1
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Russel NS, Kodali G, Stanley RJ, Narayanan M. Screening for Novel Fluorescent Nucleobase Analogues Using Computational and Experimental Methods: 2-Amino-6-chloro-8-vinylpurine (2A6Cl8VP) as a Case Study. J Phys Chem B 2023; 127:7858-7871. [PMID: 37698525 DOI: 10.1021/acs.jpcb.3c03618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/13/2023]
Abstract
Novel fluorescent nucleic acid base analogues (FBAs) with improved optical properties are needed in a variety of biological applications. 2-Amino-6-chloro-8-vinylpurine (2A6Cl8VP) is structural analogue of two existing highly fluorescent FBAs, 2-aminopurine (2AP) and 8-vinyladenine (8VA), and can therefore be expected to have similar base pairing as well as better optical properties compared to its counterparts. In order to determine the absorption and fluorescence properties of 2A6Cl8VP, as a first step, we used TD-DFT calculations and the polarizable continuum model for simulating the solvents and computationally predicted absorption and fluorescence maxima. To test the computational predictions, we also synthesized 2A6Cl8VP and measured its UV/vis absorbance, fluorescence emission, and fluorescence lifetime. The computationally predicted absorbance and fluorescence maxima of 2A6Cl8VP are in reasonable agreement to the experimental values and are significantly redshifted compared to 2AP and 8VA, allowing for its specific excitation. The fluorescence quantum yield of 2A6Cl8VP, however, is significantly lower than those of 2AP and 8VA. Overall, 2A6Cl8VP is a novel fluorescent nucleobase analogue, which can be useful in studying structural, biophysical, and biochemical applications.
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Affiliation(s)
- Nadim Shahriar Russel
- Department of Chemistry, Temple University, 1901 N. Broad Street, Philadelphia, Pennsylvania 19122, United States
| | - Goutham Kodali
- GlowDNA LLC., Malvern, Pennsylvania 19355, United States
| | - Robert J Stanley
- Department of Chemistry, Temple University, 1901 N. Broad Street, Philadelphia, Pennsylvania 19122, United States
| | - Madhavan Narayanan
- Department of Physical Sciences, Benedictine University, 5700 College Rd, Lisle, Illinois 60532, United States
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2
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Abstract
Oxidoreductases have evolved over millions of years to perform a variety of metabolic tasks crucial for life. Understanding how these tasks are engineered relies on delivering external electron donors or acceptors to initiate electron transfer reactions. This is a challenge. Small-molecule redox reagents can act indiscriminately, poisoning the cell. Natural redox proteins are more selective, but finding the right partner can be difficult due to the limited number of redox potentials and difficulty tuning them. De novo proteins offer an alternative path. They are robust and can withstand mutations that allow for tailorable changes. They are also devoid of evolutionary artifacts and readily bind redox cofactors. However, no reliable set of engineering principles have been developed that allow for these proteins to be fine-tuned so their redox midpoint potential (Em) can form donor/acceptor pairs with any natural oxidoreductase. This work dissects protein-cofactor interactions that can be tuned to modulate redox potentials of acceptors and donors using a mutable de novo designed tetrahelical protein platform with iron tetrapyrrole cofactors as a test case. We show a series of engineered heme b-binding de novo proteins and quantify their resulting effect on Em. By focusing on the surface charge and buried charges, as well as cofactor placement, chemical modification, and ligation of cofactors, we are able to achieve a broad range of Em values spanning a range of 330 mV. We anticipate this work will guide the design of proteinaceous tools that can interface with natural oxidoreductases inside and outside the cell while shedding light on how natural proteins modulate Em values of bound cofactors.
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Affiliation(s)
- Lee A. Solomon
- Department
of Chemistry and Biochemistry, George Mason
University, Fairfax, Virginia22030, United States,
| | - Joshua Witten
- Department
of Biology, George Mason University, Fairfax, Virginia22030, United States
| | - Goutham Kodali
- Department
of Biochemistry and Biophysics, University
of Pennsylvania, Philadelphia, Pennsylvania19104, United States
| | - Christopher C. Moser
- Department
of Biochemistry and Biophysics, University
of Pennsylvania, Philadelphia, Pennsylvania19104, United States
| | - P. Leslie Dutton
- Department
of Biochemistry and Biophysics, University
of Pennsylvania, Philadelphia, Pennsylvania19104, United States
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3
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Russel NS, Kodali G, Stanley R, Narayanan M. Screening for novel fluorescent nucleobase analogs (FBAs) using computational and experimental methods ‐ 2‐amino‐8‐vinylpurine (2A8VP), as a Case study. FASEB J 2022. [DOI: 10.1096/fasebj.2022.36.s1.l7432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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4
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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] [What about the content of this article? (0)] [Affiliation(s)] [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.
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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
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5
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Sheehan MM, Magaraci MS, Kuznetsov IA, Mancini JA, Kodali G, Moser CC, Dutton PL, Chow BY. Rational Construction of Compact de Novo-Designed Biliverdin-Binding Proteins. Biochemistry 2018; 57:6752-6756. [PMID: 30468389 PMCID: PMC6293442 DOI: 10.1021/acs.biochem.8b01076] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We report the rational construction of de novo-designed biliverdin-binding proteins by first principles of protein design, informed by energy minimization modeling in Rosetta. The self-assembling tetrahelical bundles bind biliverdin IXa (BV) cofactor autocatalytically in vitro, like photosensory proteins that bind BV (and related bilins or linear tetrapyrroles) despite lacking sequence and structural homology to the natural counterparts. Upon identification of a suitable site for ligation of the cofactor to the protein scaffold, stepwise placement of residues stabilized BV within the hydrophobic core. Rosetta modeling was used in the absence of a high-resolution structure to inform the structure-function relationships of the cofactor binding pocket. Holoprotein formation stabilized BV, resulting in increased far-red BV fluorescence. Via removal of segments extraneous to cofactor stabilization or bundle stability, the initial 15 kDa de novo-designed fluorescence-activating protein was truncated without any change to its optical properties, down to a miniature 10 kDa "mini", in which the protein scaffold extends only a half-heptad repeat beyond the hypothetical position of the bilin D-ring. This work demonstrates how highly compact holoprotein fluorochromes can be rationally constructed using de novo protein design technology and natural cofactors.
