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Rhys GG, Dawson WM, Beesley JL, Martin FJO, Brady RL, Thomson AR, Woolfson DN. How Coiled-Coil Assemblies Accommodate Multiple Aromatic Residues. Biomacromolecules 2021; 22:2010-2019. [PMID: 33881308 DOI: 10.1021/acs.biomac.1c00131] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Rational protein design requires understanding the contribution of each amino acid to a targeted protein fold. For a subset of protein structures, namely, α-helical coiled coils (CCs), knowledge is sufficiently advanced to allow the rational de novo design of many structures, including entirely new protein folds. Current CC design rules center on using aliphatic hydrophobic residues predominantly to drive the folding and assembly of amphipathic α helices. The consequences of using aromatic residues-which would be useful for introducing structural probes, and binding and catalytic functionalities-into these interfaces are not understood. There are specific examples of designed CCs containing such aromatic residues, e.g., phenylalanine-rich sequences, and the use of polar aromatic residues to make buried hydrogen-bond networks. However, it is not known generally if sequences rich in tyrosine can form CCs, or what CC assemblies these would lead to. Here, we explore tyrosine-rich sequences in a general CC-forming background and resolve new CC structures. In one of these, an antiparallel tetramer, the tyrosine residues are solvent accessible and pack at the interface between the core and the surface. In another more complex structure, the residues are buried and form an extended hydrogen-bond network.
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Affiliation(s)
- Guto G Rhys
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, United Kingdom.,Department of Biochemistry, University of Bayreuth, Universitätsstraße 30, 95447 Bayreuth, Germany
| | - William M Dawson
- 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
| | - Freddie J O Martin
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, United Kingdom
| | - 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.,Bristol BioDesign Institute, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, United Kingdom
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2
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Abstract
Protein-protein interactions and protein localization are essential mechanisms of cellular signal transduction. The ability to externally control such interactions using chemical and optogenetic methods has facilitated biological research and provided components for the engineering of cell-based therapies and materials. However, chemical and optical methods are limited in their ability to provide spatiotemporal specificity in light-scattering tissues. To overcome these limitations, we present "thermomers", modular protein dimerization domains controlled with temperature-a form of energy that can be delivered to cells both globally and locally in a wide variety of in vitro and in vivo contexts. Thermomers are based on a sharply thermolabile coiled-coil protein, which we engineered to heterodimerize at a tunable transition temperature within the biocompatible range of 37-42 °C. When fused to other proteins, thermomers can reversibly control their association, as demonstrated via membrane localization in mammalian cells. This technology enables remote control of intracellular protein-protein interactions with a form of energy that can be delivered with spatiotemporal precision in a wide range of biological, therapeutic, and living material scenarios.
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3
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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.
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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
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4
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Wang Z, Ding X, Li S, Shi J, Li Y. Engineered fluorescence tags for in vivo protein labelling. RSC Adv 2014. [DOI: 10.1039/c3ra46991c] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
In vivoprotein labelling with a peptide tag–fluorescent probe system is an important chemical biology strategy for studying protein distribution, interaction and function.
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Affiliation(s)
- Zhipeng Wang
- School of Medical Engineering
- Hefei University of Technology
- Hefei, China
- Department of Chemistry
- School of Life Sciences
| | - Xiaozhe Ding
- Department of Chemistry
- School of Life Sciences
- Tsinghua University
- Beijing 100084, China
| | - Sijian Li
- School of Medical Engineering
- Hefei University of Technology
- Hefei, China
| | - Jing Shi
- Department of Chemistry
- University of Science and Technology of China
- Hefei, China
| | - Yiming Li
- School of Medical Engineering
- Hefei University of Technology
- Hefei, China
- Department of Chemistry
- School of Life Sciences
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5
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Tsutsumi H, Nomura W, Abe S, Mino T, Masuda A, Ohashi N, Tanaka T, Ohba K, Yamamoto N, Akiyoshi K, Tamamura H. Fluorogenically active leucine zipper peptides as tag-probe pairs for protein imaging in living cells. Angew Chem Int Ed Engl 2010; 48:9164-6. [PMID: 19876989 DOI: 10.1002/anie.200903183] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Hiroshi Tsutsumi
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, Chiyoda-ku, Tokyo 101-0062, Japan
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6
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Tsutsumi H, Nomura W, Abe S, Mino T, Masuda A, Ohashi N, Tanaka T, Ohba K, Yamamoto N, Akiyoshi K, Tamamura H. Fluorogenically Active Leucine Zipper Peptides as Tag-Probe Pairs for Protein Imaging in Living Cells. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200903183] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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7
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Mizuno T, Suzuki K, Imai T, Kitade Y, Furutani Y, Kudou M, Oda M, Kandori H, Tsumoto K, Tanaka T. Manipulation of protein-complex function by using an engineered heterotrimeric coiled-coil switch. Org Biomol Chem 2009. [DOI: 10.1039/b901118h] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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8
