1
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Nilsen-Moe A, Reinhardt CR, Huang P, Agarwala H, Lopes R, Lasagna M, Glover S, Hammes-Schiffer S, Tommos C, Hammarström L. Switching the proton-coupled electron transfer mechanism for non-canonical tyrosine residues in a de novo protein. Chem Sci 2024; 15:3957-3970. [PMID: 38487244 PMCID: PMC10935721 DOI: 10.1039/d3sc05450k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 01/23/2024] [Indexed: 03/17/2024] Open
Abstract
The proton-coupled electron transfer (PCET) reactions of tyrosine (Y) are instrumental to many redox reactions in nature. This study investigates how the local environment and the thermodynamic properties of Y influence its PCET characteristics. Herein, 2- and 4-mercaptophenol (MP) are placed in the well-folded α3C protein (forming 2MP-α3C and 4MP-α3C) and oxidized by external light-generated [Ru(L)3]3+ complexes. The resulting neutral radicals are long-lived (>100 s) with distinct optical and EPR spectra. Calculated spin-density distributions are similar to canonical Y˙ and display very little spin on the S-S bridge that ligates the MPs to C32 inside the protein. With 2MP-α3C and 4MP-α3C we probe how proton transfer (PT) affects the PCET rate constants and mechanisms by varying the degree of solvent exposure or the potential to form an internal hydrogen bond. Solution NMR ensemble structures confirmed our intended design by displaying a major difference in the phenol OH solvent accessible surface area (≤∼2% for 2MP and 30-40% for 4MP). Additionally, 2MP-C32 is within hydrogen bonding distance to a nearby glutamate (average O-O distance is 3.2 ± 0.5 Å), which is suggested also by quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulations. Neither increased exposure of the phenol OH to solvent (buffered water), nor the internal hydrogen bond, was found to significantly affect the PCET rates. However, the lower phenol pKa values associated with the MP-α3C proteins compared to α3Y provided a sufficient change in PT driving force to alter the PCET mechanism. The PCET mechanism for 2MP-α3C and 4MP-α3C with moderately strong oxidants was predominantly step-wise PTET for pH values, but changed to concerted PCET at neutral pH values and below when a stronger oxidant was used, as found previously for α3Y. This shows how the balance of ET and PT driving forces is critical for controlling PCET mechanisms. The presented results improve our general understanding of amino-acid based PCET in enzymes.
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Affiliation(s)
- Astrid Nilsen-Moe
- Department of Chemistry, Ångström Laboratory, Uppsala University Box 523 75120 Uppsala Sweden
| | - Clorice R Reinhardt
- Department of Molecular Biophysics and Biochemistry, Yale University New Haven CT 06520 USA
| | - Ping Huang
- Department of Chemistry, Ångström Laboratory, Uppsala University Box 523 75120 Uppsala Sweden
| | - Hemlata Agarwala
- Technical University Munich, Campus Straubing for Biotechnology and Sustainability Uferstraße 53 94315 Straubing Germany
| | - Rosana Lopes
- Department of Biochemistry and Biophysics, Texas A&M University College Station TX 77843 USA
| | - Mauricio Lasagna
- Department of Biochemistry and Biophysics, Texas A&M University College Station TX 77843 USA
| | - Starla Glover
- Department of Chemistry, Ångström Laboratory, Uppsala University Box 523 75120 Uppsala Sweden
| | | | - Cecilia Tommos
- Department of Biochemistry and Biophysics, Texas A&M University College Station TX 77843 USA
| | - Leif Hammarström
- Department of Chemistry, Ångström Laboratory, Uppsala University Box 523 75120 Uppsala Sweden
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2
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Edholm F, Nandy A, Reinhardt CR, Kastner DW, Kulik HJ. Protein3D: Enabling analysis and extraction of metal-containing sites from the Protein Data Bank with molSimplify. J Comput Chem 2024; 45:352-361. [PMID: 37873926 DOI: 10.1002/jcc.27242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 09/27/2023] [Accepted: 10/03/2023] [Indexed: 10/25/2023]
Abstract
Metalloenzymes catalyze a wide range of chemical transformations, with the active site residues playing a key role in modulating chemical reactivity and selectivity. Unlike smaller synthetic catalysts, a metalloenzyme active site is embedded in a larger protein, which makes interrogation of electronic properties and geometric features with quantum mechanical calculations challenging. Here we implement the ability to fetch crystallographic structures from the Protein Data Bank and analyze the metal binding sites in the program molSimplify. We show the usefulness of the newly created protein3D class to extract the local environment around non-heme iron enzymes containing a two histidine motif and prepare 372 structures for quantum mechanical calculations. Our implementation of protein3D serves to expand the range of systems molSimplify can be used to analyze and will enable high-throughput study of metal-containing active sites in proteins.
