1
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Brennan A, Leech JT, Kad NM, Mason JM. An Approach to Derive Functional Peptide Inhibitors of Transcription Factor Activity. JACS AU 2022; 2:996-1006. [PMID: 35557753 PMCID: PMC9088798 DOI: 10.1021/jacsau.2c00105] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 03/01/2022] [Accepted: 03/01/2022] [Indexed: 06/15/2023]
Abstract
We report the development of a high-throughput, intracellular "transcription block survival" (TBS) screening platform to derive functional transcription factor antagonists. TBS is demonstrated using the oncogenic transcriptional regulator cJun, with the development of antagonists that bind cJun and prevent both dimerization and, more importantly, DNA binding remaining a primary challenge. In TBS, cognate TRE sites are introduced into the coding region of the essential gene, dihydrofolate reductase (DHFR). Introduction of cJun leads to TRE binding, preventing DHFR expression by directly blocking RNA polymerase gene transcription to abrogate cell proliferation. Peptide library screening identified a sequence that both binds cJun and antagonizes function by preventing DNA binding, as demonstrated by restored cell viability and subsequent in vitro hit validation. TBS is an entirely tag-free genotype-to-phenotype approach, selecting desirable attributes such as high solubility, target specificity, and low toxicity within a complex cellular environment. TBS facilitates rapid library screening to accelerate the identification of therapeutically valuable sequences.
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Affiliation(s)
- Andrew Brennan
- Department
of Biology & Biochemistry, University
of Bath, Bath BA2 7AY, U.K.
| | - James T. Leech
- School
of Biosciences, University of Kent, Canterbury CT2 7NH, U.K.
| | - Neil M. Kad
- School
of Biosciences, University of Kent, Canterbury CT2 7NH, U.K.
| | - Jody M. Mason
- Department
of Biology & Biochemistry, University
of Bath, Bath BA2 7AY, U.K.
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2
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Stern KL, Dalley NA, McMurray NT, Billings WM, Loftus TJ, Jones ZB, Hadfield JR, Price JL. Prerequisites for Stabilizing Long-Range Synergistic Interactions among b-, c-, and f-Residues in Coiled Coils. Biochemistry 2022; 61:319-326. [PMID: 35129961 PMCID: PMC9202806 DOI: 10.1021/acs.biochem.1c00760] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Coiled coils are among the most abundant tertiary and quaternary structures found in proteins. A growing body of evidence suggests that long-range synergistic interactions among solvent-exposed residues can contribute substantially to coiled-coil conformational stability, but our understanding of the key sequence and structural prerequisites of this effect is still developing. Here, we show that the strength of synergistic interaction involving a b-position Glu (i), an f-position Tyr (i + 4), and a c-position Lys (i + 8) depends on the identity of the f-position residue, the length and stability of the coiled coil, and its oligomerization stoichiometry/surface accessibility. Combined with previous observations, these results map out predictable sequence- and structure-based criteria for enhancing coiled-coil stability by up to -0.58 kcal/mol per monomer (or -2.32 kcal/mol per coiled-coil tetramer). Our observations expand the available tools for enhancing coiled coil stability by sequence variation at solvent-exposed b-, c-, and f-positions and suggest the need to exercise care in the choice of substitutions at these positions for application-specific purposes.
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Affiliation(s)
| | | | | | | | | | | | | | - Joshua L. Price
- Corresponding Author: Joshua L. Price, C100 BNSN, Brigham Young University, Provo, UT 84602;
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3
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Plaper T, Aupič J, Dekleva P, Lapenta F, Keber MM, Jerala R, Benčina M. Coiled-coil heterodimers with increased stability for cellular regulation and sensing SARS-CoV-2 spike protein-mediated cell fusion. Sci Rep 2021; 11:9136. [PMID: 33911109 PMCID: PMC8080620 DOI: 10.1038/s41598-021-88315-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 04/12/2021] [Indexed: 12/19/2022] Open
Abstract
Coiled-coil (CC) dimer-forming peptides are attractive designable modules for mediating protein association. Highly stable CCs are desired for biological activity regulation and assay. Here, we report the design and versatile applications of orthogonal CC dimer-forming peptides with a dissociation constant in the low nanomolar range. In vitro stability and specificity was confirmed in mammalian cells by enzyme reconstitution, transcriptional activation using a combination of DNA-binding and a transcriptional activation domain, and cellular-enzyme-activity regulation based on externally-added peptides. In addition to cellular regulation, coiled-coil-mediated reporter reconstitution was used for the detection of cell fusion mediated by the interaction between the spike protein of pandemic SARS-CoV2 and the ACE2 receptor. This assay can be used to investigate the mechanism of viral spike protein-mediated fusion or screening for viral inhibitors under biosafety level 1 conditions.
