title: Dioxane contributes to the altered conformation and oligomerization state of a designed engrailed homeodomain variant.
abstract: Our goal was to compute a stable, full-sequence design of the Drosophila melanogaster engrailed homeodomain. Thermal and chemical denaturation data indicated the design was significantly more stable than was the wild-type protein. The data were also nearly identical to those for a similar, later full-sequence design, which was shown by NMR to adopt the homeodomain fold: a three-helix, globular monomer. However, a 1.65 A crystal structure of the design described here turned out to be of a completely different fold: a four-helix, rodlike tetramer. The crystallization conditions included approximately 25% dioxane, and subsequent experiments by circular dichroism and sedimentation velocity analytical ultracentrifugation indicated that dioxane increases the helicity and oligomerization state of the designed protein. We attribute at least part of the discrepancy between the target fold and the crystal structure to the presence of a high concentration of dioxane.
authors.affiliation: Biochemistry and Molecular Biophysics Option, California Institute of Technology/HHMI 114-96, 1200 E. California Boulevard, Pasadena, CA 91125-9600, USA.
authors.forename: Geoffrey K
authors.initials: GK
authors.lastname: Hom
authors.forename: J Kyle
authors.initials: JK
authors.lastname: Lassila
authors.forename: Leonard M
authors.initials: LM
authors.lastname: Thomas
authors.forename: Stephen L
authors.initials: SL
authors.lastname: Mayo
mesh_terms: D000818:Animals; D002942:Circular Dichroism; D018360:Crystallography, X-Ray; D004146:Dioxanes / Q000737:chemistry / Q000494:pharmacology*; D029721:Drosophila Proteins; D018398:Homeodomain Proteins / Q000737:chemistry*; D008958:Models, Molecular; D011487:Protein Conformation / Q000187:drug effects; D014157:Transcription Factors / Q000737:chemistry*
chemical_list: D004146:Dioxanes; D029721:Drosophila Proteins; C063459:En protein, Drosophila; D018398:Homeodomain Proteins; D014157:Transcription Factors; C025223:1,4-dioxane
references.citation: Acta Crystallogr D Biol Crystallogr. 1999 Jan;55(Pt 1):247-55
references.pmid: 10089417
references.citation: Biophys J. 2000 Mar;78(3):1606-19
references.pmid: 10692345
references.citation: J Mol Biol. 2000 Jun 9;299(3):789-803
references.pmid: 10835284
references.citation: J Mol Biol. 2001 Jan 19;305(3):619-31
references.pmid: 11152617
references.citation: J Mol Biol. 2002 Feb 8;316(1):189-99
references.pmid: 11829512
references.citation: Proteins. 2002 Jul 1;48(1):31-43
references.pmid: 12012335
references.citation: J Comput Chem. 2003 Jan 30;24(2):232-43
references.pmid: 12497602
references.citation: Adv Protein Chem. 1961;16:401-544
references.pmid: 13995485
references.citation: Acta Crystallogr B. 1992 Aug 1;48 ( Pt 4):341-56
references.pmid: 1418817
references.citation: Proc Natl Acad Sci U S A. 2004 Feb 10;101(6):1537-42
references.pmid: 14752198
references.citation: Acta Crystallogr D Biol Crystallogr. 1994 Sep 1;50(Pt 5):760-3
references.pmid: 15299374
references.citation: J Comput Chem. 2004 Nov 15;25(14):1797-800
references.pmid: 15362137
references.citation: Acta Crystallogr A. 1991 Mar 1;47 ( Pt 2):110-9
references.pmid: 2025413
references.citation: Methods Enzymol. 1997;276:307-26
references.pmid: 27754618
references.citation: J Mol Biol. 1966 Jan;15(1):175-92
references.pmid: 5912039
references.citation: Nature. 1967 May 13;214(5089):652-6
references.pmid: 6049071
references.citation: Biotechnology (N Y). 1994 Dec;12(13):1357-60
references.pmid: 7765566
references.citation: Protein Sci. 1994 Oct;3(10):1779-87
references.pmid: 7849596
references.citation: Protein Sci. 1996 May;5(5):895-903
references.pmid: 8732761
references.citation: Protein Sci. 1996 Dec;5(12):2623-37
references.pmid: 8976571