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Affiliation(s)
- Freya Edholm
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Aditya Nandy
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Clorice R Reinhardt
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - David W Kastner
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Heather J Kulik
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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3
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Zhong J, Reinhardt CR, Hammes-Schiffer S. Direct Proton-Coupled Electron Transfer between Interfacial Tyrosines in Ribonucleotide Reductase. J Am Chem Soc 2023; 145:4784-4790. [PMID: 36802630 PMCID: PMC10344599 DOI: 10.1021/jacs.2c13615] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
Ribonucleotide reductase (RNR) regulates DNA synthesis and repair in all organisms. The mechanism of Escherichia coli RNR requires radical transfer over a proton-coupled electron transfer (PCET) pathway spanning ∼32 Å across two protein subunits. A key step along this pathway is the interfacial PCET reaction between Y356 in the β subunit and Y731 in the α subunit. Herein, this PCET reaction between two tyrosines across an aqueous interface is explored with classical molecular dynamics and quantum mechanical/molecular mechanical (QM/MM) free energy simulations. The simulations suggest that the water-mediated mechanism involving double proton transfer through an intervening water molecule is thermodynamically and kinetically unfavorable. The direct PCET mechanism between Y356 and Y731 becomes feasible when Y731 is flipped toward the interface and is predicted to be approximately isoergic with a relatively low free energy barrier. This direct mechanism is facilitated by the hydrogen bonding of water to both Y356 and Y731. These simulations provide fundamental insights into radical transfer across aqueous interfaces.
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Affiliation(s)
- Jiayun Zhong
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Clorice R. Reinhardt
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, United States
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4
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Shipps C, Thrush KL, Reinhardt CR, Siwiecki SA, Claydon JL, Noble DB, O'Hern CS. "Student-led workshop strengthens perceived discussion skills and community in an interdisciplinary graduate program". FASEB Bioadv 2023; 5:1-12. [PMID: 36643898 PMCID: PMC9832528 DOI: 10.1096/fba.2021-00165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 09/30/2022] [Accepted: 10/05/2022] [Indexed: 01/18/2023] Open
Abstract
The Integrated Graduate Program in Physical and Engineering Biology (IGPPEB) at Yale University brings together Ph.D. students from the physical, engineering, and biological sciences. The main goals of this program are for students to become comfortable working in an interdisciplinary and collaborative research environment and adept at communicating with scientists and nonscientists. To fill a student-identified learning gap in engaging in inclusive discussions, IGPPEB students developed a communication workshop to improve skills in visual engagement, citing specific content, constructive conversation entrances, and encouragement of peers. Based on short- and long-term assessment of the workshop, 100% of students reported that it should be offered to future cohorts and 63% of students perceived it to be personally helpful. Additionally, 92% of participants reported using one or more of the core skills beyond the course, with skills in "Encouraging peers" and "Constructive conversation entrances" rated the highest in perceived improvement. Based on the highest average rating of 76 ± 24 (on a scale of 0-100), students agreed that the workshop made them feel more welcome in the IGPPEB community. With a rating of 68 ± 13, they also agreed that the workshop had a positive impact on their graduate school experience. Participants provided suggestions for future improvements, such as increasing student involvement in leading discussions of course material. This study demonstrates that a student-led workshop can improve perceived discussion skills and build community across an interdisciplinary program in the sciences.