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Affiliation(s)
- Tjaša Plaper
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, 1001, Ljubljana, Slovenia.,Interfaculty Doctoral Study of Biomedicine, University of Ljubljana, Ljubljana, Slovenia
| | - Jana Aupič
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, 1001, Ljubljana, Slovenia
| | - Petra Dekleva
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, 1001, Ljubljana, Slovenia
| | - Fabio Lapenta
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, 1001, Ljubljana, Slovenia.,EN-FIST Centre of Excellence, Trg Osvobodilne Fronte 13, 1000, Ljubljana, Slovenia
| | - Mateja Manček Keber
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, 1001, Ljubljana, Slovenia.,EN-FIST Centre of Excellence, Trg Osvobodilne Fronte 13, 1000, Ljubljana, Slovenia
| | - Roman Jerala
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, 1001, Ljubljana, Slovenia. .,EN-FIST Centre of Excellence, Trg Osvobodilne Fronte 13, 1000, Ljubljana, Slovenia.
| | - Mojca Benčina
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, 1001, Ljubljana, Slovenia. .,EN-FIST Centre of Excellence, Trg Osvobodilne Fronte 13, 1000, Ljubljana, Slovenia.
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4
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Brennan A, Leech JT, Kad NM, Mason JM. Selective antagonism of cJun for cancer therapy. J Exp Clin Cancer Res 2020; 39:184. [PMID: 32917236 PMCID: PMC7488417 DOI: 10.1186/s13046-020-01686-9] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 08/20/2020] [Indexed: 01/10/2023] Open
Abstract
The activator protein-1 (AP-1) family of transcription factors modulate a diverse range of cellular signalling pathways into outputs which can be oncogenic or anti-oncogenic. The transcription of relevant genes is controlled by the cellular context, and in particular by the dimeric composition of AP-1. Here, we describe the evidence linking cJun in particular to a range of cancers. This includes correlative studies of protein levels in patient tumour samples and mechanistic understanding of the role of cJun in cancer cell models. This develops an understanding of cJun as a focal point of cancer-altered signalling which has the potential for therapeutic antagonism. Significant work has produced a range of small molecules and peptides which have been summarised here and categorised according to the binding surface they target within the cJun-DNA complex. We highlight the importance of selectively targeting a single AP-1 family member to antagonise known oncogenic function and avoid antagonism of anti-oncogenic function.
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Affiliation(s)
- Andrew Brennan
- Department of Biology & Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - James T Leech
- School of Biosciences, University of Kent, Canterbury, CT2 7NH, UK
| | - Neil M Kad
- School of Biosciences, University of Kent, Canterbury, CT2 7NH, UK
| | - Jody M Mason
- Department of Biology & Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK.
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5
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Park WM. Coiled-Coils: the Molecular Zippers that Self-Assemble Protein Nanostructures. Int J Mol Sci 2020; 21:E3584. [PMID: 32438665 PMCID: PMC7278914 DOI: 10.3390/ijms21103584] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 05/17/2020] [Accepted: 05/18/2020] [Indexed: 02/07/2023] Open
Abstract
Coiled-coils, the bundles of intertwined helical protein motifs, have drawn much attention as versatile molecular toolkits. Because of programmable interaction specificity and affinity as well as well-established sequence-to-structure relationships, coiled-coils have been used as subunits that self-assemble various molecular complexes in a range of fields. In this review, I describe recent advances in the field of protein nanotechnology, with a focus on programming assembly of protein nanostructures using coiled-coil modules. Modular design approaches to converting the helical motifs into self-assembling building blocks are described, followed by a discussion on the molecular basis and principles underlying the modular designs. This review also provides a summary of recently developed nanostructures with a variety of structural features, which are in categories of unbounded nanostructures, discrete nanoparticles, and well-defined origami nanostructures. Challenges existing in current design strategies, as well as desired improvements for controls over material properties and functionalities for applications, are also provided.
