P2 Research Unit , École Polytechnique de Montréal , P.O. Box 6079, succ. Centre-Ville, Montréal , Quebec , Canada H3C 3A7
| | - Celestine Loh
- Division of Chemical and Biomolecular Engineering , Nanyang Technological University , 50 Nanyang Avenue , Singapore , Singapore , 639798
| | - Benoit Liberelle
- Department of Chemical Engineering, Groupe de Recherche en Sciences et Technologies Biomédicales (GRSTB), Bio-P2 Research Unit , École Polytechnique de Montréal , P.O. Box 6079, succ. Centre-Ville, Montréal , Quebec , Canada H3C 3A7
| | - Araceli Garcia-Ac
- Faculty of Pharmacy , Université de Montréal , 2900 Edouard-Montpetit Boulevard , Montreal , Quebec , Canada H3C 3J7
| | - Sung Vo Duy
- Department of Chemistry , Université de Montréal , C.P. 6128, succ. Centre-Ville, Montreal , Quebec , Canada H3C 3J7
| | - Sébastien Sauvé
- Department of Chemistry , Université de Montréal , C.P. 6128, succ. Centre-Ville, Montreal , Quebec , Canada H3C 3J7
| | - Xavier Banquy
- Faculty of Pharmacy , Université de Montréal , 2900 Edouard-Montpetit Boulevard , Montreal , Quebec , Canada H3C 3J7
| | - Frederic Murschel
- Faculty of Pharmacy , Université de Montréal , 2900 Edouard-Montpetit Boulevard , Montreal , Quebec , Canada H3C 3J7
| | - Gregory De Crescenzo
- Department of Chemical Engineering, Groupe de Recherche en Sciences et Technologies Biomédicales (GRSTB), Bio-P2 Research Unit , École Polytechnique de Montréal , P.O. Box 6079, succ. Centre-Ville, Montréal , Quebec , Canada H3C 3A7
| |
Collapse
|
77
|
Rink WM, Thomas F. Decoration of Coiled-Coil Peptides with N-Cysteine Peptide Thioesters As Cyclic Peptide Precursors Using Copper-Catalyzed Azide-Alkyne Cycloaddition (CuAAC) Click Reaction. Org Lett 2018; 20:7493-7497. [PMID: 30407016 DOI: 10.1021/acs.orglett.8b03261] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The development of a copper-catalyzed azide-alkyne cycloaddition (CuAAC) protocol for the decoration of coiled coils with N-cysteine peptide thioesters as cyclic peptide precursors is presented. The reaction conditions include tert-butanol/PBS as the solvent and CuSO4/THPTA/ascorbate as the catalytic system. During these studies, partial formylation of N-terminal cysteine peptides is observed. Mechanistic analysis leads to identification of the formyl source and, hence, to the development of reaction conditions, under which the undesired side reaction was suppressed.
Collapse
Affiliation(s)
- W Mathis Rink
- Institute of Organic and Biomolecular Chemistry, Georg-August Universität Göttingen , Tammannstraße 2 , 37077 Göttingen , Germany
| | - Franziska Thomas
- Institute of Organic and Biomolecular Chemistry, Georg-August Universität Göttingen , Tammannstraße 2 , 37077 Göttingen , Germany.,Center for Biostructural Imaging of Neurodegeneration , von-Siebold-Straße 3a , 37075 Göttingen , Germany
| |
Collapse
|
78
|
Lee MJ, Mantell J, Brown IR, Fletcher JM, Verkade P, Pickersgill RW, Woolfson DN, Frank S, Warren MJ. De novo targeting to the cytoplasmic and luminal side of bacterial microcompartments. Nat Commun 2018; 9:3413. [PMID: 30143644 PMCID: PMC6109187 DOI: 10.1038/s41467-018-05922-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 07/31/2018] [Indexed: 01/05/2023] Open
Abstract
Bacterial microcompartments, BMCs, are proteinaceous organelles that encase a specific metabolic pathway within a semi-permeable protein shell. Short encapsulation peptides can direct cargo proteins to the lumen of the compartments. However, the fusion of such peptides to non-native proteins does not guarantee encapsulation and often causes aggregation. Here, we report an approach for targeting recombinant proteins to BMCs that utilizes specific de novo coiled-coil protein–protein interactions. Attachment of one coiled-coil module to PduA (a component of the BMC shell) allows targeting of a fluorescent protein fused to a cognate coiled-coil partner. This interaction takes place on the outer surface of the BMC. The redesign of PduA to generate an N-terminus on the luminal side of the BMC results in intact compartments to which proteins can still be targeted via the designed coiled-coil system. This study provides a strategy to display proteins on the surface or within the lumen of the BMCs. Bacterial microcompartments (BMCs) are protein-bound organelles encapsulating segments of metabolic pathways. Here the authors utilize specific de novo coiled-coil protein-protein interactions to display proteins on the outer or inner surface of BMCs.
Collapse
Affiliation(s)
- Matthew J Lee
- Industrial Biotechnology Centre, School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK
| | - Judith Mantell
- School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk, Bristol, BS8 1TD, UK.,Wolfson Bioimaging Facility, Medical Sciences Building, University Walk, Bristol, BS8 1TD, UK
| | - Ian R Brown
- Industrial Biotechnology Centre, School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK
| | - Jordan M Fletcher
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK
| | - Paul Verkade
- School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk, Bristol, BS8 1TD, UK.,Wolfson Bioimaging Facility, Medical Sciences Building, University Walk, Bristol, BS8 1TD, UK.,BrisSynBio, Life Sciences Building, Tyndall Avenue, Bristol, BS8 1TQ, UK
| | - Richard W Pickersgill
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Derek N Woolfson
- School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk, Bristol, BS8 1TD, UK.,School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK.,BrisSynBio, Life Sciences Building, Tyndall Avenue, Bristol, BS8 1TQ, UK
| | - Stefanie Frank
- Department of Biochemical Engineering, University College London, Bernard Katz Building, Gordon Street, London, WC1E 6BT, UK.
| | - Martin J Warren
- Industrial Biotechnology Centre, School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK.
| |
Collapse
|
79
|
Fletcher JM, Horner KA, Bartlett GJ, Rhys GG, Wilson AJ, Woolfson DN. De novo coiled-coil peptides as scaffolds for disrupting protein-protein interactions. Chem Sci 2018; 9:7656-7665. [PMID: 30393526 PMCID: PMC6182421 DOI: 10.1039/c8sc02643b] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 08/06/2018] [Indexed: 02/06/2023] Open
Abstract
Homo- and hetero-dimeric coiled coils as scaffolds for the presentation of α-helical protein-binding motifs.
