1
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Gibbs C, Fedoretz-Maxwell BP, MacNeil GA, Walsby CJ, Warren JJ. Proximal Methionine Amino Acid Residue Affects the Properties of Redox-Active Tryptophan in an Artificial Model Protein. ACS OMEGA 2023; 8:19798-19806. [PMID: 37305310 PMCID: PMC10249128 DOI: 10.1021/acsomega.3c01589] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 05/11/2023] [Indexed: 06/13/2023]
Abstract
Redox-active amino acid residues are at the heart of biological electron-transfer reactions. They play important roles in natural protein functions and are implicated in disease states (e.g., oxidative-stress-associated disorders). Tryptophan (Trp) is one such redox-active amino acid residue, and it has long been known to serve a functional role in proteins. Broadly speaking, there is still much to learn about the local features that make some Trp redox active and others inactive. Herein, we describe a new protein model system where we investigate how a methionine (Met) residue proximal to a redox-active Trp affects its reactivity and spectroscopy. We use an artificial variant of azurin from Pseudomonas aeruginosa to produce these models. We employ a series of UV-visible spectroscopy, electrochemistry, electron paramagnetic resonance, and density functional theory experiments to demonstrate the effect that placing Met near Trp radicals has in the context of redox proteins. The introduction of Met proximal to Trp lowers its reduction potential by ca. 30 mV and causes clear shifts in the optical spectra of the corresponding radicals. While the effect may be small, it is significant enough to be a way for natural systems to tune Trp reactivity.
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2
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The Potential of a Protein Model Synthesized Absent of Methionine. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27123679. [PMID: 35744804 PMCID: PMC9230714 DOI: 10.3390/molecules27123679] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 05/20/2022] [Accepted: 06/03/2022] [Indexed: 11/17/2022]
Abstract
Methionine is an amino acid long thought to be essential, but only in the case of protein synthesis initiation. In more recent years, methionine has been found to play an important role in antioxidant defense, stability, and modulation of cell and protein activity. Though these findings have expanded the previously held sentiment of methionine having a singular purpose within cells and proteins, the essential nature of methionine can still be challenged. Many of the features that give methionine its newfound functions are shared by the other sulfur-containing amino acid: cysteine. While the antioxidant, stabilizing, and cell/protein modulatory functions of cysteine have already been well established, recent findings have shown a similar hydrophobicity to methionine which suggests cysteine may be able to replace methionine in all functions outside of protein synthesis initiation with little effect on cell and protein function. Furthermore, a number of novel mechanisms for alternative initiation of protein synthesis have been identified that suggest a potential to bypass the traditional methionine-dependent initiation during times of stress. In this review, these findings are discussed with a number of examples that demonstrate a potential model for synthesizing a protein in the absence of methionine.
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3
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Gibbs CA, Fedoretz-Maxwell BP, Warren JJ. On the roles of methionine and the importance of its microenvironments in redox metalloproteins. Dalton Trans 2022; 51:4976-4985. [PMID: 35253809 DOI: 10.1039/d1dt04387k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The amino acid residue methionine (Met) is commonly thought of as a ligand in redox metalloproteins, for example in cytochromes c and in blue copper proteins. However, the roles of Met can go beyond a simple ligand. The thioether functional group of Met allows it to be considered as a hydrophobic residue as well as one that is capable of weak dipolar interactions. In addition, the lone pairs on sulphur allow Met to interact with other groups, inluding the aforementioned metal ions. Because of its properties, Met can play diverse roles in metal coordination, fine tuning of redox reactions, or supporting protein structures. These roles are strongly influenced by the nature of the surrounding medium. Herein, we describe several common interactions between Met and surrounding aromatic amino acids and how they affect the physical properties of both copper and iron metalloproteins. While the importance of interactions between Met and other groups is established in biological systems, less is known about their roles in redox metalloproteins and our view is that this is an area that is ready for greater attention.
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Affiliation(s)
- Curtis A Gibbs
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby BC V5A 1S6, Canada.
| | | | - Jeffrey J Warren
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby BC V5A 1S6, Canada.