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Affiliation(s)
- Won Min Park
- Tim Taylor Department of Chemical Engineering, Kansas State University, Manhattan, KS 66506, USA
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6
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A tunable orthogonal coiled-coil interaction toolbox for engineering mammalian cells. Nat Chem Biol 2020; 16:513-519. [PMID: 31907374 PMCID: PMC7182445 DOI: 10.1038/s41589-019-0443-y] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 10/21/2019] [Accepted: 11/25/2019] [Indexed: 02/07/2023]
Abstract
Protein interactions guide most cellular processes. Orthogonal hetero-specific protein-protein interaction domains may facilitate better control of engineered biological systems. Here, we report a tunable de novo designed set of orthogonal coiled-coil (CC) peptide heterodimers (called the NICP set) and its application for the regulation of diverse cellular processes, from cellular localization to transcriptional regulation. We demonstrate the application of CC pairs for multiplex localization in single cells and exploit the interaction strength and variable stoichiometry of CC peptides for tuning of gene transcription strength. A concatenated CC peptide tag (CCC-tag) was used to construct highly potent CRISPR-dCas9-based transcriptional activators and to amplify the response of light and small molecule-inducible transcription in cell culture as well as in vivo. The NICP set and its implementations represent a valuable toolbox of minimally disruptive modules for the recruitment of versatile functional domains and regulation of cellular processes for synthetic biology.
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7
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Biok NA, Passow AD, Wang C, Bingman CA, Abbott NL, Gellman SH. Retention of Coiled-Coil Dimer Formation in the Absence of Ion Pairing at Positions Flanking the Hydrophobic Core. Biochemistry 2019; 58:4821-4826. [DOI: 10.1021/acs.biochem.9b00668] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Naomi A. Biok
- Department of Chemistry, University of Wisconsin—Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Alexander D. Passow
- Department of Chemistry, University of Wisconsin—Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Chenxuan Wang
- Department of Chemistry, University of Wisconsin—Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
- Department of Chemical and Biological Engineering, University of Wisconsin—Madison, 1415 Engineering Drive, Madison, Wisconsin 53706, United States
| | - Craig A. Bingman
- Department of Biochemistry, University of Wisconsin—Madison, 440 Henry Mall, Madison, Wisconsin 53706, United States
| | - Nicholas L. Abbott
- Department of Chemical and Biological Engineering, University of Wisconsin—Madison, 1415 Engineering Drive, Madison, Wisconsin 53706, United States
- Smith School of Chemical and Biomolecular Engineering, Cornell University, 1 Ho Plaza, Ithaca, New York 14853, United States
| | - Samuel H. Gellman
- Department of Chemistry, University of Wisconsin—Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
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8
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Kopra K, Tong-Ochoa N, Laine M, Eskonen V, Koskinen PJ, Härmä H. Homogeneous peptide-break assay for luminescent detection of enzymatic protein post-translational modification activity utilizing charged peptides. Anal Chim Acta 2019; 1055:126-132. [PMID: 30782363 DOI: 10.1016/j.aca.2018.12.041] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 12/18/2018] [Indexed: 11/18/2022]
Abstract
We have developed a rapid and sensitive universal peptide-based time-resolved luminescence assay for detection of enzymatic post-translational modifications (PTMs). PTMs play essential roles in intracellular signaling and cell regulation, thus providing functional protein diversity in cell. Due this, impaired PTM patterns have been linked to multiple disease states. Clear link between PTMs and pathological conditions have also driven assay development further, but still today most of the methodologies are based on single-specificity or group-specific PTM-recognition. We have previously introduced leuzine-zipper based peptide-break technology as a viable option for universal PTM detection. Here, we introduce peptide-break technology utilizing single-label homogeneous quenching resonance energy transfer (QRET) and charge-based peptide-peptide interaction. We demonstrate the functionality of the new assay concept in phosphorylation, deacetylation, and citrullination. In a comparable study between previously introduced leucine-zipper and the novel charge-based approach, we found equal PTM detection performance and sensitivity, but the peptide design for new targets is simplified with the charged peptides. The new concept allows the use of short <20 amino acid peptides without limitations rising from the leucine-zipper coiled-coil structure. Introduced methodology enables wash-free PTM detection in a 384-well plate format, using low nanomolar enzyme concentrations. Potentially, the peptide-break technique using charged peptides may be applicable for natural peptide sequences directly obtained from the target protein.
