title: The association of polar residues in the DAP12 homodimer: TOXCAT and molecular dynamics simulation studies.
abstract: Dimerization of the transmembrane (TM) adaptor protein DAP12 plays a key role in mediating activation signals through TM-TM association with cell-surface receptors. Herein, we apply the TOXCAT assay and molecular dynamics simulation to analyze dynamics and dimerization of the TM helix of DAP12 in the membrane bilayer. In the TOXCAT assay, we performed site-specific mutagenesis of potential dimerization motifs in the DAP12 TM domain. Instead of the common GxxxG dimerization motif, mutating either of the polar residues Asp-50 and Thr-54 significantly decreased the TOXCAT signal for the dimerization of DAP12 TM domain. Furthermore, through the conformational difference between wild-type and mutant DAP12 TM homodimers, a combined coarse-grained and atomistic molecular dynamics simulation has identified both Asp-50 and Thr-54 at the dimerization interface. The experimental and computational results of the DAP12 TM dimer are in excellent agreement with the previously reported NMR structure obtained in detergent micelles. Such a combination of dynamics simulation and cell-based experiments can be applied to produce insights at the molecular level into the TM-TM association of many other transmembrane proteins.
authors.affiliation: Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, People's Republic of China.
authors.forename: Peng
authors.initials: P
authors.lastname: Wei
authors.forename: Bo-Kai
authors.initials: BK
authors.lastname: Zheng
authors.forename: Peng-Ru
authors.initials: PR
authors.lastname: Guo
authors.forename: Toru
authors.initials: T
authors.lastname: Kawakami
authors.forename: Shi-Zhong
authors.initials: SZ
authors.lastname: Luo
mesh_terms: D048868:Adaptor Proteins, Signal Transducing / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D000595:Amino Acid Sequence; D002462:Cell Membrane / Q000378:metabolism*; D006801:Humans; D008051:Lipid Bilayers / Q000378:metabolism*; D008565:Membrane Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D056004:Molecular Dynamics Simulation; D008969:Molecular Sequence Data; D016297:Mutagenesis, Site-Directed; D009154:Mutation; D055503:Protein Multimerization; D020836:Protein Structure, Quaternary; D017433:Protein Structure, Secondary
chemical_list: D048868:Adaptor Proteins, Signal Transducing; D008051:Lipid Bilayers; D008565:Membrane Proteins; C110546:TYROBP protein, human
references.citation: Nat Immunol. 2008 May;9(5):495-502
references.pmid: 18425106
references.citation: J Mol Biol. 2002 Jan 4;315(1):63-72
references.pmid: 11771966
references.citation: Biochem Soc Trans. 2008 Feb;36(Pt 1):27-32
references.pmid: 18208379
references.citation: Phys Chem Chem Phys. 2010 Mar 7;12(9):2254-6; author reply 2257-8
references.pmid: 20165775
references.citation: Biochemistry. 2006 Dec 5;45(48):14298-310
references.pmid: 17128969
references.citation: Protein Sci. 2011 Nov;20(11):1814-23
references.pmid: 21830242
references.citation: J Biol Chem. 2005 Jul 22;280(29):27449-57
references.pmid: 15911619
references.citation: Proc Natl Acad Sci U S A. 2010 Jan 12;107(2):703-8
references.pmid: 20080739
references.citation: Biophys J. 2004 Aug;87(2):754-63
references.pmid: 15298884
references.citation: Biochemistry. 1992 Dec 29;31(51):12726-32
references.pmid: 1463744
references.citation: Biochim Biophys Acta. 2012 Apr;1818(4):974-83
references.pmid: 22155642
references.citation: Proc Natl Acad Sci U S A. 1999 Feb 2;96(3):863-8
references.pmid: 9927659
references.citation: Biochim Biophys Acta. 2012 Feb;1818(2):183-93
references.pmid: 21910966
references.citation: Proteins. 2011 Jul;79(7):2203-13
references.pmid: 21557324
references.citation: J Chem Theory Comput. 2008 Mar;4(3):435-47
references.pmid: 26620784
references.citation: J Chem Theory Comput. 2008 May;4(5):819-34
references.pmid: 26621095
references.citation: J Chem Theory Comput. 2009 Mar 10;5(3):615-26
references.pmid: 26610227
references.citation: J Mol Graph. 1996 Feb;14(1):33-8, 27-8
references.pmid: 8744570
references.citation: Biochemistry. 2009 Oct 13;48(40):9437-47
references.pmid: 19743837
references.citation: Cell. 2006 Oct 20;127(2):355-68
references.pmid: 17055436
references.citation: J Mol Biol. 1993 Dec 5;234(3):779-815
references.pmid: 8254673
references.citation: Structure. 2008 Jul;16(7):991-1001
references.pmid: 18611372
references.citation: J Biol Chem. 2004 Jun 18;279(25):26666-73
references.pmid: 15067009
references.citation: Nature. 1998 Feb 12;391(6668):703-7
references.pmid: 9490415
references.citation: Immunity. 1998 Jun;8(6):693-701
references.pmid: 9655483
references.citation: Biochemistry. 2008 Oct 7;47(40):10503-12
references.pmid: 18783247
references.citation: Nat Rev Immunol. 2007 Nov;7(11):841-50
references.pmid: 17960150
references.citation: PLoS One. 2012;7(9):e44263
references.pmid: 22984481
references.citation: Immunol Rev. 2005 Dec;208:50-65
references.pmid: 16313340
references.citation: J Am Chem Soc. 2006 Mar 1;128(8):2697-704
references.pmid: 16492056
references.citation: Biochemistry. 1990 May 1;29(17):4031-7
references.pmid: 1694455
references.citation: Biophys J. 2009 Jun 3;96(11):4622-30
references.pmid: 19486684
references.citation: Immunol Rev. 2009 Jan;227(1):150-60
references.pmid: 19120482
references.citation: J Mol Biol. 2009 May 29;389(1):10-6
references.pmid: 19361517
references.citation: J Biol Chem. 1996 Mar 8;271(10):5941-6
references.pmid: 8621468
references.citation: Biophys J. 2012 Apr 4;102(7):L27-9
references.pmid: 22500771
references.citation: Arch Biochem Biophys. 2010 Mar 15;495(2):159-64
references.pmid: 20074546
references.citation: J Comput Chem. 2004 Oct;25(13):1656-76
references.pmid: 15264259
references.citation: J Chem Theory Comput. 2011 Apr 12;7(4):1157-66
references.pmid: 26606363
references.citation: Annu Rev Biophys Biomol Struct. 1992;21:223-42
references.pmid: 1326354
references.citation: Nat Immunol. 2010 Nov;11(11):1023-9
references.pmid: 20890284
references.citation: J Mol Biol. 2008 Oct 3;382(2):448-57
references.pmid: 18674540
references.citation: Biochim Biophys Acta. 2012 Apr;1818(4):925-6
references.pmid: 22365068
references.citation: Biochim Biophys Acta. 2012 Apr;1818(4):963-73
references.pmid: 21827736
references.citation: Proteins. 1999 Jul 1;36(1):135-43
references.pmid: 10373012
references.citation: J Phys Chem B. 2007 Jul 12;111(27):7812-24
references.pmid: 17569554