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6
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Narayanan M, Singh VR, Kodali G, Moravcevic K, Morris KJ, Stanley RJ. An Ethenoadenine FAD Analog Accelerates UV Dimer Repair by DNA Photolyase. Photochem Photobiol 2018; 93:343-354. [PMID: 27935052 DOI: 10.1111/php.12684] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 11/21/2016] [Indexed: 11/28/2022]
Abstract
Reduced anionic flavin adenine dinucleotide (FADH- ) is the critical cofactor in DNA photolyase (PL) for the repair of cyclobutane pyrimidine dimers (CPD) in UV-damaged DNA. The initial step involves photoinduced electron transfer from *FADH- to the CPD. The adenine (Ade) moiety is nearly stacked with the flavin ring, an unusual conformation compared to other FAD-dependent proteins. The role of this proximity has not been unequivocally elucidated. Some studies suggest that Ade is a radical intermediate, but others conclude that Ade modulates the electron transfer rate constant (kET ) through superexchange. No study has succeeded in removing or modifying this Ade to test these hypotheses. Here, FAD analogs containing either an ethano- or etheno-bridged Ade between the AN1 and AN6 atoms (e-FAD and ε-FAD, respectively) were used to reconstitute apo-PL, giving e-PL and ε-PL respectively. The reconstitution yield of e-PL was very poor, suggesting that the hydrophobicity of the ethano group prevented its uptake, while ε-PL showed 50% reconstitution yield. The substrate binding constants for ε-PL and rPL were identical. ε-PL showed a 15% higher steady-state repair yield compared to FAD-reconstituted photolyase (rPL). The acceleration of repair in ε-PL is discussed in terms of an ε-Ade radical intermediate vs superexchange mechanism.
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Affiliation(s)
| | - Vijay R Singh
- Postdoctoral Fellow at the Department of Nanoscience and Engineering, Indian Institute of Science, Bangalore, India
| | | | - Katarina Moravcevic
- Large Molecule Analytical Development, Janssen Research & Development, LLC, Horsham, PA
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7
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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] [What about the content of this article? (0)] [Affiliation(s)] [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.
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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
.
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8
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Zollitsch TM, Jarocha LE, Bialas C, Henbest KB, Kodali G, Dutton PL, Moser CC, Timmel CR, Hore PJ, Mackenzie SR. Magnetically Sensitive Radical Photochemistry of Non-natural Flavoproteins. J Am Chem Soc 2018; 140:8705-8713. [PMID: 29940116 DOI: 10.1021/jacs.8b03104] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
It is a remarkable fact that ∼50 μT magnetic fields can alter the rates and yields of certain free-radical reactions and that such effects might be the basis of the light-dependent ability of migratory birds to sense the direction of the Earth's magnetic field. The most likely sensory molecule at the heart of this chemical compass is cryptochrome, a flavin-containing protein that undergoes intramolecular, blue-light-induced electron transfer to produce magnetically sensitive radical pairs. To learn more about the factors that control the magnetic sensitivity of cryptochromes, we have used a set of de novo designed protein maquettes that self-assemble as four-α-helical proteins incorporating a single tryptophan residue as an electron donor placed approximately 0.6, 1.1, or 1.7 nm away from a covalently attached riboflavin as chromophore and electron acceptor. Using a specifically developed form of cavity ring-down spectroscopy, we have characterized the photochemistry of these designed flavoprotein maquettes to determine the identities and kinetics of the transient radicals responsible for the magnetic field effects. Given the gross structural and dynamic differences from the natural proteins, it is remarkable that the maquettes show magnetic field effects that are so similar to those observed for cryptochromes.
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Affiliation(s)
- Tilo M Zollitsch
- Department of Chemistry , University of Oxford, Physical and Theoretical Chemistry Laboratory , Oxford OX1 3QZ , United Kingdom
| | - Lauren E Jarocha
- Department of Chemistry , University of Oxford, Physical and Theoretical Chemistry Laboratory , Oxford OX1 3QZ , United Kingdom
| | - Chris Bialas
- Johnson Research Foundation, Department of Biochemistry and Biophysics , University of Pennsylvania , Philadelphia , Pennsylvania 19104 , United States
| | - Kevin B Henbest
- Department of Chemistry , University of Oxford, Centre for Advanced Electron Spin Resonance, Inorganic Chemistry Laboratory , Oxford OX1 3QR , United Kingdom
| | - Goutham Kodali
- Johnson Research Foundation, Department of Biochemistry and Biophysics , University of Pennsylvania , Philadelphia , Pennsylvania 19104 , United States
| | - P Leslie Dutton
- Johnson Research Foundation, Department of Biochemistry and Biophysics , University of Pennsylvania , Philadelphia , Pennsylvania 19104 , United States
| | - Christopher C Moser
- Johnson Research Foundation, Department of Biochemistry and Biophysics , University of Pennsylvania , Philadelphia , Pennsylvania 19104 , United States
| | - Christiane R Timmel
- Department of Chemistry , University of Oxford, Centre for Advanced Electron Spin Resonance, Inorganic Chemistry Laboratory , Oxford OX1 3QR , United Kingdom
| | - P J Hore
- Department of Chemistry , University of Oxford, Physical and Theoretical Chemistry Laboratory , Oxford OX1 3QZ , United Kingdom
| | - Stuart R Mackenzie
- Department of Chemistry , University of Oxford, Physical and Theoretical Chemistry Laboratory , Oxford OX1 3QZ , United Kingdom
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9
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Narayanan M, Singh VR, Kodali G, Moravcevic K, Stanley RJ. An Ethenoadenine FAD Analog Accelerates UV Dimer Repair by DNA Photolyase. Photochem Photobiol 2018; 94:195. [DOI: 10.1111/php.12870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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10
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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] [What about the content of this article? (0)] [Affiliation(s)] [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.
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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
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11
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Kodali G, Mancini JA, Solomon LA, Episova TV, Roach N, Hobbs CJ, Wagner P, Mass OA, Aravindu K, Barnsley JE, Gordon KC, Officer DL, Dutton PL, Moser CC. Design and engineering of water-soluble light-harvesting protein maquettes. Chem Sci 2017; 8:316-324. [PMID: 28261441 PMCID: PMC5330312 DOI: 10.1039/c6sc02417c] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 08/16/2016] [Indexed: 02/04/2023] Open
Abstract
Natural selection in photosynthesis has engineered tetrapyrrole based, nanometer scale, light harvesting and energy capture in light-induced charge separation. By designing and creating nanometer scale artificial light harvesting and charge separating proteins, we have the opportunity to reengineer and overcome the limitations of natural selection to extend energy capture to new wavelengths and to tailor efficient systems that better meet human as opposed to cellular energetic needs. While tetrapyrrole cofactor incorporation in natural proteins is complex and often assisted by accessory proteins for cofactor transport and insertion, artificial protein functionalization relies on a practical understanding of the basic physical chemistry of protein and cofactors that drive nanometer scale self-assembly. Patterning and balancing of hydrophobic and hydrophilic tetrapyrrole substituents is critical to avoid natural or synthetic porphyrin and chlorin aggregation in aqueous media and speed cofactor partitioning into the non-polar core of a man-made water soluble protein designed according to elementary first principles of protein folding. This partitioning is followed by site-specific anchoring of tetrapyrroles to histidine ligands strategically placed for design control of rates and efficiencies of light energy and electron transfer while orienting at least one polar group towards the aqueous phase.