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Affiliation(s)
- Kari Kopra
- Materials Chemistry and Chemical Analysis, University of Turku, Vatselankatu 2, 20500, Turku, Finland.
| | - Natalia Tong-Ochoa
- Materials Chemistry and Chemical Analysis, University of Turku, Vatselankatu 2, 20500, Turku, Finland
| | - Mari Laine
- Materials Chemistry and Chemical Analysis, University of Turku, Vatselankatu 2, 20500, Turku, Finland
| | - Ville Eskonen
- Materials Chemistry and Chemical Analysis, University of Turku, Vatselankatu 2, 20500, Turku, Finland
| | - Päivi J Koskinen
- Section of Physiology and Genetics, Department of Biology, University of Turku, Vesilinnantie 5, Turku, Finland
| | - Harri Härmä
- Materials Chemistry and Chemical Analysis, University of Turku, Vatselankatu 2, 20500, Turku, Finland
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9
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Brechun KE, Arndt KM, Woolley GA. Selection of Protein-Protein Interactions of Desired Affinities with a Bandpass Circuit. J Mol Biol 2019; 431:391-400. [PMID: 30448232 DOI: 10.1016/j.jmb.2018.11.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 11/07/2018] [Accepted: 11/08/2018] [Indexed: 11/17/2022]
Abstract
We have developed a genetic circuit in Escherichia coli that can be used to select for protein-protein interactions of different strengths by changing antibiotic concentrations in the media. The genetic circuit links protein-protein interaction strength to β-lactamase activity while simultaneously imposing tuneable positive and negative selection pressure for β-lactamase activity. Cells only survive if they express interacting proteins with affinities that fall within set high- and low-pass thresholds; i.e. the circuit therefore acts as a bandpass filter for protein-protein interactions. We show that the circuit can be used to recover protein-protein interactions of desired affinity from a mixed population with a range of affinities. The circuit can also be used to select for inhibitors of protein-protein interactions of defined strength.
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Affiliation(s)
- Katherine E Brechun
- Department of Chemistry, University of Toronto, Toronto, Canada; Molecular Biotechnology, University of Potsdam, Potsdam, Germany
| | - Katja M Arndt
- Molecular Biotechnology, University of Potsdam, Potsdam, Germany.
| | - G Andrew Woolley
- Department of Chemistry, University of Toronto, Toronto, Canada.
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10
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Härmä H, Tong-Ochoa N, van Adrichem AJ, Jelesarov I, Wennerberg K, Kopra K. Toward universal protein post-translational modification detection in high throughput format. Chem Commun (Camb) 2018; 54:2910-2913. [PMID: 29498735 DOI: 10.1039/c7cc09575a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Post-translational modification (PTM) of proteins plays essential regulatory roles in a variety of pathological conditions. Reliable and practical assays are required to accelerate the discovery of inhibitors and activators for PTM related diseases. Today, methodologies are based on specific or group-specific PTM recognition of e.g. phosphate for kinase activity without extending to other type of PTMs. Here we have established a universal time-resolved luminescence assay on a peptide-break platform for the direct detection of wide variety of PTMs. The developed assay is based on the leucine zipper concept wherein a europium-chelate labeled detection peptide and a non-labeled peptide substrate form a highly luminescent dimer. As an active PTM enzyme at sub or low nanomolar concentration modifies the substrate peptide, the luminescent signal of the detached detection peptide is quenched in the presence of soluble quenchers. The functionality of this universal assay technique has been demonstrated for the monitoring of phosphorylation, dephosphorylation, deacetylation, and citrullination with high applicability also to other PTMs in a high throughput format.
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Affiliation(s)
- Harri Härmä
- Materials Chemistry and Chemical Analysis, University of Turku, Turku, Finland.
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11
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Ferro M, Lamanna J, Ripamonti M, Racchetti G, Arena A, Spadini S, Montesano G, Cortese R, Zimarino V, Malgaroli A. Functional mapping of brain synapses by the enriching activity-marker SynaptoZip. Nat Commun 2017; 8:1229. [PMID: 29089485 PMCID: PMC5663910 DOI: 10.1038/s41467-017-01335-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 09/08/2017] [Indexed: 01/27/2023] Open
Abstract
Ideally, elucidating the role of specific brain circuits in animal behavior would require the ability to measure activity at all involved synapses, possibly with unrestricted field of view, thus even at those boutons deeply located into the brain. Here, we introduce and validate an efficient scheme reporting synaptic vesicle cycling in vivo. This is based on SynaptoZip, a genetically encoded molecule deploying in the vesicular lumen a bait moiety designed to capture upon exocytosis a labeled alien peptide, Synbond. The resulting signal is cumulative and stores the number of cycling events occurring at individual synapses. Since this functional signal is enduring and measurable both online and ex post, SynaptoZip provides a unique method for the analysis of the history of synaptic activity in regions several millimeters below the brain surface. We show its broad applicability by reporting stimulus-evoked and spontaneous circuit activity in wide cortical fields, in anesthetized and freely moving animals. Visualization of synaptic activity in the living brain is challenging. This study devises a simple and efficient scheme that reports synaptic vesicle recycling in vivo using SynaptoZip, a genetically encoded sensor of past synaptic activities.