Protein–protein interactions (PPIs) play pivotal roles in the majority of biological processes. Therefore, improved approaches to target and disrupt PPIs would provide tools for chemical biology and leads for therapeutic development. PPIs with α-helical components are appealing targets given that the secondary structure is well understood and can be mimicked or stabilised to render small-molecule and constrained-peptide-based inhibitors. Here we present a strategy to target α-helix-mediated PPIs that exploits de novo coiled-coil assemblies and test this using the MCL-1/NOXA-B PPI. First, computational alanine scanning is used to identify key α-helical residues from NOXA-B that contribute to the interface. Next, these residues are grafted onto the exposed surfaces of de novo designed homodimeric or heterodimeric coiled-coil peptides. The resulting synthetic peptides selectively inhibit a cognate MCL-1/BID complex in the mid-nM range. Furthermore, the heterodimeric system affords control as inhibition occurs only when both the grafted peptide and its designed partner are present. This establishes proof of concept for exploiting peptides stabilised in de novo coiled coils as inhibitors of PPIs. This dependence on supramolecular assembly introduces new possibilities for regulation and control.
Collapse
Affiliation(s)
- Jordan M Fletcher
- School of Chemistry , University of Bristol , Cantock's Close , Bristol BS8 1TS , UK . ;
| | - Katherine A Horner
- School of Chemistry , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK.,Astbury Centre for Structural Molecular Biology , University of Leeds , Woodhouse Lane , Leeds , LS2 9JT , UK
| | - Gail J Bartlett
- School of Chemistry , University of Bristol , Cantock's Close , Bristol BS8 1TS , UK . ;
| | - Guto G Rhys
- School of Chemistry , University of Bristol , Cantock's Close , Bristol BS8 1TS , UK . ;
| | - Andrew J Wilson
- School of Chemistry , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK.,Astbury Centre for Structural Molecular Biology , University of Leeds , Woodhouse Lane , Leeds , LS2 9JT , UK
| | - Derek N Woolfson
- 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.,BrisSynBio , University of Bristol , Life Sciences Building, Tyndall Avenue , Bristol , BS8 1TQ , UK
| |
Collapse
|
80
|
Chino M, Zhang SQ, Pirro F, Leone L, Maglio O, Lombardi A, DeGrado WF. Spectroscopic and metal binding properties of a de novo metalloprotein binding a tetrazinc cluster. Biopolymers 2018; 109:e23339. [PMID: 30203532 PMCID: PMC6218314 DOI: 10.1002/bip.23229] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 05/18/2018] [Accepted: 05/22/2018] [Indexed: 12/27/2022]
Abstract
De novo design provides an attractive approach, which allows one to test and refine the principles guiding metalloproteins in defining the geometry and reactivity of their metal ion cofactors. Although impressive progress has been made in designing proteins that bind transition metal ions including iron-sulfur clusters, the design of tetranuclear clusters with oxygen-rich environments remains in its infancy. In previous work, we described the design of homotetrameric four-helix bundles that bind tetra-Zn2+ clusters. The crystal structures of the helical proteins were in good agreement with the overall design, and the metal-binding and conformational properties of the helical bundles in solution were consistent with the crystal structures. However, the corresponding apo-proteins were not fully folded in solution. In this work, we design three peptides, based on the crystal structure of the original bundles. One of the peptides forms tetramers in aqueous solution in the absence of metal ions as assessed by CD and NMR. It also binds Zn2+ in the intended stoichiometry. These studies strongly suggest that the desired structure has been achieved in the apo state, providing evidence that the peptide is able to actively impart the designed geometry to the metal cluster.
Collapse
Affiliation(s)
- Marco Chino
- Department of Chemical Sciences, University of Napoli “Federico II”, Via Cintia, 46, 80126 Napoli, Italy
| | - Shao-Qing Zhang
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California at San Francisco, San Francisco, CA 94158-9001, United States
- Department of Chemistry, University of Pennsylvania, 209 South 33rd Street, Philadelphia, PA 19104-6396, United States
| | - Fabio Pirro
- Department of Chemical Sciences, University of Napoli “Federico II”, Via Cintia, 46, 80126 Napoli, Italy
| | - Linda Leone
- Department of Chemical Sciences, University of Napoli “Federico II”, Via Cintia, 46, 80126 Napoli, Italy
| | - Ornella Maglio
- Department of Chemical Sciences, University of Napoli “Federico II”, Via Cintia, 46, 80126 Napoli, Italy
- Institute of Biostructure and Bioimaging, National Research Council, via Mezzocannone, 16, 80134, Napoli, Italy
| | - Angela Lombardi
- Department of Chemical Sciences, University of Napoli “Federico II”, Via Cintia, 46, 80126 Napoli, Italy
| | - William F. DeGrado
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California at San Francisco, San Francisco, CA 94158-9001, United States
| |
Collapse
|
81
|
Thomas F, Dawson WM, Lang EJM, Burton AJ, Bartlett GJ, Rhys GG, Mulholland AJ, Woolfson DN. De Novo-Designed α-Helical Barrels as Receptors for Small Molecules. ACS Synth Biol 2018; 7:1808-1816. [PMID: 29944338 DOI: 10.1021/acssynbio.8b00225] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We describe de novo-designed α-helical barrels (αHBs) that bind and discriminate between lipophilic biologically active molecules. αHBs have five or more α-helices arranged around central hydrophobic channels the diameters of which scale with oligomer state. We show that pentameric, hexameric, and heptameric αHBs bind the environmentally sensitive dye 1,6-diphenylhexatriene (DPH) in the micromolar range and fluoresce. Displacement of the dye is used to report the binding of nonfluorescent molecules: palmitic acid and retinol bind to all three αHBs with submicromolar inhibitor constants; farnesol binds the hexamer and heptamer; but β-carotene binds only the heptamer. A co-crystal structure of the hexamer with farnesol reveals oriented binding in the center of the hydrophobic channel. Charged side chains engineered into the lumen of the heptamer facilitate binding of polar ligands: a glutamate variant binds a cationic variant of DPH, and introducing lysine allows binding of the biosynthetically important farnesol diphosphate.
