title: Small-angle scattering determination of the shape and localization of human cytochrome P450 embedded in a phospholipid nanodisc environment.
abstract: Membrane proteins reconstituted into phospholipid nanodiscs comprise a soluble entity accessible to solution small-angle X-ray scattering (SAXS) studies. It is demonstrated that using SAXS data it is possible to determine both the shape and localization of the membrane protein cytochrome P450 3A4 (CYP3A4) while it is embedded in the phospholipid bilayer of a nanodisc. In order to accomplish this, a hybrid approach to analysis of small-angle scattering data was developed which combines an analytical approach to describe the multi-contrast nanodisc with a free-form bead-model description of the embedded protein. The protein shape is then reconstructed ab initio to optimally fit the data. The result of using this approach is compared with the result obtained using a rigid-body description of the CYP3A4-in-nanodisc system. Here, the CYP3A4 structure relies on detailed information from crystallographic and molecular-dynamics studies of CYP3A4. Both modelling approaches arrive at very similar solutions in which the α-helical anchor of the CYP3A4 systematically stays close to the edge of the nanodisc and with the large catalytic domain leaning over the outer edge of the nanodisc. The obtained distance between the globular domains of CYP3A4 is consistent with previously published theoretical calculations.
authors.affiliation: Structural Biophysics, Niels Bohr Institute, Faculty of Science, University of Copenhagen, Copenhagen, Denmark.
authors.forename: Nicholas
authors.initials: N
authors.lastname: Skar-Gislinge
authors.affiliation: Structural Biophysics, Niels Bohr Institute, Faculty of Science, University of Copenhagen, Copenhagen, Denmark.
authors.forename: Søren A R
authors.initials: SA
authors.lastname: Kynde
authors.affiliation: Department of Biochemistry, School of Molecular and Cellular Biology, University of Illinois, 505 South Goodwin Avenue, Urbana, IL 61801, USA.
authors.forename: Ilia G
authors.initials: IG
authors.lastname: Denisov
authors.affiliation: Department of Biochemistry, School of Molecular and Cellular Biology, University of Illinois, 505 South Goodwin Avenue, Urbana, IL 61801, USA.
authors.forename: Xin
authors.initials: X
authors.lastname: Ye
authors.affiliation: Department of Biochemistry, School of Molecular and Cellular Biology, University of Illinois, 505 South Goodwin Avenue, Urbana, IL 61801, USA.
authors.forename: Ivan
authors.initials: I
authors.lastname: Lenov
authors.affiliation: Department of Biochemistry, School of Molecular and Cellular Biology, University of Illinois, 505 South Goodwin Avenue, Urbana, IL 61801, USA.
authors.forename: Stephen G
authors.initials: SG
authors.lastname: Sligar
authors.affiliation: Structural Biophysics, Niels Bohr Institute, Faculty of Science, University of Copenhagen, Copenhagen, Denmark.
authors.forename: Lise
authors.initials: L
authors.lastname: Arleth
mesh_terms: D020816:Amino Acid Motifs; D020134:Catalytic Domain; D051544:Cytochrome P-450 CYP3A / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D004339:Drug Compounding; D015870:Gene Expression; D006801:Humans; D008051:Lipid Bilayers / Q000737:chemistry*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D049329:Nanostructures / Q000737:chemistry* / Q000648:ultrastructure; D010713:Phosphatidylcholines / Q000737:chemistry*; D017433:Protein Structure, Secondary; D011994:Recombinant Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D053838:Scattering, Small Angle; D014961:X-Ray Diffraction
chemical_list: D008051:Lipid Bilayers; D010713:Phosphatidylcholines; D011994:Recombinant Proteins; D051544:Cytochrome P-450 CYP3A; C510163:CYP3A4 protein, human; C028694:1-palmitoyl-2-oleoylphosphatidylcholine
keywords: cytochrome P450 3A4; membrane proteins; nanodiscs; small-angle scattering