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Woolfson DN. Understanding a protein fold: the physics, chemistry, and biology of α-helical coiled coils. J Biol Chem 2023; 299:104579. [PMID: 36871758 PMCID: PMC10124910 DOI: 10.1016/j.jbc.2023.104579] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 02/25/2023] [Accepted: 02/27/2023] [Indexed: 03/07/2023] Open
Abstract
Protein science is being transformed by powerful computational methods for structure prediction and design: AlphaFold2 can predict many natural protein structures from sequence, and other AI methods are enabling the de novo design of new structures. This raises a question: how much do we understand the underlying sequence-to-structure/function relationships being captured by these methods? This perspective presents our current understanding of one class of protein assembly, the α-helical coiled coils. At first sight, these are straightforward: sequence repeats of hydrophobic (h) and polar (p) residues, (hpphppp)n, direct the folding and assembly of amphipathic α helices into bundles. However, many different bundles are possible: they can have two or more helices (different oligomers); the helices can have parallel, antiparallel or mixed arrangements (different topologies); and the helical sequences can be the same (homomers) or different (heteromers). Thus, sequence-to-structure relationships must be present within the hpphppp repeats to distinguish these states. I discuss the current understanding of this problem at three levels: First, physics gives a parametric framework to generate the many possible coiled-coil backbone structures. Second, chemistry provides a means to explore and deliver sequence-to-structure relationships. Third, biology shows how coiled coils are adapted and functionalized in nature, inspiring applications of coiled coils in synthetic biology. I argue that the chemistry is largely understood; the physics is partly solved, though the considerable challenge of predicting even relative stabilities of different coiled-coil states remains; but there is much more to explore in the biology and synthetic biology of coiled coils.
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Affiliation(s)
- Derek N Woolfson
- School of Chemistry, University of Bristol, Bristol, United Kingdom; School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk, Bristol, United Kingdom; BrisEngBio, School of Chemistry, University of Bristol, Bristol, United Kingdom; Max Planck-Bristol Centre for Minimal Biology, University of Bristol, Bristol, United Kingdom.
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Xie Y, Khoo KS, Chew KW, Devadas VV, Phang SJ, Lim HR, Rajendran S, Show PL. Advancement of renewable energy technologies via artificial and microalgae photosynthesis. BIORESOURCE TECHNOLOGY 2022; 363:127830. [PMID: 36029982 DOI: 10.1016/j.biortech.2022.127830] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/19/2022] [Accepted: 08/21/2022] [Indexed: 06/15/2023]
Abstract
There has been an urgent need to tackle global climate change and replace conventional fuels with alternatives from sustainable sources. This has led to the emergence of bioenergy sources like biofuels and biohydrogen extracted from microalgae biomass. Microalgae takes up carbon dioxide and absorbs sunlight, as part of its photosynthesis process, for growth and producing useful compounds for renewable energy. While, the developments in artificial photosynthesis to a chemical process that biomimics the natural photosynthesis process to fix CO2 in the air. However, the artificial photosynthesis technology is still being investigated for its implementation in large scale production. Microalgae photosynthesis can provide the same advantages as artificial photosynthesis, along with the prospect of having final microalgae products suitable for various application. There are significant potential to adapt either microalgae photosynthesis or artificial photosynthesis to reduce the CO2 in the climate and contribute to a cleaner and green cultivation method.
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Affiliation(s)
- Youping Xie
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350108, China
| | - Kuan Shiong Khoo
- Department of Chemical Engineering and Materials Science, Yuan Ze University, Taoyuan, Taiwan
| | - Kit Wayne Chew
- School of Energy and Chemical Engineering, Xiamen University Malaysia, Jalan Sunsuria, Bandar Sunsuria, 43900 Sepang, Selangor Darul Ehsan, Malaysia
| | - Vishno Vardhan Devadas
- Department of Chemical and Environmental Engineering, Faculty of Science and Engineering, University of Nottingham Malaysia, Jalan Broga, 43500 Semenyih, Selangor Darul Ehsan, Malaysia
| | - Sue Jiun Phang
- School of Engineering and Physical Sciences, Heriot-Watt University Malaysia, Jalan Venna P5/2, Precinct 5, 62200 Putrajaya, Malaysia
| | - Hooi Ren Lim
- Department of Chemical and Environmental Engineering, Faculty of Science and Engineering, University of Nottingham Malaysia, Jalan Broga, 43500 Semenyih, Selangor Darul Ehsan, Malaysia
| | - Saravanan Rajendran
- Faculty of Engineering, Department of Mechanical Engineering, University of Tarapacá, Avda. General Velasquez, 1775 Arica, Chile
| | - Pau Loke Show
- Department of Chemical and Environmental Engineering, Faculty of Science and Engineering, University of Nottingham Malaysia, Jalan Broga, 43500 Semenyih, Selangor Darul Ehsan, Malaysia; Zhejiang Provincial Key Laboratory for Subtropical Water Environment and Marine Biological Resources Protection, Wenzhou University, Wenzhou 325035, China; Department of Sustainable Engineering, Saveetha School of Engineering, SIMATS, Chennai 602105, India.