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Mizuno T, Hasegawa C, Tanabe Y, Hamajima K, Muto T, Nishi Y, Oda M, Kobayashi Y, Tanaka T. Organic ligand binding by a hydrophobic cavity in a designed tetrameric coiled-coil protein. Chemistry 2008; 15:1491-8. [PMID: 19115294 DOI: 10.1002/chem.200800855] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The design and characterization of a hydrophobic cavity in de novo designed proteins provides a wide range of information about the functions of de novo proteins. We designed a de novo tetrameric coiled-coil protein with a hydrophobic pocketlike cavity. Tetrameric coiled coils with hydrophobic cavities have previously been reported. By replacing one Leu residue at the a position with Ala, hydrophobic cavities that did not flatten out due to loose peptide chains were reliably created. To perform a detailed examination of the ligand-binding characteristics of the cavities, we originally designed two other coiled-coil proteins: AM2, with eight Ala substitutions at the adjacent a and d positions at the center of a bundled structure, and AM2W, with one Trp and seven Ala substitutions at the same positions. To increase the association of the helical peptides, each helical peptide was connected with flexible linkers, which resulted in a single peptide chain. These proteins exhibited CD spectra corresponding to superhelical structures, despite weakened hydrophobic packing. AM2W exhibited binding affinity for size-complementary organic compounds. The dissociation constants, K(d), of AM2W were 220 nM for adamantane, 81 microM for 1-adamantanol, and 294 microM for 1-adamantaneacetic acid, as measured by fluorescence titration analyses. Although it was contrary to expectations, AM2 did not exhibit any binding affinity, probably due to structural defects around the designed hydrophobic cavity. Interestingly, AM2W exhibited incremental structure stability through ligand binding. Plugging of structural defects with organic ligands would be expected to facilitate protein folding.
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Affiliation(s)
- Toshihisa Mizuno
- Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-cho, Nagoya, Aichi, 466-8555, Japan.
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9
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Diss ML, Kennan AJ. Simultaneous directed assembly of three distinct heterodimeric coiled coils. Org Lett 2008; 10:3797-800. [PMID: 18693746 DOI: 10.1021/ol801461a] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We describe simultaneous formation of three distinct heterodimeric coiled coils from a mixture of six different peptides. The choice among electrostatically viable complexes is governed by alignment of buried core residues, including a fundamentally new interaction that exploits urea-terminated side chains. Buried urea/urea contacts lead to extremely stable dimeric coiled coils, with T(m) values between 63 and 79 degrees C. Core ureas can also form stable complexes with a variety of other polar groups, including guanidines, acids, and amides.
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Affiliation(s)
- Maria L Diss
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, USA
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10
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Marsden HR, Korobko AV, van Leeuwen ENM, Pouget EM, Veen SJ, Sommerdijk NAJM, Kros A. Noncovalent Triblock Copolymers Based on a Coiled-Coil Peptide Motif. J Am Chem Soc 2008; 130:9386-93. [DOI: 10.1021/ja800254w] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hana Robson Marsden
- Department of Soft Matter Chemistry, Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands, Soft Matter cryoTEM Research Unit, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands, and Van’t Hoff Laboratory, Debye Research Institute, Utrecht University, N-701 Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Alexander V. Korobko
- Department of Soft Matter Chemistry, Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands, Soft Matter cryoTEM Research Unit, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands, and Van’t Hoff Laboratory, Debye Research Institute, Utrecht University, N-701 Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Ellen N. M. van Leeuwen
- Department of Soft Matter Chemistry, Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands, Soft Matter cryoTEM Research Unit, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands, and Van’t Hoff Laboratory, Debye Research Institute, Utrecht University, N-701 Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Emilie M. Pouget
- Department of Soft Matter Chemistry, Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands, Soft Matter cryoTEM Research Unit, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands, and Van’t Hoff Laboratory, Debye Research Institute, Utrecht University, N-701 Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Sandra J. Veen
- Department of Soft Matter Chemistry, Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands, Soft Matter cryoTEM Research Unit, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands, and Van’t Hoff Laboratory, Debye Research Institute, Utrecht University, N-701 Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Nico A. J. M. Sommerdijk
- Department of Soft Matter Chemistry, Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands, Soft Matter cryoTEM Research Unit, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands, and Van’t Hoff Laboratory, Debye Research Institute, Utrecht University, N-701 Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Alexander Kros
- Department of Soft Matter Chemistry, Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands, Soft Matter cryoTEM Research Unit, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands, and Van’t Hoff Laboratory, Debye Research Institute, Utrecht University, N-701 Padualaan 8, 3584 CH Utrecht, The Netherlands
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11
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Sakamoto S, Kudo K. Supramolecular Control of Split-GFP Reassembly by Conjugation of β-Cyclodextrin and Coumarin Units. J Am Chem Soc 2008; 130:9574-82. [DOI: 10.1021/ja802313a] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Seiji Sakamoto
- Institute of Industrial Science, University of Tokyo, Komaba 4-6-1, Meguro-ku, Tokyo 153-8505, Japan
| | - Kazuaki Kudo
- Institute of Industrial Science, University of Tokyo, Komaba 4-6-1, Meguro-ku, Tokyo 153-8505, Japan
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12
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Grigoryan G, Keating AE. Structural specificity in coiled-coil interactions. Curr Opin Struct Biol 2008; 18:477-83. [PMID: 18555680 DOI: 10.1016/j.sbi.2008.04.008] [Citation(s) in RCA: 204] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2008] [Revised: 04/14/2008] [Accepted: 04/29/2008] [Indexed: 10/22/2022]
Abstract
Coiled coils have a rich history in the field of protein design and engineering. Novel structures, such as the first seven-helix coiled coil, continue to provide surprises and insights. Large-scale datasets quantifying the influence of systematic mutations on coiled-coil stability are a valuable new asset to the area. Scoring methods based on sequence and/or structure can predict interaction preferences in coiled-coil-mediated bZIP transcription factor dimerization. Experimental and computational methods for dealing with the near-degeneracy of many coiled-coil structures appear promising for future design applications.
