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Treuheit NA, Redhair M, Kwon H, McClary WD, Guttman M, Sumida JP, Atkins WM. Membrane Interactions, Ligand-Dependent Dynamics, and Stability of Cytochrome P4503A4 in Lipid Nanodiscs. Biochemistry 2016; 55:1058-69. [PMID: 26814638 DOI: 10.1021/acs.biochem.5b01313] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Membrane-bound cytochrome P4503A4 (CYP3A4) is the major source of enzymatic drug metabolism. Although several structural models of CYP3A4 in various ligand complexes are available, none includes a lipid bilayer. Details of the effects of the membrane on protein dynamics and solvation, and access channels for ligands, remain uncertain. H/D exchange mass spectrometry (H/DXMS) with ligand free CYP3A4 containing a deletion of residues 3-12, compared to that of the full length wild type, in lipid nanodiscs afforded 91% sequence coverage. Deuterium exchange was fast in the F- and G-helices, HI loop, and C-terminal loop. In contrast, there is very low exchange in the F'- and G'-helices. The results are consistent with the overall membrane orientation of CYP3A4 suggested by published MD simulations and spectroscopic results, and the solvent accessibility of the F/G loop suggests that it is not deeply membrane-embedded. Addition of ketoconazole results in only modest, but global, changes in solvent accessibility. Interestingly, with ketoconazole bound some peptides become less solvent accessible or dynamic, including the F- and G-helices, but several peptides demonstrate modestly increased accessibility. Differential scanning calorimetry (DSC) of CYP3A4-nanodiscs suggests membrane-induced stabilization compared to that of aggregated CYP3A4 in buffer, and this stabilization is enhanced upon addition of the ligand ketoconazole. This ligand-induced stabilization is accompanied by a very large increase in ΔH for CYP3A4 denaturation in nanodiscs, possibly due to increased CYP3A4-membrane interactions. Together, the results suggest a distinct orientation of CYP3A4 on the lipid membrane, and they highlight likely solvent access channels, which are consistent with several MD simulations.
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Affiliation(s)
- Nicholas A Treuheit
- Department of Medicinal Chemistry, University of Washington , Box 357610, Seattle, Washington 98195-7610, United States
| | - Michelle Redhair
- Department of Medicinal Chemistry, University of Washington , Box 357610, Seattle, Washington 98195-7610, United States
| | - Hyewon Kwon
- Department of Medicinal Chemistry, University of Washington , Box 357610, Seattle, Washington 98195-7610, United States
| | - Wynton D McClary
- Department of Medicinal Chemistry, University of Washington , Box 357610, Seattle, Washington 98195-7610, United States
| | - Miklos Guttman
- Department of Medicinal Chemistry, University of Washington , Box 357610, Seattle, Washington 98195-7610, United States
| | - John P Sumida
- Department of Medicinal Chemistry, University of Washington , Box 357610, Seattle, Washington 98195-7610, United States
| | - William M Atkins
- Department of Medicinal Chemistry, University of Washington , Box 357610, Seattle, Washington 98195-7610, United States
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Goormaghtigh E, Raussens V, Ruysschaert JM. Attenuated total reflection infrared spectroscopy of proteins and lipids in biological membranes. BIOCHIMICA ET BIOPHYSICA ACTA 1999; 1422:105-85. [PMID: 10393271 DOI: 10.1016/s0304-4157(99)00004-0] [Citation(s) in RCA: 452] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- E Goormaghtigh
- Laboratoire de Chimie-Physique des Macromolécules aux Interfaces, P. O. Box 206/2, Université Libre de Bruxelles, Campus Plaine, B-1050, Brussels, Belgium.