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Affiliation(s)
- Catharine Shipps
- Integrated Graduate Program in Physical and Engineering Biology Yale University New Haven Connecticut USA
- Department of Molecular Biophysics and Biochemistry Yale University New Haven Connecticut USA
| | - Kyra L Thrush
- Integrated Graduate Program in Physical and Engineering Biology Yale University New Haven Connecticut USA
- Graduate Program in Computational Biology and Bioinformatics Yale University New Haven Connecticut USA
| | - Clorice R Reinhardt
- Integrated Graduate Program in Physical and Engineering Biology Yale University New Haven Connecticut USA
- Department of Molecular Biophysics and Biochemistry Yale University New Haven Connecticut USA
| | - Sara A Siwiecki
- Integrated Graduate Program in Physical and Engineering Biology Yale University New Haven Connecticut USA
- Department of Molecular Biophysics and Biochemistry Yale University New Haven Connecticut USA
| | - Jennifer L Claydon
- Poorvu Center for Teaching and Learning Yale University New Haven Connecticut USA
- Combined Graduate Program in Biological and Biomedical Sciences Yale University New Haven Connecticut USA
| | - Dorottya B Noble
- Integrated Graduate Program in Physical and Engineering Biology Yale University New Haven Connecticut USA
- Program in Physics, Engineering, and Biology Yale University New Haven Connecticut USA
| | - Corey S O'Hern
- Integrated Graduate Program in Physical and Engineering Biology Yale University New Haven Connecticut USA
- Graduate Program in Computational Biology and Bioinformatics Yale University New Haven Connecticut USA
- Program in Physics, Engineering, and Biology Yale University New Haven Connecticut USA
- Department of Mechanical Engineering & Materials Science Yale University New Haven Connecticut USA
- Department of Physics Yale University New Haven Connecticut USA
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5
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Zhong J, Reinhardt CR, Hammes-Schiffer S. Role of Water in Proton-Coupled Electron Transfer between Tyrosine and Cysteine in Ribonucleotide Reductase. J Am Chem Soc 2022; 144:7208-7214. [PMID: 35426309 PMCID: PMC9197590 DOI: 10.1021/jacs.1c13455] [Citation(s) in RCA: 2] [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: 12/11/2022]
Abstract
Ribonucleotide reductase (RNR) catalyzes the reduction of ribonucleotides to deoxyribonucleotides and is critical for DNA synthesis and repair in all organisms. Its mechanism requires radical transfer along a ∼32 Å pathway through a series of proton-coupled electron transfer (PCET) steps. Previous simulations suggested that a glutamate residue (E623) mediates the PCET reaction between two stacked tyrosine residues (Y730 and Y731) through a proton relay mechanism. This work focuses on the adjacent PCET reaction between Y730 and a cysteine residue (C439). Quantum mechanical/molecular mechanical free energy simulations illustrate that when Y730 and Y731 are stacked, E623 stabilizes the radical on C439 through hydrogen bonding with the Y730 hydroxyl group. When Y731 is flipped away from Y730, a water molecule stabilizes the radical on C439 through hydrogen bonding with Y730 and lowers the free energy barrier for radical transfer from Y730 to C439 through electrostatic interactions with the transferring hydrogen but does not directly accept the proton. These simulations indicate that the conformational motions and electrostatic interactions of the tyrosines, cysteine, glutamate, and water strongly impact the thermodynamics and kinetics of these two coupled PCET reactions. Such insights are important for protein engineering efforts aimed at altering radical transfer in RNR.
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Affiliation(s)
- Jiayun Zhong
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, United States
| | - Clorice R. Reinhardt
- Department of Molecular Biophysics & Biochemistry, Yale University, 266 Whitney Avenue, New Haven, Connecticut 06520, United States
| | - Sharon Hammes-Schiffer
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, United States
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6
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Reinhardt CR, Sayfutyarova ER, Zhong J, Hammes-Schiffer S. Glutamate Mediates Proton-Coupled Electron Transfer Between Tyrosines 730 and 731 in Escherichia coli Ribonucleotide Reductase. J Am Chem Soc 2021; 143:6054-6059. [DOI: 10.1021/jacs.1c02152] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Clorice R. Reinhardt
- Department of Molecular Biophysics & Biochemistry, Yale University, 266 Whitney Avenue, New Haven, Connecticut 06520, United States
| | - Elvira R. Sayfutyarova
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, United States
| | - Jiayun Zhong
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, United States
| | - Sharon Hammes-Schiffer
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, United States
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7
