title: Insights into the transmembrane helix associations of kit ligand by molecular dynamics simulation and TOXCAT.
abstract: Kit ligand (KITL) plays important roles in cell proliferation, differentiation, and survival via interaction with its receptor Kit. The previous studies demonstrated that KITL formed a noncovalent homodimer through transmembrane (TM) domain; however, the undergoing mechanism of transmembrane association that determines KITL TM dimerization is still not clear. Herein, molecular dynamics (MD) simulation strategy and TOXCAT assay were combined to characterize the dimerization interface and structure of KITL TM in details. KITL TM formed a more energetically favorable noncovalent dimer through a conserved SxxxGxxxG motif in the MD simulation. Furthermore, the TOXCAT results demonstrated that KITL TM self-associated strongly in the bilayer membrane environment. Mutating any one of the small residues Ser11, Gly15 or Gly19 to Ile disrupted KITL TM dimerization dramatically, which further validated our MD simulation results. In addition, our results showed that Tyr22 could help to stabilize the TM interactions via interacting with the phosphoric group in the bilayer membrane. Pro7 did not induce helix kinks or swivel angles in KITL TM, but it was related with the pitch of the turn around this residue so as to affect the dimer formation. Combining the results of computer modeling and experimental mutagenesis studies on the KITL TM provide new insights for the transmembrane helix association of KITL dimerization. Proteins 2017; 85:1362-1370. © 2017 Wiley Periodicals, Inc.
authors.affiliation: Beijing Key Laboratory of Bioprocess College of Life Science and Technology, Beijing, University of Chemical Technology, Beijing, 100029, China.
authors.forename: Mengya
authors.identifier: 0000-0001-8722-6296
authors.initials: M
authors.lastname: Chai
authors.affiliation: Beijing Key Laboratory of Bioprocess College of Life Science and Technology, Beijing, University of Chemical Technology, Beijing, 100029, China.
authors.forename: Bo
authors.initials: B
authors.lastname: Liu
authors.affiliation: Beijing Key Laboratory of Bioprocess College of Life Science and Technology, Beijing, University of Chemical Technology, Beijing, 100029, China.
authors.forename: Fude
authors.initials: F
authors.lastname: Sun
authors.affiliation: Beijing Key Laboratory of Bioprocess College of Life Science and Technology, Beijing, University of Chemical Technology, Beijing, 100029, China.|School of Basic Medical Science, Beijing University of Chinese Medicine, Beijing, 100029, China.
authors.forename: Peng
authors.initials: P
authors.lastname: Wei
authors.affiliation: Beijing Key Laboratory of Bioprocess College of Life Science and Technology, Beijing, University of Chemical Technology, Beijing, 100029, China.
authors.forename: Peng
authors.initials: P
authors.lastname: Chen
authors.affiliation: Beijing Key Laboratory of Bioprocess College of Life Science and Technology, Beijing, University of Chemical Technology, Beijing, 100029, China.
authors.forename: Lida
authors.initials: L
authors.lastname: Xu
authors.affiliation: Beijing Key Laboratory of Bioprocess College of Life Science and Technology, Beijing, University of Chemical Technology, Beijing, 100029, China.
authors.forename: Shi-Zhong
authors.initials: SZ
authors.lastname: Luo
mesh_terms: D015060:1,2-Dipalmitoylphosphatidylcholine / Q000737:chemistry; D000595:Amino Acid Sequence; D000818:Animals; D001665:Binding Sites; D002417:Cattle; D015500:Chloramphenicol O-Acetyltransferase / Q000235:genetics / Q000378:metabolism*; D003001:Cloning, Molecular; D004285:Dogs; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism; D015870:Gene Expression; D017930:Genes, Reporter; D006801:Humans; D007700:Kinetics; D008051:Lipid Bilayers / Q000737:chemistry; D051379:Mice; D056004:Molecular Dynamics Simulation; D009154:Mutation; D011485:Protein Binding; D000072756:Protein Conformation, alpha-Helical; D000072757:Protein Conformation, beta-Strand; D055503:Protein Multimerization; D051381:Rats; D011993:Recombinant Fusion Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D011994:Recombinant Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D016415:Sequence Alignment; D019089:Stem Cell Factor / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D013379:Substrate Specificity; D013552:Swine; D013816:Thermodynamics
chemical_list: D008051:Lipid Bilayers; D011993:Recombinant Fusion Proteins; D011994:Recombinant Proteins; D019089:Stem Cell Factor; D015060:1,2-Dipalmitoylphosphatidylcholine; D015500:Chloramphenicol O-Acetyltransferase
keywords: SxxxGxxxG motif; TOXCAT; dimerization; kit ligand; molecular dynamic simulation; transmembrane domain