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Backbone structure of Yersinia pestis Ail determined in micelles by NMR-restrained simulated annealing with implicit membrane solvation

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Abstract

The outer membrane protein Ail (attachment invasion locus) is a virulence factor of Yersinia pestis that mediates cell invasion, cell attachment and complement resistance. Here we describe its three-dimensional backbone structure determined in decyl-phosphocholine (DePC) micelles by NMR spectroscopy. The NMR structure was calculated using the membrane function of the implicit solvation potential, eefxPot, which we have developed to facilitate NMR structure calculations in a physically realistic environment. We show that the eefxPot force field guides the protein towards its native fold. The resulting structures provide information about the membrane-embedded global position of Ail, and have higher accuracy, higher precision and improved conformational properties, compared to the structures calculated with the standard repulsive potential.

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References

  • Bartra SS, Styer KL, O’Bryant DM, Nilles ML, Hinnebusch BJ, Aballay A, Plano GV (2008) Resistance of Yersinia pestis to complement-dependent killing is mediated by the Ail outer membrane protein. Infect Immun 76(2):612–622. doi:10.1128/IAI.01125-07

    Article  Google Scholar 

  • Bermejo GA, Clore GM, Schwieters CD (2012) Smooth statistical torsion angle potential derived from a large conformational database via adaptive kernel density estimation improves the quality of NMR protein structures. Protein Sci 21(12):1824–1836. doi:10.1002/pro.2163

    Article  Google Scholar 

  • Brubaker RR (2004) The recent emergence of plague: a process of felonious evolution. Microb Ecol 47(3):293–299. doi:10.1007/s00248-003-1022-y

    Article  Google Scholar 

  • Chen VB, Arendall WB 3rd, Headd JJ, Keedy DA, Immormino RM, Kapral GJ, Murray LW, Richardson JS, Richardson DC (2010) MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr D Biol Crystallogr 66(Pt 1):12–21. doi:10.1107/S0907444909042073

    Article  Google Scholar 

  • Clore GM, Gronenborn AM (1989) Determination of three-dimensional structures of proteins and nucleic acids in solution by nuclear magnetic resonance spectroscopy. Crit Rev Biochem Mol Biol 24(5):479–564

    Article  Google Scholar 

  • Cornelis GR (2000) Molecular and cell biology aspects of plague. Proc Natl Acad Sci USA 97(16):8778–8783

    Article  ADS  Google Scholar 

  • de Planque MR, Killian JA (2003) Protein-lipid interactions studied with designed transmembrane peptides: role of hydrophobic matching and interfacial anchoring. Mol Membr Biol 20(4):271–284. doi:10.1080/09687680310001605352

    Article  Google Scholar 

  • DeLano WL (2005) PyMol. https://www.pymol.org

  • Ding Y, Fujimoto LM, Yao Y, Marassi FM (2015a) Solid-state NMR of the Yersinia pestis outer membrane protein Ail in lipid bilayer nanodiscs sedimented by ultracentrifugation. J Biomol NMR 61(3–4):275–286. doi:10.1007/s10858-014-9893-4

    Article  Google Scholar 

  • Ding Y, Fujimoto LM, Yao Y, Plano GV, Marassi FM (2015b) Influence of the lipid membrane environment on structure and activity of the outer membrane protein Ail from Yersinia pestis. Biochim Biophys Acta 1842(2):712–720. doi:10.1016/j.bbamem.2014.11.021

    Article  Google Scholar 

  • Doreleijers JF, Sousa da Silva AW, Krieger E, Nabuurs SB, Spronk CA, Stevens TJ, Vranken WF, Vriend G, Vuister GW (2012) CING: an integrated residue-based structure validation program suite. J Biomol NMR 54(3):267–283. doi:10.1007/s10858-012-9669-7

    Article  Google Scholar 

  • Felek S, Tsang TM, Krukonis ES (2010) Three Yersinia pestis adhesins facilitate Yop delivery to eukaryotic cells and contribute to plague virulence. Infect Immun 78(10):4134–4150. doi:10.1128/IAI.00167-10

    Article  Google Scholar 

  • Fox DA, Larsson P, Lo RH, Kroncke BM, Kasson PM, Columbus L (2014) Structure of the Neisserial outer membrane protein Opa(6)(0): loop flexibility essential to receptor recognition and bacterial engulfment. J Am Chem Soc 136(28):9938–9946. doi:10.1021/ja503093y

    Article  Google Scholar 

  • Gong XM, Ding Y, Yu J, Yao Y, Marassi FM (2015) Structure of the Na, K-ATPase regulatory protein FXYD2b in micelles: implications for membrane-water interfacial arginines. Biochim Biophys Acta 1848(1 Pt B):299–306. doi:10.1016/j.bbamem.2014.04.021

