1
|
Serrano GP, Echavarría CF, Mejias SH. Development of artificial photosystems based on designed proteins for mechanistic insights into photosynthesis. Protein Sci 2024; 33:e5164. [PMID: 39276008 PMCID: PMC11400635 DOI: 10.1002/pro.5164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2024] [Revised: 08/14/2024] [Accepted: 08/19/2024] [Indexed: 09/16/2024]
Abstract
This review aims to provide an overview of the progress in protein-based artificial photosystem design and their potential to uncover the underlying principles governing light-harvesting in photosynthesis. While significant advances have been made in this area, a gap persists in reviewing these advances. This review provides a perspective of the field, pinpointing knowledge gaps and unresolved challenges that warrant further inquiry. In particular, it delves into the key considerations when designing photosystems based on the chromophore and protein scaffold characteristics, presents the established strategies for artificial photosystems engineering with their advantages and disadvantages, and underscores the recent breakthroughs in understanding the molecular mechanisms governing light-harvesting, charge separation, and the role of the protein motions in the chromophore's excited state relaxation. By disseminating this knowledge, this article provides a foundational resource for defining the field of bio-hybrid photosystems and aims to inspire the continued exploration of artificial photosystems using protein design.
Collapse
Affiliation(s)
- Gonzalo Pérez Serrano
- Madrid Institute for Advanced Studies (IMDEA‐Nanoscience)Ciudad Universitaria de CantoblancoMadridSpain
| | - Claudia F. Echavarría
- Madrid Institute for Advanced Studies (IMDEA‐Nanoscience)Ciudad Universitaria de CantoblancoMadridSpain
| | - Sara H. Mejias
- Madrid Institute for Advanced Studies (IMDEA‐Nanoscience)Ciudad Universitaria de CantoblancoMadridSpain
| |
Collapse
|
2
|
Ennist NM, Wang S, Kennedy MA, Curti M, Sutherland GA, Vasilev C, Redler RL, Maffeis V, Shareef S, Sica AV, Hua AS, Deshmukh AP, Moyer AP, Hicks DR, Swartz AZ, Cacho RA, Novy N, Bera AK, Kang A, Sankaran B, Johnson MP, Phadkule A, Reppert M, Ekiert D, Bhabha G, Stewart L, Caram JR, Stoddard BL, Romero E, Hunter CN, Baker D. De novo design of proteins housing excitonically coupled chlorophyll special pairs. Nat Chem Biol 2024; 20:906-915. [PMID: 38831036 PMCID: PMC11213709 DOI: 10.1038/s41589-024-01626-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Accepted: 04/15/2024] [Indexed: 06/05/2024]
Abstract
Natural photosystems couple light harvesting to charge separation using a 'special pair' of chlorophyll molecules that accepts excitation energy from the antenna and initiates an electron-transfer cascade. To investigate the photophysics of special pairs independently of the complexities of native photosynthetic proteins, and as a first step toward creating synthetic photosystems for new energy conversion technologies, we designed C2-symmetric proteins that hold two chlorophyll molecules in closely juxtaposed arrangements. X-ray crystallography confirmed that one designed protein binds two chlorophylls in the same orientation as native special pairs, whereas a second designed protein positions them in a previously unseen geometry. Spectroscopy revealed that the chlorophylls are excitonically coupled, and fluorescence lifetime imaging demonstrated energy transfer. The cryo-electron microscopy structure of a designed 24-chlorophyll octahedral nanocage with a special pair on each edge closely matched the design model. The results suggest that the de novo design of artificial photosynthetic systems is within reach of current computational methods.
Collapse
Affiliation(s)
- Nathan M Ennist
- Institute for Protein Design, University of Washington, Seattle, WA, USA.
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
| | - Shunzhi Wang
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Madison A Kennedy
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Mariano Curti
- Institute of Chemical Research of Catalonia (ICIQ-CERCA), Barcelona Institute of Science and Technology (BIST), Tarragona, Spain
| | | | | | - Rachel L Redler
- Department of Cell Biology and Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY, USA
| | - Valentin Maffeis
- Institute of Chemical Research of Catalonia (ICIQ-CERCA), Barcelona Institute of Science and Technology (BIST), Tarragona, Spain
| | - Saeed Shareef
- Institute of Chemical Research of Catalonia (ICIQ-CERCA), Barcelona Institute of Science and Technology (BIST), Tarragona, Spain
- Departament de Química Física i Inorgànica, Universitat Rovira i Virgili, Tarragona, Spain
| | - Anthony V Sica
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Ash Sueh Hua
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Arundhati P Deshmukh
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Adam P Moyer
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Derrick R Hicks
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Avi Z Swartz
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Ralph A Cacho
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Nathan Novy
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Asim K Bera
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Alex Kang
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Banumathi Sankaran
- Molecular Biophysics and Integrated Bioimaging, Berkeley Center for Structural Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | - Amala Phadkule
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
| | - Mike Reppert
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
| | - Damian Ekiert
- Department of Cell Biology and Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY, USA
- Department of Microbiology, New York University School of Medicine, New York, NY, USA
| | - Gira Bhabha
- Department of Cell Biology and Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY, USA
| | - Lance Stewart
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Justin R Caram
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Barry L Stoddard
- Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Elisabet Romero
- Institute of Chemical Research of Catalonia (ICIQ-CERCA), Barcelona Institute of Science and Technology (BIST), Tarragona, Spain
| | - C Neil Hunter
- School of Biosciences, University of Sheffield, Sheffield, UK
| | - David Baker
- Institute for Protein Design, University of Washington, Seattle, WA, USA.
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
| |
Collapse
|
3
|
Ennist N, Wang S, Kennedy M, Curti M, Sutherland G, Vasilev C, Redler R, Maffeis V, Shareef S, Sica A, Hua A, Deshmukh A, Moyer A, Hicks D, Swartz A, Cacho R, Novy N, Bera A, Kang A, Sankaran B, Johnson M, Reppert M, Ekiert D, Bhabha G, Stewart L, Caram J, Stoddard B, Romero E, Hunter CN, Baker D. De novo design of energy transfer proteins housing excitonically coupled chlorophyll special pairs. RESEARCH SQUARE 2023:rs.3.rs-2736786. [PMID: 37131790 PMCID: PMC10153362 DOI: 10.21203/rs.3.rs-2736786/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Natural photosystems couple light harvesting to charge separation using a "special pair" of chlorophyll molecules that accepts excitation energy from the antenna and initiates an electron-transfer cascade. To investigate the photophysics of special pairs independent of complexities of native photosynthetic proteins, and as a first step towards synthetic photosystems for new energy conversion technologies, we designed C2-symmetric proteins that precisely position chlorophyll dimers. X-ray crystallography shows that one designed protein binds two chlorophylls in a binding orientation matching native special pairs, while a second positions them in a previously unseen geometry. Spectroscopy reveals excitonic coupling, and fluorescence lifetime imaging demonstrates energy transfer. We designed special pair proteins to assemble into 24-chlorophyll octahedral nanocages; the design model and cryo-EM structure are nearly identical. The design accuracy and energy transfer function of these special pair proteins suggest that de novo design of artificial photosynthetic systems is within reach of current computational methods.