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4
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Albanese KI, Leaver-Fay A, Treacy JW, Park R, Houk KN, Kuhlman B, Waters ML. Comparative Analysis of Sulfonium-π, Ammonium-π, and Sulfur-π Interactions and Relevance to SAM-Dependent Methyltransferases. J Am Chem Soc 2022; 144:2535-2545. [PMID: 35108000 PMCID: PMC8923077 DOI: 10.1021/jacs.1c09902] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report the measurement and analysis of sulfonium-π, thioether-π, and ammonium-π interactions in a β-hairpin peptide model system, coupled with computational investigation and PDB analysis. These studies indicated that the sulfonium-π interaction is the strongest and that polarizability contributes to the stronger interaction with sulfonium relative to ammonium. Computational studies demonstrate that differences in solvation of the trimethylsulfonium versus the trimethylammonium group also contribute to the stronger sulfonium-π interaction. In comparing sulfonium-π versus sulfur-π interactions in proteins, analysis of SAM- and SAH-bound enzymes in the PDB suggests that aromatic residues are enriched in close proximity to the sulfur of both SAM and SAH, but the populations of aromatic interactions of the two cofactors are not significantly different, with the exception of the Me-π interactions in SAM, which are the most prevalent interaction in SAM but are not possible for SAH. This suggests that the weaker interaction energies due to loss of the cation-π interaction in going from SAM to SAH may contribute to turnover of the cofactor.
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Affiliation(s)
- Katherine I. Albanese
- Department of Chemistry, CB 3290, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599
| | - Andrew Leaver-Fay
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599
| | - Joseph W. Treacy
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA, 90095-1569
| | - Rodney Park
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599
| | - K. N. Houk
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA, 90095-1569
| | - Brian Kuhlman
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599
| | - Marcey L. Waters
- Department of Chemistry, CB 3290, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599
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5
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Orabi EA, Öztürk TN, Bernhardt N, Faraldo-Gómez JD. Corrections in the CHARMM36 Parametrization of Chloride Interactions with Proteins, Lipids, and Alkali Cations, and Extension to Other Halide Anions. J Chem Theory Comput 2021; 17:6240-6261. [PMID: 34516741 DOI: 10.1021/acs.jctc.1c00550] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The nonpolarizable CHARMM force field is one of the most widely used energy functions for all-atom biomolecular simulations. Chloride is the only halide ion included in the latest version, CHARMM36m, and is used widely in simulation studies, often as an electrolyte ion but also as the biological substrate of transport proteins and enzymes. Here, we find that existing parameters systematically underestimate the interaction of Cl- with proteins and lipids. Accordingly, when examined in solution, little to no Cl-association can be observed with most components of the protein, including backbone, polar side chains and aromatic rings. The strength of the interaction with cationic side chains and with alkali ions is also incongruent with experimental measurements, specifically osmotic coefficients of concentrated solutions. Consistent with these findings, a 4-μs trajectory of the Cl--specific transport protein CLC-ec1 shows irreversible Cl- dissociation from the so-called Scen binding site, even in a 150 mM NaCl buffer. To correct for these deficiencies, we formulate a series of pair-specific Lennard-Jones parameters that override those resulting from the conventional Lorentz-Berthelot combination rules. These parameters, referred to as NBFIX, are systematically calibrated against available experimental data as well as ab initio geometry optimizations and energy evaluations, for a wide set of binary and ternary Cl- complexes with protein and lipid analogs and alkali cations. Analogously, we also formulate parameter sets for the other three biological halide ions, namely, fluoride, bromide, and iodide. The resulting parameters are used to calculate the potential of mean force defining the interaction of each anion and each of the protein and lipid analogues in bulk water, revealing association free energies in the range of -0.3 to -3.3 kcal/mol, with the F- complexes being the least stable. The NBFIX corrections also preserve the Cl- occupancy of CLC-ec1 in a second 4-μs trajectory. We posit that these optimized molecular-mechanics models provide a more realistic foundation for all-atom simulation studies of processes entailing changes in hydration, recognition, or transport of halide anions.