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Affiliation(s)
- 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 .
| | - Lee A. Solomon
- The Johnson Research Foundation and Department of Biochemistry and Biophysics , University of Pennsylvania , Philadelphia , PA 10104 , USA .
| | - Tatiana V. Episova
- The Johnson Research Foundation and Department of Biochemistry and Biophysics , University of Pennsylvania , Philadelphia , PA 10104 , USA .
| | - Nicholas Roach
- The ARC Centre of Excellence for Electromaterials Science and the Intelligent Polymer Research Institute , University of Wollongong , NSW 2522 , Australia
| | - Christopher J. Hobbs
- The ARC Centre of Excellence for Electromaterials Science and the Intelligent Polymer Research Institute , University of Wollongong , NSW 2522 , Australia
| | - Pawel Wagner
- The ARC Centre of Excellence for Electromaterials Science and the Intelligent Polymer Research Institute , University of Wollongong , NSW 2522 , Australia
| | - Olga A. Mass
- N Carolina State University , Department of Chemistry , Raleigh , NC 27695 , USA
| | - Kunche Aravindu
- N Carolina State University , Department of Chemistry , Raleigh , NC 27695 , USA
| | | | - Keith C. Gordon
- University of Otago , Department of Chemistry , Dunedin 9016 , New Zealand
| | - David L. Officer
- The ARC Centre of Excellence for Electromaterials Science and the Intelligent Polymer Research Institute , University of Wollongong , NSW 2522 , Australia
| | - P. Leslie Dutton
- The Johnson Research Foundation and Department of Biochemistry and Biophysics , University of Pennsylvania , Philadelphia , PA 10104 , USA .
| | - Christopher C. Moser
- The Johnson Research Foundation and Department of Biochemistry and Biophysics , University of Pennsylvania , Philadelphia , PA 10104 , USA .
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12
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Bialas C, Jarocha LE, Henbest KB, Zollitsch TM, Kodali G, Timmel CR, Mackenzie SR, Dutton PL, Moser CC, Hore PJ. Engineering an Artificial Flavoprotein Magnetosensor. J Am Chem Soc 2016; 138:16584-16587. [PMID: 27958724 DOI: 10.1021/jacs.6b09682] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Migratory birds use the Earth's magnetic field as a source of navigational information. This light-dependent magnetic compass is thought to be mediated by cryptochrome proteins in the retina. Upon light activation, electron transfer between the flavin adenine dinucleotide cofactor and tryptophan residues leads to the formation of a spin-correlated radical pair, whose subsequent fate is sensitive to external magnetic fields. To learn more about the functional requirements of this complex chemical compass, we have created a family of simplified, adaptable proteins-maquettes-that contain a single tryptophan residue at different distances from a covalently bound flavin. Despite the complete absence of structural resemblance to the native cryptochrome fold or sequence, the maquettes exhibit a strong magnetic field effect that rivals those observed in the natural proteins in vitro. These novel maquette designs offer unprecedented flexibility to explore the basic requirements for magnetic sensing in a protein environment.
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Affiliation(s)
- Chris Bialas
- Johnson Research Foundation, Department of Biochemistry and Biophysics, University of Pennsylvania , Philadelphia, Pennsylvania 19104, United States
| | - Lauren E Jarocha
- Department of Chemistry, University of Oxford , Physical and Theoretical Chemistry Laboratory, Oxford OX1 3QZ, United Kingdom
| | - Kevin B Henbest
- Department of Chemistry, University of Oxford , Inorganic Chemistry Laboratory, Oxford OX1 3QR, United Kingdom
| | - Tilo M Zollitsch
- Department of Chemistry, University of Oxford , Physical and Theoretical Chemistry Laboratory, Oxford OX1 3QZ, United Kingdom
| | - Goutham Kodali
- Johnson Research Foundation, Department of Biochemistry and Biophysics, University of Pennsylvania , Philadelphia, Pennsylvania 19104, United States
| | - Christiane R Timmel
- Department of Chemistry, University of Oxford , Inorganic Chemistry Laboratory, Oxford OX1 3QR, United Kingdom
| | - Stuart R Mackenzie
- Department of Chemistry, University of Oxford , Physical and Theoretical Chemistry Laboratory, Oxford OX1 3QZ, United Kingdom
| | - P Leslie Dutton
- Johnson Research Foundation, Department of Biochemistry and Biophysics, University of Pennsylvania , Philadelphia, Pennsylvania 19104, United States
| | - Christopher C Moser
- Johnson Research Foundation, Department of Biochemistry and Biophysics, University of Pennsylvania , Philadelphia, Pennsylvania 19104, United States
| | - P J Hore
- Department of Chemistry, University of Oxford , Physical and Theoretical Chemistry Laboratory, Oxford OX1 3QZ, United Kingdom
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13
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Tsargorodska A, Cartron ML, Vasilev C, Kodali G, Mass OA, Baumberg JJ, Dutton PL, Hunter CN, Törmä P, Leggett GJ. Strong Coupling of Localized Surface Plasmons to Excitons in Light-Harvesting Complexes. Nano Lett 2016; 16:6850-6856. [PMID: 27689237 PMCID: PMC5135229 DOI: 10.1021/acs.nanolett.6b02661] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 09/28/2016] [Indexed: 05/24/2023]
Abstract
Gold nanostructure arrays exhibit surface plasmon resonances that split after attaching light harvesting complexes 1 and 2 (LH1 and LH2) from purple bacteria. The splitting is attributed to strong coupling between the localized surface plasmon resonances and excitons in the light-harvesting complexes. Wild-type and mutant LH1 and LH2 from Rhodobacter sphaeroides containing different carotenoids yield different splitting energies, demonstrating that the coupling mechanism is sensitive to the electronic states in the light harvesting complexes. Plasmon-exciton coupling models reveal different coupling strengths depending on the molecular organization and the protein coverage, consistent with strong coupling. Strong coupling was also observed for self-assembling polypeptide maquettes that contain only chlorins. However, it is not observed for monolayers of bacteriochlorophyll, indicating that strong plasmon-exciton coupling is sensitive to the specific presentation of the pigment molecules.
