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Bara‐Estaún A, Harder MC, Lyall CL, Lowe JP, Suturina E, Hintermair U. Paramagnetic Relaxation Agents for Enhancing Temporal Resolution and Sensitivity in Multinuclear FlowNMR Spectroscopy. Chemistry 2023; 29:e202300215. [PMID: 36946535 PMCID: PMC10962566 DOI: 10.1002/chem.202300215] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Revised: 03/22/2023] [Accepted: 03/22/2023] [Indexed: 03/23/2023]
Abstract
Sensitivity in FlowNMR spectroscopy for reaction monitoring often suffers from low levels of pre-magnetisation due to limited residence times of the sample in the magnetic field. While this in-flow effect is tolerable for high sensitivity nuclei such as 1 H and 19 F, it significantly reduces the signal-to-noise ratio in 31 P and 13 C spectra, making FlowNMR impractical for low sensititvity nuclei at low concentrations. Paramagnetic relaxation agents (PRAs), which enhance polarisation and spin-lattice relaxation, could eliminate the adverse in-flow effect and improve the signal-to-noise ratio. Herein, [Co(acac)3 ], [Mn(acac)3 ], [Fe(acac)3 ], [Cr(acac)3 ], [Ni(acac)2 ]3, [Gd(tmhd)3 ] and [Cr(tmhd)3 ] are investigated for their effectiveness in improving signal intensity per unit time in FlowNMR applications under the additional constraint of chemical inertness towards catalytically active transition metal complexes. High-spin Cr(III) acetylacetonates emerged as the most effective compounds, successfully reducing 31 P T1 values four- to five-fold at PRA concentrations as low as 10 mM without causing adverse line broadening. Whereas [Cr(acac)3 ] showed signs of chemical reactivity with a mixture of triphenylphosphine, triphenylphosphine oxide and triphenylphosphate over the course of several hours at 80° C, the bulkier [Cr(tmhd)3 ] was stable and equally effective as a PRA under these conditions. Compatibility with a range of representative transition metal complexes often used in homogeneous catalysis has been investigated, and application of [Cr(tmhd)3 ] in significantly improving 1 H and 31 P{1 H} FlowNMR data quality in a Rh-catalysed hydroformylation reaction has been demonstrated. With the PRA added, 13 C relaxation times were reduced more than six-fold, allowing quantitative reaction monitoring of substrate consumption and product formation by 13 C{1 H} FlowNMR spectroscopy at natural abundance.
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Affiliation(s)
- Alejandro Bara‐Estaún
- Department of ChemistryUniversity of Bath Claverton DownBathBA2 7AYUnited Kingdom
- Dynamic Reaction Monitoring FacilityUniversity of Bath, Claverton DownBathBA2 7AYUnited Kingdom
| | - Marie C. Harder
- Department of ChemistryUniversity of Bath Claverton DownBathBA2 7AYUnited Kingdom
- Dynamic Reaction Monitoring FacilityUniversity of Bath, Claverton DownBathBA2 7AYUnited Kingdom
| | - Catherine L. Lyall
- Department of ChemistryUniversity of Bath Claverton DownBathBA2 7AYUnited Kingdom
- Dynamic Reaction Monitoring FacilityUniversity of Bath, Claverton DownBathBA2 7AYUnited Kingdom
| | - John P. Lowe
- Department of ChemistryUniversity of Bath Claverton DownBathBA2 7AYUnited Kingdom
- Dynamic Reaction Monitoring FacilityUniversity of Bath, Claverton DownBathBA2 7AYUnited Kingdom
| | - Elizaveta Suturina
- Department of ChemistryUniversity of Bath Claverton DownBathBA2 7AYUnited Kingdom
| | - Ulrich Hintermair
- Department of ChemistryUniversity of Bath Claverton DownBathBA2 7AYUnited Kingdom
- Dynamic Reaction Monitoring FacilityUniversity of Bath, Claverton DownBathBA2 7AYUnited Kingdom
- Institute for SustainabilityUniversity of BathBathBA2 7AYUnited Kingdom
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Gardner PR. Ordered Motions in the Nitric-Oxide Dioxygenase Mechanism of Flavohemoglobin and Assorted Globins with Tightly Coupled Reductases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1414:45-96. [PMID: 36520413 DOI: 10.1007/5584_2022_751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Nitric-oxide dioxygenases (NODs) activate and combine O2 with NO to form nitrate. A variety of oxygen-binding hemoglobins with associated partner reductases or electron donors function as enzymatic NODs. Kinetic and structural investigations of the archetypal two-domain microbial flavohemoglobin-NOD have illuminated an allosteric mechanism that employs selective tunnels for O2 and NO, gates for NO and nitrate, transient O2 association with ferric heme, and an O2 and NO-triggered, ferric heme spin crossover-driven, motion-controlled, and dipole-regulated electron-transfer switch. The proposed mechanism facilitates radical-radical coupling of ferric-superoxide with NO to form nitrate while preventing suicidal ferrous-NO formation. Diverse globins display the structural and functional motifs necessary for a similar allosteric NOD mechanism. In silico docking simulations reveal monomeric erythrocyte hemoglobin alpha-chain and beta-chain intrinsically matched and tightly coupled with NADH-cytochrome b5 oxidoreductase and NADPH-cytochrome P450 oxidoreductase, respectively, forming membrane-bound flavohemoglobin-like mammalian NODs. The neuroprotective neuroglobin manifests a potential NOD role in a close-fitting ternary complex with membrane-bound NADH-cytochrome b5 oxidoreductase and cytochrome b5. Cytoglobin interfaces weakly with cytochrome b5 for O2 and NO-regulated electron-transfer and coupled NOD activity. The mechanistic model also provides insight into the evolution of O2 binding cooperativity in hemoglobin and a basis for the discovery of allosteric NOD inhibitors.
