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Rakotoharisoa RV, Seifinoferest B, Zarifi N, Miller JDM, Rodriguez JM, Thompson MC, Chica RA. Design of Efficient Artificial Enzymes Using Crystallographically Enhanced Conformational Sampling. J Am Chem Soc 2024; 146:10001-10013. [PMID: 38532610 DOI: 10.1021/jacs.4c00677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/28/2024]
Abstract
The ability to create efficient artificial enzymes for any chemical reaction is of great interest. Here, we describe a computational design method for increasing the catalytic efficiency of de novo enzymes by several orders of magnitude without relying on directed evolution and high-throughput screening. Using structural ensembles generated from dynamics-based refinement against X-ray diffraction data collected from crystals of Kemp eliminases HG3 (kcat/KM 125 M-1 s-1) and KE70 (kcat/KM 57 M-1 s-1), we design from each enzyme ≤10 sequences predicted to catalyze this reaction more efficiently. The most active designs display kcat/KM values improved by 100-250-fold, comparable to mutants obtained after screening thousands of variants in multiple rounds of directed evolution. Crystal structures show excellent agreement with computational models, with catalytic contacts present as designed and transition-state root-mean-square deviations of ≤0.65 Å. Our work shows how ensemble-based design can generate efficient artificial enzymes by exploiting the true conformational ensemble to design improved active sites.
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Affiliation(s)
- Rojo V Rakotoharisoa
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
- Center for Catalysis Research and Innovation, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Behnoush Seifinoferest
- Department of Chemistry and Biochemistry, University of California Merced, Merced, California 95343, United States
| | - Niayesh Zarifi
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
- Center for Catalysis Research and Innovation, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Jack D M Miller
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
- Center for Catalysis Research and Innovation, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Joshua M Rodriguez
- Department of Chemistry and Biochemistry, University of California Merced, Merced, California 95343, United States
| | - Michael C Thompson
- Department of Chemistry and Biochemistry, University of California Merced, Merced, California 95343, United States
| | - Roberto A Chica
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
- Center for Catalysis Research and Innovation, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
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Mukherjee S, Douglas N, Jimenez R. Influence of Fluorescence Lifetime Selections and Conformational Flexibility on Brightness of FusionRed Variants. J Phys Chem Lett 2024; 15:1644-1651. [PMID: 38315162 DOI: 10.1021/acs.jpclett.3c02765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
Abstract
Fluorescent proteins (FPs) for bioimaging are typically developed by screening mutant libraries for clones with improved photophysical properties. This approach has resulted in FPs with high brightness, but the mechanistic origins of the improvements are often unclear. We focused on improving the molecular brightness in the FusionRed family of FPs with fluorescence lifetime selections on targeted libraries, with the aim of reducing nonradiative decay rates. Our new variants show fluorescence quantum yields of up to 75% and lifetimes >3.5 ns. We present a comprehensive analysis of these new FPs, including trends in spectral shifts, photophysical data, photostability, and cellular brightness resulting from codon optimization. We also performed all-atom molecular dynamics simulations to investigate the impact of side chain mutations. The trajectories reveal that individual mutations reduce the flexibility of the chromophore and side chains, leading to an overall reduction in nonradiative rates.
