title: Dynamics and ligand-induced solvent accessibility changes in human retinoid X receptor homodimer determined by hydrogen deuterium exchange and mass spectrometry.
abstract: Receptors for retinoic acid act as ligand activated transcription factors. The three-dimensional structure of the retinoid X receptor (RXR) ligand binding domain has been determined, but little information is available concerning the properties of the protein in solution. Hydrogen/deuterium exchange followed by electrospray ionization mass spectrometry was used to probe the solution conformation of the recombinant human RXRalpha homodimer ligand binding domain in the presence and absence of 9-cis-retinoic acid (9-cis-RA). Within the experimental time domain (0.25-180 min), about 20 amide hydrogens showed decreased exchange rates in the presence of saturating concentrations of 9-cis-RA as compared to those found for the homodimer in the absence of ligand. Most of the amides were located in peptides derived from regions of the protein shown by the X-ray structure to interact with the bound ligand: the amino termini of helices 3 and 9, the two beta sheets, helix 8, the H8-H9 loop, and the carboxyl terminus of helix 11. Unexpectedly, protection was also observed in peptides derived from helices 7, 10, 11, and the H7-H8 and H10-H11 loops, regions that are not directly in contact with bound 9-cis-RA. These results suggest that the binding of ligand results in additional effects on the conformation or dynamics of the homodimer in solution as compared to those observed for the X-ray structure. Overall, the change in deuterium exchange induced by the binding of 9-cis-RA correlated reasonably well with changes in hydrogen bonding, residue depth, and/or solvent accessibility predicted from the crystal structure.
authors.affiliation: Department of Chemistry, Oregon State University, Corvallis, Oregon 97331, USA.
authors.forename: Xuguang
authors.initials: X
authors.lastname: Yan
authors.forename: David
authors.initials: D
authors.lastname: Broderick
authors.forename: Mark E
authors.initials: ME
authors.lastname: Leid
authors.forename: Michael I
authors.initials: MI
authors.lastname: Schimerlik
authors.forename: Max L
authors.initials: ML
authors.lastname: Deinzer
mesh_terms: D000077556:Alitretinoin; D000595:Amino Acid Sequence; D002850:Chromatography, Gel; D018360:Crystallography, X-Ray; D041961:Deuterium Exchange Measurement / Q000379:methods; D019281:Dimerization; D006801:Humans; D008024:Ligands; D008969:Molecular Sequence Data; D010446:Peptide Fragments / Q000737:chemistry; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D021122:Protein Subunits / Q000737:chemistry; D018168:Receptors, Retinoic Acid / Q000819:agonists / Q000737:chemistry*; D011993:Recombinant Fusion Proteins / Q000819:agonists / Q000737:chemistry; D047488:Retinoid X Receptors; D012996:Solutions; D012997:Solvents / Q000737:chemistry*; D021241:Spectrometry, Mass, Electrospray Ionization / Q000379:methods; D013816:Thermodynamics; D014157:Transcription Factors / Q000819:agonists / Q000737:chemistry*; D014212:Tretinoin / Q000737:chemistry
chemical_list: D008024:Ligands; D010446:Peptide Fragments; D021122:Protein Subunits; D018168:Receptors, Retinoic Acid; D011993:Recombinant Fusion Proteins; D047488:Retinoid X Receptors; D012996:Solutions; D012997:Solvents; D014157:Transcription Factors; D000077556:Alitretinoin; D014212:Tretinoin