Collapse
Affiliation(s)
| | | | | | - Mariano Curti
- Institute of Chemical Research of Catalonia (ICIQ-CERCA)
| | | | | | | | | | - Saeed Shareef
- Institute of Chemical Research of Catalonia (ICIQ-CERCA)
| | | | - Ash Hua
- University of California, Los Angeles
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
4
|
Hanreich S, Bonandi E, Drienovská I. Design of Artificial Enzymes: Insights into Protein Scaffolds. Chembiochem 2023; 24:e202200566. [PMID: 36418221 DOI: 10.1002/cbic.202200566] [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: 09/27/2022] [Revised: 11/18/2022] [Accepted: 11/21/2022] [Indexed: 11/25/2022]
Abstract
The design of artificial enzymes has emerged as a promising tool for the generation of potent biocatalysts able to promote new-to-nature reactions with improved catalytic performances, providing a powerful platform for wide-ranging applications and a better understanding of protein functions and structures. The selection of an appropriate protein scaffold plays a key role in the design process. This review aims to give a general overview of the most common protein scaffolds that can be exploited for the generation of artificial enzymes. Several examples are discussed and categorized according to the strategy used for the design of the artificial biocatalyst, namely the functionalization of natural enzymes, the creation of a new catalytic site in a protein scaffold bearing a wide hydrophobic pocket and de novo protein design. The review is concluded by a comparison of these different methods and by our perspective on the topic.
Collapse
Affiliation(s)
- Stefanie Hanreich
- Department of Chemistry and Pharmaceutical Sciences Vrije Universiteit, Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam (The, Netherlands
| | - Elisa Bonandi
- Department of Chemistry and Pharmaceutical Sciences Vrije Universiteit, Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam (The, Netherlands
| | - Ivana Drienovská
- Department of Chemistry and Pharmaceutical Sciences Vrije Universiteit, Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam (The, Netherlands
| |
Collapse
|
5
|
Abstract
Biological pigment-protein complexes (PPCs) exhibit a remarkable ability to tune the optical properties of biological excitons (bioexcitons) through specific pigment-protein interactions. While such fine-tuning allows natural systems (e.g., photosynthetic proteins) to carry out their native functions with near-optimal performance, native function itself is often suboptimal for applications such as biofuel production or quantum technology development. This perspective offers a look at near-term prospects for the rational reoptimization of PPC bioexcitons for new functions using site-directed mutagenesis. The primary focus is on the "structure-spectrum" challenge of understanding the relationships between structural features and spectroscopic properties. While recent examples demonstrate that site-directed mutagenesis can be used to tune nearly all key bioexciton parameters (e.g., site energies, interpigment couplings, and electronic-vibrational interactions), critical challenges remain before we achieve truly rational design of bioexciton properties.
Collapse
Affiliation(s)
- Mike Reppert
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| |
Collapse
|
6
|
Curti M, Maffeis V, Teixeira Alves Duarte LG, Shareef S, Hallado LX, Curutchet C, Romero E. Engineering excitonically coupled dimers in an artificial protein for light harvesting via computational modeling. Protein Sci 2023; 32:e4579. [PMID: 36715022 PMCID: PMC9951196 DOI: 10.1002/pro.4579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 01/23/2023] [Accepted: 01/25/2023] [Indexed: 01/31/2023]
Abstract
In photosynthesis, pigment-protein complexes achieve outstanding photoinduced charge separation efficiencies through a set of strategies in which excited states delocalization over multiple pigments ("excitons") and charge-transfer states play key roles. These concepts, and their implementation in bioinspired artificial systems, are attracting increasing attention due to the vast potential that could be tapped by realizing efficient photochemical reactions. In particular, de novo designed proteins provide a diverse structural toolbox that can be used to manipulate the geometric and electronic properties of bound chromophore molecules. However, achieving excitonic and charge-transfer states requires closely spaced chromophores, a non-trivial aspect since a strong binding with the protein matrix needs to be maintained. Here, we show how a general-purpose artificial protein can be optimized via molecular dynamics simulations to improve its binding capacity of a chlorophyll derivative, achieving complexes in which chromophores form two closely spaced and strongly interacting dimers. Based on spectroscopy results and computational modeling, we demonstrate each dimer is excitonically coupled, and propose they display signatures of charge-transfer state mixing. This work could open new avenues for the rational design of chromophore-protein complexes with advanced functionalities.
Collapse
Affiliation(s)
- Mariano Curti
- Institute of Chemical Research of Catalonia (ICIQ), Barcelona Institute of Science and Technology (BIST)TarragonaSpain
| | - Valentin Maffeis
- Institute of Chemical Research of Catalonia (ICIQ), Barcelona Institute of Science and Technology (BIST)TarragonaSpain
- Laboratoire de Chimie, UMR 5182, ENS Lyon, CNRSUniversité Lyon 1LyonFrance
| | | | - Saeed Shareef
- Institute of Chemical Research of Catalonia (ICIQ), Barcelona Institute of Science and Technology (BIST)TarragonaSpain
- Departament de Química Física i InorgànicaUniversitat Rovira i VirgiliTarragonaSpain
| | - Luisa Xiomara Hallado
- Institute of Chemical Research of Catalonia (ICIQ), Barcelona Institute of Science and Technology (BIST)TarragonaSpain
- Departament de Química Física i InorgànicaUniversitat Rovira i VirgiliTarragonaSpain
| | - Carles Curutchet
- Departament de Farmàcia i Tecnologia Farmacèutica i Fisicoquímica, Facultat de Farmàcia i Ciències de l'AlimentacióUniversitat de Barcelona (UB)BarcelonaSpain
- Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona (UB)BarcelonaSpain
| | - Elisabet Romero
- Institute of Chemical Research of Catalonia (ICIQ), Barcelona Institute of Science and Technology (BIST)TarragonaSpain
| |
Collapse
|
7
|
Hancock AM, Swainsbury DJK, Meredith SA, Morigaki K, Hunter CN, Adams PG. Enhancing the spectral range of plant and bacterial light-harvesting pigment-protein complexes with various synthetic chromophores incorporated into lipid vesicles. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 2022; 237:112585. [PMID: 36334507 DOI: 10.1016/j.jphotobiol.2022.112585] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 09/16/2022] [Accepted: 10/11/2022] [Indexed: 11/06/2022]
Abstract
The Light-Harvesting (LH) pigment-protein complexes found in photosynthetic organisms have the role of absorbing solar energy with high efficiency and transferring it to reaction centre complexes. LH complexes contain a suite of pigments that each absorb light at specific wavelengths, however, the natural combinations of pigments within any one protein complex do not cover the full range of solar radiation. Here, we provide an in-depth comparison of the relative effectiveness of five different organic "dye" molecules (Texas Red, ATTO, Cy7, DiI, DiR) for enhancing the absorption range of two different LH membrane protein complexes (the major LHCII from plants and LH2 from purple phototrophic bacteria). Proteoliposomes were self-assembled from defined mixtures of lipids, proteins and dye molecules and their optical properties were quantified by absorption and fluorescence spectroscopy. Both lipid-linked dyes and alternative lipophilic dyes were found to be effective excitation energy donors to LH protein complexes, without the need for direct chemical or generic modification of the proteins. The Förster theory parameters (e.g., spectral overlap) were compared between each donor-acceptor combination and found to be good predictors of an effective dye-protein combination. At the highest dye-to-protein ratios tested (over 20:1), the effective absorption strength integrated over the full spectral range was increased to ∼180% of its natural level for both LH complexes. Lipophilic dyes could be inserted into pre-formed membranes although their effectiveness was found to depend upon favourable physicochemical interactions. Finally, we demonstrated that these dyes can also be effective at increasing the spectral range of surface-supported models of photosynthetic membranes, using fluorescence microscopy. The results of this work provide insight into the utility of self-assembled lipid membranes and the great flexibility of LH complexes for interacting with different dyes.