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Nakayoshi T, Kato K, Kurimoto E, Oda A. Theoretical Studies on the Effect of Isomerized Aspartic Acid Residues on the Three-Dimensional Structures of Bovine Pancreatic Ribonucleases A. Biol Pharm Bull 2021; 44:967-975. [PMID: 34193692 DOI: 10.1248/bpb.b21-00083] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Isomerized aspartic acid (Asp) residues have previously been identified in various aging tissues, and are suspected to contribute to age-related diseases. Asp-residue isomerization occurs nonenzymatically under physiological conditions, resulting in the formation of three types of isomerized Asp (i.e., L-isoAsp, D-Asp, and D-isoAsp) residues. Asp-residue isomerization often accelerates protein aggregation and insolubilization, making structural biology analyses difficult. Recently, Sakaue et al. reported the synthesis of a ribonuclease A (RNase A) in which Asp121 was artificially replaced with different isomerized Asp residues, and experimentally demonstrated that the enzymatic activities of these artificial mutants were completely lost. However, their structural features have not yet been elucidated. In the present study, the three-dimensional (3D) structures of these artificial-mutant RNases A were predicted using molecular dynamics (MD) simulations. The 3D structures of wild-type and artificial-mutant RNases A were converged by 3000-ns MD simulations. Our computational data show that the structures of the active site and the formation frequencies of the appropriate catalytic dyad structures in the artificial-mutant RNases A were quite different from wild-type RNase A. These computational findings may provide an explanation for the experimental data which show that artificial-mutant RNases A lack enzymatic activity. Herein, MD simulations have been used to evaluate the influences of isomerized Asp residues on the 3D structures of proteins.
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Affiliation(s)
- Tomoki Nakayoshi
- Graduate School of Pharmacy, Meijo University.,Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University
| | - Koichi Kato
- Graduate School of Pharmacy, Meijo University.,College of Pharmacy, Kinjo Gakuin University
| | | | - Akifumi Oda
- Graduate School of Pharmacy, Meijo University.,Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University.,Institute for Protein Research, Osaka University
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Gardner AM, Gardner PR. Allostery in the nitric oxide dioxygenase mechanism of flavohemoglobin. J Biol Chem 2020; 296:100186. [PMID: 33310705 PMCID: PMC7948479 DOI: 10.1074/jbc.ra120.016637] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 12/09/2020] [Accepted: 12/11/2020] [Indexed: 12/12/2022] Open
Abstract
The substrates O2 and NO cooperatively activate the NO dioxygenase function of Escherichia coli flavohemoglobin. Steady-state and transient kinetic measurements support a structure-based mechanistic model in which O2 and NO movements and conserved amino acids at the E11, G8, E2, E7, B10, and F7 positions within the globin domain control activation. In the cooperative and allosteric mechanism, O2 migrates to the catalytic heme site via a long hydrophobic tunnel and displaces LeuE11 away from the ferric iron, which forces open a short tunnel to the catalytic site gated by the ValG8/IleE15 pair and LeuE11. NO permeates this tunnel and leverages upon the gating side chains triggering the CD loop to furl, which moves the E and F-helices and switches an electron transfer gate formed by LysF7, GlnE7, and water. This allows FADH2 to reduce the ferric iron, which forms the stable ferric–superoxide–TyrB10/GlnE7 complex. This complex reacts with internalized NO with a bimolecular rate constant of 1010 M−1 s−1 forming nitrate, which migrates to the CD loop and unfurls the spring-like structure. To restart the cycle, LeuE11 toggles back to the ferric iron. Actuating electron transfer with O2 and NO movements averts irreversible NO poisoning and reductive inactivation of the enzyme. Together, structure snapshots and kinetic constants provide glimpses of intermediate conformational states, time scales for motion, and associated energies.