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Affiliation(s)
- Esam A Orabi
- Theoretical Molecular Biophysics Laboratory, National Heart, Lung and Blood Institute, National Institutes of Health, 10 Center Drive, Bethesda, Maryland 20814, United States
| | - Tuǧba N Öztürk
- Theoretical Molecular Biophysics Laboratory, National Heart, Lung and Blood Institute, National Institutes of Health, 10 Center Drive, Bethesda, Maryland 20814, United States.,Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, United States
| | - Nathan Bernhardt
- Theoretical Molecular Biophysics Laboratory, National Heart, Lung and Blood Institute, National Institutes of Health, 10 Center Drive, Bethesda, Maryland 20814, United States
| | - José D Faraldo-Gómez
- Theoretical Molecular Biophysics Laboratory, National Heart, Lung and Blood Institute, National Institutes of Health, 10 Center Drive, Bethesda, Maryland 20814, United States
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6
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Aledo JC. The Role of Methionine Residues in the Regulation of Liquid-Liquid Phase Separation. Biomolecules 2021; 11:biom11081248. [PMID: 34439914 PMCID: PMC8394241 DOI: 10.3390/biom11081248] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Revised: 08/12/2021] [Accepted: 08/18/2021] [Indexed: 02/07/2023] Open
Abstract
Membraneless organelles are non-stoichiometric supramolecular structures in the micron scale. These structures can be quickly assembled/disassembled in a regulated fashion in response to specific stimuli. Membraneless organelles contribute to the spatiotemporal compartmentalization of the cell, and they are involved in diverse cellular processes often, but not exclusively, related to RNA metabolism. Liquid-liquid phase separation, a reversible event involving demixing into two distinct liquid phases, provides a physical framework to gain insights concerning the molecular forces underlying the process and how they can be tuned according to the cellular needs. Proteins able to undergo phase separation usually present a modular architecture, which favors a multivalency-driven demixing. We discuss the role of low complexity regions in establishing networks of intra- and intermolecular interactions that collectively control the phase regime. Post-translational modifications of the residues present in these domains provide a convenient strategy to reshape the residue-residue interaction networks that determine the dynamics of phase separation. Focus will be placed on those proteins with low complexity domains exhibiting a biased composition towards the amino acid methionine and the prominent role that reversible methionine sulfoxidation plays in the assembly/disassembly of biomolecular condensates.
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Affiliation(s)
- Juan Carlos Aledo
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, 29071 Málaga, Spain
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7
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Molecular basis for lipid recognition by the prostaglandin D 2 receptor CRTH2. Proc Natl Acad Sci U S A 2021; 118:2102813118. [PMID: 34341104 DOI: 10.1073/pnas.2102813118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Prostaglandin D2 (PGD2) signals through the G protein-coupled receptor (GPCR) CRTH2 to mediate various inflammatory responses. CRTH2 is the only member of the prostanoid receptor family that is phylogenetically distant from others, implying a nonconserved mechanism of lipid action on CRTH2. Here, we report a crystal structure of human CRTH2 bound to a PGD2 derivative, 15R-methyl-PGD2 (15mPGD2), by serial femtosecond crystallography. The structure revealed a "polar group in"-binding mode of 15mPGD2 contrasting the "polar group out"-binding mode of PGE2 in its receptor EP3. Structural comparison analysis suggested that these two lipid-binding modes, associated with distinct charge distributions of ligand-binding pockets, may apply to other lipid GPCRs. Molecular dynamics simulations together with mutagenesis studies also identified charged residues at the ligand entry port that function to capture lipid ligands of CRTH2 from the lipid bilayer. Together, our studies suggest critical roles of charge environment in lipid recognition by GPCRs.
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8
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Chatterjee KS, Das R. An "up" oriented methionine-aromatic structural motif in SUMO is critical for its stability and activity. J Biol Chem 2021; 297:100970. [PMID: 34274315 PMCID: PMC8353491 DOI: 10.1016/j.jbc.2021.100970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 07/09/2021] [Accepted: 07/14/2021] [Indexed: 11/25/2022] Open
Abstract
Protein structural bioinformatic analyses suggest preferential associations between methionine and aromatic amino acid residues in proteins. Ab initio energy calculations highlight a conformation-dependent stabilizing interaction between the interacting sulfur-aromatic molecular pair. However, the relevance of buried methionine-aromatic motifs to protein folding and function is relatively unexplored. The Small Ubiquitin-Like Modifier (SUMO) is a β-grasp fold protein and a common posttranslational modifier that affects diverse cellular processes, including transcriptional regulation, chromatin remodeling, metabolic regulation, mitosis, and meiosis. SUMO is a member of the Ubiquitin-Like (UBL) protein family. Herein, we report that a highly conserved and buried methionine-phenylalanine motif is a unique signature of SUMO proteins but absent in other homologous UBL proteins. We also detect that a specific "up" conformation between the methionine-phenylalanine pair of interacting residues in SUMO is critical to its β-grasp fold. The noncovalent interactions of SUMO with its ligands are dependent on the methionine-phenylalanine pair. MD simulations, NMR, and biophysical and biochemical studies suggest that perturbation of the methionine-aromatic motif disrupts native contacts, modulates noncovalent interactions, and attenuates SUMOylation activity. Our results highlight the importance of conserved orientations of Met-aromatic structural motifs inside a protein core for its structure and function.
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Affiliation(s)
- Kiran Sankar Chatterjee
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru, India
| | - Ranabir Das
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru, India.