Collapse
Affiliation(s)
- Ashley M Hancock
- School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, UK; Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - David J K Swainsbury
- School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK; School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK
| | - Sophie A Meredith
- School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, UK; Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Kenichi Morigaki
- Graduate School of Agricultural Science and Biosignal Research Center, Kobe University, Rokkodaicho 1-1, Nada, Kobe 657-8501, Japan
| | - C Neil Hunter
- School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Peter G Adams
- School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, UK; Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK.
| |
Collapse
|
8
|
Qing R, Hao S, Smorodina E, Jin D, Zalevsky A, Zhang S. Protein Design: From the Aspect of Water Solubility and Stability. Chem Rev 2022; 122:14085-14179. [PMID: 35921495 PMCID: PMC9523718 DOI: 10.1021/acs.chemrev.1c00757] [Citation(s) in RCA: 56] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Indexed: 12/13/2022]
Abstract
Water solubility and structural stability are key merits for proteins defined by the primary sequence and 3D-conformation. Their manipulation represents important aspects of the protein design field that relies on the accurate placement of amino acids and molecular interactions, guided by underlying physiochemical principles. Emulated designer proteins with well-defined properties both fuel the knowledge-base for more precise computational design models and are used in various biomedical and nanotechnological applications. The continuous developments in protein science, increasing computing power, new algorithms, and characterization techniques provide sophisticated toolkits for solubility design beyond guess work. In this review, we summarize recent advances in the protein design field with respect to water solubility and structural stability. After introducing fundamental design rules, we discuss the transmembrane protein solubilization and de novo transmembrane protein design. Traditional strategies to enhance protein solubility and structural stability are introduced. The designs of stable protein complexes and high-order assemblies are covered. Computational methodologies behind these endeavors, including structure prediction programs, machine learning algorithms, and specialty software dedicated to the evaluation of protein solubility and aggregation, are discussed. The findings and opportunities for Cryo-EM are presented. This review provides an overview of significant progress and prospects in accurate protein design for solubility and stability.
Collapse
Affiliation(s)
- Rui Qing
- State
Key Laboratory of Microbial Metabolism, School of Life Sciences and
Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- Media
Lab, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- The
David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Shilei Hao
- Media
Lab, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- Key
Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400030, China
| | - Eva Smorodina
- Department
of Immunology, University of Oslo and Oslo
University Hospital, Oslo 0424, Norway
| | - David Jin
- Avalon GloboCare
Corp., Freehold, New Jersey 07728, United States
| | - Arthur Zalevsky
- Laboratory
of Bioinformatics Approaches in Combinatorial Chemistry and Biology, Shemyakin−Ovchinnikov Institute of Bioorganic
Chemistry RAS, Moscow 117997, Russia
| | - Shuguang Zhang
- Media
Lab, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| |
Collapse
|
9
|
Ennist NM, Stayrook SE, Dutton PL, Moser CC. Rational design of photosynthetic reaction center protein maquettes. Front Mol Biosci 2022; 9:997295. [PMID: 36213121 PMCID: PMC9532970 DOI: 10.3389/fmolb.2022.997295] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 08/18/2022] [Indexed: 11/20/2022] Open
Abstract
New technologies for efficient solar-to-fuel energy conversion will help facilitate a global shift from dependence on fossil fuels to renewable energy. Nature uses photosynthetic reaction centers to convert photon energy into a cascade of electron-transfer reactions that eventually produce chemical fuel. The design of new reaction centers de novo deepens our understanding of photosynthetic charge separation and may one day allow production of biofuels with higher thermodynamic efficiency than natural photosystems. Recently, we described the multi-step electron-transfer activity of a designed reaction center maquette protein (the RC maquette), which can assemble metal ions, tyrosine, a Zn tetrapyrrole, and heme into an electron-transport chain. Here, we detail our modular strategy for rational protein design and show that the intended RC maquette design agrees with crystal structures in various states of assembly. A flexible, dynamic apo-state collapses by design into a more ordered holo-state upon cofactor binding. Crystal structures illustrate the structural transitions upon binding of different cofactors. Spectroscopic assays demonstrate that the RC maquette binds various electron donors, pigments, and electron acceptors with high affinity. We close with a critique of the present RC maquette design and use electron-tunneling theory to envision a path toward a designed RC with a substantially higher thermodynamic efficiency than natural photosystems.
Collapse
Affiliation(s)
- Nathan M. Ennist
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, United States
- Institute for Protein Design, University of Washington, Seattle, WA, United States
- Department of Biochemistry, University of Washington, Seattle, WA, United States
- *Correspondence: Nathan M. Ennist,
| | - Steven E. Stayrook
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, United States
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, United States
- Yale Cancer Biology Institute, Yale University West Campus, West Haven, CT, United States
| | - P. Leslie Dutton
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, United States
| | - Christopher C. Moser
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, United States
| |
Collapse
|
10
|
Ennist NM, Zhao Z, Stayrook SE, Discher BM, Dutton PL, Moser CC. De novo protein design of photochemical reaction centers. Nat Commun 2022; 13:4937. [PMID: 35999239 PMCID: PMC9399245 DOI: 10.1038/s41467-022-32710-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 08/12/2022] [Indexed: 11/09/2022] Open
Abstract
Natural photosynthetic protein complexes capture sunlight to power the energetic catalysis that supports life on Earth. Yet these natural protein structures carry an evolutionary legacy of complexity and fragility that encumbers protein reengineering efforts and obfuscates the underlying design rules for light-driven charge separation. De novo development of a simplified photosynthetic reaction center protein can clarify practical engineering principles needed to build new enzymes for efficient solar-to-fuel energy conversion. Here, we report the rational design, X-ray crystal structure, and electron transfer activity of a multi-cofactor protein that incorporates essential elements of photosynthetic reaction centers. This highly stable, modular artificial protein framework can be reconstituted in vitro with interchangeable redox centers for nanometer-scale photochemical charge separation. Transient absorption spectroscopy demonstrates Photosystem II-like tyrosine and metal cluster oxidation, and we measure charge separation lifetimes exceeding 100 ms, ideal for light-activated catalysis. This de novo-designed reaction center builds upon engineering guidelines established for charge separation in earlier synthetic photochemical triads and modified natural proteins, and it shows how synthetic biology may lead to a new generation of genetically encoded, light-powered catalysts for solar fuel production.