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Affiliation(s)
- Anne M Gardner
- Research and Development Division, Miami Valley Biotech, Dayton, Ohio, USA; Division of Critical Care Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Paul R Gardner
- Research and Development Division, Miami Valley Biotech, Dayton, Ohio, USA; Division of Critical Care Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA; Chemistry and Biochemistry Department, University of Dayton, Dayton, Ohio, USA.
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Di Pietrantonio C, Pandey A, Gould J, Hasabnis A, Prosser RS. Understanding Protein Function Through an Ensemble Description: Characterization of Functional States by 19F NMR. Methods Enzymol 2019; 615:103-130. [DOI: 10.1016/bs.mie.2018.09.029] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Kitahara R, Sakuraba S, Kameda T, Okuda S, Xue M, Mulder FAA. Nuclear magnetic resonance-based determination of dioxygen binding sites in protein cavities. Protein Sci 2018; 27:769-779. [PMID: 29271012 DOI: 10.1002/pro.3371] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 11/28/2017] [Accepted: 12/20/2017] [Indexed: 11/06/2022]
Abstract
The location and ligand accessibility of internal cavities in cysteine-free wild-type T4 lysozyme was investigated using O2 gas-pressure NMR spectroscopy and molecular dynamics (MD) simulation. Upon increasing the concentration of dissolved O2 in solvent to 8.9 mM, O2 -induced paramagnetic relaxation enhancements (PREs) to the backbone amide and side chain methyl protons were observed, specifically around two cavities in the C-terminal domain. To determine the number of O2 binding sites and their atomic coordinates from the 1/r6 distance dependence of the PREs, we established an analytical procedure using Akaike's Information Criterion, in combination with a grid-search. Two O2 -accessible sites were identified in internal cavities: One site was consistent with the xenon-binding site in the protein in crystal, and the other site was established to be a novel ligand-binding site. MD simulations performed at 10 and 100 mM O2 revealed dioxygen ingress and egress as well as rotational and translational motions of O2 in the cavities. It is therefore suggested that conformational fluctuations within the ground-state ensemble transiently develop channels for O2 association with the internal protein cavities.
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Affiliation(s)
- Ryo Kitahara
- Department of Pharmaceutical Sciences, College of Pharmaceutical Sciences, Ritsumeikan University, Kusatsu, 525-8577, Japan
| | - Shun Sakuraba
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8561, Japan
| | - Tomoshi Kameda
- Computational Omics Research Team, Artificial Intelligence Research Center, Advanced Industrial Science and Technology, Koto, Tokyo, 135-0064, Japan
| | - Sanshiro Okuda
- Graduate School of Life Sciences, Ritsumeikan University, Kusatsu, 525-8577, Japan
| | - Mengjun Xue
- Department of Chemistry and Interdisciplinary Nanoscience Center (iNANO), University of Aarhus, Aarhus C, DK-8000, Denmark
| | - Frans A A Mulder
- Department of Chemistry and Interdisciplinary Nanoscience Center (iNANO), University of Aarhus, Aarhus C, DK-8000, Denmark
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Analysis of O 2-binding Sites in Proteins Using Gas-Pressure NMR Spectroscopy: Outer Surface Protein A. Biophys J 2017; 112:1820-1828. [PMID: 28494953 DOI: 10.1016/j.bpj.2017.03.029] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 03/22/2017] [Accepted: 03/29/2017] [Indexed: 11/22/2022] Open
Abstract
Internal cavities in proteins produce conformational fluctuations and enable the binding of small ligands. Here, we report a NMR analysis of O2-binding sites by O2-induced paramagnetic relaxation enhancements (PREs) on amide groups of proteins in solution. Outer surface protein A contains a nonglobular single-layer β-sheet that connects the N- and C-terminal globular domains. Several cavities have been observed in both domains of the crystallized protein structure. The receptor-binding sites are occluded and line the largest cavity of the C-terminal domain. We observed significant O2-induced PREs for amide protons located around the largest cavity and at the central β-sheet. We suggested three potential O2-accessible sites in the protein based on the 1/r6 distance dependence of the PRE. Two sites were in or close to the largest cavity and the third site was in the surface crevice of the central β-sheet. These results provide, to our knowledge, the first evidence of ligand binding to the surface crevice and cavity of the protein in solution. Because O2 generally binds more specifically to hydrophobic rather than hydrophilic cavities within a protein, the results also indicated that the receptor-binding sites lining the largest cavity were in the hydrophobic environment in the ground-state conformation. Molecular dynamics simulations permitted the visualization of the rotational and translational motions of O2 within the largest cavity, egress of O2 from the cavity, and ingress of O2 in the surface crevice of the β-sheet. These molecular dynamics simulation results qualitatively explained the O2-induced changes in NMR observations. Exploring cavities that are sufficiently dynamic to enable access by small molecules can be a useful strategy for the design of stable proteins and their ligands.