Collapse
Affiliation(s)
- Franziska Thomas
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K
- Institute of Organic and Biomolecular Chemistry, Georg-August-Universität Göttingen, Tammannstrasse 2, 37077 Göttingen, Germany
| | - William M. Dawson
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K
| | - Eric J. M. Lang
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K
- BrisSynBio, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, U.K
| | - Antony J. Burton
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K
- Frick Chemistry Laboratory, Princeton, New Jersey 084544, United States
| | - Gail J. Bartlett
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K
| | - Guto G. Rhys
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K
| | - Adrian J. Mulholland
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K
- BrisSynBio, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, U.K
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K
| | - Derek N. Woolfson
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K
- BrisSynBio, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, U.K
- School of Biochemistry, University of Bristol, Biomedical Sciences Building, University Walk, Bristol BS8 1TD, U.K
| |
Collapse
|
82
|
Skyttner C, Enander K, Aronsson C, Aili D. Tuning Liposome Membrane Permeability by Competitive Coiled Coil Heterodimerization and Heterodimer Exchange. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:6529-6537. [PMID: 29758162 DOI: 10.1021/acs.langmuir.8b00592] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Membrane-active peptides that enable the triggered release of liposomal cargo are of great interest for the development of liposome-based drug delivery systems but require peptide-lipid membrane interactions that are highly defined and tunable. To this end, we have explored the possibility to use the competing interactions between membrane partitioning and heterodimerization and the folding of a set of four different de novo designed coiled coil peptides. Covalent conjugation of the cationic peptides triggered rapid destabilization of membrane integrity and the release of encapsulated species. The release was inhibited when introducing complementary peptides as a result of heterodimerization and folding into coiled coils. The degree of inhibition was shown to be dictated by the coiled coil peptide heterodimer dissociation constants, and liposomal release could be reactivated by a heterodimer exchange to render the membrane bound peptide free and thus membrane-active. The possibility to tune the permeability of lipid membranes using highly specific peptide-folding-dependent interactions delineates a new possible approach for the further development of responsive liposome-based drug delivery systems.
Collapse
Affiliation(s)
- Camilla Skyttner
- Division of Molecular Physics, Department of Physics, Chemistry and Biology , Linköping University , 581 83 Linköping , Sweden
| | - Karin Enander
- Division of Molecular Physics, Department of Physics, Chemistry and Biology , Linköping University , 581 83 Linköping , Sweden
| | - Christopher Aronsson
- Division of Molecular Physics, Department of Physics, Chemistry and Biology , Linköping University , 581 83 Linköping , Sweden
| | - Daniel Aili
- Division of Molecular Physics, Department of Physics, Chemistry and Biology , Linköping University , 581 83 Linköping , Sweden
| |
Collapse
|
83
|
Anderson G, Shriver-Lake LC, Liu JL, Goldman ER. Orthogonal Synthetic Zippers as Protein Scaffolds. ACS OMEGA 2018; 3:4810-4815. [PMID: 30023904 PMCID: PMC6045340 DOI: 10.1021/acsomega.8b00156] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 03/21/2018] [Indexed: 06/08/2023]
Abstract
Protein scaffolds have proven useful for co-localization of enzymes, providing control over stoichiometry and leading to higher local enzyme concentrations, which have led to improved product formation. To broaden their usefulness, it is necessary to have a wide choice of building blocks to mix and match for scaffold generation. Ideally, the scaffold building blocks should function at any location within the scaffold and have high affinity interactions with their binding partners. We examined the utility of orthogonal synthetic coiled coils (zippers) as scaffold components. The orthogonal zippers are coiled coil domains that form heterodimers only with their specific partner and not with other zipper domains. Focusing on two orthogonal zipper pairs, we demonstrated that they are able to function on either end or in the middle of a multiblock assembly. Surface plasmon resonance was employed to assess the binding kinetics of zipper pairs placed at the start, middle, or end of a construct. Size-exclusion chromatography was used to demonstrate the ability of a scaffold with two zipper domains to bind their partners simultaneously. We then expanded the study to examine the binding kinetics and cross-reactivities of three additional zipper pairs. By validating the affinities and specificities of synthetic zipper pairs, we demonstrated the potential for zipper domains to provide an expanded library of scaffolding parts for tethering enzymes in complex pathways for synthetic biology applications.
Collapse
Affiliation(s)
- George
P. Anderson
- Center for BioMolecular Science
and Engineering, U.S. Naval Research Laboratory, 4555 Overlook Avenue SW, Washington, District of Columbia 20375, United States
| | - Lisa C. Shriver-Lake
- Center for BioMolecular Science
and Engineering, U.S. Naval Research Laboratory, 4555 Overlook Avenue SW, Washington, District of Columbia 20375, United States
| | - Jinny L. Liu
- Center for BioMolecular Science
and Engineering, U.S. Naval Research Laboratory, 4555 Overlook Avenue SW, Washington, District of Columbia 20375, United States
| | - Ellen R. Goldman
- Center for BioMolecular Science
and Engineering, U.S. Naval Research Laboratory, 4555 Overlook Avenue SW, Washington, District of Columbia 20375, United States
| |
Collapse
|
84
|
Groth MC, Rink WM, Meyer NF, Thomas F. Kinetic studies on strand displacement in de novo designed parallel heterodimeric coiled coils. Chem Sci 2018; 9:4308-4316. [PMID: 29780562 PMCID: PMC5944379 DOI: 10.1039/c7sc05342h] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Accepted: 04/14/2018] [Indexed: 12/14/2022] Open
Abstract
Among the protein folding motifs, which are accessible by de novo design, the parallel heterodimeric coiled coil is most frequently used in bioinspired applications and chemical biology in general. This is due to the straightforward sequence-to-structure relationships, which it has in common with all coiled-coil motifs, and the heterospecificity, which allows control of association. Whereas much focus was laid on designing orthogonal coiled coils, systematic studies on controlling association, for instance by strand displacement, are rare. As a contribution to the design of dynamic coiled-coil-based systems, we studied the strand-displacement mechanism in obligate heterodimeric coiled coils to investigate the suitability of the dissociation constants (KD) as parameters for the prediction of the outcome of strand-displacement reactions. We use two sets of heterodimeric coiled coils, the previously reported N-A x B y and the newly characterized C-A x B y . Both comprise KD values in the μM to sub-nM regime. Strand displacement is explored by CD titration and a FRET-based kinetic assay and is proved to be an equilibrium reaction with half-lifes from a few seconds up to minutes. We could fit the displacement data by a competitive binding model, giving rate constants and overall affinities of the underlying association and dissociation reactions. The overall affinities correlate well with the ratios of KD values determined by CD-thermal denaturation experiments and, hence, support the dissociative mechanism of strand displacement in heterodimeric coiled coils. From the results of more than 100 different displacement reactions we are able to classify three categories of overall affinities, which allow for easy prediction of the equilibrium of strand displacement in two competing heterodimeric coiled coils.