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Affiliation(s)
- Anna Tsargorodska
- Department
of Chemistry, University of Sheffield, Brook Hill, Sheffield S3 7HF, U.K.
| | - Michaël L. Cartron
- Department
of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Sheffield S10 2TN, U.K.
| | - Cvetelin Vasilev
- Department
of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Sheffield S10 2TN, U.K.
| | - Goutham Kodali
- The
Johnson Research Foundation and Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 10104, United States
| | - Olga A. Mass
- Department
of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Jeremy J. Baumberg
- Cavendish
Laboratory, Dept. of Physics, University
of Cambridge, J. J. Thomson
Ave, Cambridge, CB3 0HE, U.K.
| | - P. Leslie Dutton
- The
Johnson Research Foundation and Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 10104, United States
| | - C. Neil Hunter
- Department
of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Sheffield S10 2TN, U.K.
| | - 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, U.K.
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14
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Pauszek RF, Kodali G, Siddiqui MSU, Stanley RJ. Overlapping Electronic States with Nearly Parallel Transition Dipole Moments in Reduced Anionic Flavin Can Distort Photobiological Dynamics. J Am Chem Soc 2016; 138:14880-14889. [PMID: 27686753 DOI: 10.1021/jacs.6b06449] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Chromophoric biomolecules are exploited as reporters of a diverse set of phenomena, acting as internal distance monitors, environment and redox sensors, and endogenous imaging probes. The extent to which they can be exploited is dependent on an accurate knowledge of their fundamental electronic properties. Arguably of greatest importance is a precise knowledge of the direction(s) of the absorption transition dipole moment(s) (TDMs) in the molecular frame of reference. Such is the case for flavins, fluorescent redox cofactors utilized for ground- and excited-state redox and photochemical processes. The directions of the TDMs in oxidized and semiquinone flavins were characterized decades ago, and the details of charge redistribution in these forms have also been studied by Stark spectroscopy. The electronic structure of the fully reduced hydroquinone anionic state, FlH-, however, has been the subject of unfounded assumptions and estimates about the number and direction of TDMs in FlH-, as well the electronic structure changes that occur upon light absorption. Here we have used Stark spectroscopy to measure the magnitude and direction of charge redistribution in FlH- upon optical excitation. These data were analyzed using TD-DFT calculations. The results show unequivocally that not one but two nearly orientation-degenerate electronic transitions are required to explain the 340-500 nm absorption spectral range, demolishing the commonly held assumption of a single transition. The difference dipole moments for these states show that electron density shifts toward the xylene ring for both transitions. These measurements force a reappraisal of previous studies that have used erroneous assumptions and unsubstantiated estimates of these quantities. The results put future optical studies of reduced flavins/flavoproteins on a firm photophysical footing.
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Affiliation(s)
- Raymond F Pauszek
- Department of Chemistry, Temple University , 250B Beury Hall, 1901 North 13th Street, Philadelphia, Pennsylvania 19122, United States
| | - Goutham Kodali
- Department of Chemistry, Temple University , 250B Beury Hall, 1901 North 13th Street, Philadelphia, Pennsylvania 19122, United States
| | - M Salim U Siddiqui
- Department of Chemistry, Temple University , 250B Beury Hall, 1901 North 13th Street, Philadelphia, Pennsylvania 19122, United States
| | - Robert J Stanley
- Department of Chemistry, Temple University , 250B Beury Hall, 1901 North 13th Street, Philadelphia, Pennsylvania 19122, United States
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15
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Abstract
Relatively simple principles can be used to plan and construct de novo proteins that bind redox cofactors and participate in a range of electron-transfer reactions analogous to those seen in natural oxidoreductase proteins. These designed redox proteins are called maquettes. Hydrophobic/hydrophilic binary patterning of heptad repeats of amino acids linked together in a single-chain self-assemble into 4-alpha-helix bundles. These bundles form a robust and adaptable frame for uncovering the default properties of protein embedded cofactors independent of the complexities introduced by generations of natural selection and allow us to better understand what factors can be exploited by man or nature to manipulate the physical chemical properties of these cofactors. Anchoring of redox cofactors such as hemes, light active tetrapyrroles, FeS clusters, and flavins by His and Cys residues allow cofactors to be placed at positions in which electron-tunneling rates between cofactors within or between proteins can be predicted in advance. The modularity of heptad repeat designs facilitates the construction of electron-transfer chains and novel combinations of redox cofactors and new redox cofactor assisted functions. Developing de novo designs that can support cofactor incorporation upon expression in a cell is needed to support a synthetic biology advance that integrates with natural bioenergetic pathways.
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Affiliation(s)
- C C Moser
- University of Pennsylvania, Philadelphia, PA, United States
| | - M M Sheehan
- University of Pennsylvania, Philadelphia, PA, United States
| | - N M Ennist
- University of Pennsylvania, Philadelphia, PA, United States
| | - G Kodali
- University of Pennsylvania, Philadelphia, PA, United States
| | - C Bialas
- University of Pennsylvania, Philadelphia, PA, United States
| | - M T Englander
- University of Pennsylvania, Philadelphia, PA, United States
| | - B M Discher
- University of Pennsylvania, Philadelphia, PA, United States
| | - P L Dutton
- University of Pennsylvania, Philadelphia, PA, United States.
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16
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Lee W, Kodali G, Stanley RJ, Matsika S. Coexistence of Different Electron-Transfer Mechanisms in the DNA Repair Process by Photolyase. Chemistry 2016; 22:11371-81. [PMID: 27362906 DOI: 10.1002/chem.201600656] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Revised: 05/18/2016] [Indexed: 11/07/2022]
Abstract
DNA photolyase has been the topic of extensive studies due to its important role of repairing photodamaged DNA, and its unique feature of using light as an energy source. A crucial step in the repair by DNA photolyase is the forward electron transfer from its cofactor (FADH(-) ) to the damaged DNA, and the detailed mechanism of this process has been controversial. In the present study, we examine the forward electron transfer in DNA photolyase by carrying out high-level ab initio calculations in combination with a quantum mechanical/molecular mechanical (QM/MM) approach, and by measuring fluorescence emission spectra at low temperature. On the basis of these computational and experimental results, we demonstrate that multiple decay pathways exist in DNA photolyase depending on the wavelength at excitation and the subsequent transition. This implies that the forward electron transfer in DNA photolyase occurs not only by superexchange mechanism but also by sequential electron transfer.