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Abstract
Internal cavities are important elements in protein structure, dynamics, stability and function. Here we use NMR spectroscopy to investigate the binding of molecular oxygen (O2) to cavities in a well-studied model for ligand binding, the L99A mutant of T4 lysozyme. On increasing the O2 concentration to 8.9 mM, changes in 1H, 15N, and 13C chemical shifts and signal broadening were observed specifically for backbone amide and side chain methyl groups located around the two hydrophobic cavities of the protein. O2-induced longitudinal relaxation enhancements for amide and methyl protons could be adequately accounted for by paramagnetic dipolar relaxation. These data provide the first experimental demonstration that O2 binds specifically to the hydrophobic, and not the hydrophilic cavities, in a protein. Molecular dynamics simulations visualized the rotational and translational motions of O2 in the cavities, as well as the binding and egress of O2, suggesting that the channel consisting of helices D, E, G, H, and J could be the potential gateway for ligand binding to the protein. Due to strong paramagnetic relaxation effects, O2 gas-pressure NMR measurements can detect hydrophobic cavities when populated to as little as 1%, and thereby provide a general and highly sensitive method for detecting oxygen binding in proteins.
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Kitevski-LeBlanc JL, Hoang J, Thach W, Larda ST, Prosser RS. 19F NMR Studies of a Desolvated Near-Native Protein Folding Intermediate. Biochemistry 2013; 52:5780-9. [DOI: 10.1021/bi4010057] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Julianne L. Kitevski-LeBlanc
- Department of Chemistry, University of Toronto, UTM, 3359 Mississauga Road North,
Mississauga, Ontario L5L 1C6, Canada
| | - Joshua Hoang
- Department of Chemistry, University of Toronto, UTM, 3359 Mississauga Road North,
Mississauga, Ontario L5L 1C6, Canada
| | - William Thach
- Department of Biochemistry, University of Toronto, 1 King’s College Circle,
Toronto, Ontario M5S 1A8, Canada
| | - Sacha Thierry Larda
- Department of Chemistry, University of Toronto, UTM, 3359 Mississauga Road North,
Mississauga, Ontario L5L 1C6, Canada
| | - R. Scott Prosser
- Department of Chemistry, University of Toronto, UTM, 3359 Mississauga Road North,
Mississauga, Ontario L5L 1C6, Canada
- Department of Biochemistry, University of Toronto, 1 King’s College Circle,
Toronto, Ontario M5S 1A8, Canada
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Sun Y, Friedman JI, Stivers JT. Cosolute paramagnetic relaxation enhancements detect transient conformations of human uracil DNA glycosylase (hUNG). Biochemistry 2011; 50:10724-31. [PMID: 22077282 DOI: 10.1021/bi201572g] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The human DNA repair enzyme uracil DNA glycosylase (hUNG) locates and excises rare uracil bases that arise in DNA from cytosine deamination or through dUTP incorporation by DNA polymerases. Previous NMR studies of hUNG have revealed millisecond time scale dynamic transitions in the enzyme-nonspecific DNA complex, but not the free enzyme, that were ascribed to a reversible clamping motion of the enzyme as it scans along short regions of duplex DNA in its search for uracil. Here we further probe the properties of the nonspecific DNA binding surface of {(2)H(12)C}{(15)N}-labeled hUNG using a neutral chelate of a paramagnetic Gd(3+) cosolute (Gd(HP-DO3A)). Overall, the measured paramagnetic relaxation enhancements (PREs) on R(2) of the backbone amide protons for free hUNG and its DNA complex were in good agreement with those calculated based on their relative exposure observed in the crystal structures of both enzyme forms. However, the calculated PREs systematically underestimated the experimental PREs by large amounts in discrete regions implicated in DNA recognition and catalysis: active site loops involved in DNA recognition (268-274, 246-250), the uracil binding pocket (143-148, 169-170), a transient extrahelical base binding site (214-216), and a remote hinge region (129-132) implicated in dynamic clamping. These reactive hot spots were not correlated with structural, hydrophobic, or solvent exchange properties that might be common to these regions, leaving the possibility that the effects arise from dynamic sampling of exposed conformations that are distinct from the static structures. Consistent with this suggestion, the above regions have been previously shown to be flexible based on relaxation dispersion measurements and course-grained normal-mode analysis. A model is suggested where the intrinsic dynamic properties of these regions allows sampling of transient conformations where the backbone amide groups have greater average exposure to the cosolute as compared to the static structures. We conclude that PREs derived from the paramagnetic cosolute reveal dynamic hot spots in hUNG and that these regions are highly correlated with substrate binding and recognition.