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A bound iron porphyrin is redox active in hybrid bacterial reaction centers modified to possess a four-helix bundle domain. Photochem Photobiol Sci 2021; 21:91-99. [PMID: 34850374 DOI: 10.1007/s43630-021-00142-7] [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: 09/29/2021] [Accepted: 11/16/2021] [Indexed: 10/19/2022]
Abstract
In this paper we report the design of hybrid reaction centers with a novel redox-active cofactor. Reaction centers perform the primary photochemistry of photosynthesis, namely the light-induced transfer of an electron from the bacteriochlorophyll dimer to a series of electron acceptors. Hybrid complexes were created by the fusion of an artificial four-helix bundle to the M-subunit of the reaction center. Despite the large modification, optical spectra show that the purified hybrid reaction centers assemble as active complexes that retain the characteristic cofactor absorption peaks and are capable of light-induced charge separation. The four-helix bundle could bind iron-protoporphyrin in either a reduced and oxidized state. After binding iron-protoporphyrin to the hybrid reaction centers, light excitation results in a new derivative signal with a maximum at 402 nm and minimum at 429 nm. This signal increases in amplitude with longer light durations and persists in the dark. No signal is observed when iron-protoporphyrin is added to reaction centers without the four-helix bundle domain or when a redox-inactive zinc-protoporphyrin is bound. The results are consistent with the signal arising from a new redox reaction, electron transfer from the iron-protoporphyrin to the oxidized bacteriochlorophyll dimer. These outcomes demonstrate the feasibility of binding porphyrins to the hybrid reaction centers to gain new light-driven functions.
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Edgell CL, Savery NJ, Woolfson DN. Robust De Novo-Designed Homotetrameric Coiled Coils. Biochemistry 2020; 59:1087-1092. [DOI: 10.1021/acs.biochem.0c00082] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Caitlin L. Edgell
- School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, United Kingdom
| | - Nigel J. Savery
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, United Kingdom
- BrisSynBio, University of Bristol, Life Sciences Building, Bristol BS8 1TQ, United Kingdom
| | - Derek N. Woolfson
- School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
- School of Biochemistry, University of Bristol, Bristol BS8 1TD, United Kingdom
- BrisSynBio, University of Bristol, Life Sciences Building, Bristol BS8 1TQ, United Kingdom
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Edgell CL, Smith AJ, Beesley JL, Savery NJ, Woolfson DN. De Novo Designed Protein-Interaction Modules for In-Cell Applications. ACS Synth Biol 2020; 9:427-436. [PMID: 31977192 DOI: 10.1021/acssynbio.9b00453] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Protein-protein interactions control a wide variety of natural biological processes. α-Helical coiled coils frequently mediate such protein-protein interactions. Due to the relative simplicity of their sequences and structures and the ease with which properties such as strength and specificity of interaction can be controlled, coiled coils can be designed de novo to deliver a variety of non-natural protein-protein interaction domains. Herein, several de novo designed coiled coils are tested for their ability to mediate protein-protein interactions in Escherichia coli cells. The set includes a parallel homodimer, a parallel homotetramer, an antiparallel homotetramer, and a newly designed heterotetramer, all of which have been characterized in vitro by biophysical and structural methods. Using a transcription repression assay based on reconstituting the Lac repressor, we find that the modules behave as designed in the cellular environment. Each design imparts a different property to the resulting Lac repressor-coiled coil complexes, resulting in the benefit of being able to reconfigure the system in multiple ways. Modification of the system also allows the interactions to be controlled: assembly can be tuned by controlling the expression of the constituent components, and complexes can be disrupted through helix sequestration. The small and straightforward de novo designed components that we deliver are highly versatile and have considerable potential as protein-protein interaction domains in synthetic biology where proteins must be assembled in highly specific ways. The relative simplicity of the designs makes them amenable to future modifications to introduce finer control over their assembly and to adapt them for different contexts.