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9
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Orabi EA. Molecular dynamics investigation of the structural flexibility of H2O2 and H2S2 in response to medium polarity. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.115469] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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10
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Orabi EA, English AM. Modeling Shows that Rotation about the Peroxide O-O Bond Assists Protein and Lipid Functional Groups in Discriminating between H 2O 2 and H 2O. J Phys Chem B 2020; 125:137-147. [PMID: 33356279 DOI: 10.1021/acs.jpcb.0c10326] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Long associated with cell death, hydrogen peroxide (H2O2) is now known to perform many physiological roles. Unraveling its biological mechanisms of action requires atomic-level knowledge of its association with proteins and lipids, which we address here. High-level [MP2(full)/6-311++G(3df,3pd)] ab initio calculations reveal skew rotamers as the lowest-energy states of isolated H2O2 (ϕHOOH ∼ 112°) with minimum and maximum electrostatic potentials (kcal/mol) of -24.8 (Vs,min) and 36.5 (Vs,max), respectively. Transition-state, nonpolar trans rotamers (ϕHOOH ∼ 180°) at 1.2 kcal/mol higher in energy are poorer H-bond acceptors (Vs,min = -16.6) than the skew rotamers, while highly polar cis rotamers (ϕHOOH ∼ 0°) at 7.8 kcal/mol are much better H-bond donors (Vs,max = 52.7). Modeling H2O2 association with neutral and charged analogs of protein residues and lipid groups (e.g., ester, phosphate, choline) reveals that skew rotamers (ϕHOOH = 84-122°) are favored in the neutral and cationic complexes, which display gas-phase interaction energies (ECP, kcal/mol) of -1.5 to -18. The neutral and cationic complexes of H2O exhibit a similar range of stabilities (ECP ∼ -1 to -18). However, considerably higher energies (ECP ∼ -14 to -36) are found for the H2O2 complexes of the anionic ligands, which are stabilized by charge-assisted H-bond donation from cis and distorted cis rotamers (ϕHOOH = 0-60°). H2O is a much poorer H-bond donor (Vs,max = 33.4) than cis-H2O2, so its anionic complexes are significantly weaker (ECP ∼ -11 to -20). Thus, by dictating the rotamer preference of H2O2, functional groups in biomolecules can discriminate between H2O2 and H2O. Finally, exploiting the present ab initio data, we calibrated and validated our published molecular mechanics model for H2O2 (Orabi, E. A.; English, A. M. J. Chem. Theory Comput. 2018, 14, 2808-2821) to provide an important tool for simulating H2O2 in biology.
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Affiliation(s)
- Esam A Orabi
- Department of Chemistry, Faculty of Science, Assiut University, Assiut 71516, Egypt.,Department of Chemistry and Biochemistry, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec H4B 1R6, Canada
| | - Ann M English
- Department of Chemistry and Biochemistry, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec H4B 1R6, Canada.,Center for Research in Molecular Modeling (CERMM) and Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Concordia University, Montreal, Quebec H4B 1R6, Canada
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11
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Orabi EA, Faraldo-Gómez JD. New Molecular-Mechanics Model for Simulations of Hydrogen Fluoride in Chemistry and Biology. J Chem Theory Comput 2020; 16:5105-5126. [PMID: 32615034 DOI: 10.1021/acs.jctc.0c00247] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Hydrogen fluoride (HF) is the most polar diatomic molecule and one of the simplest molecules capable of hydrogen-bonding. HF deviates from ideality both in the gas phase and in solution and is thus of great interest from a fundamental standpoint. Pure and aqueous HF solutions are broadly used in chemical and industrial processes, despite their high toxicity. HF is a stable species also in some biological conditions, because it does not readily dissociate in water unlike other hydrogen halides; yet, little is known about how HF interacts with biomolecules. Here, we set out to develop a molecular-mechanics model to enable computer simulations of HF in chemical and biological applications. This model is based on a comprehensive high-level ab initio quantum chemical investigation of the structure and energetics of the HF monomer and dimer; (HF)n clusters, for n = 3-7; various clusters of HF and H2O; and complexes of HF with analogs of all 20 amino acids and of several commonly occurring lipids, both neutral and ionized. This systematic analysis explains the unique properties of this molecule: for example, that interacting HF molecules favor nonlinear geometries despite being diatomic and that HF is a strong H-bond donor but a poor acceptor. The ab initio data also enables us to calibrate a three-site molecular-mechanics model, with which we investigate the structure and thermodynamic properties of gaseous, liquid, and supercritical HF in a wide range of temperatures and pressures; the solvation structure of HF in water and of H2O in liquid HF; and the free diffusion of HF across a lipid bilayer, a key process underlying the high cytotoxicity of HF. Despite its inherent simplifications, the model presented significantly improves upon previous efforts to capture the properties of pure and aqueous HF fluids by molecular-mechanics methods and to our knowledge constitutes the first parameter set calibrated for biomolecular simulations.