Collapse
Affiliation(s)
- Mike C Groth
- Georg-August-Universität Göttingen , Institute of Organic and Biomolecular Chemistry , Tammannstraße 2 , 37077 Göttingen , Germany .
| | - W Mathis Rink
- Georg-August-Universität Göttingen , Institute of Organic and Biomolecular Chemistry , Tammannstraße 2 , 37077 Göttingen , Germany .
| | - Nils F Meyer
- Georg-August-Universität Göttingen , Institute of Organic and Biomolecular Chemistry , Tammannstraße 2 , 37077 Göttingen , Germany .
| | - Franziska Thomas
- Georg-August-Universität Göttingen , Institute of Organic and Biomolecular Chemistry , Tammannstraße 2 , 37077 Göttingen , Germany .
- Center for Biostructural Imaging of Neurodegeneration , Von-Siebold-Straße 3a , 37075 Göttingen , Germany
| |
Collapse
|
85
|
Goktas M, Luo C, Sullan RMA, Bergues-Pupo AE, Lipowsky R, Vila Verde A, Blank KG. Molecular mechanics of coiled coils loaded in the shear geometry. Chem Sci 2018; 9:4610-4621. [PMID: 29899954 PMCID: PMC5969510 DOI: 10.1039/c8sc01037d] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Accepted: 04/19/2018] [Indexed: 01/25/2023] Open
Abstract
Coiled coils are important nanomechanical building blocks in biological and biomimetic materials. A mechanistic molecular understanding of their structural response to mechanical load is essential for elucidating their role in tissues and for utilizing and tuning these building blocks in materials applications. Using a combination of single-molecule force spectroscopy (SMFS) and steered molecular dynamics (SMD) simulations, we have investigated the mechanics of synthetic heterodimeric coiled coils of different length (3-4 heptads) when loaded in shear geometry. Upon shearing, we observe an initial rise in the force, which is followed by a constant force plateau and ultimately strand separation. The force required for strand separation depends on the coiled coil length and the applied loading rate, suggesting that coiled coil shearing occurs out of equilibrium. This out-of-equilibrium behaviour is determined by a complex structural response which involves helix uncoiling, uncoiling-assisted sliding of the helices relative to each other in the direction of the applied force as well as uncoiling-assisted dissociation perpendicular to the force axis. These processes follow a hierarchy of timescales with helix uncoiling being faster than sliding and sliding being faster than dissociation. In SMFS experiments, strand separation is dominated by uncoiling-assisted dissociation and occurs at forces between 25-45 pN for the shortest 3-heptad coiled coil and between 35-50 pN for the longest 4-heptad coiled coil. These values are highly similar to the forces required for shearing apart short double-stranded DNA oligonucleotides, reinforcing the potential role of coiled coils as nanomechanical building blocks in applications where protein-based structures are desired.
Collapse
Affiliation(s)
- Melis Goktas
- Max Planck Institute of Colloids and Interfaces , Mechano(bio)chemistry , Science Park Potsdam-Golm , 14424 Potsdam , Germany .
| | - Chuanfu Luo
- Max Planck Institute of Colloids and Interfaces , Department of Theory & Bio-Systems , Science Park Potsdam-Golm , 14424 Potsdam , Germany .
| | - Ruby May A Sullan
- Max Planck Institute of Colloids and Interfaces , Mechano(bio)chemistry , Science Park Potsdam-Golm , 14424 Potsdam , Germany .
| | - Ana E Bergues-Pupo
- Max Planck Institute of Colloids and Interfaces , Department of Theory & Bio-Systems , Science Park Potsdam-Golm , 14424 Potsdam , Germany .
| | - Reinhard Lipowsky
- Max Planck Institute of Colloids and Interfaces , Department of Theory & Bio-Systems , Science Park Potsdam-Golm , 14424 Potsdam , Germany .
| | - Ana Vila Verde
- Max Planck Institute of Colloids and Interfaces , Department of Theory & Bio-Systems , Science Park Potsdam-Golm , 14424 Potsdam , Germany .
| | - Kerstin G Blank
- Max Planck Institute of Colloids and Interfaces , Mechano(bio)chemistry , Science Park Potsdam-Golm , 14424 Potsdam , Germany .
| |
Collapse
|
86
|
Mann FA, Horlebein J, Meyer NF, Meyer D, Thomas F, Kruss S. Carbon Nanotubes Encapsulated in Coiled-Coil Peptide Barrels. Chemistry 2018; 24:12241-12245. [DOI: 10.1002/chem.201800993] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Indexed: 11/06/2022]
Affiliation(s)
- Florian A. Mann
- Institute of Physical Chemistry; Georg-August Universität Göttingen; Tammannstraße 6 37077 Göttingen Germany
| | - Jan Horlebein
- Institute of Physical Chemistry; Georg-August Universität Göttingen; Tammannstraße 6 37077 Göttingen Germany
| | - Nils Frederik Meyer
- Institute of Organic and Biomolecular Chemistry; Georg-August Universität Göttingen; Tammannstraße 2 37077 Göttingen Germany
| | - Daniel Meyer
- Institute of Physical Chemistry; Georg-August Universität Göttingen; Tammannstraße 6 37077 Göttingen Germany
| | - Franziska Thomas
- Institute of Organic and Biomolecular Chemistry; Georg-August Universität Göttingen; Tammannstraße 2 37077 Göttingen Germany
- Center for Biostructural Imaging of Neurodegeneration; Von-Siebold-Strasse 3a 37075 Göttingen Germany
| | - Sebastian Kruss
- Institute of Physical Chemistry; Georg-August Universität Göttingen; Tammannstraße 6 37077 Göttingen Germany
- Center for Nanoscale Microscopy and Molecular Physiology of the Brain (CNMPB); Humboldtallee 23 37073 Göttingen Germany
| |
Collapse
|
87
|
Oba M, Ito C, Tanaka M. Effects of five-membered ring amino acid incorporation into peptides for coiled coil formation. Bioorg Med Chem Lett 2018; 28:875-877. [PMID: 29433922 DOI: 10.1016/j.bmcl.2018.02.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 02/01/2018] [Indexed: 12/22/2022]
Abstract
A five-membered ring amino acid (Ac5c), the peptides of which exhibit a preference for helical secondary structures, was introduced into peptides for the purpose of designing coiled coil peptides with high binding affinities. We prepared five types of peptides containing Ac5c with different numbers or at different positions. The incorporation of Ac5c into peptides enhanced their α-helicities; however, in contrast to our expectations, it did not result in stable coiled coil formation. The structures of side chains in hydrophobic amino acids, not α-helicities appeared to be important for stable hydrophobic interactions between peptides. Although we were unable to develop coiled coil peptides with high binding affinities, the present results will be useful for designing novel coiled coil peptides.