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Affiliation(s)
- Mattia Ferro
- Università Vita-Salute San Raffaele, Milan, 20132, Italy.,Neurobiology of Learning Unit, Division of Neuroscience, Scientific Institute Ospedale San Raffaele, Milan, 20132, Italy
| | - Jacopo Lamanna
- Università Vita-Salute San Raffaele, Milan, 20132, Italy.,Neurobiology of Learning Unit, Division of Neuroscience, Scientific Institute Ospedale San Raffaele, Milan, 20132, Italy
| | - Maddalena Ripamonti
- Università Vita-Salute San Raffaele, Milan, 20132, Italy.,Neurobiology of Learning Unit, Division of Neuroscience, Scientific Institute Ospedale San Raffaele, Milan, 20132, Italy
| | - Gabriella Racchetti
- Università Vita-Salute San Raffaele, Milan, 20132, Italy.,Psychiatry and Clinical Psychobiology Unit, Division of Neuroscience, Scientific Institute Ospedale San Raffaele, Milan, 20132, Italy
| | - Alessandro Arena
- Università Vita-Salute San Raffaele, Milan, 20132, Italy.,Neurobiology of Learning Unit, Division of Neuroscience, Scientific Institute Ospedale San Raffaele, Milan, 20132, Italy.,Department of Physiology, Institute of Basal Medical Sciences, University of Oslo, Oslo, 0315, Norway
| | - Sara Spadini
- Università Vita-Salute San Raffaele, Milan, 20132, Italy.,Neurobiology of Learning Unit, Division of Neuroscience, Scientific Institute Ospedale San Raffaele, Milan, 20132, Italy
| | - Giovanni Montesano
- Università Vita-Salute San Raffaele, Milan, 20132, Italy.,Neurobiology of Learning Unit, Division of Neuroscience, Scientific Institute Ospedale San Raffaele, Milan, 20132, Italy.,Dipartimento Testa-Collo, San Paolo Hospital, University of Milan, Milan, 20122, Italy
| | | | - Vincenzo Zimarino
- Neurobiology of Learning Unit, Division of Neuroscience, Scientific Institute Ospedale San Raffaele, Milan, 20132, Italy
| | - Antonio Malgaroli
- Università Vita-Salute San Raffaele, Milan, 20132, Italy. .,Neurobiology of Learning Unit, Division of Neuroscience, Scientific Institute Ospedale San Raffaele, Milan, 20132, Italy.
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12
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Small LSR, Bruning M, Thomson AR, Boyle AL, Davies RB, Curmi PMG, Forde NR, Linke H, Woolfson DN, Bromley EHC. Construction of a Chassis for a Tripartite Protein-Based Molecular Motor. ACS Synth Biol 2017; 6:1096-1102. [PMID: 28221767 PMCID: PMC5477008 DOI: 10.1021/acssynbio.7b00037] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Improving our understanding of biological
motors, both to fully
comprehend their activities in vital processes, and to exploit their
impressive abilities for use in bionanotechnology, is highly desirable.
One means of understanding these systems is through the production
of synthetic molecular motors. We demonstrate the use of orthogonal
coiled-coil dimers (including both parallel and antiparallel coiled
coils) as a hub for linking other components of a previously described
synthetic molecular motor, the Tumbleweed. We use circular dichroism,
analytical ultracentrifugation, dynamic light scattering, and disulfide
rearrangement studies to demonstrate the ability of this six-peptide
set to form the structure designed for the Tumbleweed motor. The successful
formation of a suitable hub structure is both a test of the transferability
of design rules for protein folding as well as an important step in
the production of a synthetic protein-based molecular motor.