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Hu QH, Williams MT, Shulgina I, Fossum CJ, Weeks KM, Adams LM, Reinhardt CR, Musier-Forsyth K, Hati S, Bhattacharyya S. Editing Domain Motions Preorganize the Synthetic Active Site of Prolyl-tRNA Synthetase. ACS Catal 2020; 10:10229-10242. [PMID: 34295570 DOI: 10.1021/acscatal.0c02381] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Prolyl-tRNA synthetases (ProRSs) catalyze the covalent attachment of proline onto cognate tRNAs, an indispensable step for protein synthesis in all living organisms. ProRSs are modular enzymes and the "prokaryotic-like" ProRSs are distinguished from "eukaryotic-like" ProRSs by the presence of an editing domain (INS) inserted between motifs 2 and 3 of the main catalytic domain. Earlier studies suggested the presence of coupled-domain dynamics could contribute to catalysis; however, the role that the distal, highly mobile INS domain plays in catalysis at the synthetic active site is not completely understood. In the present study, a combination of theoretical and experimental approaches has been used to elucidate the precise role of INS domain dynamics. Quantum mechanical/molecular mechanical simulations were carried out to model catalytic Pro-AMP formation by Enterococcus faecalis ProRS. The energetics of the adenylate formation by the wild-type enzyme was computed and contrasted with variants containing active site mutations, as well as a deletion mutant lacking the INS domain. The combined results revealed that two distinct types of dynamics contribute to the enzyme's catalytic power. One set of motions is intrinsic to the INS domain and leads to conformational preorganization that is essential for catalysis. A second type of motion, stemming from the electrostatic reorganization of active site residues, impacts the height and width of the energy profile and has a critical role in fine tuning the substrate orientation to facilitate reactive collisions. Thus, motions in a distal domain can preorganize the active site of an enzyme to optimize catalysis.
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Affiliation(s)
- Quin H. Hu
- Department of Chemistry and Biochemistry, University of Wisconsin, Eau Claire, Wisconsin 54701, United States
| | - Murphi T. Williams
- Department of Chemistry and Biochemistry, University of Wisconsin, Eau Claire, Wisconsin 54701, United States
| | - Irina Shulgina
- Department of Chemistry and Biochemistry and Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Carl J. Fossum
- Department of Chemistry and Biochemistry, University of Wisconsin, Eau Claire, Wisconsin 54701, United States
| | - Katelyn M. Weeks
- Department of Chemistry and Biochemistry, University of Wisconsin, Eau Claire, Wisconsin 54701, United States
| | - Lauren M. Adams
- Department of Chemistry and Biochemistry, University of Wisconsin, Eau Claire, Wisconsin 54701, United States
| | - Clorice R. Reinhardt
- Department of Chemistry and Biochemistry, University of Wisconsin, Eau Claire, Wisconsin 54701, United States
| | - Karin Musier-Forsyth
- Department of Chemistry and Biochemistry and Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Sanchita Hati
- Department of Chemistry and Biochemistry, University of Wisconsin, Eau Claire, Wisconsin 54701, United States
| | - Sudeep Bhattacharyya
- Department of Chemistry and Biochemistry, University of Wisconsin, Eau Claire, Wisconsin 54701, United States
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8
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Reinhardt CR, Li P, Kang G, Stubbe J, Drennan CL, Hammes-Schiffer S. Conformational Motions and Water Networks at the α/β Interface in E. coli Ribonucleotide Reductase. J Am Chem Soc 2020; 142:13768-13778. [PMID: 32631052 DOI: 10.1021/jacs.0c04325] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Ribonucleotide reductases (RNRs) catalyze the conversion of all four ribonucleotides to deoxyribonucleotides and are essential for DNA synthesis in all organisms. The active form of E. coli Ia RNR is composed of two homodimers that form the active α2β2 complex. Catalysis is initiated by long-range radical translocation over a ∼32 Å proton-coupled electron transfer (PCET) pathway involving Y356β and Y731α at the interface. Resolving the PCET pathway at the α/β interface has been a long-standing challenge due to the lack of structural data. Herein, molecular dynamics simulations based on a recently solved cryogenic-electron microscopy structure of an active α2β2 complex are performed to examine the structure and fluctuations of interfacial water, as well as the hydrogen-bonding interactions and conformational motions of interfacial residues along the PCET pathway. Our free energy simulations reveal that Y731 is able to sample both a flipped-out conformation, where it points toward the interface to facilitate interfacial PCET with Y356, and a stacked conformation with Y730 to enable collinear PCET with this residue. Y356 and Y731 exhibit hydrogen-bonding interactions with interfacial water molecules and, in some conformations, share a bridging water molecule, suggesting that the primary proton acceptor for PCET from Y356 and from Y731 is interfacial water. The conformational flexibility of Y731 and the hydrogen-bonding interactions of both Y731 and Y356 with interfacial water and hydrogen-bonded water chains appear critical for effective radical translocation along the PCET pathway. These simulations are consistent with biochemical and spectroscopic data and provide previously unattainable atomic-level insights into the fundamental mechanism of RNR.