Collapse
Affiliation(s)
- Nathan M Ennist
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, 19104-6058, USA. .,Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA. .,Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA.
| | - Zhenyu Zhao
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, 19104-6058, USA
| | - Steven E Stayrook
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, 19104-6058, USA.,Department of Pharmacology, Yale University School of Medicine, New Haven, CT, 06510, USA.,Yale Cancer Biology Institute, Yale University West Campus, West Haven, CT, 06516, USA
| | - Bohdana M Discher
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, 19104-6058, USA
| | - P Leslie Dutton
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, 19104-6058, USA
| | - Christopher C Moser
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, 19104-6058, USA
| |
Collapse
|
11
|
Lebedeva NS, Koifman OI. Supramolecular Systems Based on Macrocyclic Compounds with Proteins: Application Prospects. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2022. [DOI: 10.1134/s1068162022010071] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
|
12
|
Lishchuk A, Csányi E, Darroch B, Wilson C, Nabok A, Leggett GJ. Active control of strong plasmon-exciton coupling in biomimetic pigment-polymer antenna complexes grown by surface-initiated polymerisation from gold nanostructures. Chem Sci 2022; 13:2405-2417. [PMID: 35310503 PMCID: PMC8864694 DOI: 10.1039/d1sc05842h] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 02/03/2022] [Indexed: 11/24/2022] Open
Abstract
Plexcitonic antenna complexes, inspired by photosynthetic light-harvesting complexes, are formed by attachment of chlorophylls (Chl) to poly(cysteine methacrylate) (PCysMA) scaffolds grown by atom-transfer radical polymerisation from gold nanostructure arrays. In these pigment–polymer antenna complexes, localised surface plasmon resonances on gold nanostructures are strongly coupled to Chl excitons, yielding hybrid light–matter states (plexcitons) that are manifested in splitting of the plasmon band. Modelling of the extinction spectra of these systems using a simple coupled oscillator model indicates that their coupling energies are up to twice as large as those measured for LHCs from plants and bacteria. Coupling energies are correlated with the exciton density in the grafted polymer layer, consistent with the collective nature of strong plasmon–exciton coupling. Steric hindrance in fully-dense PCysMA brushes limits binding of bulky chlorophylls, but the chlorophyll concentration can be increased to ∼2 M, exceeding that in biological light-harvesting complexes, by controlling the grafting density and polymerisation time. Moreover, synthetic plexcitonic antenna complexes display pH- and temperature-responsiveness, facilitating active control of plasmon–exciton coupling. Because of the wide range of compatible polymer chemistries and the mild reaction conditions, plexcitonic antenna complexes may offer a versatile route to programmable molecular photonic materials. Excitons in pigment–polymer antenna complexes formed by attachment of chlorophyll to surface grafted polymers are coupled strongly to plasmon modes, with coupling energies twice those for biological light-harvesting complexes and active control of plasmon–exciton coupling.![]()
Collapse
Affiliation(s)
- Anna Lishchuk
- Department of Chemistry, University of Sheffield Brook Hill Sheffield S3 7HF UK
| | - Evelin Csányi
- Department of Chemistry, University of Sheffield Brook Hill Sheffield S3 7HF UK
| | - Brice Darroch
- Department of Chemistry, University of Sheffield Brook Hill Sheffield S3 7HF UK
| | - Chloe Wilson
- Department of Chemistry, University of Sheffield Brook Hill Sheffield S3 7HF UK
| | - Alexei Nabok
- Materials and Engineering Research Institute, Sheffield Hallam University City Campus Sheffield S1 1WB UK
| | - Graham J Leggett
- Department of Chemistry, University of Sheffield Brook Hill Sheffield S3 7HF UK
| |
Collapse
|
13
|
Lemon CM, Marletta MA. Designer Heme Proteins: Achieving Novel Function with Abiological Heme Analogues. Acc Chem Res 2021; 54:4565-4575. [PMID: 34890183 PMCID: PMC8754152 DOI: 10.1021/acs.accounts.1c00588] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Heme proteins have proven to be a convenient platform for the development of designer proteins with novel functionalities. This is achieved by substituting the native iron porphyrin cofactor with a heme analogue that possesses the desired properties. Replacing the iron center of the porphyrin with another metal provides one inroad to novel protein function. A less explored approach is substitution of the porphyrin cofactor with an alternative tetrapyrrole macrocycle or a related ligand. In general, these ligands exhibit chemical properties and reactivity that are distinct from those of porphyrins. While these techniques have most prominently been utilized to develop artificial metalloenzymes, there are many other applications of this methodology to problems in biochemistry, health, and medicine. Incorporation of synthetic cofactors into protein environments represents a facile way to impart water solubility and biocompatibility. It circumvents the laborious synthesis of water-soluble cofactors, which often introduces substantial charge that leads to undesired bioaccumulation. To this end, the incorporation of unnatural cofactors in heme proteins has enabled the development of designer proteins as optical oxygen sensors, MRI contrast agents, spectroscopic probes, tools to interrogate protein function, antibiotics, and fluorescent proteins.Incorporation of an artificial cofactor is frequently accomplished by denaturing the holoprotein with removal of the heme; the refolded apoprotein is then reconstituted with the artificial cofactor. This process often results in substantial protein loss and does not necessarily guarantee that the refolded protein adopts the native structure. To circumvent these issues, our laboratory has pioneered the use of the RP523 strain of E. coli to incorporate artificial cofactors into heme proteins using expression-based methods. This strain lacks the ability to biosynthesize heme, and the bacterial cell wall is permeable to heme and related molecules. In this way, heme analogues supplemented in the growth medium are incorporated into heme proteins. This approach can also be leveraged for the direct expression of the apoprotein for subsequent reconstitution.These methodologies have been exploited to incorporate non-native cofactors into heme proteins that are resistant to harsh environmental conditions: the heme nitric oxide/oxygen binding protein (H-NOX) from Caldanaerobacter subterraneus (Cs) and the heme acquisition system protein A (HasA) from Pseudomonas aeruginosa (Pa). The exceptional stability of these proteins makes them ideal scaffolds for biomedical applications. Optical oxygen sensing has been accomplished using a phosphorescent ruthenium porphyrin as the artificial heme cofactor. Paramagnetic manganese and gadolinium porphyrins yield high-relaxivity, protein-based MRI contrast agents. A fluorescent phosphorus corrole serves as a heme analogue to produce fluorescent proteins. Iron complexes of nonporphyrin cofactors bound to HasA inhibit the growth of pathogenic bacteria. Moreover, HasA can deliver a gallium phthalocyanine into the bacterial cytosol to serve as a sensitizer for photochemical sterilization. Together, these examples illustrate the potential for designer heme proteins to address burgeoning problems in the areas of health and medicine. The concepts and methodologies presented in this Account can be extended to the development of next-generation biomedical sensing and imaging agents to identify and quantify clinically relevant metabolites and other key disease biomarkers.
Collapse
|
14
|
Bialas D, Kirchner E, Röhr MIS, Würthner F. Perspectives in Dye Chemistry: A Rational Approach toward Functional Materials by Understanding the Aggregate State. J Am Chem Soc 2021; 143:4500-4518. [DOI: 10.1021/jacs.0c13245] [Citation(s) in RCA: 87] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- David Bialas
- Center for Nanosystems Chemistry, Universität Würzburg, Theodor-Boveri-Weg, 97074 Würzburg, Germany
- Institut für Organische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Eva Kirchner
- Institut für Organische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Merle I. S. Röhr
- Center for Nanosystems Chemistry, Universität Würzburg, Theodor-Boveri-Weg, 97074 Würzburg, Germany
| | - Frank Würthner
- Center for Nanosystems Chemistry, Universität Würzburg, Theodor-Boveri-Weg, 97074 Würzburg, Germany
- Institut für Organische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
| |
Collapse
|
15
|
Ferrando J, Solomon LA. Recent Progress Using De Novo Design to Study Protein Structure, Design and Binding Interactions. Life (Basel) 2021; 11:life11030225. [PMID: 33802210 PMCID: PMC7999464 DOI: 10.3390/life11030225] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 03/04/2021] [Accepted: 03/05/2021] [Indexed: 12/14/2022] Open
Abstract
De novo protein design is a powerful methodology used to study natural functions in an artificial-protein context. Since its inception, it has been used to reproduce a plethora of reactions and uncover biophysical principles that are often difficult to extract from direct studies of natural proteins. Natural proteins are capable of assuming a variety of different structures and subsequently binding ligands at impressively high levels of both specificity and affinity. Here, we will review recent examples of de novo design studies on binding reactions for small molecules, nucleic acids, and the formation of protein-protein interactions. We will then discuss some new structural advances in the field. Finally, we will discuss some advancements in computational modeling and design approaches and provide an overview of some modern algorithmic tools being used to design these proteins.