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Affiliation(s)
- Lara S. R. Small
- Department
of Physics, Durham University, Durham, DH1 3LE, United Kingdom
| | - Marc Bruning
- School
of Chemistry, University of Bristol, BS8 1TS, Bristol, United Kingdom
| | - Andrew R. Thomson
- School
of Chemistry, University of Glasgow, Glasgow, G12 8QQ, United Kingdom
| | - Aimee L. Boyle
- Faculty
of Science, Leiden Institute of Chemistry, Leiden, 2333 CC, Netherlands
| | - Roberta B. Davies
- Structural
Biology Laboratory, Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales 2010, Australia
| | - Paul M. G. Curmi
- School of
Physics, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Nancy R. Forde
- Department
of Physics, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Heiner Linke
- NanoLund
and Solid State Physics, Lund University, Box 118, 22100 Lund, Sweden
| | - Derek N. Woolfson
- School
of Chemistry, University of Bristol, BS8 1TS, Bristol, United Kingdom
- School
of Biochemistry, University of Bristol, BS8 1TD, Bristol, United Kingdom
- BrisSynBio,
Life Sciences Building, University of Bristol, BS8 1TQ, Bristol, United Kingdom
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13
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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.
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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
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14
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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.
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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.
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15
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Boyken SE, Chen Z, Groves B, Langan RA, Oberdorfer G, Ford A, Gilmore JM, Xu C, DiMaio F, Pereira JH, Sankaran B, Seelig G, Zwart PH, Baker D. De novo design of protein homo-oligomers with modular hydrogen-bond network-mediated specificity. Science 2016; 352:680-7. [PMID: 27151862 PMCID: PMC5497568 DOI: 10.1126/science.aad8865] [Citation(s) in RCA: 222] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 03/23/2016] [Indexed: 12/26/2022]
Abstract
In nature, structural specificity in DNA and proteins is encoded differently: In DNA, specificity arises from modular hydrogen bonds in the core of the double helix, whereas in proteins, specificity arises largely from buried hydrophobic packing complemented by irregular peripheral polar interactions. Here, we describe a general approach for designing a wide range of protein homo-oligomers with specificity determined by modular arrays of central hydrogen-bond networks. We use the approach to design dimers, trimers, and tetramers consisting of two concentric rings of helices, including previously not seen triangular, square, and supercoiled topologies. X-ray crystallography confirms that the structures overall, and the hydrogen-bond networks in particular, are nearly identical to the design models, and the networks confer interaction specificity in vivo. The ability to design extensive hydrogen-bond networks with atomic accuracy enables the programming of protein interaction specificity for a broad range of synthetic biology applications; more generally, our results demonstrate that, even with the tremendous diversity observed in nature, there are fundamentally new modes of interaction to be discovered in proteins.
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Affiliation(s)
- Scott E Boyken
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA. Institute for Protein Design, University of Washington, Seattle, WA 98195, USA. Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Zibo Chen
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA. Institute for Protein Design, University of Washington, Seattle, WA 98195, USA. Graduate Program in Biological Physics, Structure, and Design, University of Washington, Seattle, WA 98195, USA
| | - Benjamin Groves
- Department of Electrical Engineering, University of Washington, Seattle, WA 98195, USA
| | - Robert A Langan
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA. Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Gustav Oberdorfer
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA. Institute for Protein Design, University of Washington, Seattle, WA 98195, USA. Department of Computer Science and Engineering, University of Washington, Seattle, WA 98195, USA
| | - Alex Ford
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA. Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Jason M Gilmore
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA. Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Chunfu Xu
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA. Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Frank DiMaio
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA. Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Jose Henrique Pereira
- Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50/3, 8010-Graz, Austria. Joint BioEnergy Institute, Emeryville, CA 94608, USA
| | - Banumathi Sankaran
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Georg Seelig
- Department of Electrical Engineering, University of Washington, Seattle, WA 98195, USA. Berkeley Center for Structural Biology, Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Peter H Zwart
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA. The Center for Advanced Mathematics for Energy Research Applications, Lawrence Berkeley National Laboratories, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA. Institute for Protein Design, University of Washington, Seattle, WA 98195, USA. Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA.
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16
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Rezaei Araghi R, Keating AE. Designing helical peptide inhibitors of protein-protein interactions. Curr Opin Struct Biol 2016; 39:27-38. [PMID: 27123812 DOI: 10.1016/j.sbi.2016.04.001] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Revised: 03/28/2016] [Accepted: 04/03/2016] [Indexed: 02/04/2023]
Abstract
Short helical peptides combine characteristics of small molecules and large proteins and provide an exciting area of opportunity in protein design. A growing number of studies report novel helical peptide inhibitors of protein-protein interactions. New techniques have been developed for peptide design and for chemically stabilizing peptides in a helical conformation, which frequently improves protease resistance and cell permeability. We summarize advances in peptide crosslinking chemistry and give examples of peptide design studies targeting coiled-coil transcription factors, Bcl-2 family proteins, MDM2/MDMX, and HIV gp41, among other targets.