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Affiliation(s)
- Wook Lee
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania, 19122, USA.
| | - Goutham Kodali
- Teva Pharmaceuticals USA, Inc, 145 Brandywine Pkwy, West Chester, Pennsylvania, 19380, USA
| | - Robert J Stanley
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania, 19122, USA
| | - Spiridoula Matsika
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania, 19122, USA
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17
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Leslie Dutton P, Kodali G, Mancini JA, Ennist NM, Stayrook S, Zhao Z, Englander M, Sheehan MM, Fry BA, Bialas C, Esipovo TV, Vinogradov SA, Goparaju G, Watkins DW, Armstrong CT, Ross Anderson J, Discher BM, Moser CC. Toward the biogenesis of manmade oxidoreductases working in cells. Biochimica et Biophysica Acta (BBA) - Bioenergetics 2014. [DOI: 10.1016/j.bbabio.2014.05.138] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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18
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Pauszek RF, Kodali G, Stanley RJ. Excited state electronic structures of 5,10-methenyltetrahydrofolate and 5,10-methylenetetrahydrofolate determined by Stark spectroscopy. J Phys Chem A 2014; 118:8320-8. [PMID: 24814224 DOI: 10.1021/jp501143u] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Folates are ubiquitous cofactors that participate in a wide variety of critical biological processes. 5,10-Methenyltetrahydrofolate and its photodegradation product 5,10-methylenetetrahydrofolate are both associated with the light-driven DNA repair protein DNA photolyase and its homologues (e.g., cryptochromes). The excited state electronic properties of these folate molecules have been studied here using Stark spectroscopy and complementary quantum calculations. The tetrahydrofolates have relatively large difference dipole moments (ca. 6-8 Debye) and difference polarizabilities (ca. 100 Å(3)). This extensive excited state charge redistribution appears to be due largely to the pendant p-aminobenzoic acid group, which helps shuttle charge over the entirety of the molecule. Simple calculations based on the experimental difference dipole moments suggest that tetrahydrofolates should have large two photon cross sections sufficient to enable two photon microscopy to selectively detect and follow folate-containing proteins both in vitro and in vivo.
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Affiliation(s)
- Raymond F Pauszek
- Department of Chemistry, Temple University , Philadelphia, Pennsylvania 19122, United States
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19
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Abstract
Timely ligation of one or more chemical cofactors at preselected locations in proteins is a critical preamble for catalysis in many natural enzymes, including the oxidoreductases and allied transport and signaling proteins. Likewise, ligation strategies must be directly addressed when designing oxidoreductase and molecular transport functions in man-made, first-principle protein constructs intended to operate in vitro or in vivo. As one of the most common catalytic cofactors in biology, we have chosen heme B, along with its chemical analogues, to determine the kinetics and barriers to cofactor incorporation and bishistidine ligation in a range of 4-α-helix proteins. We compare five elementary synthetic designs (maquettes) and the natural cytochrome b562 that differ in oligomeric forms, apo- and holo-tertiary structural stability; qualities that we show can either assist or hinder assembly. The cofactor itself also imposes an assembly barrier if amphiphilicity ranges toward too hydrophobic or hydrophilic. With progressive removal of identified barriers, we achieve maquette assembly rates as fast as native cytochrome b562, paving the way to in vivo assembly of man-made hemoprotein maquettes and integration of artificial proteins into enzymatic pathways.
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Affiliation(s)
- Lee A Solomon
- The Johnson Research Foundation, Department of Biochemistry and Biophysics, University of Pennsylvania , Philadelphia, Pennsylvania 19104, United States
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20
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Farid TA, Kodali G, Solomon LA, Lichtenstein BR, Sheehan MM, Fry BA, Bialas C, Ennist NM, Siedlecki JA, Zhao Z, Stetz MA, Valentine KG, Anderson JLR, Wand AJ, Discher BM, Moser CC, Dutton PL. Erratum: Corrigendum: Elementary tetrahelical protein design for diverse oxidoreductase functions. Nat Chem Biol 2014. [DOI: 10.1038/nchembio0214-164b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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21
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Anderson JLR, Armstrong CT, Kodali G, Lichtenstein BR, Watkins DW, Mancini JA, Boyle AL, Farid TA, Crump MP, Moser CC, Dutton PL. Constructing a man-made c-type cytochrome maquette in vivo: electron transfer, oxygen transport and conversion to a photoactive light harvesting maquette. Chem Sci 2013; 5:507-514. [PMID: 24634717 DOI: 10.1039/c3sc52019f] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The successful use of man-made proteins to advance synthetic biology requires both the fabrication of functional artificial proteins in a living environment, and the ability of these proteins to interact productively with other proteins and substrates in that environment. Proteins made by the maquette method integrate sophisticated oxidoreductase function into evolutionarily naive, non-computationally designed protein constructs with sequences that are entirely unrelated to any natural protein. Nevertheless, we show here that we can efficiently interface with the natural cellular machinery that covalently incorporates heme into natural cytochromes c to produce in vivo an artificial c-type cytochrome maquette. Furthermore, this c-type cytochrome maquette is designed with a displaceable histidine heme ligand that opens to allow functional oxygen binding, the primary event in more sophisticated functions ranging from oxygen storage and transport to catalytic hydroxylation. To exploit the range of functions that comes from the freedom to bind a variety of redox cofactors within a single maquette framework, this c-type cytochrome maquette is designed with a second, non-heme C, tetrapyrrole binding site, enabling the construction of an elementary electron transport chain, and when the heme C iron is replaced with zinc to create a Zn porphyrin, a light-activatable artificial redox protein. The work we describe here represents a major advance in de novo protein design, offering a robust platform for new c-type heme based oxidoreductase designs and an equally important proof-of-principle that cofactor-equipped man-made proteins can be expressed in living cells, paving the way for constructing functionally useful man-made proteins in vivo.