Collapse
Affiliation(s)
- Juan Ferrando
- Department of Biology, George Mason University, 4400 University Dr, Fairfax, VA 22030, USA;
| | - Lee A. Solomon
- Department of Chemistry and Biochemistry, George Mason University, 10920 George Mason Circle, Manassas, VA 20110, USA
- Correspondence: ; Tel.: +703-993-6418
| |
Collapse
|
16
|
Klein AS, Zeymer C. Design and engineering of artificial metalloproteins: from de novo metal coordination to catalysis. Protein Eng Des Sel 2021; 34:6150309. [PMID: 33635315 DOI: 10.1093/protein/gzab003] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 01/15/2021] [Accepted: 01/19/2021] [Indexed: 11/13/2022] Open
Abstract
Metalloproteins are essential to sustain life. Natural evolution optimized them for intricate structural, regulatory and catalytic functions that cannot be fulfilled by either a protein or a metal ion alone. In order to understand this synergy and the complex design principles behind the natural systems, simpler mimics were engineered from the bottom up by installing de novo metal sites in either natural or fully designed, artificial protein scaffolds. This review focuses on key challenges associated with this approach. We discuss how proteins can be equipped with binding sites that provide an optimal coordination environment for a metal cofactor of choice, which can be a single metal ion or a complex multinuclear cluster. Furthermore, we highlight recent studies in which artificial metalloproteins were engineered towards new functions, including electron transfer and catalysis. In this context, the powerful combination of de novo protein design and directed evolution is emphasized for metalloenzyme development.
Collapse
Affiliation(s)
- Andreas S Klein
- Department of Chemistry, Technische Universität München, 85747 Garching, Germany
| | - Cathleen Zeymer
- Department of Chemistry, Technische Universität München, 85747 Garching, Germany
| |
Collapse
|
17
|
Abstract
The field of de novo protein design has met with considerable success over the past few decades. Heme, a cofactor, has often been introduced to impart a diverse array of functions to a protein, ranging from electron transport to respiration. In nature, heme is found to occur predominantly in α-helical structures over β-sheets, which has resulted in significant designs of heme proteins utilizing coiled-coil helices. By contrast, there are only a few known β-sheet proteins that bind heme and designs of β-sheets frequently result in amyloid-like aggregates. This review reflects on our success in designing a series of multistranded β-sheet heme binding peptides that are well folded in both aqueous and membrane-like environments. Initially, we designed a β-hairpin peptide that self-assembles to bind heme and performs peroxidase activity in membrane. The β-hairpin was optimized further to accommodate a heme binding pocket within multistranded β-sheets for catalysis and electron transfer in membranes. Furthermore, we de novo designed and characterized β-sheet peptides and miniproteins that are soluble in an aqueous environment capable of binding single and multiple hemes with high affinity and stability. Collectively, these studies highlight the substantial progress made toward the design of functional β-sheets.
Collapse
Affiliation(s)
- Areetha D'Souza
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Surajit Bhattacharjya
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| |
Collapse
|
18
|
Sutherland GA, Polak D, Swainsbury DJK, Wang S, Spano FC, Auman DB, Bossanyi DG, Pidgeon JP, Hitchcock A, Musser AJ, Anthony JE, Dutton PL, Clark J, Hunter CN. A Thermostable Protein Matrix for Spectroscopic Analysis of Organic Semiconductors. J Am Chem Soc 2020; 142:13898-13907. [PMID: 32672948 DOI: 10.1021/jacs.0c05477] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Advances in protein design and engineering have yielded peptide assemblies with enhanced and non-native functionalities. Here, various molecular organic semiconductors (OSCs), with known excitonic up- and down-conversion properties, are attached to a de novo-designed protein, conferring entirely novel functions on the peptide scaffolds. The protein-OSC complexes form similarly sized, stable, water-soluble nanoparticles that are robust to cryogenic freezing and processing into the solid-state. The peptide matrix enables the formation of protein-OSC-trehalose glasses that fix the proteins in their folded states under oxygen-limited conditions. The encapsulation dramatically enhances the stability of protein-OSC complexes to photodamage, increasing the lifetime of the chromophores from several hours to more than 10 weeks under constant illumination. Comparison of the photophysical properties of astaxanthin aggregates in mixed-solvent systems and proteins shows that the peptide environment does not alter the underlying electronic processes of the incorporated materials, exemplified here by singlet exciton fission followed by separation into weakly bound, localized triplets. This adaptable protein-based approach lays the foundation for spectroscopic assessment of a broad range of molecular OSCs in aqueous solutions and the solid-state, circumventing the laborious procedure of identifying the experimental conditions necessary for aggregate generation or film formation. The non-native protein functions also raise the prospect of future biocompatible devices where peptide assemblies could complex with native and non-native systems to generate novel functional materials.
Collapse
Affiliation(s)
- George A Sutherland
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, U.K
| | - Daniel Polak
- Department of Physics and Astronomy, University of Sheffield, Sheffield S3 7RH, U.K
| | - David J K Swainsbury
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, U.K
| | - Shuangqing Wang
- Department of Physics and Astronomy, University of Sheffield, Sheffield S3 7RH, U.K
| | - Frank C Spano
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Dirk B Auman
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - David G Bossanyi
- Department of Physics and Astronomy, University of Sheffield, Sheffield S3 7RH, U.K
| | - James P Pidgeon
- Department of Physics and Astronomy, University of Sheffield, Sheffield S3 7RH, U.K
| | - Andrew Hitchcock
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, U.K
| | - Andrew J Musser
- Department of Physics and Astronomy, University of Sheffield, Sheffield S3 7RH, U.K
| | - John E Anthony
- Department of Chemistry, University of Kentucky, Kentucky 40511, United States
| | - P Leslie Dutton
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Jenny Clark
- Department of Physics and Astronomy, University of Sheffield, Sheffield S3 7RH, U.K
| | - C Neil Hunter
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, U.K
| |
Collapse
|
19
|
Huang X, Vasilev C, Hunter CN. Excitation energy transfer between monomolecular layers of light harvesting LH2 and LH1-reaction centre complexes printed on a glass substrate. LAB ON A CHIP 2020; 20:2529-2538. [PMID: 32662473 DOI: 10.1039/d0lc00156b] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Light-harvesting 2 (LH2) and light-harvesting 1 - reaction centre (RCLH1) complexes purified from the photosynthetic bacterium Rhodobacter (Rba.) sphaeroides were cross-patterned on glass surfaces for energy transfer studies. Atomic force microscopy (AFM) images of the RCLH1 and LH2 patterns show the deposition of monomolecular layers of complexes on the glass substrate. Spectral imaging and fluorescence life-time imaging microscopy (FLIM) revealed that RCLH1 and LH2 complexes, sealed under physiological conditions, retained their native light-harvesting and energy transfer functions. Measurements of the amplitude and lifetime decay of fluorescence emission from LH2 complexes, the energy transfer donors, and gain of fluorescence emission from acceptor RCLH1 complexes, provide evidence for excitation energy transfer from LH2 to RCLH1. Directional energy transfer on the glass substrate was unequivocally established by using LH2-carotenoid complexes and RCLH1 complexes with genetically removed carotenoids. Specific excitation of carotenoids in donor LH2 complexes elicited fluorescence emission from RCLH1 acceptors. To explore the longevity of this novel nanoprinted photosynthetic unit, RCLH1 and LH2 complexes were cross-patterned on a glass surface and sealed under a protective argon atmosphere. The results show that both complexes retained their individual and collective functions and are capable of directional excitation energy transfer for at least 60 days.