Collapse
Affiliation(s)
- Makoto Oba
- Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan.
| | - Chika Ito
- Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan
| | - Masakazu Tanaka
- Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan
| |
Collapse
|
88
|
Fujita S, Matsuura K. Self-assembled artificial viral capsids bearing coiled-coils at the surface. Org Biomol Chem 2018; 15:5070-5077. [PMID: 28574073 DOI: 10.1039/c7ob00998d] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
In order to construct artificial viral capsids bearing complementary dimeric coiled-coils on the surface, a β-annulus peptide bearing a coiled-coil forming sequence at the C-terminus (β-annulus-coiled-coil-B) was synthesized by a native chemical ligation of a β-annulus-SBn peptide with a Cys-containing coiled-coil-B peptide. Dynamic light scattering (DLS) measurements and transmission electron microscopy (TEM) images revealed that the β-annulus-coiled-coil-B peptide self-assembled into spherical structures of about 50 nm in 10 mM Tris-HCl buffer. Circular dichroism (CD) spectra indicated the formation of the complementary coiled-coil structure on the spherical assemblies. Addition of 0.25 equivalent of the complementary coiled-coil-A peptide to the β-annulus-coiled-coil-B peptide showed the formation of spherical assemblies of 46 ± 14 nm with grains of 5 nm at the surface, whereas addition of 1 equivalent of the complementary coiled-coil-A peptide generated fibrous assemblies.
Collapse
Affiliation(s)
- Seiya Fujita
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori, 680-8552, Japan.
| | | |
Collapse
|
89
|
Thomas F, Niitsu A, Oregioni A, Bartlett GJ, Woolfson DN. Conformational Dynamics of Asparagine at Coiled-Coil Interfaces. Biochemistry 2017; 56:6544-6554. [PMID: 29166010 PMCID: PMC5916467 DOI: 10.1021/acs.biochem.7b00848] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 10/25/2017] [Indexed: 12/19/2022]
Abstract
Coiled coils (CCs) are among the best-understood protein folds. Nonetheless, there are gaps in our knowledge of CCs. Notably, CCs are likely to be structurally more dynamic than often considered. Here, we explore this in an abundant class of CCs, parallel dimers, focusing on polar asparagine (Asn) residues in the hydrophobic interface. It is well documented that such inclusions discriminate between different CC oligomers, which has been rationalized in terms of whether the Asn can make side-chain hydrogen bonds. Analysis of parallel CC dimers in the Protein Data Bank reveals a variety of Asn side-chain conformations, but not all of these make the expected inter-side-chain hydrogen bond. We probe the structure and dynamics of a de novo-designed coiled-coil homodimer, CC-Di, by multidimensional nuclear magnetic resonance spectroscopy, including model-free dynamical analysis and relaxation-dispersion experiments. We find dynamic exchange on the millisecond time scale between Asn conformers with the side chains pointing into and out of the core. We perform molecular dynamics simulations that are consistent with this, revealing that the side chains are highly dynamic, exchanging between hydrogen-bonded-paired conformations in picoseconds to nanoseconds. Combined, our data present a more dynamic view for Asn at CC interfaces. Although inter-side-chain hydrogen bonding states are the most abundant, Asn is not always buried or engaged in such interactions. Because interfacial Asn residues are key design features for modulating CC stability and recognition, these further insights into how they are accommodated within CC structures will aid their predictive modeling, engineering, and design.
Collapse
Affiliation(s)
- Franziska Thomas
- School
of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K.
- Institute
for Organic and Biomolecular Chemistry, Georg-August-Universität Göttingen, Tammannstraße 2, 37077 Göttingen, Germany
| | - Ai Niitsu
- School
of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K.
| | - Alain Oregioni
- MRC
Biomedical NMR Centre, The Francis Crick
Institute, 1 Midland
Road, London NW1 1AT, U.K.
| | - Gail J. Bartlett
- School
of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K.
| | - Derek N. Woolfson
- School
of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K.
- School
of Biochemistry, University of Bristol, Medical Sciences Building, University
Walk, Bristol BS8 1TD, U.K.
- BrisSynBio, University
of Bristol, Life Sciences
Building, Tyndall Avenue, Bristol BS8 1TQ, U.K.
| |
Collapse
|
90
|
Lee MJ, Mantell J, Hodgson L, Alibhai D, Fletcher JM, Brown IR, Frank S, Xue WF, Verkade P, Woolfson DN, Warren MJ. Engineered synthetic scaffolds for organizing proteins within the bacterial cytoplasm. Nat Chem Biol 2017; 14:142-147. [DOI: 10.1038/nchembio.2535] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 11/01/2017] [Indexed: 12/21/2022]
|
91
|
Ross JF, Bridges A, Fletcher JM, Shoemark D, Alibhai D, Bray HEV, Beesley JL, Dawson WM, Hodgson LR, Mantell J, Verkade P, Edge CM, Sessions RB, Tew D, Woolfson DN. Decorating Self-Assembled Peptide Cages with Proteins. ACS NANO 2017; 11:7901-7914. [PMID: 28686416 DOI: 10.1021/acsnano.7b02368] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
An ability to organize and encapsulate multiple active proteins into defined objects and spaces at the nanoscale has potential applications in biotechnology, nanotechnology, and synthetic biology. Previously, we have described the design, assembly, and characterization of peptide-based self-assembled cages (SAGEs). These ≈100 nm particles comprise thousands of copies of de novo designed peptide-based hubs that array into a hexagonal network and close to give caged structures. Here, we show that, when fused to the designed peptides, various natural proteins can be co-assembled into SAGE particles. We call these constructs pSAGE for protein-SAGE. These particles tolerate the incorporation of multiple copies of folded proteins fused to either the N or the C termini of the hubs, which modeling indicates form the external and internal surfaces of the particles, respectively. Up to 15% of the hubs can be functionalized without compromising the integrity of the pSAGEs. This corresponds to hundreds of copies giving mM local concentrations of protein in the particles. Moreover, and illustrating the modularity of the SAGE system, we show that multiple different proteins can be assembled simultaneously into the same particle. As the peptide-protein fusions are made via recombinant expression of synthetic genes, we envisage that pSAGE systems could be developed modularly to actively encapsulate or to present a wide variety of functional proteins, allowing them to be developed as nanoreactors through the immobilization of enzyme cascades or as vehicles for presenting whole antigenic proteins as synthetic vaccine platforms.