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Affiliation(s)
- Clorice R Reinhardt
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven Connecticut 06520, United States
| | - Pengfei Li
- Department of Chemistry, Yale University, New Haven Connecticut 06520, United States
| | - Gyunghoon Kang
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge Massachusetts 02139, United States.,Department of Chemistry, Massachusetts Institute of Technology, Cambridge Massachusetts 02139, United States
| | - JoAnne Stubbe
- Department of Biology, Massachusetts Institute of Technology, Cambridge Massachusetts 02139, United States.,Department of Chemistry, Massachusetts Institute of Technology, Cambridge Massachusetts 02139, United States
| | - Catherine L Drennan
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge Massachusetts 02139, United States.,Department of Biology, Massachusetts Institute of Technology, Cambridge Massachusetts 02139, United States.,Department of Chemistry, Massachusetts Institute of Technology, Cambridge Massachusetts 02139, United States.,Fellow, Bio-inspired Solar Energy Program, Canadian Institute for Advanced Research (CIFAR), Toronto, ON M5G 1M1, Canada
| | - Sharon Hammes-Schiffer
- Department of Chemistry, Yale University, New Haven Connecticut 06520, United States.,Fellow, Bio-inspired Solar Energy Program, Canadian Institute for Advanced Research (CIFAR), Toronto, ON M5G 1M1, Canada
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9
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Nilsen-Moe A, Reinhardt CR, Glover SD, Liang L, Hammes-Schiffer S, Hammarström L, Tommos C. Proton-Coupled Electron Transfer from Tyrosine in the Interior of a de novo Protein: Mechanisms and Primary Proton Acceptor. J Am Chem Soc 2020; 142:11550-11559. [PMID: 32479070 PMCID: PMC7315633 DOI: 10.1021/jacs.0c04655] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
![]()
Proton-coupled
electron transfer (PCET) from tyrosine produces
a neutral tyrosyl radical (Y•) that is vital to
many catalytic redox reactions. To better understand how the protein
environment influences the PCET properties of tyrosine, we have studied
the radical formation behavior of Y32 in the α3Y model protein. The previously solved α3Y solution NMR structure shows that Y32 is sequestered
∼7.7 ± 0.3 Å below the protein surface without any
primary proton acceptors nearby. Here we present transient absorption
kinetic data and molecular dynamics (MD) simulations to resolve the
PCET mechanism associated with Y32 oxidation. Y32• was generated in a bimolecular reaction with
[Ru(bpy)3]3+ formed by flash photolysis. At
pH > 8, the rate constant of Y32• formation
(kPCET) increases by one order of magnitude
per pH unit, corresponding to a proton-first mechanism via tyrosinate
(PTET). At lower pH < 7.5, the pH dependence is weak and shows
a previously measured KIE ≈ 2.5, which best fits a concerted
mechanism. kPCET is independent of phosphate
buffer concentration at pH 6.5. This provides clear evidence that
phosphate buffer is not the primary proton acceptor. MD simulations
show that one to two water molecules can enter the hydrophobic cavity
of α3Y and hydrogen bond to Y32, as well
as the possibility of hydrogen-bonding interactions between Y32 and E13, through structural fluctuations that
reorient surrounding side chains. Our results illustrate how protein
conformational motions can influence the redox reactivity of a tyrosine
residue and how PCET mechanisms can be tuned by changing the pH even
when the PCET occurs within the interior of a protein.