Collapse
Affiliation(s)
- Xia Huang
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK.
| | | | | |
Collapse
|
20
|
Abstract
Proteins are molecular machines whose function depends on their ability to achieve complex folds with precisely defined structural and dynamic properties. The rational design of proteins from first-principles, or de novo, was once considered to be impossible, but today proteins with a variety of folds and functions have been realized. We review the evolution of the field from its earliest days, placing particular emphasis on how this endeavor has illuminated our understanding of the principles underlying the folding and function of natural proteins, and is informing the design of macromolecules with unprecedented structures and properties. An initial set of milestones in de novo protein design focused on the construction of sequences that folded in water and membranes to adopt folded conformations. The first proteins were designed from first-principles using very simple physical models. As computers became more powerful, the use of the rotamer approximation allowed one to discover amino acid sequences that stabilize the desired fold. As the crystallographic database of protein structures expanded in subsequent years, it became possible to construct proteins by assembling short backbone fragments that frequently recur in Nature. The second set of milestones in de novo design involves the discovery of complex functions. Proteins have been designed to bind a variety of metals, porphyrins, and other cofactors. The design of proteins that catalyze hydrolysis and oxygen-dependent reactions has progressed significantly. However, de novo design of catalysts for energetically demanding reactions, or even proteins that bind with high affinity and specificity to highly functionalized complex polar molecules remains an importnant challenge that is now being achieved. Finally, the protein design contributed significantly to our understanding of membrane protein folding and transport of ions across membranes. The area of membrane protein design, or more generally of biomimetic polymers that function in mixed or non-aqueous environments, is now becoming increasingly possible.
Collapse
|
21
|
Kulyk O, Rocard L, Maggini L, Bonifazi D. Synthetic strategies tailoring colours in multichromophoric organic nanostructures. Chem Soc Rev 2020; 49:8400-8424. [PMID: 33107504 DOI: 10.1039/c9cs00555b] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Mimicking nature to develop light-harvesting materials is a timely challenge. This tutorial review examines the chemical strategies to engineer and customise innovative multi-coloured architectures with specific light-absorbing and emitting properties.
Collapse
Affiliation(s)
- Olesia Kulyk
- School of Chemistry
- Cardiff University
- Main Building
- Park Place
- Cardiff
| | - Lou Rocard
- School of Chemistry
- Cardiff University
- Main Building
- Park Place
- Cardiff
| | - Laura Maggini
- Institute of Organic Chemistry
- Faculty of Chemistry, University of Vienna, Währinger Strasse 38
- Vienna
- Austria
| | - Davide Bonifazi
- School of Chemistry
- Cardiff University
- Main Building
- Park Place
- Cardiff
| |
Collapse
|
22
|
Engineering Metalloprotein Functions in Designed and Native Scaffolds. Trends Biochem Sci 2019; 44:1022-1040. [DOI: 10.1016/j.tibs.2019.06.006] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 06/05/2019] [Accepted: 06/11/2019] [Indexed: 12/15/2022]
|
23
|
Grayson KJ, Anderson JLR. Designed for life: biocompatible de novo designed proteins and components. J R Soc Interface 2019; 15:rsif.2018.0472. [PMID: 30158186 PMCID: PMC6127164 DOI: 10.1098/rsif.2018.0472] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 08/01/2018] [Indexed: 12/30/2022] Open
Abstract
A principal goal of synthetic biology is the de novo design or redesign of biomolecular components. In addition to revealing fundamentally important information regarding natural biomolecular engineering and biochemistry, functional building blocks will ultimately be provided for applications including the manufacture of valuable products and therapeutics. To fully realize this ambitious goal, the designed components must be biocompatible, working in concert with natural biochemical processes and pathways, while not adversely affecting cellular function. For example, de novo protein design has provided us with a wide repertoire of structures and functions, including those that can be assembled and function in vivo. Here we discuss such biocompatible designs, as well as others that have the potential to become biocompatible, including non-protein molecules, and routes to achieving full biological integration.
Collapse
Affiliation(s)
- Katie J Grayson
- School of Biochemistry, University of Bristol, Biomedical Sciences Building, Bristol BS8 1TD, UK
| | - J L Ross Anderson
- School of Biochemistry, University of Bristol, Biomedical Sciences Building, Bristol BS8 1TD, UK .,BrisSynBio Synthetic Biology Research Centre, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
| |
Collapse
|
24
|
Towards functional de novo designed proteins. Curr Opin Chem Biol 2019; 52:102-111. [DOI: 10.1016/j.cbpa.2019.06.011] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 04/25/2019] [Accepted: 06/06/2019] [Indexed: 12/31/2022]
|
25
|
Mancini JA, Sheehan M, Kodali G, Chow BY, Bryant DA, Dutton PL, Moser CC. De novo synthetic biliprotein design, assembly and excitation energy transfer. J R Soc Interface 2019; 15:rsif.2018.0021. [PMID: 29618529 DOI: 10.1098/rsif.2018.0021] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 03/13/2018] [Indexed: 12/26/2022] Open
Abstract
Bilins are linear tetrapyrrole chromophores with a wide range of visible and near-visible light absorption and emission properties. These properties are tuned upon binding to natural proteins and exploited in photosynthetic light-harvesting and non-photosynthetic light-sensitive signalling. These pigmented proteins are now being manipulated to develop fluorescent experimental tools. To engineer the optical properties of bound bilins for specific applications more flexibly, we have used first principles of protein folding to design novel, stable and highly adaptable bilin-binding four-α-helix bundle protein frames, called maquettes, and explored the minimal requirements underlying covalent bilin ligation and conformational restriction responsible for the strong and variable absorption, fluorescence and excitation energy transfer of these proteins. Biliverdin, phycocyanobilin and phycoerythrobilin bind covalently to maquette Cys in vitro A blue-shifted tripyrrole formed from maquette-bound phycocyanobilin displays a quantum yield of 26%. Although unrelated in fold and sequence to natural phycobiliproteins, bilin lyases nevertheless interact with maquettes during co-expression in Escherichia coli to improve the efficiency of bilin binding and influence bilin structure. Bilins bind in vitro and in vivo to Cys residues placed in loops, towards the amino end or in the middle of helices but bind poorly at the carboxyl end of helices. Bilin-binding efficiency and fluorescence yield are improved by Arg and Asp residues adjacent to the ligating Cys on the same helix and by His residues on adjacent helices.