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Affiliation(s)
- Raheleh Rezaei Araghi
- MIT Department of Biology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States
| | - Amy E Keating
- MIT Department of Biology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States; MIT Department of Biological Engineering, 77 Massachusetts Avenue, Cambridge, MA 02139, United States.
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17
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Lee S, Kaku Y, Inoue S, Nagamune T, Kawahara M. Growth signalobody selects functional intrabodies in the mammalian cytoplasm. Biotechnol J 2016; 11:565-73. [PMID: 26647155 DOI: 10.1002/biot.201500364] [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: 06/15/2015] [Revised: 09/03/2015] [Accepted: 12/08/2015] [Indexed: 12/18/2022]
Abstract
A versatile strategy to inhibit protein functions in the cytoplasmic environment is eagerly anticipated for drug discovery. In this study, we demonstrate a novel system to directly select functional intrabodies from a library in the mammalian cytoplasm. In this system, a target homo-oligomeric antigen is expressed together with a single-chain Fv (scFv) library that is linked to the cytoplasmic domain of a receptor tyrosine kinase (RTK) in the cytoplasm of murine interleukin-3 (IL-3)-dependent cells. As the tyrosine kinase is activated by dimerization, only scFv-RTK clones that can bind to the target antigen would be oligomerized and transduce a growth signal under the IL-3-deprived condition, which leads to selection of functional intrabodies. To demonstrate this system, we used rabies virus phosphoprotein (RV-P) that forms dimers in the cytoplasm as a target antigen. As a result, functional intrabodies were selected using our system from a naïve scFv library as well as from a pre-selected anti-RV-P library generated by phage display. This system may be applied for screening intrabodies that can prevent progression of various severe diseases.
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Affiliation(s)
- Songhee Lee
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Yoshihiro Kaku
- Department of Veterinary Science, National Institute of Infectious Diseases, Tokyo, Japan
| | - Satoshi Inoue
- Department of Veterinary Science, National Institute of Infectious Diseases, Tokyo, Japan
| | - Teruyuki Nagamune
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Masahiro Kawahara
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan.
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18
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Self-sorting heterodimeric coiled coil peptides with defined and tuneable self-assembly properties. Sci Rep 2015; 5:14063. [PMID: 26370878 PMCID: PMC4570195 DOI: 10.1038/srep14063] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 08/17/2015] [Indexed: 01/23/2023] Open
Abstract
Coiled coils with defined assembly properties and dissociation constants are highly attractive components in synthetic biology and for fabrication of peptide-based hybrid nanomaterials and nanostructures. Complex assemblies based on multiple different peptides typically require orthogonal peptides obtained by negative design. Negative design does not necessarily exclude formation of undesired species and may eventually compromise the stability of the desired coiled coils. This work describe a set of four promiscuous 28-residue de novo designed peptides that heterodimerize and fold into parallel coiled coils. The peptides are non-orthogonal and can form four different heterodimers albeit with large differences in affinities. The peptides display dissociation constants for dimerization spanning from the micromolar to the picomolar range. The significant differences in affinities for dimerization make the peptides prone to thermodynamic social self-sorting as shown by thermal unfolding and fluorescence experiments, and confirmed by simulations. The peptides self-sort with high fidelity to form the two coiled coils with the highest and lowest affinities for heterodimerization. The possibility to exploit self-sorting of mutually complementary peptides could hence be a viable approach to guide the assembly of higher order architectures and a powerful strategy for fabrication of dynamic and tuneable nanostructured materials.
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19
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Jones KA, Li DJ, Hui E, Sellmyer MA, Prescher JA. Visualizing cell proximity with genetically encoded bioluminescent reporters. ACS Chem Biol 2015; 10:933-8. [PMID: 25643167 DOI: 10.1021/cb5007773] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Cell-cell interactions underlie diverse physiological processes ranging from immune function to cell migration. Dysregulated cellular crosstalk also potentiates numerous pathologies, including infections and metastases. Despite their ubiquity in organismal biology, cell-cell interactions are difficult to examine in tissues and whole animals without invasive procedures. Here, we report a strategy to noninvasively image cell proximity using engineered bioluminescent probes. These tools comprise "split" fragments of Gaussia luciferase (Gluc) fused to the leucine zipper domains of Fos and Jun. When cells secreting the fragments draw near one another, Fos and Jun drive the assembly of functional, light-emitting Gluc. Photon production thus provides a readout on the distance between two cell types. We used the split fragments to visualize cell-cell interactions over time in vitro and in macroscopic models of cell migration. Further application of these tools in live organisms will refine our understanding of cell contacts relevant to basic biology and disease.