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Affiliation(s)
- Yan Sun
- Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, United States
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Abstract
Stable nitroxyl radicals are important tools in chemistry, biophysics, biology, and materials science. Their stability and the sensitivity of their EPR spectra to the local environment make them valuable molecular probes. This review seeks to give an overview of the developments in the field of nitroxide spin probes and their various applications, with the main focus on the pH-sensitive imidazoline nitroxide family.
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Affiliation(s)
- Evelyn Zottler
- Institute of Physical and Theoretical Chemistry, Graz University of Technology, Stremayrgasse 9, 8010 Graz, Austria
| | - Georg Gescheidt
- Institute of Physical and Theoretical Chemistry, Graz University of Technology, Stremayrgasse 9, 8010 Graz, Austria
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Al-Abdul-Wahid MS, Evanics F, Prosser RS. Dioxygen transmembrane distributions and partitioning thermodynamics in lipid bilayers and micelles. Biochemistry 2011; 50:3975-83. [PMID: 21510612 DOI: 10.1021/bi200168n] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cellular respiration, mediated by the passive diffusion of oxygen across lipid membranes, is key to many basic cellular processes. In this work, we report the detailed distribution of oxygen across lipid bilayers and examine the thermodynamics of oxygen partitioning via NMR studies of lipids in a small unilamellar vesicle (SUV) morphology. Dissolved oxygen gives rise to paramagnetic chemical shift perturbations and relaxation rate enhancements, both of which report on local oxygen concentration. From SUVs containing the phospholipid sn-2-perdeuterio-1-myristelaidoyl, 2-myristoyl-sn-glycero-3-phosphocholine (MLMPC), an analogue of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC), we deduced the complete trans-bilayer oxygen distribution by measuring (13)C paramagnetic chemical shifts perturbations for 18 different sites on MLMPC arising from oxygen at a partial pressure of 30 bar. The overall oxygen solubility at 45 °C spans a factor of 7 between the bulk water (23.7 mM) and the bilayer center (170 mM) and is lowest in the vicinity of the phosphocholine headgroup, suggesting that oxygen diffusion across the glycerol backbone should be the rate-limiting step in diffusion-mediated passive transport of oxygen across the lipid bilayer. Lowering of the temperature from 45 to 25 °C gave rise to a slight decrease of the oxygen solubility within the hydrocarbon interior of the membrane. An analysis of the temperature dependence of the oxygen solubility profile, as measured by (1)H paramagnetic relaxation rate enhancements, reveals that oxygen partitioning into the bilayer is entropically favored (ΔS° = 54 ± 3 J K(-1) mol(-1)) and must overcome an enthalpic barrier (ΔH° = 12.0 ± 0.9 kJ mol(-1)).