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Affiliation(s)
- Srijit Mukherjee
- JILA, University of Colorado, Boulder, and National Institute of Standards and Technology, 440 UCB, Boulder, Colorado 80309, United States
- Department of Chemistry, University of Colorado, Boulder, 215 UCB, Boulder, Colorado 80309, United States
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Nancy Douglas
- Department of Chemistry, University of Colorado, Boulder, 215 UCB, Boulder, Colorado 80309, United States
| | - Ralph Jimenez
- JILA, University of Colorado, Boulder, and National Institute of Standards and Technology, 440 UCB, Boulder, Colorado 80309, United States
- Department of Chemistry, University of Colorado, Boulder, 215 UCB, Boulder, Colorado 80309, United States
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Patrian M, Shaukat A, Nieddu M, Banda-Vázquez JA, Timonen JVI, Fuenzalida Werner JP, Anaya-Plaza E, Kostiainen MA, Costa RD. Supercharged Fluorescent Protein-Apoferritin Cocrystals for Lighting Applications. ACS NANO 2023; 17:21206-21215. [PMID: 37902649 PMCID: PMC10684032 DOI: 10.1021/acsnano.3c05284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 10/12/2023] [Indexed: 10/31/2023]
Abstract
The application of fluorescent proteins (FPs) in optoelectronics is hindered by the need for effective protocols to stabilize them under device preparation and operational conditions. Factors such as high temperatures, irradiation, and organic solvent exposure contribute to the denaturation of FPs, resulting in a low device performance. Herein, we focus on addressing the photoinduced heat generation associated with FP motion and rapid heat transfer. This leads to device temperatures of approximately 65 °C, causing FP-denaturation and a subsequent loss of device functionality. We present a FP stabilization strategy involving the integration of electrostatically self-assembled FP-apoferritin cocrystals within a silicone-based color down-converting filter. Three key achievements characterize this approach: (i) an engineering strategy to design positively supercharged FPs (+22) without compromising photoluminescence and thermal stability compared to their native form, (ii) a carefully developed crystallization protocol resulting in highly emissive cocrystals that retain the essential photoluminescence features of the FPs, and (iii) a strong reduction of the device's working temperature to 40 °C, leading to a 40-fold increase in Bio-HLEDs stability compared to reference devices.
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Affiliation(s)
- Marta Patrian
- Chair
of Biogenic Functional Materials, 6 Technical
University of Munich, Schulgasse, 22, Straubing 94315, Germany
| | - Ahmed Shaukat
- Department
of Bioproducts and Biosystems, Aalto University, 00076 Aalto, Finland
| | - Mattia Nieddu
- Chair
of Biogenic Functional Materials, 6 Technical
University of Munich, Schulgasse, 22, Straubing 94315, Germany
| | - Jesús Agustín Banda-Vázquez
- Chair
of Biogenic Functional Materials, 6 Technical
University of Munich, Schulgasse, 22, Straubing 94315, Germany
| | - Jaakko V. I. Timonen
- Department
of Applied Physics, Aalto University School
of Science, P.O. Box 15100, Espoo FI-02150, Finland
| | - Juan Pablo Fuenzalida Werner
- Chair
of Biogenic Functional Materials, 6 Technical
University of Munich, Schulgasse, 22, Straubing 94315, Germany
| | - Eduardo Anaya-Plaza
- Department
of Bioproducts and Biosystems, Aalto University, 00076 Aalto, Finland
| | - Mauri A. Kostiainen
- Department
of Bioproducts and Biosystems, Aalto University, 00076 Aalto, Finland
| | - Rubén D. Costa
- Chair
of Biogenic Functional Materials, 6 Technical
University of Munich, Schulgasse, 22, Straubing 94315, Germany
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Rakotoharisoa RV, Seifinoferest B, Zarifi N, Miller JD, Rodriguez JM, Thompson MC, Chica RA. Design of efficient artificial enzymes using crystallographically-enhanced conformational sampling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.01.564846. [PMID: 37961474 PMCID: PMC10635043 DOI: 10.1101/2023.11.01.564846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
The ability to create efficient artificial enzymes for any chemical reaction is of great interest. Here, we describe a computational design method for increasing catalytic efficiency of de novo enzymes to a level comparable to their natural counterparts without relying on directed evolution. Using structural ensembles generated from dynamics-based refinement against X-ray diffraction data collected from crystals of Kemp eliminases HG3 (kcat/KM 125 M-1 s-1) and KE70 (kcat/KM 57 M-1 s-1), we design from each enzyme ≤10 sequences predicted to catalyze this reaction more efficiently. The most active designs display kcat/KM values improved by 100-250-fold, comparable to mutants obtained after screening thousands of variants in multiple rounds of directed evolution. Crystal structures show excellent agreement with computational models. Our work shows how computational design can generate efficient artificial enzymes by exploiting the true conformational ensemble to more effectively stabilize the transition state.