Collapse
Affiliation(s)
- Joshua A Mancini
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA
| | - Molly Sheehan
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
| | - Goutham Kodali
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA
| | - Brian Y Chow
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
| | - Donald A Bryant
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
| | - P Leslie Dutton
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA
| | - Christopher C Moser
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA
| |
Collapse
|
26
|
Rhys GG, Wood CW, Beesley JL, Zaccai NR, Burton AJ, Brady RL, Thomson AR, Woolfson DN. Navigating the Structural Landscape of De Novo α-Helical Bundles. J Am Chem Soc 2019; 141:8787-8797. [PMID: 31066556 DOI: 10.1021/jacs.8b13354] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The association of amphipathic α helices in water leads to α-helical-bundle protein structures. However, the driving force for this-the hydrophobic effect-is not specific and does not define the number or the orientation of helices in the associated state. Rather, this is achieved through deeper sequence-to-structure relationships, which are increasingly being discerned. For example, for one structurally extreme but nevertheless ubiquitous class of bundle-the α-helical coiled coils-relationships have been established that discriminate between all-parallel dimers, trimers, and tetramers. Association states above this are known, as are antiparallel and mixed arrangements of the helices. However, these alternative states are less well understood. Here, we describe a synthetic-peptide system that switches between parallel hexamers and various up-down-up-down tetramers in response to single-amino-acid changes and solution conditions. The main accessible states of each peptide variant are characterized fully in solution and, in most cases, to high resolution with X-ray crystal structures. Analysis and inspection of these structures helps rationalize the different states formed. This navigation of the structural landscape of α-helical coiled coils above the dimers and trimers that dominate in nature has allowed us to design rationally a well-defined and hyperstable antiparallel coiled-coil tetramer (apCC-Tet). This robust de novo protein provides another scaffold for further structural and functional designs in protein engineering and synthetic biology.
Collapse
Affiliation(s)
- Guto G Rhys
- School of Chemistry , University of Bristol , Cantock's Close , Bristol BS8 1TS , United Kingdom
| | - Christopher W Wood
- School of Chemistry , University of Bristol , Cantock's Close , Bristol BS8 1TS , United Kingdom
| | - Joseph L Beesley
- School of Chemistry , University of Bristol , Cantock's Close , Bristol BS8 1TS , United Kingdom
| | - Nathan R Zaccai
- School of Biochemistry , University of Bristol , Medical Sciences Building, University Walk , Bristol BS8 1TD , United Kingdom
| | - Antony J Burton
- School of Chemistry , University of Bristol , Cantock's Close , Bristol BS8 1TS , United Kingdom
- Frick Chemistry Laboratory , Princeton University , Princeton , New Jersey 08544 , United States
| | - R Leo Brady
- School of Biochemistry , University of Bristol , Medical Sciences Building, University Walk , Bristol BS8 1TD , United Kingdom
| | - Andrew R Thomson
- School of Chemistry , University of Bristol , Cantock's Close , Bristol BS8 1TS , United Kingdom
- School of Chemistry , University of Glasgow , Glasgow G12 8QQ , United Kingdom
| | - Derek N Woolfson
- School of Chemistry , University of Bristol , Cantock's Close , Bristol BS8 1TS , United Kingdom
- School of Biochemistry , University of Bristol , Medical Sciences Building, University Walk , Bristol BS8 1TD , United Kingdom
- BrisSynBio , University of Bristol , Life Sciences Building, Tyndall Avenue , Bristol BS8 1TQ , United Kingdom
| |
Collapse
|
27
|
Sun Z, Diebolder CA, Renault L, de Groot H. A Semisynthetic Peptide−Metalloporphyrin Responsive Matrix for Artificial Photosynthesis. CHEMPHOTOCHEM 2019. [DOI: 10.1002/cptc.201900063] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Zhongwu Sun
- Leiden University Leiden Institute of Chemistry 2333 AL Leiden The Netherlands
| | - Christoph A. Diebolder
- Leiden University The Netherlands Centre for Electron Nanoscopy (NeCEN) 2333 AL Leiden The Netherlands
| | - Ludovic Renault
- Leiden University The Netherlands Centre for Electron Nanoscopy (NeCEN) 2333 AL Leiden The Netherlands
| | - Huub de Groot
- Leiden University Leiden Institute of Chemistry 2333 AL Leiden The Netherlands
| |
Collapse
|
28
|
Solomon LA, Wood AR, Sykes ME, Diroll BT, Wiederrecht GP, Schaller RD, Fry HC. Microenvironment control of porphyrin binding, organization, and function in peptide nanofiber assemblies. NANOSCALE 2019; 11:5412-5421. [PMID: 30855041 DOI: 10.1039/c8nr09556f] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
To take peptide materials from predominantly structural to functional assemblies, variations in cofactor binding sites must be engineered and controlled. Here, we have employed the peptide sequence c16-AHX3K3-CO2H where X3 represents the aliphatic structural component of the peptide design that dictates β-sheet formation and upon self-assembly yields a change in the overall microenvironment surrounding the Zn protoporphyrin IX ((PPIX)Zn) binding site. All peptides studied yield β-sheet rich nanofibers highlighting the materials' resiliency to amino acid substitution. We highlight that the (PPIX)Zn binding constants correlate strongly with amino acid side chain volume, where X = L or I yields the lowest dissociation constant values (KD). The resulting microenvironment highlights the materials' ability to control interchromophore electronic interactions such that slip-stacked cofacial arrangements are observed via exciton splitting in UV/visible and circular dichroism spectroscopy. Steady state and time-resolved photoluminescence suggests that greater interchromophore packing yields larger excimer populations and corresponding longer excimer association lifetimes (τA) which directly translates to shorter exciton diffusion lengths. In comparison to synthetic porphyrin molecular assemblies, this work demonstrates the ability to employ the peptide assembly to modulate the degree of cofactor arrangement, extent of excimer formation, and the exciton hopping rates all while in a platform amenable for producing polymer-like materials.
Collapse
Affiliation(s)
- Lee A Solomon
- Center for Nanoscale Materials, Argonne National Laboratory, Lemont, IL 60439, USA.
| | | | | | | | | | | | | |
Collapse
|
29
|
D’Souza A, Torres J, Bhattacharjya S. Expanding heme-protein folding space using designed multi-heme β-sheet mini-proteins. Commun Chem 2018. [DOI: 10.1038/s42004-018-0078-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
|
30
|
Grayson KJ, Anderson JR. The ascent of man(made oxidoreductases). Curr Opin Struct Biol 2018; 51:149-155. [PMID: 29754103 PMCID: PMC6227378 DOI: 10.1016/j.sbi.2018.04.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 04/24/2018] [Indexed: 11/09/2022]
Abstract
Though established 40 years ago, the field of de novo protein design has recently come of age, with new designs exhibiting an unprecedented level of sophistication in structure and function. With respect to catalysis, de novo enzymes promise to revolutionise the industrial production of useful chemicals and materials, while providing new biomolecules as plug-and-play components in the metabolic pathways of living cells. To this end, there are now de novo metalloenzymes that are assembled in vivo, including the recently reported C45 maquette, which can catalyse a variety of substrate oxidations with efficiencies rivalling those of closely related natural enzymes. Here we explore the successful design of this de novo enzyme, which was designed to minimise the undesirable complexity of natural proteins using a minimalistic bottom-up approach.