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Affiliation(s)
- J L Ross Anderson
- School of Biochemistry, University of Bristol, University Walk, Bristol, BS8 1TD, UK.,The Johnson Research Foundation, Dept. of Biochemistry and Biophysics, University of Pennsylvania, PA19104-6059, USA
| | - Craig T Armstrong
- School of Biochemistry, University of Bristol, University Walk, Bristol, BS8 1TD, UK
| | - Goutham Kodali
- The Johnson Research Foundation, Dept. of Biochemistry and Biophysics, University of Pennsylvania, PA19104-6059, USA
| | - Bruce R Lichtenstein
- The Johnson Research Foundation, Dept. of Biochemistry and Biophysics, University of Pennsylvania, PA19104-6059, USA
| | - Daniel W Watkins
- School of Biochemistry, University of Bristol, University Walk, Bristol, BS8 1TD, UK
| | - Joshua A Mancini
- The Johnson Research Foundation, Dept. of Biochemistry and Biophysics, University of Pennsylvania, PA19104-6059, USA
| | - Aimee L Boyle
- School of Chemistry, University of Bristol, Bristol, BS8 1TS, UK
| | - Tammer A Farid
- The Johnson Research Foundation, Dept. of Biochemistry and Biophysics, University of Pennsylvania, PA19104-6059, USA
| | - Matthew P Crump
- School of Chemistry, University of Bristol, Bristol, BS8 1TS, UK
| | - Christopher C Moser
- The Johnson Research Foundation, Dept. of Biochemistry and Biophysics, University of Pennsylvania, PA19104-6059, USA
| | - P Leslie Dutton
- The Johnson Research Foundation, Dept. of Biochemistry and Biophysics, University of Pennsylvania, PA19104-6059, USA
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22
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Farid TA, Kodali G, Solomon LA, Lichtenstein BR, Sheehan MM, Fry BA, Bialas C, Ennist NM, Siedlecki JA, Zhao Z, Stetz MA, Valentine KG, Anderson JLR, Wand AJ, Discher BM, Moser CC, Dutton PL. Elementary tetrahelical protein design for diverse oxidoreductase functions. Nat Chem Biol 2013; 9:826-833. [PMID: 24121554 DOI: 10.1038/nchembio.1362] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Accepted: 09/09/2013] [Indexed: 11/09/2022]
Abstract
Emulating functions of natural enzymes in man-made constructs has proven challenging. Here we describe a man-made protein platform that reproduces many of the diverse functions of natural oxidoreductases without importing the complex and obscure interactions common to natural proteins. Our design is founded on an elementary, structurally stable 4-α-helix protein monomer with a minimalist interior malleable enough to accommodate various light- and redox-active cofactors and with an exterior tolerating extensive charge patterning for modulation of redox cofactor potentials and environmental interactions. Despite its modest size, the construct offers several independent domains for functional engineering that targets diverse natural activities, including dioxygen binding and superoxide and peroxide generation, interprotein electron transfer to natural cytochrome c and light-activated intraprotein energy transfer and charge separation approximating the core reactions of photosynthesis, cryptochrome and photolyase. The highly stable, readily expressible and biocompatible characteristics of these open-ended designs promise development of practical in vitro and in vivo applications.
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Affiliation(s)
- Tammer A Farid
- Department of Biochemistry and Biophysics, Johnson Research Foundation, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Goutham Kodali
- Department of Biochemistry and Biophysics, Johnson Research Foundation, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Lee A Solomon
- Department of Biochemistry and Biophysics, Johnson Research Foundation, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Bruce R Lichtenstein
- Department of Biochemistry and Biophysics, Johnson Research Foundation, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Molly M Sheehan
- Department of Biochemistry and Biophysics, Johnson Research Foundation, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Bryan A Fry
- Department of Biochemistry and Biophysics, Johnson Research Foundation, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Chris Bialas
- Department of Biochemistry and Biophysics, Johnson Research Foundation, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Nathan M Ennist
- Department of Biochemistry and Biophysics, Johnson Research Foundation, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jessica A Siedlecki
- Department of Biochemistry and Biophysics, Johnson Research Foundation, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Zhenyu Zhao
- Department of Biochemistry and Biophysics, Johnson Research Foundation, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Matthew A Stetz
- Department of Biochemistry and Biophysics, Johnson Research Foundation, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Kathleen G Valentine
- Department of Biochemistry and Biophysics, Johnson Research Foundation, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - J L Ross Anderson
- Department of Biochemistry and Biophysics, Johnson Research Foundation, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,School of Biochemistry, University of Bristol, Bristol, UK
| | - A Joshua Wand
- Department of Biochemistry and Biophysics, Johnson Research Foundation, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Bohdana M Discher
- Department of Biochemistry and Biophysics, Johnson Research Foundation, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Christopher C Moser
- Department of Biochemistry and Biophysics, Johnson Research Foundation, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - P Leslie Dutton
- Department of Biochemistry and Biophysics, Johnson Research Foundation, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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23
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Pauszek RF, Kodali G, Caldwell ST, Fitzpatrick B, Zainalabdeen NY, Cooke G, Rotello VM, Stanley RJ. Excited state charge redistribution and dynamics in the donor-π-acceptor flavin derivative ABFL. J Phys Chem B 2013; 117:15684-94. [PMID: 24020957 DOI: 10.1021/jp406420h] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Chromophores containing a donor-π-acceptor (D-π-A) motif have been shown to exhibit many interesting photophysical properties. The lowest electronic transition of a flavin derivative containing this motif, azobenzylflavin (ABFL), has previously been shown to be highly sensitive to solvent environment and hydrogen bonding ligands. To better understand this sensitivity, we have investigated the excited state charge redistribution and dynamics of ABFL in a low-dielectric, non-hydrogen bonding solvent by steady-state Stark and femtosecond optical transient absorption spectroscopies. The Stark measurements reveal the difference dipole moment, Δμ01, between the ground and first excited states to be 22.3 ± 0.9 D. The direction of Δμ01 in the molecular frame was assigned with the aid of TD-DFT and finite field calculations, verifying the hypothesis that electron density moves from the diethylaniline donor to the flavin acceptor in the excited state. The magnitude of the difference dipole moment was used to estimate the hyperpolarizability of ABFL, β0 = 720 × 10(-30) esu. Subsequent excited state decay via charge recombination was shown to take place in a few picoseconds. The data was best fit to a kinetic model composed of a sub-picosecond internal conversion step from S2→S1, followed by a 5 ps decay to the ground state. A competing process involving formation of an additional long-lived state from S1 was also observed. Cyclic voltammetry shows one oxidation and two reduction waves and is completely reversible. This analysis lays the groundwork for developing new flavin dyads with the desired excited electronic state properties for applications such as nonlinear optical devices, molecular electronics applications, or dye-sensitized solar cells.