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Tüchsen E, Woodward C. Hydrogen exchange kinetics of surface peptide amides in bovine pancreatic trypsin inhibitor. J Mol Biol 1987; 193:793-802. [PMID: 2441070 DOI: 10.1016/0022-2836(87)90359-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The acid and base catalytic rate constants, kH, obs and kOH, obs and the pH at the minimum rate, pHmin, of 25 rapidly exchanging protons in bovine pancreatic trypsin inhibitor have been determined. Here we report the labeling procedure giving 1H nuclear magnetic resonance spectral resolution of seven additional rapidly exchanging NH protons and the pH dependence of their chemical shifts. Values of kH,obs kOH,obs and pHmin are given for Ala16, Gly28 and Arg53 NH groups, the only backbone amide protons with static accessibility of more than zero in the crystal structure not previously reports, and for Gly56 NH, buried at the C terminus of an alpha-helix. All four protons reported here have pH min greater than or equal to 3. Conclusions of the previous study predict that peptide protons with pHmin higher than those of model compounds have greater static accessibility of the peptide O than of the peptide N atom. The locations in the crystal structure of the four NH groups whose exchange rates are reported here are in qualitative agreement with these predictions. The ionic strength dependence of Ala16 at pH 5.5 shows a sharp increase in the exchange rate with decreasing salt concentration, as expected for base-catalyzed exchange in a positive electrostatic field.
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Tüchsen E, Woodward C. Mechanism of surface peptide proton exchange in bovine pancreatic trypsin inhibitor. Salt effects and O-protonation. J Mol Biol 1985; 185:421-30. [PMID: 2414452 DOI: 10.1016/0022-2836(85)90413-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The acid-catalyzed hydrogen exchange rate constants kH, and the base-catalyzed rate constants kOH, have been determined (in the preceding paper) for the 25 most rapidly exchanging NH groups of bovine pancreatic trypsin inhibitor. Most of these NH groups are at the protein-solvent interface. The correlation of kH, but not kOH, with the static accessibility and hydrogen bonding of the peptide carbonyl O atom indicates that the mechanism of acid catalysis in proteins involves O-protonation. Agreement between the ionic strength dependence observed for kH and kOH and the ionic strength dependence calculated for an O-protonation mechanism supports this conclusion. N-protonation for acid catalysis, as well as N-deprotonation for base catalysis, have traditionally been assumed in the mechanism of the chemical step in peptide amide proton exchange. A preference for the alternative O-protonation mechanism has far-reaching implications in the interpretation of protein hydrogen exchange kinetics. With an O-protonation mechanism, acid-catalyzed rates of surface NH groups are primarily a function of the average solvent accessibility of the carbonyl O atoms in the dynamic solution structure, while base-catalyzed rates of surface NH groups measure solvent accessibility of the peptide N. The relative dynamic accessibilities of peptide O atoms, as measured by relative values of kH (corrected for electrostatic effects), correlate with O static accessibilities in the crystal structure. A lower correlation of static accessibility of N atoms with kOH is observed for surface NH groups in peptide groups in which the carbonyl O is not hydrogen bonded. For some surface NH groups, the observed pH of minimum rate, pHmin, deviates widely from the pHmin of model compounds. This is explained as the combined result of electrostatic effects and of the differences in accessibility of the carbonyl O and N atoms that result in a change in the relative values of kH and kOH as compared to those of model peptides. A mechanism whereby exchange of interior sites is catalyzed by interactions of catalysis ions with protein surface atoms via charge transfer is suggested.
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Tüchsen E, Hvidt A, Ottesen M. Enzymes immobilized as crystals. Hydrogen isotope exchange of crystalline lysozyme. Biochimie 1980; 62:563-6. [PMID: 7417590 DOI: 10.1016/s0300-9084(80)80101-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Immobilization of enzymes by crystallization and subsequent cross-linking provide structures characterized by a regular three-dimensional molecular arrangement and a high packing density. Compared to randomly immobilized enzymes, such structures permit more detailed analysis of the variations in kinetic properties arising from the three-dimensional network or perturbations of the molecular conformations. To obtain information on the effect of crystallization on the dynamic properties of the folded peptide chain in an enzyme molecule, hydrogen exchange rates were measured for both dissolved and crystalline lysozyme over a wide range of pH. Using this method, which reflects molecular oscillations between closely related conformations, no differences were detected between lysozyme in crystalline and dissolved state.
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