Collapse
Affiliation(s)
- Katie J Grayson
- School of Biochemistry, Biomedical Sciences Building, University of Bristol, BS8 1TD, UK
| | - Jl Ross Anderson
- School of Biochemistry, Biomedical Sciences Building, University of Bristol, BS8 1TD, UK; BrisSynBio Synthetic Biology Research Centre, Life Sciences Building, University of Bristol, Tyndall Avenue, Bristol BS8 1TQ, UK.
| |
Collapse
|
31
|
Lishchuk A, Kodali G, Mancini JA, Broadbent M, Darroch B, Mass OA, Nabok A, Dutton PL, Hunter CN, Törmä P, Leggett GJ. A synthetic biological quantum optical system. NANOSCALE 2018; 10:13064-13073. [PMID: 29956712 PMCID: PMC6044288 DOI: 10.1039/c8nr02144a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 06/06/2018] [Indexed: 06/08/2023]
Abstract
In strong plasmon-exciton coupling, a surface plasmon mode is coupled to an array of localized emitters to yield new hybrid light-matter states (plexcitons), whose properties may in principle be controlled via modification of the arrangement of emitters. We show that plasmon modes are strongly coupled to synthetic light-harvesting maquette proteins, and that the coupling can be controlled via alteration of the protein structure. For maquettes with a single chlorin binding site, the exciton energy (2.06 ± 0.07 eV) is close to the expected energy of the Qy transition. However, for maquettes containing two chlorin binding sites that are collinear in the field direction, an exciton energy of 2.20 ± 0.01 eV is obtained, intermediate between the energies of the Qx and Qy transitions of the chlorin. This observation is attributed to strong coupling of the LSPR to an H-dimer state not observed under weak coupling.
Collapse
Affiliation(s)
- Anna Lishchuk
- Department of Chemistry
, University of Sheffield
,
Brook Hill
, Sheffield S3 7HF
, UK
.
| | - Goutham Kodali
- The Johnson Research Foundation and Department of Biochemistry and Biophysics
, University of Pennsylvania
,
Philadelphia
, PA 10104
, USA
| | - Joshua A. Mancini
- The Johnson Research Foundation and Department of Biochemistry and Biophysics
, University of Pennsylvania
,
Philadelphia
, PA 10104
, USA
| | - Matthew Broadbent
- Department of Chemistry
, University of Sheffield
,
Brook Hill
, Sheffield S3 7HF
, UK
.
| | - Brice Darroch
- Department of Chemistry
, University of Sheffield
,
Brook Hill
, Sheffield S3 7HF
, UK
.
| | - Olga A. Mass
- N. Carolina State University
, Department of Chemistry
,
Raleigh
, NC 27695
, USA
| | - Alexei Nabok
- Materials and Engineering Research Institute
, Sheffield Hallam University
,
Howard St
, Sheffield S1 1WB
, UK
| | - P. Leslie Dutton
- The Johnson Research Foundation and Department of Biochemistry and Biophysics
, University of Pennsylvania
,
Philadelphia
, PA 10104
, USA
| | - C. Neil Hunter
- Department of Molecular Biology and Biotechnology
, University of Sheffield
,
Western Bank
, Sheffield S10 2TN
, UK
| | - Päivi Törmä
- COMP Centre of Excellence
, Department of Applied Physics
, Aalto University
, School of Science
,
P.O. Box 15100
, 00076 Aalto
, Finland
| | - Graham J. Leggett
- Department of Chemistry
, University of Sheffield
,
Brook Hill
, Sheffield S3 7HF
, UK
.
| |
Collapse
|
32
|
Hecht MH, Zarzhitsky S, Karas C, Chari S. Are natural proteins special? Can we do that? Curr Opin Struct Biol 2018; 48:124-132. [DOI: 10.1016/j.sbi.2017.11.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 11/29/2017] [Indexed: 12/23/2022]
|
33
|
Banal JL, Kondo T, Veneziano R, Bathe M, Schlau-Cohen GS. Photophysics of J-Aggregate-Mediated Energy Transfer on DNA. J Phys Chem Lett 2017; 8:5827-5833. [PMID: 29144136 DOI: 10.1021/acs.jpclett.7b01898] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Achieving nanoscale spatial and electronic control over the formation of dye aggregates is a major synthetic challenge due to their typically inhomogeneous self-assembly, which limits control over their higher-order organization. To address these challenges, synthetic DNA-templated pseudoisocyanine (PIC) J-aggregates were recently introduced. However, the dependence of the photophysics of the superradiant exciton on the underlying DNA template length and the impact of static disorder on energy transfer through these PIC J-aggregates remain unknown. We examine the delocalization length progression of superradiant PIC excitons by varying the length of poly-A DNA tracts that template PIC J-aggregates. We then investigate the energy-transfer efficiency from PIC J-aggregates with DNA duplex template length, which we found to be limited by static disorder. Utilizing the self-assembled and selective formation of superradiant excitons on DNA provides a platform to determine the function of delocalized excitons in the context of nanoscale energy transport.
Collapse
Affiliation(s)
- James L Banal
- Energy Frontier Research Center for Excitonics, ‡Department of Biological Engineering, and §Department of Chemistry, Massachusetts Institute of Technology , 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Toru Kondo
- Energy Frontier Research Center for Excitonics, ‡Department of Biological Engineering, and §Department of Chemistry, Massachusetts Institute of Technology , 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Rémi Veneziano
- Energy Frontier Research Center for Excitonics, ‡Department of Biological Engineering, and §Department of Chemistry, Massachusetts Institute of Technology , 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Mark Bathe
- Energy Frontier Research Center for Excitonics, ‡Department of Biological Engineering, and §Department of Chemistry, Massachusetts Institute of Technology , 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Gabriela S Schlau-Cohen
- Energy Frontier Research Center for Excitonics, ‡Department of Biological Engineering, and §Department of Chemistry, Massachusetts Institute of Technology , 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| |
Collapse
|
34
|
Mancini JA, Kodali G, Jiang J, Reddy KR, Lindsey JS, Bryant DA, Dutton PL, Moser CC. Multi-step excitation energy transfer engineered in genetic fusions of natural and synthetic light-harvesting proteins. J R Soc Interface 2017; 14:rsif.2016.0896. [PMID: 28179548 DOI: 10.1098/rsif.2016.0896] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 01/16/2017] [Indexed: 11/12/2022] Open
Abstract
Synthetic proteins designed and constructed from first principles with minimal reference to the sequence of any natural protein have proven robust and extraordinarily adaptable for engineering a range of functions. Here for the first time we describe the expression and genetic fusion of a natural photosynthetic light-harvesting subunit with a synthetic protein designed for light energy capture and multi-step transfer. We demonstrate excitation energy transfer from the bilin of the CpcA subunit (phycocyanin α subunit) of the cyanobacterial photosynthetic light-harvesting phycobilisome to synthetic four-helix-bundle proteins accommodating sites that specifically bind a variety of selected photoactive tetrapyrroles positioned to enhance energy transfer by relay. The examination of combinations of different bilin, chlorin and bacteriochlorin cofactors has led to identification of the preconditions for directing energy from the bilin light-harvesting antenna into synthetic protein-cofactor constructs that can be customized for light-activated chemistry in the cell.
Collapse
Affiliation(s)
- Joshua A Mancini
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Goutham Kodali
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jianbing Jiang
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA
| | | | - Jonathan S Lindsey
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - Donald A Bryant
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - P Leslie Dutton
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Christopher C Moser
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| |
Collapse
|