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Affiliation(s)
- Rojo V. Rakotoharisoa
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario, Canada, K1N 6N5
- Center for Catalysis Research and Innovation, University of Ottawa, Ottawa, Ontario, Canada, K1N 6N5
| | - Behnoush Seifinoferest
- Department of Chemistry and Biochemistry, University of California Merced, Merced, California 95343, United States
| | - Niayesh Zarifi
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario, Canada, K1N 6N5
- Center for Catalysis Research and Innovation, University of Ottawa, Ottawa, Ontario, Canada, K1N 6N5
| | - Jack D.M. Miller
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario, Canada, K1N 6N5
- Center for Catalysis Research and Innovation, University of Ottawa, Ottawa, Ontario, Canada, K1N 6N5
| | - Joshua M. Rodriguez
- Department of Chemistry and Biochemistry, University of California Merced, Merced, California 95343, United States
| | - Michael C. Thompson
- Department of Chemistry and Biochemistry, University of California Merced, Merced, California 95343, United States
| | - Roberto A. Chica
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario, Canada, K1N 6N5
- Center for Catalysis Research and Innovation, University of Ottawa, Ottawa, Ontario, Canada, K1N 6N5
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Mukherjee S, Manna P, Hung ST, Vietmeyer F, Friis P, Palmer AE, Jimenez R. Directed Evolution of a Bright Variant of mCherry: Suppression of Nonradiative Decay by Fluorescence Lifetime Selections. J Phys Chem B 2022; 126:4659-4668. [PMID: 35709514 DOI: 10.1021/acs.jpcb.2c01956] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The approximately linear scaling of fluorescence quantum yield (ϕ) with fluorescence lifetime (τ) in fluorescent proteins (FPs) has inspired engineering of brighter fluorophores based on screening for increased lifetimes. Several recently developed FPs such as mTurquoise2, mScarlet, and FusionRed-MQV which have become useful for live cell imaging are products of lifetime selection strategies. However, the underlying photophysical basis of the improved brightness has not been scrutinized. In this study, we focused on understanding the outcome of lifetime-based directed evolution of mCherry, which is a popular red-FP (RFP). We identified four positions (W143, I161, Q163, and I197) near the FP chromophore that can be mutated to create mCherry-XL (eXtended Lifetime: ϕ = 0.70; τ = 3.9 ns). The 3-fold higher quantum yield of mCherry-XL is on par with that of the brightest RFP to date, mScarlet. We examined selected variants within the evolution trajectory and found a near-linear scaling of lifetime with quantum yield and consistent blue-shifts of the absorption and emission spectra. We find that the improvement in brightness is primarily due to a decrease in the nonradiative decay of the excited state. In addition, our analysis revealed the decrease in nonradiative rate is not limited to the blue-shift of the energy gap and changes in the excited state reorganization energy. Our findings suggest that nonradiative mechanisms beyond the scope of energy-gap models such the Englman-Jortner model are suppressed in this lifetime evolution trajectory.
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Affiliation(s)
- Srijit Mukherjee
- JILA, University of Colorado, Boulder and National Institute of Standards and Technology, 440 UCB, Boulder, Colorado 80309, United States.,Department of Chemistry, University of Colorado, Boulder, 215 UCB, Boulder, Colorado 80309, United States
| | - Premashis Manna
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Sheng-Ting Hung
- Department of Physics, National Sun Yat-sen University, Kaohsiung 80424, Taiwan
| | - Felix Vietmeyer
- JILA, University of Colorado, Boulder and National Institute of Standards and Technology, 440 UCB, Boulder, Colorado 80309, United States
| | - Pia Friis
- JILA, University of Colorado, Boulder and National Institute of Standards and Technology, 440 UCB, Boulder, Colorado 80309, United States
| | - Amy E Palmer
- Department of Biochemistry, University of Colorado at Boulder, 596 UCB, Boulder, Colorado 80309, United States.,BioFrontiers Institute, University of Colorado, Boulder, 596 UCB, Boulder, Colorado 80309, United States
| | - Ralph Jimenez
- JILA, University of Colorado, Boulder and National Institute of Standards and Technology, 440 UCB, Boulder, Colorado 80309, United States.,Department of Chemistry, University of Colorado, Boulder, 215 UCB, Boulder, Colorado 80309, United States
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