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Affiliation(s)
| | | | | | - Mark A. Sellmyer
- Department
of Radiology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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20
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Chica RA. Protein engineering in the 21st century. Protein Sci 2015; 24:431-3. [PMID: 25644972 DOI: 10.1002/pro.2656] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 01/30/2015] [Indexed: 12/24/2022]
Affiliation(s)
- Roberto A Chica
- Department of Chemistry, University of Ottawa, Ottawa, Ontario, Canada, K1N 6N5
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21
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Potapov V, Kaplan JB, Keating AE. Data-driven prediction and design of bZIP coiled-coil interactions. PLoS Comput Biol 2015; 11:e1004046. [PMID: 25695764 PMCID: PMC4335062 DOI: 10.1371/journal.pcbi.1004046] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Accepted: 11/19/2014] [Indexed: 11/18/2022] Open
Abstract
Selective dimerization of the basic-region leucine-zipper (bZIP) transcription factors presents a vivid example of how a high degree of interaction specificity can be achieved within a family of structurally similar proteins. The coiled-coil motif that mediates homo- or hetero-dimerization of the bZIP proteins has been intensively studied, and a variety of methods have been proposed to predict these interactions from sequence data. In this work, we used a large quantitative set of 4,549 bZIP coiled-coil interactions to develop a predictive model that exploits knowledge of structurally conserved residue-residue interactions in the coiled-coil motif. Our model, which expresses interaction energies as a sum of interpretable residue-pair and triplet terms, achieves a correlation with experimental binding free energies of R = 0.68 and significantly out-performs other scoring functions. To use our model in protein design applications, we devised a strategy in which synthetic peptides are built by assembling 7-residue native-protein heptad modules into new combinations. An integer linear program was used to find the optimal combination of heptads to bind selectively to a target human bZIP coiled coil, but not to target paralogs. Using this approach, we designed peptides to interact with the bZIP domains from human JUN, XBP1, ATF4 and ATF5. Testing more than 132 candidate protein complexes using a fluorescence resonance energy transfer assay confirmed the formation of tight and selective heterodimers between the designed peptides and their targets. This approach can be used to make inhibitors of native proteins, or to develop novel peptides for applications in synthetic biology or nanotechnology.
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Affiliation(s)
- Vladimir Potapov
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Jenifer B. Kaplan
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Amy E. Keating
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- * E-mail:
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22
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Negron C, Keating AE. A set of computationally designed orthogonal antiparallel homodimers that expands the synthetic coiled-coil toolkit. J Am Chem Soc 2014; 136:16544-56. [PMID: 25337788 PMCID: PMC4277747 DOI: 10.1021/ja507847t] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Indexed: 12/11/2022]
Abstract
Molecular engineering of protein assemblies, including the fabrication of nanostructures and synthetic signaling pathways, relies on the availability of modular parts that can be combined to give different structures and functions. Currently, a limited number of well-characterized protein interaction components are available. Coiled-coil interaction modules have been demonstrated to be useful for biomolecular design, and many parallel homodimers and heterodimers are available in the coiled-coil toolkit. In this work, we sought to design a set of orthogonal antiparallel homodimeric coiled coils using a computational approach. There are very few antiparallel homodimers described in the literature, and none have been measured for cross-reactivity. We tested the ability of the distance-dependent statistical potential DFIRE to predict orientation preferences for coiled-coil dimers of known structure. The DFIRE model was then combined with the CLASSY multistate protein design framework to engineer sets of three orthogonal antiparallel homodimeric coiled coils. Experimental measurements confirmed the successful design of three peptides that preferentially formed antiparallel homodimers that, furthermore, did not interact with one additional previously reported antiparallel homodimer. Two designed peptides that formed higher-order structures suggest how future design protocols could be improved. The successful designs represent a significant expansion of the existing protein-interaction toolbox for molecular engineers.
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Affiliation(s)
- Christopher Negron
- Program
in Computational and Systems Biology and Departments of Biology and Biological
Engineering, Massachusetts Institute of
Technology, 77 Massachusetts
Avenue, Cambridge, Massachusetts 021393, United States
| | - Amy E. Keating
- Program
in Computational and Systems Biology and Departments of Biology and Biological
Engineering, Massachusetts Institute of
Technology, 77 Massachusetts
Avenue, Cambridge, Massachusetts 021393, United States
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