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Affiliation(s)
- Raymond F Pauszek
- Department of Chemistry, Temple University , Philadelphia, Pennsylvania 19122, United States
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24
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Pauszek RF, Kodali G, Siddiqui MS, Jacoby K, Stanley RJ. Investigation of Excited State Charge Redistribution of the Reduced Anionic Flavin in DNA Photolyase and Simple Solvents by Stark Spectroscopy. Biophys J 2013. [DOI: 10.1016/j.bpj.2012.11.2692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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25
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Ennist NM, Kodali G, Moser CC, Dutton P. Assembly of a Photoactivatable Cofactor Triad within a Designed Protein. Biophys J 2013. [DOI: 10.1016/j.bpj.2012.11.3112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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26
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Mancini JA, Kodali G, Solomon LA, Roach N, Anderson JR, Esipova TV, Vinogradov SA, Wagner P, Discher BM, Officer DL, Moser CC, Dutton PL. Light Harvesting and Light Activatable Protein Maquettes Designed from Scratch. Biophys J 2013. [DOI: 10.1016/j.bpj.2012.11.2937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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27
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Kodali G, Englander MT, Solomon LA, Moser CC, Dutton P. Hemoproteins Designed from Scratch for O2 Transport, Co, No Signaling, Oxidoreductase and Cytochrome P450 Oxygenase Catalysis. Biophys J 2013. [DOI: 10.1016/j.bpj.2012.11.3110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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28
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Sheehan MM, Solomon LA, Kodali G, Moser CC, Dutton PL. Engineering and Tuning of Oxygen Reactivity in Heme Protein Maquettes. Biophys J 2013. [DOI: 10.1016/j.bpj.2012.11.2693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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29
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Kodali G, Solomon LA, Englander MT, Lichtenstein BR, Farid TA, Sheehan MM, Ennist NM, Fry BA, Bialas CP, Mancini JA, Zhao Z, Siedlecki JA, Discher BM, Moser CC, Dutton PL. Design and Engineering of Protein Platforms for Multiple Functions. Biophys J 2013. [DOI: 10.1016/j.bpj.2012.11.3648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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30
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Solomon LA, Kodali G, Moser CC, Dutton PL. Physical Chemical and Engineering Principles underlying the Construction and Electrochemical Properties of Man-Made Protein Maquettes. Biophys J 2013. [DOI: 10.1016/j.bpj.2012.11.2694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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31
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Kodali G, Narayanan M, Stanley RJ. Excited-state electronic properties of 6-methylisoxanthopterin (6-MI): an experimental and theoretical study. J Phys Chem B 2012; 116:2981-9. [PMID: 22276652 DOI: 10.1021/jp2110083] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
6-Methylisoxanthopterin (6-MI) is a pteridine-based guanine analog that has a red-shifted absorption and high fluorescence quantum yield. Its Watson-Crick base-pairing and base stacking properties are similar to guanine. The fluorescence quantum yield of 6-MI is sensitive to its nearest neighbors and base stacking, making it a very useful real-time probe of DNA structure. The fundamental photophysics underlying this fluorescence quenching by base stacking is not well understood. We have explored the excited-state electronic structure of the 6-MI in frozen 77 K LiCl glasses using Stark spectroscopy. These measurements yielded the direction and degree of charge redistribution for the S(0)→S(1) transition as manifested in the difference dipole moment, Δμ(01), and difference static polarizability, TrΔα. TDDFT (time-dependent density functional theory) was employed to calculate the transition energy, oscillator strength, and the dipole moments of the ground and lowest optically bright excited state of 6-MI (S(0)→S(1)). The direction of Δμ(01) was assigned in the molecular frame based on the Stark data and calculations. These results suggest that the C4═O and C2-NH(2) groups are electron-deficient in the excited state, a very different outcome compared with guanine. This implies that Watson-Crick hydrogen bonding in 6-MI may be modulated by absorption of a photon so as to strengthen base pairing, if only transiently. Solvatochromism was also obtained for the absorption and emission spectra of 6-MI in various solvents and compared with the Stark spectroscopic results using both the Lippert-Mataga and Bakhshiev models.
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Affiliation(s)
- Goutham Kodali
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, USA
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32
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Kodali G, Lu Y, Goparaju G, Moser CC, Dutton PL, Johnson AC, Discher BM. Interfacing Natural and Artificial Proteins with Electronic Devices. Biophys J 2012. [DOI: 10.1016/j.bpj.2011.11.3880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022] Open
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33
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Ennist NM, Farid T, Kodali G, Dutton PL. Design and Characterization of a Multi-Cofactor Binding Protein with Implications for Photoactivated Water Oxidation. Biophys J 2012. [DOI: 10.1016/j.bpj.2011.11.3132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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34
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Narayanan M, Kodali G, Singh V, Xing Y, Hawkins ME, Stanley RJ. Correction to “Differential Fluorescence Quenching of Fluorescent Nucleic Acid Base Analogs by Native Nucleic Acid Monophosphates”. J Phys Chem B 2011. [DOI: 10.1021/jp203370g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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35
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Narayanan M, Kodali G, Xing Y, Stanley RJ. Photoinduced electron transfer occurs between 2-aminopurine and the DNA nucleic acid monophosphates: results from cyclic voltammetry and fluorescence quenching. J Phys Chem B 2010; 114:10573-80. [PMID: 20734496 DOI: 10.1021/jp102355v] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
2-Aminopurine (2AP) is a fluorescent adenine analogue that is useful in part because its substantial fluorescence quantum yield is sensitive to base stacking with native bases in ss- and ds-DNA. However, the degree of quenching is sequence dependent and the mechanism of quenching is still a matter of some debate. Here we show that the most likely quenching mechanism in aqueous solution involves photoinduced electron transfer (PET), as revealed by cyclic voltammetry (CV) performed in aprotic organic solvents. These potentials were used with spectroscopic data to obtain excited-state reduction and oxidation potentials. Stern-Volmer (S-V) experiments using the native base monophosphate nucleotides (NMPs) rGMP, rAMP, rCMP, and dTMP were performed in aqueous solution to obtain quenching rate constants kq. The results suggest that 2AP* can act as either an electron donor or an electron acceptor depending on the particular NMP but that PET proceeds for all NMPs tested.