Collapse
Affiliation(s)
- James F Ross
- School of Chemistry, University of Bristol , Cantock's Close, Bristol BS8 1TS, United Kingdom
| | - Angela Bridges
- GlaxoSmithKline (GSK) , Gunnels Wood Rd, Stevenage SG21 2NY, United Kingdom
| | - Jordan M Fletcher
- School of Chemistry, University of Bristol , Cantock's Close, Bristol BS8 1TS, United Kingdom
| | - Deborah Shoemark
- BrisSynBio, Life Sciences Building, University of Bristol , Tyndall Avenue, Bristol BS8 1TQ, United Kingdom
| | | | - Harriet E V Bray
- School of Chemistry, University of Bristol , Cantock's Close, Bristol BS8 1TS, United Kingdom
| | - Joseph L Beesley
- School of Chemistry, University of Bristol , Cantock's Close, Bristol BS8 1TS, United Kingdom
| | - William M Dawson
- School of Chemistry, University of Bristol , Cantock's Close, Bristol BS8 1TS, United Kingdom
| | | | | | | | - Colin M Edge
- GlaxoSmithKline (GSK) , Gunnels Wood Rd, Stevenage SG21 2NY, United Kingdom
| | - Richard B Sessions
- BrisSynBio, Life Sciences Building, University of Bristol , Tyndall Avenue, Bristol BS8 1TQ, United Kingdom
| | - David Tew
- GlaxoSmithKline (GSK) , Gunnels Wood Rd, Stevenage SG21 2NY, United Kingdom
| | - Derek N Woolfson
- School of Chemistry, University of Bristol , Cantock's Close, Bristol BS8 1TS, United Kingdom
- BrisSynBio, Life Sciences Building, University of Bristol , Tyndall Avenue, Bristol BS8 1TQ, United Kingdom
| |
Collapse
|
92
|
Drobnak I, Gradišar H, Ljubetič A, Merljak E, Jerala R. Modulation of Coiled-Coil Dimer Stability through Surface Residues while Preserving Pairing Specificity. J Am Chem Soc 2017; 139:8229-8236. [PMID: 28553984 DOI: 10.1021/jacs.7b01690] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The coiled-coil dimer is a widespread protein structural motif and, due to its designability, represents an attractive building block for assembling modular nanostructures. The specificity of coiled-coil dimer pairing is mainly based on hydrophobic and electrostatic interactions between residues at positions a, d, e, and g of the heptad repeat. Binding affinity, on the other hand, can also be affected by surface residues that face away from the dimerization interface. Here we show how design of the local helical propensity of interacting peptides can be used to tune the stabilities of coiled-coil dimers over a wide range. By designing intramolecular charge pairs, regions of high local helical propensity can be engineered to form trigger sequences, and dimer stability is adjusted without changing the peptide length or any of the directly interacting residues. This general principle is demonstrated by a change in thermal stability by more than 30 °C as a result of only two mutations outside the binding interface. The same approach was successfully used to modulate the stabilities in an orthogonal set of coiled-coils without affecting their binding preferences. The stability effects of local helical propensity and peptide charge are well described by a simple linear model, which should help improve current coiled-coil stability prediction algorithms. Our findings enable tuning the stabilities of coiled-coil-based building modules match a diverse range of applications in synthetic biology and nanomaterials.
Collapse
Affiliation(s)
- Igor Drobnak
- Department of Synthetic Biology and Immunology, National Institute of Chemistry , Hajdrihova 19, SI-1000 Ljubljana, Slovenia
| | - Helena Gradišar
- Department of Synthetic Biology and Immunology, National Institute of Chemistry , Hajdrihova 19, SI-1000 Ljubljana, Slovenia.,EN-FIST Centre of Excellence , Trg OF 13, SI-1000 Ljubljana, Slovenia
| | - Ajasja Ljubetič
- Department of Synthetic Biology and Immunology, National Institute of Chemistry , Hajdrihova 19, SI-1000 Ljubljana, Slovenia
| | - Estera Merljak
- Department of Synthetic Biology and Immunology, National Institute of Chemistry , Hajdrihova 19, SI-1000 Ljubljana, Slovenia
| | - Roman Jerala
- Department of Synthetic Biology and Immunology, National Institute of Chemistry , Hajdrihova 19, SI-1000 Ljubljana, Slovenia.,EN-FIST Centre of Excellence , Trg OF 13, SI-1000 Ljubljana, Slovenia
| |
Collapse
|
93
|
Fletcher JM, Bartlett GJ, Boyle AL, Danon JJ, Rush LE, Lupas AN, Woolfson DN. N@a and N@d: Oligomer and Partner Specification by Asparagine in Coiled-Coil Interfaces. ACS Chem Biol 2017; 12:528-538. [PMID: 28026921 DOI: 10.1021/acschembio.6b00935] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The α-helical coiled coil is one of the best-studied protein-protein interaction motifs. As a result, sequence-to-structure relationships are available for the prediction of natural coiled-coil sequences and the de novo design of new ones. However, coiled coils adopt a wide range of oligomeric states and topologies, and our understanding of the specification of these and the discrimination between them remains incomplete. Gaps in our knowledge assume more importance as coiled coils are used increasingly to construct biomimetic systems of higher complexity; for this, coiled-coil components need to be robust, orthogonal, and transferable between contexts. Here, we explore how the polar side chain asparagine (Asn, N) is tolerated within otherwise hydrophobic helix-helix interfaces of coiled coils. The long-held view is that Asn placed at certain sites of the coiled-coil sequence repeat selects one oligomer state over others, which is rationalized by the ability of the side chain to make hydrogen bonds, or interactions with chelated ions within the coiled-coil interior of the favored state. We test this with experiments on de novo peptide sequences traditionally considered as directing parallel dimers and trimers, and more widely through bioinformatics analysis of natural coiled-coil sequences and structures. We find that when located centrally, rather than near the termini of such coiled-coil sequences, Asn does exert the anticipated oligomer-specifying influence. However, outside of these bounds, Asn is observed less frequently in the natural sequences, and the synthetic peptides are hyperthermostable and lose oligomer-state specificity. These findings highlight that not all regions of coiled-coil repeat sequences are equivalent, and that care is needed when designing coiled-coil interfaces.