    Article  Google Scholar 

  • Hinnebusch BJ, Jarrett CO, Callison JA, Gardner D, Buchanan SK, Plano GV (2011) Role of the Yersinia pestis Ail protein in preventing a protective polymorphonuclear leukocyte response during bubonic plague. Infect Immun. doi:10.1128/IAI.05307-11

    Google Scholar 

  • Ho DK, Skurnik M, Blom AM, Meri S (2014) Yersinia pestis Ail recruitment of C4b-binding protein leads to factor I-mediated inactivation of covalently and noncovalently bound C4b. Eur J Immunol 44(3):742–751. doi:10.1002/eji.201343552

    Article  Google Scholar 

  • Kleinschmidt JH (2015) Folding of beta-barrel membrane proteins in lipid bilayers—unassisted and assisted folding and insertion. Biochim Biophys Acta. doi:10.1016/j.bbamem.2015.05.004

    Google Scholar 

  • Kolodziejek AM, Schnider DR, Rohde HN, Wojtowicz AJ, Bohach GA, Minnich SA, Hovde CJ (2010) Outer membrane protein X (Ail) contributes to Yersinia pestis virulence in pneumonic plague and its activity is dependent on the lipopolysaccharide core length. Infect Immun 78(12):5233–5243. doi:10.1128/IAI.00783-10

    Article  Google Scholar 

  • Kucerka N, Nieh MP, Katsaras J (2011) Fluid phase lipid areas and bilayer thicknesses of commonly used phosphatidylcholines as a function of temperature. Biochim Biophys Acta 1808(11):2761–2771. doi:10.1016/j.bbamem.2011.07.022

    Article  Google Scholar 

  • Lazaridis T (2003) Effective energy function for proteins in lipid membranes. Proteins 52(2):176–192. doi:10.1002/prot.10410

    Article  Google Scholar 

  • Lazaridis T (2005) Structural determinants of transmembrane β-barrels. J Chem Theory Comput 1(4):716–722. doi:10.1021/ct050055x

    Article  Google Scholar 

  • Lazaridis T, Karplus M (1999) Effective energy function for proteins in solution. Proteins 35(2):133–152. doi:10.1002/(SICI)1097-0134(19990501)35:2<133:AID-PROT1>3.0.CO;2-N

    Article  Google Scholar 

  • Luzzati V, Husson F (1962) The structure of the liquid-crystalline phasis of lipid-water systems. J Cell Biol 12:207–219

    Article  Google Scholar 

  • Marsh D (2013) Handbook of lipid bilayers. 2nd edn. CRC Press, Boca Raton

  • Miller VL, Bliska JB, Falkow S (1990) Nucleotide sequence of the Yersinia enterocolitica Ail gene and characterization of the Ail protein product. J Bacteriol 172(2):1062–1069

    Google Scholar 

  • Miller VL, Beer KB, Heusipp G, Young BM, Wachtel MR (2001) Identification of regions of Ail required for the invasion and serum resistance phenotypes. Mol Microbiol 41(5):1053–1062

    Article  Google Scholar 

  • Mouritsen OG, Bloom M (1984) Mattress model of lipid-protein interactions in membranes. Biophys J 46(2):141–153. doi:10.1016/S0006-3495(84)84007-2

    Article  Google Scholar 

  • Nagle JF (2013) Introductory lecture: basic quantities in model biomembranes. Faraday Discuss 161:11–29 (discussion 113–150)

    Article  ADS  Google Scholar 

  • Nagle JF, Tristram-Nagle S (2000) Structure of lipid bilayers. Biochim Biophys Acta 1469(3):159–195

    Article  Google Scholar 

  • Nilges M, Gronenborn AM, Brunger AT, Clore GM (1988) Determination of three-dimensional structures of proteins by simulated annealing with interproton distance restraints. application to crambin, potato carboxypeptidase inhibitor and barley serine proteinase inhibitor 2. Protein Eng 2(1):27–38

    Article  Google Scholar 

  • Perry RD, Fetherston JD (1997) Yersinia pestis—etiologic agent of plague. Clin Microbiol Rev 10(1):35–66

    Google Scholar 

  • Schwieters CD, Clore GM (2001) Internal coordinates for molecular dynamics and minimization in structure determination and refinement. J Magn Reson 152(2):288–302

    Article  ADS  Google Scholar 

  • Schwieters CD, Kuszewski JJ, Tjandra N, Clore GM (2003) The Xplor-NIH NMR molecular structure determination package. J Magn Reson 160(1):65–73

    Article  ADS  Google Scholar 

  • Schwieters CD, Kuszewski JJ, Marius Clore G (2006) Using Xplor, ÄìNIH for NMR molecular structure determination. Prog Nucl Magn Reson Spectrosc 48(1):47–62. doi:10.1016/j.pnmrs.2005.10.001

    Article  Google Scholar 

  • Shen Y, Bax A (2013) Protein backbone and sidechain torsion angles predicted from NMR chemical shifts using artificial neural networks. J Biomol NMR 56(3):227–241. doi:10.1007/s10858-013-9741-y