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Affiliation(s)
- Madhavan Narayanan
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, USA
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Narayanan M, Kodali G, Singh V, Xing Y, Hawkins ME, Stanley RJ. Differential fluorescence quenching of fluorescent nucleic acid base analogues by native nucleic acid monophosphates. J Phys Chem B 2010; 114:5953-63. [PMID: 20387838 DOI: 10.1021/jp1011507] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Fluorescent nucleic acid base analogues (FBAs) are used widely as probes of DNA and RNA structure and dynamics. Of increasing utility are the pteridone adenosine analogues (6MAP, DMAP) and pteridine guanosine analogues (3MI, 6MI). These FBAs (collectively referred to as PTERs) are useful, in part, because their fluorescence quantum yields, Phi(f), are modulated by base stacking with native bases (NBs), making them sensitive reporters of DNA structure. The quenching mechanism has been hypothesized to be photoinduced electron transfer following selective excitation of the FBA, but hard evidence for this has been lacking. The degree of quenching shows some dependence on the neighboring bases, but there has been no real determination as to whether FBA*:NB complexes satisfy the basic thermodynamic requirement for spontaneous PET: a negative free energy for the electron transfer reaction. Indeed, quenching may result from entirely different mechanisms. To address these questions, Stern-Volmer (S-V) experiments were performed using the native-base monophosphate nucleotides (NMPs) GMP, AMP, CMP, and dTMP in aqueous solutions as quenchers to obtain quenching rate constants, k(q). Cyclic voltammetry (CV) and optical absorption and emission data of the PTERS were obtained in aprotic organic solvents. These data were used to obtain excited-state redox potentials from which electron transfer free energies were derived using the Rehm-Weller equation. The reorganization energies for PET were obtained using the Scandola-Balzani equation, taking into account the free energy contribution due to water. 6MAP*, DMAP*, and 3MI* gave negative free energies between -0.1 and -0.2 eV and reorganization energies of about 0.13 eV. They all displayed ET activation energies below the accessible thermal energy (0.038 eV = 3/2k(B)T, where k(B) is Boltzmann's constant) for all NMPs with the exception of CMP, whose activation barrier was only about 35% higher (approximately 0.05 eV). Thus, we conclude that these PTERs act as electron acceptors and promote NMP oxidation. However, 6MI* had positive ET free energies for all NMPs with the exception of GMP (and then only for nucleobase oxidation). The magnitudes of these free energies (> or = 0.45 eV for AMP, CMP, and dTMP) suggest that 6MI* may not quenched by PET.
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Affiliation(s)
- Madhavan Narayanan
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, USA
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Kodali G, Kistler KA, Narayanan M, Matsika S, Stanley RJ. Change in Electronic Structure upon Optical Excitation of 8-Vinyladenosine: An Experimental and Theoretical Study. J Phys Chem A 2009; 114:256-67. [DOI: 10.1021/jp908055h] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Goutham Kodali
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122
| | - Kurt A. Kistler
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122
| | - Madhavan Narayanan
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122
| | - Spiridoula Matsika
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122
| | - Robert J. Stanley
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122
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Kodali G, Siddiqui SU, Stanley RJ. Charge redistribution in oxidized and semiquinone E. coli DNA photolyase upon photoexcitation: stark spectroscopy reveals a rationale for the position of Trp382. J Am Chem Soc 2009; 131:4795-807. [PMID: 19292445 DOI: 10.1021/ja809214r] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The electronic structure of the two lowest excited electronic states of FAD and FADH(*) in folate-depleted E. coli DNA photolyase (PL(OX) and PL(SQ), respectively) was measured using absorption Stark spectroscopy. The experimental analysis was supported by TDDFT calculations of both the charge redistribution and the difference dipole moments for the transitions of both oxidation states using lumiflavin as a model. The difference dipole moments and polarizabilities for PL(OX) are similar to those obtained in our previous work for flavins in simple solvents and in an FMN-containing flavoprotein. No such comparison can be made for PL(SQ), as we believe this to be the first experimental report of the direction and magnitude of excited-state charge redistribution in any flavosemiquinone. The picture that emerges from these studies is discussed in the context of electron transfer in photolyase, particularly for the semiquinone photoreduction process, which involves nearby tryptophan residues as electron donors. The direction of charge displacement derived from an analysis of the Stark spectra rationalizes the positioning of the critical Trp382 residue relative to the flavin for efficient vectorial electron transfer leading to photoreduction. The ramifications of vectorial charge redistribution are discussed in the context of the wider class of flavoprotein blue light photoreceptors.
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Affiliation(s)
- Goutham Kodali
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, USA
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Kodali G, Kistler KA, Matsika S, Stanley RJ. 2-Aminopurine Excited State Electronic Structure Measured by Stark Spectroscopy. J Phys Chem B 2008; 112:1789-95. [DOI: 10.1021/jp076374x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Goutham Kodali
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122
| | - Kurt A. Kistler
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122
| | - Spiridoula Matsika
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122
| | - Robert J. Stanley
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122
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Siddiqui MSU, Kodali G, Stanley RJ. Electronic transition dipole moment directions of reduced anionic flavin in stretched poly(vinyl alcohol) films. J Phys Chem B 2007; 112:119-26. [PMID: 18069812 DOI: 10.1021/jp075830e] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The IR and UV/vis linear dichroic spectra of reduced anionic flavin mononucleotide (FMNH-) partially oriented in poly(vinyl alcohol) (PVA) films have been measured to determine the direction of the major electronic transition dipole moments. The IR linear dichroism (LD) was measured in the 1750-1350 cm(-1) region to provide the overall molecular orientation of the FMNH- in the stretched films. Time-dependent density functional theory using the B3LYP functional was used to calculate the normal modes and the transition dipole moments of reduced lumiflavin. The calculated normal modes assisted in IR band assignments and in the determination of the IR transition dipole moment directions which were required for the determination of the orientation parameters for FMNH- in PVA films. The UV/vis LD spectrum was measured over the 200-700 nm region and was resolved into contributions from three pi-->pi* transitions. The directions of the transitions are 90 degrees+/-4 degrees at 440 nm, 79 degrees+/-4 degrees at 350 nm, and 93 degrees+/-4 degrees at 290 nm with counterclockwise rotations with respect to the N5-N10 axis. Comparison of the calculated and experimentally determined transition dipole moments allowed for refined assignment of the transition dipole moment directions. To our knowledge, this is the first experimental evidence that the 350-450 nm absorption arises from two unique transitions. Remarkably, the two lowest energy transition dipole moments for FMNH- are nearly parallel to those obtained in prior studies for both oxidized and semiquinone flavin.
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Affiliation(s)
- M Salim U Siddiqui
- Department of Biochemistry and Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, USA
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