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Affiliation(s)
- Esam A Orabi
- Theoretical Molecular Biophysics Laboratory, National Heart, Lung and Blood Institute, National Institutes of Health, 10 Center Drive, Bethesda, Maryland 20814, United States
| | - José D Faraldo-Gómez
- Theoretical Molecular Biophysics Laboratory, National Heart, Lung and Blood Institute, National Institutes of Health, 10 Center Drive, Bethesda, Maryland 20814, United States
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12
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Sørensen MLH, Sanders BC, Hicks LP, Rasmussen MH, Vishart AL, Kongsted J, Winkler JR, Gray HB, Hansen T. Hole Hopping through Cytochrome P450. J Phys Chem B 2020; 124:3065-3073. [PMID: 32175746 DOI: 10.1021/acs.jpcb.9b09414] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
High-potential iron-oxo species are intermediates in the catalytic cycles of oxygenase enzymes. They can cause heme degradation and irreversible oxidation of nearby amino acids. We have proposed that there are protective mechanisms in which hole hopping from oxidized hemes through tryptophan/tyrosine chains generates a surface-exposed amino-acid oxidant that could be rapidly disarmed by reaction with cellular reductants. In investigations of cytochrome P450BM3, we identified Trp96 as a critical residue that could play such a protective role. This Trp is cation-π paired with Arg398 in 81% of mammalian P450s. Here we report on the effect of the Trp/Arg cation-π interaction on Trp96 formal potentials as well as on electronic coupling strengths between Trp96 and the heme both for wild type cytochrome P450 and selected mutants. Mutation of Arg398 to His, which decreases the Trp96 formal potential, increases Trp-heme electronic coupling; however, surprisingly, the rate of phototriggered electron transfer from a Ru-sensitizer (through Trp96) to the P450BM3 heme was unaffected by the Arg398His mutation. We conclude that Trp96 has moved away from Arg398, suggesting that the protective mechanism for P450s with this Trp-Arg pair is conformationally gated.
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Affiliation(s)
- Mette L H Sørensen
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK 2100 Copenhagen Ø, Denmark
| | - Brian C Sanders
- Environmental Sciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, United States
| | - L Perry Hicks
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States
| | - Maria H Rasmussen
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK 2100 Copenhagen Ø, Denmark
| | - Andreas L Vishart
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK 2100 Copenhagen Ø, Denmark
| | - Jacob Kongsted
- Department of Physics, Chemistry, and Pharmacy, University of Southern Denmark, Campusvej 55, DK 5230 Odense M, Denmark
| | - Jay R Winkler
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States
| | - Harry B Gray
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, United States
| | - Thorsten Hansen
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK 2100 Copenhagen Ø, Denmark
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13
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Chen Q, Xu S, Lu X, Boeri MV, Pepelyayeva Y, Diaz EL, Soni SD, Allaire M, Forstner MB, Bahnson BJ, Rozovsky S. 77Se NMR Probes the Protein Environment of Selenomethionine. J Phys Chem B 2020; 124:601-616. [PMID: 31846581 DOI: 10.1021/acs.jpcb.9b07466] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Sulfur is critical for the correct structure and proper function of proteins. Yet, lacking a sensitive enough isotope, nuclear magnetic resonance (NMR) experiments are unable to deliver for sulfur in proteins the usual wealth of chemical, dynamic, and structural information. This limitation can be circumvented by substituting sulfur with selenium, which has similar physicochemical properties and minimal impact on protein structures but possesses an NMR compatible isotope (77Se). Here we exploit the sensitivity of 77Se NMR to the nucleus' chemical milieu and use selenomethionine as a probe for its proteinaceous environment. However, such selenium NMR spectra of proteins currently resist a reliable interpretation because systematic connections between variations of system variables and changes in 77Se NMR parameters are still lacking. To start narrowing this knowledge gap, we report here on a biological 77Se magnetic resonance data bank based on a systematically designed library of GB1 variants in which a single selenomethionine was introduced at different locations within the protein. We recorded the resulting isotropic 77Se chemical shifts and relaxation times for six GB1 variants by solution-state 77Se NMR. For four of the GB1 variants we were also able to determine the chemical shift anisotropy tensor of SeM by solid-state 77Se NMR. To enable interpretation of the NMR data, the structures of five of the GB1 variants were solved by X-ray crystallography to a resolution of 1.2 Å, allowing us to unambiguously determine the conformation of the selenomethionine. Finally, we combine our solution- and solid-state NMR data with the structural information to arrive at general insights regarding the execution and interpretation of 77Se NMR experiments that exploit selenomethionine to probe proteins.