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13
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Diss ML, Kennan AJ. Orthogonal recognition in dimeric coiled coils via buried polar-group modulation. J Am Chem Soc 2008; 130:1321-7. [PMID: 18171063 DOI: 10.1021/ja076265w] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We describe the design and exploration of new buried polar groups to control coiled-coil dimerization. Employing our recently described method for on-resin guanidinylation, we have prepared coiled-coil peptides with a single core guanidine, spaced from the backbone by 1-3 methylene groups. Heterodimeric mixtures of these sequences with guanidine, amide, and carboxylic acid binding partners form a large number of reasonably stable coiled coils (T(m) > or = 60 degrees C). A detailed stability trend examination reveals that asparagine/acid pairs are sharply sensitive to acid residue chain length (Asn/Asp much worse than Asn/Glu), while guanidine/acid pairs are largely insensitive. This has been exploited to create orthogonal recognition pairs which establish the capacity to form two distinct heterodimeric coiled coils by simple mixing of four different peptides. One dimer has buried core asparagines, while the other pairs aspartic acid with any of three guanidinylated side chains. Specificity of this behavior is underscored by failure of glutamic acid substituted sequences to perform accordingly. The successful alternate pairs are further characterized by various biophysical methods (circular dichroism, ultracentrifugation, thermal and chemical denaturation, affinity tags).
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Affiliation(s)
- Maria L Diss
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, USA
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14
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Mizuno T, Murao K, Tanabe Y, Oda M, Tanaka T. Metal-ion-dependent GFP emission in vivo by combining a circularly permutated green fluorescent protein with an engineered metal-ion-binding coiled-coil. J Am Chem Soc 2007; 129:11378-83. [PMID: 17722917 DOI: 10.1021/ja0685102] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Coordination of metal ions significantly contributes to protein structures and functions. Here we constructed a fusion protein, consisting of a de novo designed, metal-ion-binding, trimeric coiled-coil and a circularly permutated green fluorescent protein (cpGFP), where the fluorescent emission from cpGFP was induced by metal ion coordination to the coiled-coil. A circularly permutated GFP, (191)cpGFP(190), was constructed by connecting the original N- and C-termini of GFP(UV) by a GGSGG linker and cleaving it between Asp(190) and Gly(191). The metal-ion-binding coiled-coil, IZ-HH, was designed to have three alpha-helical structures, with 12 His residues in the hydrophobic core of the coiled-coil structure. IZ-HH exhibited an unfolded structure, whereas it formed the trimeric coiled-coil structure in the presence of divalent metal ions, such as Cu(2+), Ni(2+), or Zn(2+). The fusion protein (191)cpGFP(190)-IZ-HH was constructed, in which (191)cpGFP(190) was inserted between the second and third alpha-helices of IZ-HH. Escherichia coli cells, expressing (191)cpGFP(190)-IZ-HH, exhibited strong fluorescence when the Cu(2+) and Zn(2+) ions were present in the medium, indicating that they passed through the cell membrane and induced the proper folding of the (191)cpGFP(190) domain. This strategy, in which protein function is regulated by a metal-ion-responsive coiled-coil, should be applicable to the design of various metal-ion-responsive, nonnatural proteins that work both in vitro and in vivo.
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Affiliation(s)
- Toshihisa Mizuno
- Graduate School of Engineering, Nagoya Institute of Technology, Nagoya 466-8555, Japan.
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