Collapse
Affiliation(s)
- Jordan M. Fletcher
- School
of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, United Kingdom
| | - Gail J. Bartlett
- School
of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, United Kingdom
| | - Aimee L. Boyle
- School
of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, United Kingdom
| | - Jonathan J. Danon
- School
of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, United Kingdom
| | - Laura E. Rush
- School
of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, United Kingdom
| | - Andrei N. Lupas
- Department
of Protein Evolution, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Derek N. Woolfson
- School
of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, United Kingdom
- School
of Biochemistry, University of Bristol, Medical Sciences Building, University
Walk, Bristol BS8 1TD, United Kingdom
- BrisSynBio, University of Bristol, Life Science
Building, Tyndall Avenue, Bristol BS8 1TQ, United Kingdom
| |
Collapse
|
94
|
Affiliation(s)
| | | | | | - Ting Xu
- Material
Science Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| |
Collapse
|
95
|
Murschel F, Fortier C, Jolicoeur M, Hodges RS, De Crescenzo G. Two Complementary Approaches for the Controlled Release of Biomolecules Immobilized via Coiled-Coil Interactions: Peptide Core Mutations and Multivalent Presentation. Biomacromolecules 2017; 18:965-975. [DOI: 10.1021/acs.biomac.6b01830] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Frederic Murschel
- Department
of Chemical Engineering, Groupe de Recherche en Sciences et Technologies
Biomédicales (GRSTB), Bio-P2 Research Unit, École Polytechnique de Montréal, P.O. Box 6079, succursale Centre-Ville, Montréal, Quebec H3C 3A7, Canada
| | - Charles Fortier
- Department
of Chemical Engineering, Groupe de Recherche en Sciences et Technologies
Biomédicales (GRSTB), Bio-P2 Research Unit, École Polytechnique de Montréal, P.O. Box 6079, succursale Centre-Ville, Montréal, Quebec H3C 3A7, Canada
| | - Mario Jolicoeur
- Department
of Chemical Engineering, Groupe de Recherche en Sciences et Technologies
Biomédicales (GRSTB), Bio-P2 Research Unit, École Polytechnique de Montréal, P.O. Box 6079, succursale Centre-Ville, Montréal, Quebec H3C 3A7, Canada
| | - Robert S. Hodges
- Department
of Biochemistry and Molecular Genetics, University of Colorado, School of Medicine, Anschutz Medical Campus, Aurora, Colorado 80045, United States
| | - Gregory De Crescenzo
- Department
of Chemical Engineering, Groupe de Recherche en Sciences et Technologies
Biomédicales (GRSTB), Bio-P2 Research Unit, École Polytechnique de Montréal, P.O. Box 6079, succursale Centre-Ville, Montréal, Quebec H3C 3A7, Canada
| |
Collapse
|
96
|
Abstract
α-Helical coiled coils are ubiquitous protein-folding and protein-interaction domains in which two or more α-helical chains come together to form bundles. Through a combination of bioinformatics analysis of many thousands of natural coiled-coil sequences and structures, plus empirical protein engineering and design studies, there is now a deep understanding of the sequence-to-structure relationships for this class of protein architecture. This has led to considerable success in rational design and what might be termed in biro de novo design of simple coiled coils, which include homo- and hetero-meric parallel dimers, trimers and tetramers. In turn, these provide a toolkit for directing the assembly of both natural proteins and more complex designs in protein engineering, materials science and synthetic biology. Moving on, the increased and improved use of computational design is allowing access to coiled-coil structures that are rare or even not observed in nature, for example α-helical barrels, which comprise five or more α-helices and have central channels into which different functions may be ported. This chapter reviews all of these advances, outlining improvements in our knowledge of the fundamentals of coiled-coil folding and assembly, and highlighting new coiled coil-based materials and applications that this new understanding is opening up. Despite considerable progress, however, challenges remain in coiled-coil design, and the next decade promises to be as productive and exciting as the last.
Collapse
Affiliation(s)
- Derek N Woolfson
- School of Chemistry, University of Bristol, BS8 1TS, Bristol, UK.
- School of Biochemistry, University of Bristol, BS8 1TD, Bristol, UK.
- BrisSynBio, Life Sciences Building, University of Bristol, BS8 1TQ, Bristol, UK.
| |
Collapse
|
97
|
Suyama K, Taniguchi S, Tatsubo D, Maeda I, Nose T. Dimerization effects on coacervation property of an elastin-derived synthetic peptide (FPGVG)5. J Pept Sci 2016; 22:236-43. [PMID: 27028208 DOI: 10.1002/psc.2876] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 02/11/2016] [Accepted: 02/23/2016] [Indexed: 11/08/2022]
Abstract
Elastin, a core protein of the elastic fibers, exhibits the coacervation (temperature-dependent reversible association/dissociation) under physiological conditions. Because of this characteristic, elastin and elastin-derived peptides have been considered to be useful as base materials for developing various biomedical products, skin substitutes, synthetic vascular grafts, and drug delivery systems. Although elastin-derived polypeptide (Val-Pro-Gly-Val-Gly)n also has been known to demonstrate coacervation property, a sufficiently high (VPGVG)n repetition number (n>40) is required for coacervation. In the present study, a series of elastin-derived peptide (Phe-Pro-Gly-Val-Gly)5 dimers possessing high coacervation potential were newly developed. These novel dimeric peptides exhibited coacervation at significantly lower concentrations and temperatures than the commonly used elastin-derived peptide analogs; this result suggests that the coacervation ability of the peptides is enhanced by dimerization. Circular dichroism (CD) measurements indicate that the dimers undergo similar temperature-dependent and reversible conformational changes when coacervation occurs. The molecular dynamics calculation results reveal that the sheet-turn-sheet motif involving a type II β-turn-like structure commonly observed among the dimers and caused formation of globular conformation of them. These synthesized peptide dimers may be useful not only as model peptides for structural analysis of elastin and elastin-derived peptides, but also as base materials for developing various temperature-sensitive biomedical and industrial products.