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Affiliation(s)
- Qingqing Chen
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States
| | - Shiping Xu
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States
| | - Xingyu Lu
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States.,Instrumentation and Service Center for Physical Sciences , Westlake University , Hangzhou , Zhejiang 310024 , China
| | - Michael V Boeri
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States.,Neuroscience Department, Medical Toxicology Research Division , U.S. Army Medical Research Institute of Chemical Defense , 8350 Ricketts Point Road , Gunpowder , Maryland 21010 , United States
| | - Yuliya Pepelyayeva
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States.,Department of Microbiology & Molecular Genetics, College of Osteopathic Medicine , Michigan State University , East Lansing , Michigan 48824 , United States
| | - Elizabeth L Diaz
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States
| | - Sunil-Datta Soni
- Neuroscience Department, Medical Toxicology Research Division , U.S. Army Medical Research Institute of Chemical Defense , 8350 Ricketts Point Road , Gunpowder , Maryland 21010 , United States
| | - Marc Allaire
- Berkeley Center for Structural Biology, Molecular Biophysics & Integrated Bioimaging , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States
| | - Martin B Forstner
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States
| | - Brian J Bahnson
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States
| | - Sharon Rozovsky
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States
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14
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Orabi EA, Davis RL, Lamoureux G. Drude polarizable force field for cation–π interactions of alkali and quaternary ammonium ions with aromatic amino acid side chains. J Comput Chem 2019; 41:472-481. [DOI: 10.1002/jcc.26084] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 08/14/2019] [Accepted: 09/16/2019] [Indexed: 11/08/2022]
Affiliation(s)
- Esam A. Orabi
- Department of ChemistryFaculty of Science, Assiut University Assiut 71516 Egypt
- Department of ChemistryUniversity of Manitoba Winnipeg Manitoba R3T 2N2 Canada
| | - Rebecca L. Davis
- Department of ChemistryUniversity of Manitoba Winnipeg Manitoba R3T 2N2 Canada
| | - Guillaume Lamoureux
- Department of Chemistry and Center for Computational and Integrative Biology (CCIB)Rutgers University Camden New Jersey 08102
- Centre for Research in Molecular Modeling (CERMM), Concordia University Montréal Québec H4B 1R6 Canada
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15
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The interaction between methionine and two aromatic amino acids is an abundant and multifunctional motif in proteins. Arch Biochem Biophys 2019; 672:108053. [DOI: 10.1016/j.abb.2019.07.018] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 07/08/2019] [Accepted: 07/24/2019] [Indexed: 12/29/2022]
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16
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Aledo JC. Methionine in proteins: The Cinderella of the proteinogenic amino acids. Protein Sci 2019; 28:1785-1796. [PMID: 31359525 DOI: 10.1002/pro.3698] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 07/18/2019] [Accepted: 07/22/2019] [Indexed: 11/09/2022]
Abstract
Methionine in proteins, apart from its role in the initiation of translation, is assumed to play a simple structural role in the hydrophobic core, in a similar way to other hydrophobic amino acids such as leucine, isoleucine, and valine. However, research from a number of laboratories supports the concept that methionine serves as an important cellular antioxidant, stabilizes the structure of proteins, participates in the sequence-independent recognition of protein surfaces, and can act as a regulatory switch through reversible oxidation and reduction. Despite all these evidences, the role of methionine in protein structure and function is largely overlooked by most biochemists. Thus, the main aim of the current article is not so much to carry out an exhaustive review of the many and diverse processes in which methionine residues are involved, but to review some illustrative examples that may help the nonspecialized reader to form a richer and more precise insight regarding the role-played by methionine residues in such processes.