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Affiliation(s)
- M Sameer Al-Abdul-Wahid
- Department of Chemistry, University of Toronto, UTM, North Mississauga, Ontario, Canada L5L 1C6
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Diakova G, Goddard Y, Korb JP, Bryant RG. Water-proton-spin-lattice-relaxation dispersion of paramagnetic protein solutions. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2011; 208:195-203. [PMID: 21134772 PMCID: PMC3026090 DOI: 10.1016/j.jmr.2010.11.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2010] [Revised: 09/29/2010] [Accepted: 11/03/2010] [Indexed: 05/23/2023]
Abstract
The paramagnetic contributions to water-proton-spin-lattice relaxation rate constants in protein systems spin-labeled with nitroxide radicals were re-examined. As noted by others, the strength of the dipolar coupling between water protons and the protein-bound nitroxide radical often appears to be larger than physically reasonable when the relaxation is assumed to be controlled by 3-dimensional diffusive processes in the vicinity of the spin label. We examine the effects of the surface in biasing the diffusive exploration of the radical region and derive a relaxation model that incorporates 2-dimensional dynamics at the interfacial layer. However, we find that the local 2-dimensional dynamics changes the shape of the relaxation dispersion profile but does not necessarily reproduce the low-field relaxation efficiency found by experiment. We examine the contributions of long-range dipolar couplings between the paramagnetic center and protein-bound-water molecules and find that the contributions from these several long range couplings may be competitive with translational contributions because the correlation time for global rotation of the protein is approximately 1000 times longer than that for the diffusive motion of water at the interfacial region. As a result the electron-proton dipolar coupling to rare protein-bound-water-molecule protons may be significant for protein systems that accommodate long-lived-water molecules. Although the estimate of local diffusion coefficients is not seriously compromised because it derives from the Larmor frequency dependence, these several contributions confound efforts to fit relaxation data quantitatively with unique models.
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Affiliation(s)
| | | | - Jean-Pierre Korb
- Physique de la Matière Condensée, Ecole Polytechnique, CNRS, 91128, Palaiseau, France
| | - Robert G. Bryant
- Chemistry Department University of Virginia Charlottesville, VA, USA
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Linser R, Fink U, Reif B. Probing Surface Accessibility of Proteins Using Paramagnetic Relaxation in Solid-State NMR Spectroscopy. J Am Chem Soc 2009; 131:13703-8. [DOI: 10.1021/ja903892j] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Rasmus Linser
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Str. 10, D-13125 Berlin, Germany and Charité Universitätsmedizin, D-10115 Berlin, Germany
| | - Uwe Fink
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Str. 10, D-13125 Berlin, Germany and Charité Universitätsmedizin, D-10115 Berlin, Germany
| | - Bernd Reif
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Str. 10, D-13125 Berlin, Germany and Charité Universitätsmedizin, D-10115 Berlin, Germany
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Al-Abdul-Wahid MS, Neale C, Pomès R, Prosser RS. A solution NMR approach to the measurement of amphiphile immersion depth and orientation in membrane model systems. J Am Chem Soc 2009; 131:6452-9. [PMID: 19415935 DOI: 10.1021/ja808964e] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Oxygen and Ni(II) are ideal paramagnetic species for NMR studies of immersion depth since they establish prominent concentration gradients across the membrane-water interface of either bilayers or micelles. Corresponding gradients of paramagnetic shifts and relaxation rates are observed by NMR for membrane embedded amphiphiles. Specifically, upon dissolution of oxygen at a partial pressure of 20 bar or more, (13)C NMR spectra of membrane embedded amphiphiles reveal chemical shift perturbations which depend sensitively on average immersion depth in the membrane. Similarly, depth-dependent enhancements of spin-lattice relaxation rates can be detected by (1)H NMR. Generally, such paramagnetic effects depend both on steric or accessibility factors and on the local concentration of the paramagnet. The steric terms can be factored out by combining paramagnetic rates arising from O(2) and Ni, in the form of a ratio, R(1P)(O(2))/R(1P)(Ni). The natural logarithm of this ratio is shown to depend linearly on immersion depth in a micelle. The analysis is verified using molecular dynamics simulations of dodecylphosphocholine in a detergent micelle, while thorough consideration of the paramagnetic rate data also allows for the determination of the orientation of imipramine in the micelle. Thus, a complete picture of topology arises from this approach which is readily applicable to studies of drugs and amphiphiles in fast-tumbling bicelles, small unilamellar vesicles, and micelles.