Collapse
Affiliation(s)
- Keitaro Suyama
- Faculty of Arts and Science, Kyushu University, Fukuoka, 819-0395, Japan
| | - Suguru Taniguchi
- Department of Bioscience and Bioinformatics, Graduate School of Computer Science and Systems Engineering, Kyushu Institute of Technology, Iizuka, Fukuoka, 820-8502, Japan
| | - Daiki Tatsubo
- Department of Chemistry, Faculty and Graduate School of Science, Kyushu University, Fukuoka, 819-0395, Japan
| | - Iori Maeda
- Department of Bioscience and Bioinformatics, Graduate School of Computer Science and Systems Engineering, Kyushu Institute of Technology, Iizuka, Fukuoka, 820-8502, Japan
| | - Takeru Nose
- Faculty of Arts and Science, Kyushu University, Fukuoka, 819-0395, Japan.,Department of Chemistry, Faculty and Graduate School of Science, Kyushu University, Fukuoka, 819-0395, Japan
| |
Collapse
|
98
|
Jeong WJ, Choi SH, Jin KS, Lim YB. Tuning Oligovalent Biomacromolecular Interfaces Using Double-Layered α-Helical Coiled-Coil Nanoassemblies from Lariat-Type Building Blocks. ACS Macro Lett 2016; 5:1406-1410. [PMID: 35651205 DOI: 10.1021/acsmacrolett.6b00746] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The target affinity and selectivity of many biomacromolecules depend on the three-dimensional (3D) distribution of multiple ligands on their surfaces. Here, we devised a self-assembly strategy to control the target-tailored 3D distribution of multiple α-helical ligands on a coiled-coil core scaffold using novel lariat-type supramolecular building blocks. Depending on the coiled-coil composition and ligand grafting sites in the lariat building blocks, the structural and functional features of the self-assembled peptide nanostructures (SPNs) could be variably fine-tuned. Using oligovalent protein-RNA (Rev-RRE) interactions as a model system, we demonstrate that longer grafting reinforces the helicity of the peptide ligands, whereas shorter grafting strengthens the target binding affinity of the SPNs in both monovalent and oligovalent interactions. This supramolecular approach should be useful in developing precisely controllable multivalent ligands for biomacromolecular interactions.
Collapse
Affiliation(s)
- Woo-jin Jeong
- Department of Materials Science & Engineering, Yonsei University, Seoul 120-749, Korea
| | - Se-Hwan Choi
- Department of Materials Science & Engineering, Yonsei University, Seoul 120-749, Korea
| | - Kyeong Sik Jin
- Pohang
Accelerator Laboratory, Pohang University of Science and Technology, Pohang 790-784, Korea
| | - Yong-beom Lim
- Department of Materials Science & Engineering, Yonsei University, Seoul 120-749, Korea
| |
Collapse
|
99
|
Abstract
![]()
In
this paper, we investigate the coassembly of peptides derived
from the central and C-terminal regions of the β-amyloid peptide
(Aβ). In the preceding paper, J. Am. Chem. Soc.2016, DOI: 10.1021/jacs.6b06000, we established that peptides containing residues 17–23 (LVFFAED)
from the central region of Aβ and residues 30–36 (AIIGLMV)
from the C-terminal region of Aβ assemble to form homotetramers
consisting of two hydrogen-bonded dimers. Here, we mix these tetramer-forming
peptides and determine how they coassemble. Incorporation of a single 15N isotopic label into each peptide provides a spectroscopic
probe with which to elucidate the coassembly of the peptides by 1H,15N HSQC. Job’s method of continuous variation
and nonlinear least-squares fitting reveal that the peptides form
a mixture of heterotetramers in 3:1, 2:2, and 1:3 stoichiometries,
in addition to the homotetramers. These studies also establish the
relative stability of each tetramer and show that the 2:2 heterotetramer
predominates. 15N-Edited NOESY shows the 2:2 heterotetramer
comprises two different homodimers, rather than two heterodimers.
The peptides within the heterotetramer segregate in forming the homodimer
subunits, but the two homodimers coassemble in forming the heterotetramer.
These studies show that the central and C-terminal regions of Aβ
can preferentially segregate within β-sheets and that the resulting
segregated β-sheets can further coassemble.
Collapse
Affiliation(s)
- Nicholas L Truex
- Department of Chemistry, University of California, Irvine , Irvine, California 92697-2025, United States
| | - James S Nowick
- Department of Chemistry, University of California, Irvine , Irvine, California 92697-2025, United States
| |
Collapse
|
100
|
Truex NL, Wang Y, Nowick JS. Assembly of Peptides Derived from β-Sheet Regions of β-Amyloid. J Am Chem Soc 2016; 138:13882-13890. [PMID: 27642651 PMCID: PMC5089065 DOI: 10.1021/jacs.6b06000] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
![]()
In
Alzheimer’s disease, aggregation of the β-amyloid
peptide (Aβ) results in the formation of oligomers and fibrils
that are associated with neurodegeneration. Aggregation of Aβ
occurs through interactions between different regions of the peptide.
This paper and the accompanying paper constitute a two-part investigation
of two key regions of Aβ: the central region and the C-terminal
region. These two regions promote aggregation and adopt β-sheet
structure in the fibrils, and may also do so in the oligomers. In
this paper, we study the assembly of macrocyclic β-sheet peptides
that contain residues 17–23 (LVFFAED) from the central region
and residues 30–36 (AIIGLMV) from the C-terminal region. These
peptides assemble to form tetramers. Each tetramer consists of two
hydrogen-bonded dimers that pack through hydrophobic interactions
in a sandwich-like fashion. Incorporation of a single 15N isotopic label into each peptide provides a spectroscopic probe
with which to elucidate the β-sheet assembly and interaction: 1H,15N HSQC studies facilitate the identification
of the monomers and tetramers; 15N-edited NOESY studies
corroborate the pairing of the dimers within the tetramers. In the
following paper, J. Am. Chem. Soc.2016, DOI: 10.1021/jacs.6b06001, we will extend these studies to elucidate the coassembly of the
peptides to form heterotetramers.
Collapse
Affiliation(s)
- Nicholas L Truex
- Department of Chemistry, University of California, Irvine , Irvine, California 92697-2025, United States
| | - Yilin Wang
- Department of Chemistry, University of California, Irvine , Irvine, California 92697-2025, United States
| | - James S Nowick
- Department of Chemistry, University of California, Irvine , Irvine, California 92697-2025, United States
| |
Collapse
|