    Article  Google Scholar 

  • Shi L, Traaseth NJ, Verardi R, Cembran A, Gao J, Veglia G (2009) A refinement protocol to determine structure, topology, and depth of insertion of membrane proteins using hybrid solution and solid-state NMR restraints. J Biomol NMR 44(4):195–205. doi:10.1007/s10858-009-9328-9

    Article  Google Scholar 

  • Teriete P, Franzin CM, Choi J, Marassi FM (2007) Structure of the Na, K-ATPase regulatory protein FXYD1 in micelles. Biochemistry 46(23):6774–6783. doi:10.1021/bi700391b

    Article  Google Scholar 

  • Tian Y, Schwieters CD, Opella SJ, Marassi FM (2014) A practical implicit solvent potential for NMR structure calculation. J Magn Reson 243:54–64. doi:10.1016/j.jmr.2014.03.011

    Article  ADS  Google Scholar 

  • Tian Y, Schwieters CD, Opella SJ, Marassi FM (2015) A practical implicit membrane potential for NMR structure calculations of membrane proteins. Biophys J (in press)

  • Tsang TM, Felek S, Krukonis ES (2010) Ail binding to fibronectin facilitates Yersinia pestis binding to host cells and Yop delivery. Infect Immun 78(8):3358–3368. doi:10.1128/IAI.00238-10

    Article  Google Scholar 

  • Tsang TM, Annis DS, Kronshage M, Fenno JT, Usselman LD, Mosher DF, Krukonis ES (2012) Ail protein binds ninth type III fibronectin repeat (9FNIII) within central 120-kDa region of fibronectin to facilitate cell binding by Yersinia pestis. J Biol Chem 287(20):16759–16767. doi:10.1074/jbc.M112.358978

    Article  Google Scholar 

  • Tsang TM, Wiese JS, Felek S, Kronshage M, Krukonis ES (2013) Ail proteins of Yersinia pestis and Y. pseudotuberculosis have different cell binding and invasion activities. PLoS ONE 8(12):e83621. doi:10.1371/journal.pone.0083621

    Article  ADS  Google Scholar 

  • Versace RE, Lazaridis T (2015) Modeling Protein-Micelle Systems in Implicit Water. J Phys Chem B. doi:10.1021/acs.jpcb.5b00171

    Google Scholar 

  • Vriend G (1990) WHAT IF: a molecular modeling and drug design program. J Mol Graph 8(1):52–56

    Article  Google Scholar 

  • Vriend G, Sander C (1993) Quality control of protein models: directional atomic contact analysis. J Appl Crystallogr 26(1):47–60. doi:10.1107/S0021889892008240

    Article  Google Scholar 

  • Word JM, Lovell SC, LaBean TH, Taylor HC, Zalis ME, Presley BK, Richardson JS, Richardson DC (1999) Visualizing and quantifying molecular goodness-of-fit: small-probe contact dots with explicit hydrogen atoms. J Mol Biol 285(4):1711–1733. doi:10.1006/jmbi.1998.2400

    Article  Google Scholar 

  • Xu C, Gagnon E, Call ME, Schnell JR, Schwieters CD, Carman CV, Chou JJ, Wucherpfennig KW (2008) Regulation of T cell receptor activation by dynamic membrane binding of the CD3epsilon cytoplasmic tyrosine-based motif. Cell 135(4):702–713. doi:10.1016/j.cell.2008.09.044

    Article  Google Scholar 

  • Yamashita S, Lukacik P, Barnard TJ, Noinaj N, Felek S, Tsang TM, Krukonis ES, Hinnebusch BJ, Buchanan SK (2011) Structural insights into Ail-mediated adhesion in Yersinia pestis. Structure 19(11):1672–1682. doi:10.1016/j.str.2011.08.010

    Article  Google Scholar 

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Acknowledgments

This research was supported by grants from the National Institutes of Health (NIH: R01GM110658, R01GM100265, P41EB002031, P30CA030199). CDS was supported by funds from the NIH Intramural Research Program of The Center for Information Technology.

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Authors and Affiliations

  1. Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA, 92037, USA

    Francesca M. Marassi, Yi Ding, Ye Tian & Yong Yao

  2. Division of Computational Bioscience, Center for Information Technology, National Institutes of Health, Building 12A, Bethesda, MD, 20892-5624, USA

    Charles D. Schwieters

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  1. Francesca M. Marassi
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  2. Yi Ding
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Correspondence to Francesca M. Marassi.

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Marassi, F.M., Ding, Y., Schwieters, C.D. et al. Backbone structure of Yersinia pestis Ail determined in micelles by NMR-restrained simulated annealing with implicit membrane solvation. J Biomol NMR 63, 59–65 (2015). https://doi.org/10.1007/s10858-015-9963-2

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