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Affiliation(s)
- Caitlin L. Edgell
- School of Chemistry, University of Bristol, Bristol, BS8 1TS, United Kingdom
- School of Biochemistry, University of Bristol, Bristol, BS8 1TD, United Kingdom
| | - Abigail J. Smith
- School of Biochemistry, University of Bristol, Bristol, BS8 1TD, United Kingdom
- BrisSynBio, Life Sciences Building, University of Bristol, Bristol, BS8 1TQ, United Kingdom
| | - Joseph L. Beesley
- School of Chemistry, University of Bristol, Bristol, BS8 1TS, United Kingdom
| | - Nigel J. Savery
- School of Biochemistry, University of Bristol, Bristol, BS8 1TD, United Kingdom
- BrisSynBio, Life Sciences Building, University of Bristol, Bristol, BS8 1TQ, United Kingdom
| | - Derek N. Woolfson
- School of Chemistry, University of Bristol, Bristol, BS8 1TS, United Kingdom
- School of Biochemistry, University of Bristol, Bristol, BS8 1TD, United Kingdom
- BrisSynBio, Life Sciences Building, University of Bristol, Bristol, BS8 1TQ, United Kingdom
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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.
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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
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Swainsbury DJK, Scheidelaar S, Foster N, van Grondelle R, Killian JA, Jones MR. The effectiveness of styrene-maleic acid (SMA) copolymers for solubilisation of integral membrane proteins from SMA-accessible and SMA-resistant membranes. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2017; 1859:2133-2143. [PMID: 28751090 PMCID: PMC5593810 DOI: 10.1016/j.bbamem.2017.07.011] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2017] [Revised: 07/14/2017] [Accepted: 07/23/2017] [Indexed: 11/27/2022]
Abstract
Solubilisation of biological lipid bilayer membranes for analysis of their protein complement has traditionally been carried out using detergents, but there is increasing interest in the use of amphiphilic copolymers such as styrene maleic acid (SMA) for the solubilisation, purification and characterisation of integral membrane proteins in the form of protein/lipid nanodiscs. Here we survey the effectiveness of various commercially-available formulations of the SMA copolymer in solubilising Rhodobacter sphaeroides reaction centres (RCs) from photosynthetic membranes. We find that formulations of SMA with a 2:1 or 3:1 ratio of styrene to maleic acid are almost as effective as detergent in solubilising RCs, with the best solubilisation by short chain variants (<30kDa weight average molecular weight). The effectiveness of 10kDa 2:1 and 3:1 formulations of SMA to solubilise RCs gradually declined when genetically-encoded coiled-coil bundles were used to artificially tether normally monomeric RCs into dimeric, trimeric and tetrameric multimers. The ability of SMA to solubilise reaction centre-light harvesting 1 (RC-LH1) complexes from densely packed and highly ordered photosynthetic membranes was uniformly low, but could be increased through a variety of treatments to increase the lipid:protein ratio. However, proteins isolated from such membranes comprised clusters of complexes in small membrane patches rather than individual proteins. We conclude that short-chain 2:1 and 3:1 formulations of SMA are the most effective in solubilising integral membrane proteins, but that solubilisation efficiencies are strongly influenced by the size of the target protein and the density of packing of proteins in the membrane.
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Affiliation(s)
- David J K Swainsbury
- School of Biochemistry, University of Bristol, Biomedical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom
| | - Stefan Scheidelaar
- Membrane Biochemistry & Biophysics, Utrecht University, Bijvoet Center for Biomolecular Research, Utrecht, The Netherlands
| | - Nicholas Foster
- School of Biochemistry, University of Bristol, Biomedical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom
| | - Rienk van Grondelle
- Division of Physics and Astronomy, VU University Amsterdam, De Boelelaan 1081, Amsterdam 1081 HV, The Netherlands
| | - J Antoinette Killian
- Membrane Biochemistry & Biophysics, Utrecht University, Bijvoet Center for Biomolecular Research, Utrecht, The Netherlands
| | - Michael R Jones
- School of Biochemistry, University of Bristol, Biomedical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom.
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