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Affiliation(s)
- Astrid Nilsen-Moe
- Department of Chemistry, Ångström Laboratory, Uppsala University, Box 523, Uppsala 75120, Sweden
| | - Clorice R Reinhardt
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Starla D Glover
- Department of Chemistry, Ångström Laboratory, Uppsala University, Box 523, Uppsala 75120, Sweden
| | - Li Liang
- Departments of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6059, United States
| | | | - Leif Hammarström
- Department of Chemistry, Ångström Laboratory, Uppsala University, Box 523, Uppsala 75120, Sweden
| | - Cecilia Tommos
- Departments of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6059, United States.,Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843-2128, United States
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10
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Reinhardt CR, Hu QH, Bresnahan CG, Hati S, Bhattacharyya S. Cyclic Changes in Active Site Polarization and Dynamics Drive the 'Ping-pong' Kinetics in NRH:Quinone Oxidoreductase 2: An Insight from QM/MM Simulations. ACS Catal 2018; 8:12015-12029. [PMID: 31583178 DOI: 10.1021/acscatal.8b04193] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Quinone reductases belong to the family of flavin-dependent oxidoreductases. With the redox active cofactor, flavin adenine dinucleotide, quinone reductases are known to utilize a 'ping-pong' kinetic mechanism during catalysis in which a hydride is bounced back and forth between flavin and its two substrates. However, the continuation of this catalytic cycle requires product displacement steps, where the product of one redox half-cycle is displaced by the substrate of the next half-cycle. Using improved hybrid quantum mechanical/molecular mechanical simulations, both the catalytic hydride transfer and the product displacement reactions were studied in NRH:quinone oxidoreductase 2. Initially, the self-consistent charge-density functional tight binding theory was used to describe flavin ring and the substrate atoms, while embedded in the molecular mechanically-treated solvated active site. Then, for each step of the catalytic cycle, a further improvement of energetics was made using density functional theory-based corrections. The present study showcases an integrated interplay of solvation, protonation, and protein matrix-induced polarization as the driving force behind the thermodynamic wheel of the 'ping-pong' kinetics. Reported here is the first-principles model of the 'ping-pong' kinetics that portrays how cyclic changes in the active site polarization and dynamics govern the oscillatory hydride transfer and product displacement in this enzyme.
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Affiliation(s)
- Clorice R. Reinhardt
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin 54702, United States
| | - Quin H. Hu
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin 54702, United States
| | - Caitlin G. Bresnahan
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin 54702, United States
| | - Sanchita Hati
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin 54702, United States
| | - Sudeep Bhattacharyya
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, Wisconsin 54702, United States
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11
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Goings JJ, Reinhardt CR, Hammes-Schiffer S. Propensity for Proton Relay and Electrostatic Impact of Protein Reorganization in Slr1694 BLUF Photoreceptor. J Am Chem Soc 2018; 140:15241-15251. [DOI: 10.1021/jacs.8b07456] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Joshua J. Goings
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, United States
| | - Clorice R. Reinhardt
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, United States
| | - Sharon Hammes-Schiffer
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, United States
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12
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Reinhardt CR, Jaglinski TC, Kastenschmidt AM, Song EH, Gross AK, Krause AJ, Gollmar JM, Meise KJ, Stenerson ZS, Weibel TJ, Dison A, Finnegan MR, Griesi DS, Heltne MD, Hughes TG, Hunt CD, Jansen KA, Xiong AH, Hati S, Bhattacharyya S. Insight into the kinetics and thermodynamics of the hydride transfer reactions between quinones and lumiflavin: a density functional theory study. J Mol Model 2016; 22:199. [PMID: 27491848 DOI: 10.1007/s00894-016-3074-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [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: 03/24/2016] [Accepted: 07/17/2016] [Indexed: 12/14/2022]
Abstract
The kinetics and equilibrium of the hydride transfer reaction between lumiflavin and a number of substituted quinones was studied using density functional theory. The impact of electron withdrawing/donating substituents on the redox potentials of quinones was studied. In addition, the role of these substituents on the kinetics of the hydride transfer reaction with lumiflavin was investigated in detail under the transition state (TS) theory assumption. The hydride transfer reactions were found to be more favorable for an electron-withdrawing substituent. The activation barrier exhibited a quadratic relationship with the driving force of these reactions as derived under the formalism of modified Marcus theory. The present study found a significant extent of electron delocalization in the TS that is stabilized by enhanced electrostatic, polarization, and exchange interactions. Analysis of geometry, bond-orders, and energetics revealed a predominant parallel (Leffler-Hammond) effect on the TS. Closer scrutiny reveals that electron-withdrawing substituents, although located on the acceptor ring, reduce the N-H bond order of the donor fragment in the precursor complex. Carried out in the gas-phase, this is the first ever report of a theoretical study of flavin's hydride transfer reactions with quinones, providing an unfiltered view of the electronic effect on the nuclear reorganization of donor-acceptor complexes.