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Affiliation(s)
- Juan C Aledo
- Departamento de Biología Molecular y Bioquímica. Facultad de Ciencias, Universidad de Málaga, Málaga, Spain
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Wang D, Chopra P, Wategaonkar S, Fujii A. Electronic and Infrared Spectroscopy of Benzene-(H2S)n (n = 1 and 2): The Prototype of the SH-π Interaction. J Phys Chem A 2019; 123:7255-7260. [DOI: 10.1021/acs.jpca.9b02199] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Dandan Wang
- Department of Chemistry, Graduate school of Science, Tohoku University, Sendai 980-8578, Japan
| | - Pragya Chopra
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400 005, India
| | - Sanjay Wategaonkar
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400 005, India
| | - Asuka Fujii
- Department of Chemistry, Graduate school of Science, Tohoku University, Sendai 980-8578, Japan
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Orabi EA, Peslherbe GH. Computational insight into hydrogen persulfide and a new additive model for chemical and biological simulations. Phys Chem Chem Phys 2019; 21:15988-16004. [PMID: 31297500 DOI: 10.1039/c9cp02998b] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
S-Sulfhydration of cysteine to the Cys-SSH persulfide is an oxidative post-translational modification that plays an important regulatory role in many physiological systems. Though hydrogen persulfide (H2S2) has recently been established as a signaling and cellular sulfhydration reagent, the chemistry and chemical biology of persulfides remain poorly explored. We first report an extensive high-level ab initio quantum chemical investigation of (H2S2)n, (H2S2)m·H2O, and (H2O)m·H2S2 clusters (n = 1-3 and m = 1, 2) and of H2S2 complexes with 19 compounds that model the side chains of naturally-occurring amino acids. The high polarizability of S necessitates the use of large, very diffuse, basis sets for proper description of H2S2 and its complexes. H2S2 possesses a skewed equilibrium geometry, with nonpolar trans and more polar cis conformers 6 and 8 kcal mol-1 higher in energy, respectively; the skewed conformation is preserved in all neutral and cationic complexes while a cis geometry prevails in some anionic complexes. H2S2 is found to be a better H-bond donor and a poorer acceptor than H2S, and that in complexes with H2O, alcohols and amines, H2S2 is a better H-bond donor. Radical delocalization on both S atoms stabilizes the perthiyl (HSS˙) over the thiyl (HS˙) radical and results in a ∼20 kcal mol-1 lower S-H homolytic bond dissociation in H2S2, making it a potential antioxidant. A simple additive model is optimized for H2S2 and used together with the TIP3P model and the CHARMM36 all-atom force field (FF) to investigate the structure and thermodynamic properties of liquid H2S2 and the solubility of H2S2 in water, and to model H2S2-protein interactions (for which new FF parameters are further developed). Very weak H-bonding characterizes liquid H2S2 and it is found immiscible in liquid water with a trend in H-bonding strengths between H2S2 and H2O in the order O-HO ≫ S-HO > O-HS. This work does not only provide a thorough description of the structure and energetics of H2S2 and its various complexes, but also yields a reliable FF for investigating H2S2 in chemistry and biology.
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Affiliation(s)
- Esam A Orabi
- Centre for Research in Molecular Modeling and Department of Chemistry and Biochemistry, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec H4B 1R6, Canada.
| | - Gilles H Peslherbe
- Centre for Research in Molecular Modeling and Department of Chemistry and Biochemistry, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec H4B 1R6, Canada.
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Orabi EA, English AM. Expanding the range of binding energies and oxidizability of biologically relevant S-aromatic interactions: imidazolium and phenolate binding to sulfoxide and sulfone. Phys Chem Chem Phys 2019; 21:14620-14628. [PMID: 31214677 DOI: 10.1039/c9cp02332a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Oxidation and protonation/deprotonation strongly impact intermolecular noncovalent interactions. For example, S-aromatic interactions are stabilized up to three-fold in the gas phase on oxidation of the sulfur ligand or protonation/deprotonation of the aromatic. To probe if such stabilizing effects are additive and to model interactions of oxidized methionine (MetOn) with protonated histidine and deprotonated tyrosine residues in proteins, we examined Me2SOn (n = 1, 2) binding to imidazolium, phenolate and their 4-methylated forms. Ab initio MP2(full)/6-311++G(d,p) gas-phase calculations reveal that the Me2SOn-imidazolium complexes adopt edge-on geometry with σ-type (N/C-HarO) H-bonding and interaction energies of -17.2 to -31.1 kcal mol-1. The less stable (-13.8 to -21.0 kcal mol-1) Me2SOn-phenolates possess en-face geometry stabilized by π-type (C-Hπar) H-bonding. Comparing these energies with those reported for the Me2S-neutral aromatics affirms the additive effects of ligand protonation/deprotonation and oxidation on gas-phase stability. However, this is not the case in water although the aqueous complexes retain their preferred gas-phase σ- and π-type H-bonded structures. Binding free energies (kcal mol-1) calculated from molecular dynamics simulations in bulk water (preceded by CHARMM36 force field calibration where necessary) reveal that Me2SO-imidazolium (-4.4) is more stable than Me2SO-phenolate (-2.4) but Me2SO2-imidazolium (-0.6) is less stable than Me2SO2-phenolate (-3.8). Vertical ionization potentials (IPV) calculated for the gas-phase complexes indicate that the Me2SOn-phenolates, but not the Me2SOn-imidazoles, are oxidizable under biological conditions. Charge transfer from the phenolate increases its IPV by ∼20%, decreasing its susceptibility to oxidation. Overall, this work provides fundamental data to predict the behaviour of protein-based MetOn-aromatic-ion interactions.