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Affiliation(s)
- M Sameer Al-Abdul-Wahid
- Department of Chemistry, University of Toronto Mississauga, 3359 Mississauga Road North, Mississauga, Ontario, Canada, L5L 1C6
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Bernini A, Venditti V, Spiga O, Ciutti A, Prischi F, Consonni R, Zetta L, Arosio I, Fusi P, Guagliardi A, Niccolai N. NMR studies on the surface accessibility of the archaeal protein Sso7d by using TEMPOL and Gd(III)(DTPA-BMA) as paramagnetic probes. Biophys Chem 2008; 137:71-5. [DOI: 10.1016/j.bpc.2008.07.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2008] [Revised: 07/08/2008] [Accepted: 07/08/2008] [Indexed: 11/27/2022]
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Venditti V, Niccolai N, Butcher SE. Measuring the dynamic surface accessibility of RNA with the small paramagnetic molecule TEMPOL. Nucleic Acids Res 2007; 36:e20. [PMID: 18056080 PMCID: PMC2275091 DOI: 10.1093/nar/gkm1062] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The surface accessibility of macromolecules plays a key role in modulating molecular recognition events. RNA is a complex and dynamic molecule involved in many aspects of gene expression. However, there are few experimental methods available to measure the accessible surface of RNA. Here, we investigate the accessible surface of RNA using NMR and the small paramagnetic molecule TEMPOL. We investigated two RNAs with known structures, one that is extremely stable and one that is dynamic. For helical regions, the TEMPOL probing data correlate well with the predicted RNA surface, and the method is able to distinguish subtle variations in atom depths, such as the relative accessibility of pyrimidine versus purine aromatic carbon atoms. Dynamic motions are also detected by TEMPOL probing, and the method accurately reports a previously characterized pH-dependent conformational transition involving formation of a protonated C-A pair and base flipping. Some loop regions are observed to exhibit anomalously high accessibility, reflective of motions that are not evident within the ensemble of NMR structures. We conclude that TEMPOL probing can provide valuable insights into the surface accessibility and dynamics of RNA, and can also be used as an independent means of validating RNA structure and dynamics in solution.
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Affiliation(s)
- Vincenzo Venditti
- Biomolecular Structure Research Center and Dipartimento di Biologia Molecolare, Università di Siena, via Fiorentina 1, 53100 Siena, Italy
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Teng CL, Hinderliter B, Bryant RG. Oxygen accessibility to ribonuclease a: quantitative interpretation of nuclear spin relaxation induced by a freely diffusing paramagnet. J Phys Chem A 2007; 110:580-8. [PMID: 16405330 DOI: 10.1021/jp0526593] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The nuclear spin relaxation induced by a freely diffusing paramagnetic center provides a direct measure of intermolecular accessibility. A number of factors are involved in a quantitative interpretation of relaxation data including excluded volume effects, solvation differences, and the details of the electron spin relaxation in the paramagnetic center. In the case where the electron relaxation time is short compared with correlation times describing the electron-nuclear coupling, the nuclear spin relaxation rates may be related to the effective local concentration of the paramagnetic center at different locations about the solute of interest. The local concentrations may in turn be related to differences in the local free energies of interaction between the diffusing paramagnet and the cosolute. We demonstrate this approach for the case of ribonuclease A and deduce surface free energy differences for a large number of protein proton sites. We find that the oxygen accessibility is poorly represented by hard-sphere models such as computed solvent or steric accessibility. There is a distribution of local intermolecular interactions with a width of the order of RT that dominates the report of the intermolecular exploration of the protein by this simple solute.
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Affiliation(s)
- Ching-Ling Teng
- The Biophysics Program and Chemistry Department, University of Virginia, Charlottesville, Virginia 22904-4319, USA
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Fumino K, Diakova G, Andersen JD, Brown ML, Bryant RG. Solvation and Intermolecular Exploration of Drug Molecule Fragments. J SOLUTION CHEM 2007. [DOI: 10.1007/s10953-007-9142-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Venditti V, Bernini A, De Simone A, Spiga O, Prischi F, Niccolai N. MD and NMR studies of alpha-bungarotoxin surface accessibility. Biochem Biophys Res Commun 2007; 356:114-7. [PMID: 17336923 DOI: 10.1016/j.bbrc.2007.02.094] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2007] [Accepted: 02/20/2007] [Indexed: 11/27/2022]
Abstract
Protein surface accessibility represents a dimension of structural biology which has not been discussed in details so far, in spite of its fundamental role in controlling the molecular recognition process. In the present report the surface accessibility of alpha-bungarotoxin, a small and well characterized protein, has been investigated by analyzing its interaction with solvent and paramagnetic molecules in an integrated way. The presence of strong hydration sites, identified by a combined analysis of MD simulation and NMR results, seems to prevent the access of Gd(III)DTPA-BMA to the protein surface. On the contrary, the limited hydration of the alpha-bungarotoxin active site favors frequent encounters between the paramagnetic probe and the protein in the latter region. All the data obtained here for alpha-bungarotoxin suggest that shape and stability of the solvation shell control its surface accessibility and, hence, intermolecular interactions in a way which could be common to many other proteins.