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Affiliation(s)
- Clorice R Reinhardt
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, WI, 54702, USA
| | - Tanner C Jaglinski
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, WI, 54702, USA
| | - Ashly M Kastenschmidt
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, WI, 54702, USA
| | - Eun H Song
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, WI, 54702, USA
| | - Adam K Gross
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, WI, 54702, USA
| | - Alyssa J Krause
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, WI, 54702, USA
| | - Jonathan M Gollmar
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, WI, 54702, USA
| | - Kristin J Meise
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, WI, 54702, USA
| | - Zachary S Stenerson
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, WI, 54702, USA
| | - Tyler J Weibel
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, WI, 54702, USA
| | - Andrew Dison
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, WI, 54702, USA
| | - Mackenzie R Finnegan
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, WI, 54702, USA
| | - Daniel S Griesi
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, WI, 54702, USA
| | - Michael D Heltne
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, WI, 54702, USA
| | - Tom G Hughes
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, WI, 54702, USA
| | - Connor D Hunt
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, WI, 54702, USA
| | - Kayla A Jansen
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, WI, 54702, USA
| | - Adam H Xiong
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, WI, 54702, USA
| | - Sanchita Hati
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, WI, 54702, USA
| | - Sudeep Bhattacharyya
- Department of Chemistry, University of Wisconsin-Eau Claire, Eau Claire, WI, 54702, USA.
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Franzoso M, Karbach S, Prando V, Zaglia T, Pianca N, Vitiello L, Mongillo M, Hoermann NH, Jaeckel SJ, Schoenfelder TS, Schueler RS, Finger SF, Kossmann SK, Knorr MK, Brandt MB, Wilms EW, Waisman AW, Muenzel TM, Baekhed FB, Reinhardt CR, Wenzel PW, Pianca N, Incensi A, Franzoso M, Donadio V, Scorrano L, Zaglia T, Mongillo M. Sciences within European Young Researcher Community272The neuro-cardiac interaction defines an extracellular microdomain required for neurotrophic signaling273Gut microbiota is important in the development of angiotensin II driven arterial hypertension and vascular dysfunction in mice274Role of the mitochondrial protein Opa1 in the regulation of the cardiac sympathetic neuron physiology. Cardiovasc Res 2016. [DOI: 10.1093/cvr/cvw151] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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14
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Bresnahan CG, Reinhardt CR, Bartholow TG, Rumpel JP, North M, Bhattacharyya S. Effect of stacking interactions on the thermodynamics and kinetics of lumiflavin: a study with improved density functionals and density functional tight-binding protocol. J Phys Chem A 2014; 119:172-82. [PMID: 25490119 DOI: 10.1021/jp510020v] [Citation(s) in RCA: 12] [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: 02/02/2023]
Abstract
The π-π stacking interaction between lumiflavin and a number of π-electron-rich molecules has been studied by density functional theory using several new-generation density functionals. Six known lumiflavin-aromatic adducts were used and the models were evaluated by comparing the geometry and energetics with experimental results. The study found that dispersion-corrected and hybrid functionals with larger (>50%) Hartree-Fock exchanges produced superior results in modeling thermodynamic characteristics of these complexes. The functional producing the best energetics for these model systems was used to study the stacking interactions of lumiflavin with biologically relevant aromatic groups. Additionally, the reduction of flavin-in the presence of both a hydride donor and a nondonor π-electronic system was also studied. Weak interactions were observed in the stacked lumiflavin complexes of benzene, phenol, and indole, mimicking phenyl alanine, tryptophan, and tyrosine side chains, respectively, of an enzyme. The stacked complex of naphthalene and flavin showed little change in flavin's redox potential indicating insignificant effect on the thermodynamics of the hydride transfer reaction. In contrast, the hydride transfer reaction with the hydride donor N-methyl nicotinamide tells a different story, as the transition state was found to be strongly impacted by the stacking interactions. A comparison of performance between the density functional theory (DFT) and the computationally less expensive dispersion-corrected self-consistent density functional tight-binding (SCC-DFTB-D) theory revealed that the latter produces consistent energetics for this hydride transfer reaction and additional DFT-computed perturbative corrections could significantly improve these results.
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Affiliation(s)
- Caitlin G Bresnahan
- Department of Chemistry, University of Wisconsin-Eau Claire , Eau Claire, Wisconsin 54702, United States
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