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Affiliation(s)
- Esam A Orabi
- Center for Research in Molecular Modeling (CERMM), Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), and Department of Chemistry and Biochemistry, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec H4B 1R6, Canada.
| | - Ann M English
- Center for Research in Molecular Modeling (CERMM), Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), and Department of Chemistry and Biochemistry, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec H4B 1R6, Canada.
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Kathiresan M, English AM. LC-MS/MS Proteoform Profiling Exposes Cytochrome c Peroxidase Self-Oxidation in Mitochondria and Functionally Important Hole Hopping from Its Heme. J Am Chem Soc 2018; 140:12033-12039. [PMID: 30145880 DOI: 10.1021/jacs.8b05966] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
LC-MS/MS profiling reveals that the proteoforms of cytochrome c peroxidase (Ccp1) isolated from respiring yeast mitochondria are oxidized at numerous Met, Trp, and Tyr residues. In vitro oxidation of recombinant Ccp1 by H2O2 in the absence of its reducing substrate, ferrocytochrome c, gives rise to similar proteoforms, indicating uncoupling of Ccp1 oxidation and reduction in mitochondria. The oxidative modifications found in the Ccp1 proteoforms are consistent with radical transfer (hole hopping) from the heme along several chains of redox-active residues (Trp, Met, Tyr). These modifications delineate likely hole-hopping pathways to novel substrate-binding sites. Moreover, a decrease in recombinant Ccp1 oxidation by H2O2 in vitro in the presence of glutathione supports a protective role for hole hopping to this antioxidant. Isolation and characterization of extramitochondrial Ccp1 proteoforms reveals that hole hopping from the heme in these proteoforms results in selective oxidation of the proximal heme ligand (H175) and heme labilization. Previously, we demonstrated that this labilized heme is recruited for catalase maturation (Kathiresan, M.; Martins, D.; English, A. M. Respiration triggers heme transfer from cytochrome c peroxidase to catalase in yeast mitochondria. Proc. Natl. Acad. Sci. U. S. A. 2014, 111, 17468-17473; DOI: 10.1073/pnas.1409692111 ). Following heme release, apoCcp1 exits mitochondria, yielding the extramitochondrial proteoforms that we characterize here. The targeting of Ccp1 for selective H175 oxidation may be linked to the phosphorylation status of Y153 close to the heme since pY153 is abundant in certain proteoforms. In sum, when insufficient electrons from ferrocytochrome c are available to Ccp1 in mitochondria, hole hopping from its heme expands its physiological functions. Specifically, we observe an unprecedented hole-hopping sequence for heme labilization and identify hole-hopping pathways from the heme to novel substrates and to glutathione at Ccp1's surface. Furthermore, our results underscore the power of proteoform profiling by LC-MS/MS in exploring the cellular roles of oxidoreductases.
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Affiliation(s)
- Meena Kathiresan
- Quebec Network for Research on Protein Function, Structure and Engineering (PROTEO), and Department of Chemistry and Biochemistry , Concordia University , Montreal , QC H4B 1R6 , Canada
| | - Ann M English
- Quebec Network for Research on Protein Function, Structure and Engineering (PROTEO), and Department of Chemistry and Biochemistry , Concordia University , Montreal , QC H4B 1R6 , Canada
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Orabi EA, English AM. Predicting structural and energetic changes in Met–aromatic motifs on methionine oxidation to the sulfoxide and sulfone. Phys Chem Chem Phys 2018; 20:23132-23141. [DOI: 10.1039/c8cp03277g] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Methionine oxidation increases its affinity for aromatics in the gas phase but lowers it for most complexes in water.
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Affiliation(s)
- Esam A. Orabi
- Center for Research in Molecular Modeling (CERMM)
- Quebec Network for Research on Protein Function
- Engineering, and Applications (PROTEO), and Department of Chemistry and Biochemistry
- Concordia University
- Montréal
| | - Ann M. English
- Center for Research in Molecular Modeling (CERMM)
- Quebec Network for Research on Protein Function
- Engineering, and Applications (PROTEO), and Department of Chemistry and Biochemistry
- Concordia University
- Montréal
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