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Affiliation(s)
- Vincenzo Venditti
- Biomolecular Structure Research Center and Dipartimento di Biologia Molecolare, Università di Siena, via A. Fiorentina 1, 53100 Siena, Italy
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Ferreri C, Manco I, Faraone-Mennella MR, Torreggiani A, Tamba M, Manara S, Chatgilialoglu C. The Reaction of Hydrogen Atoms with Methionine Residues: A Model of Reductive Radical Stress Causing Tandem Protein-Lipid Damage. Chembiochem 2006; 7:1738-44. [PMID: 16977666 DOI: 10.1002/cbic.200600188] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The occurrence of tandem damage, due to reductive radical stress involving proteins and lipids, is shown by using a biomimetic model. It is made of unsaturated lipid vesicle suspensions in phosphate buffer in the presence of methionine, either as a single amino acid or as part of a protein such as RNase A, which contains four methionine residues. The radical process starts with the formation of H(.) atoms by reaction of solvated electrons with dihydrogen phosphate anions, which selectively attack the thioether function of methionine. The modification of methionine to alpha-aminobutyric acid is accompanied by the formation of thiyl radicals, which in turn cause the isomerization of the cis fatty acid residues to the trans isomers. The relationship between methionine modification and lipid damage and some details of the reductive radical stress obtained by proteomic analysis of irradiated RNase A are presented.
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Affiliation(s)
- Carla Ferreri
- ISOF, Consiglio Nazionale delle Ricerche, Via P. Gobetti 101, 40129 Bologna, Italy.
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Teng CL, Bryant RG. Spin relaxation measurements of electrostatic bias in intermolecular exploration. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2006; 179:199-205. [PMID: 16386442 DOI: 10.1016/j.jmr.2005.12.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2005] [Revised: 12/09/2005] [Accepted: 12/09/2005] [Indexed: 05/05/2023]
Abstract
We utilize the paramagnetic contribution to proton spin-lattice relaxation rate constants induced by freely diffusing charged paramagnetic centers to investigate the effect of charge on the intermolecular exploration of a protein by the small molecule. The proton NMR spectrum provided 255 resolved resonances that report how the explorer molecule local concentration varies with position on the surface. The measurements integrate over local dielectric constant variations, and, in principle, provide an experimental characterization of the surface free energy sampling biases introduced by the charge distribution on the protein. The experimental results for ribonuclease A obtained using positive, neutral, and negatively charged small nitroxide radicals are qualitatively similar to those expected from electrostatic calculations. However, while systematic electrostatic trends are apparent, the three different combinations of the data sets do not yield internally consistent values for the electrostatic contribution to the intermolecular free energy. We attribute this failure to the weakness of the electrostatic sampling bias for charged nitroxides in water and local variations in effective translational diffusion constant at the water-protein interface, which enters the nuclear spin relaxation equations for the nitroxide-proton dipolar coupling.
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Affiliation(s)
- Ching-Ling Teng
- Chemistry Department, Biophysics Program, University of Virginia, Charlottesville, VA 22904-4319, USA
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Sakakura M, Noba S, Luchette PA, Shimada I, Prosser RS. An NMR Method for the Determination of Protein-Binding Interfaces Using Dioxygen-Induced Spin−Lattice Relaxation Enhancement. J Am Chem Soc 2005; 127:5826-32. [PMID: 15839680 DOI: 10.1021/ja047825j] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Using oxygen as a paramagnetic probe, researchers can routinely study topologies and protein-binding interfaces by NMR. The paramagnetic contribution to the amide (1)H spin-lattice relaxation rates (R(1)(P)) have been studied for uniformly (2)H,(15)N-labeled FB protein, a 60-residue three-helix bundle, constituting the B domain of protein A. Through TROSY versions of inversion-recovery experiments, R(1)(P) could be determined. R(1)(P) was then measured in the presence of a stoichiometric equivalent of an unlabeled Fc fragment of immunoglobulin (Ig) G, and the ratio of R(1)(P) of the FB-Fc complex to that of free FB [i.e., R(1)(P)(complex)/R(1)(P)(free)] was determined for each observable residue. Regions of helix I and helix II, which were previously known to interact with Fc, were readily identified as belonging to the binding interface by their characteristically reduced values of R(1)(P)(complex)/R(1)(P)(free). The method of comparing oxygen-induced spin-lattice relaxation rates of free protein and protein-protein complexes, to detect binding interfaces, offers greater sensitivity than chemical shift perturbation, while it is not necessary to heavily deuterate the labeled protein, as is the case in cross saturation experiments.
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Affiliation(s)
- M Sakakura
- Contribution from the Graduate School of Pharmaceutical Sciences, University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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Phosphorescence of individual horseradish peroxidases proteins having a modified heme group. Chem Phys Lett 2005. [DOI: 10.1016/j.cplett.2004.10.133] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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