All Title Author
Keywords Abstract


A New Model for Pore Formation by Cholesterol-Dependent Cytolysins

DOI: doi/10.1371/journal.pcbi.1003791

Full-Text   Cite this paper   Add to My Lib

Abstract:

Cholesterol Dependent Cytolysins (CDCs) are important bacterial virulence factors that form large (200–300 ?) membrane embedded pores in target cells. Currently, insights from X-ray crystallography, biophysical and single particle cryo-Electron Microscopy (cryo-EM) experiments suggest that soluble monomers first interact with the membrane surface via a C-terminal Immunoglobulin-like domain (Ig; Domain 4). Membrane bound oligomers then assemble into a prepore oligomeric form, following which the prepore assembly collapses towards the membrane surface, with concomitant release and insertion of the membrane spanning subunits. During this rearrangement it is proposed that Domain 2, a region comprising three β-strands that links the pore forming region (Domains 1 and 3) and the Ig domain, must undergo a significant yet currently undetermined, conformational change. Here we address this problem through a systematic molecular modeling and structural bioinformatics approach. Our work shows that simple rigid body rotations may account for the observed collapse of the prepore towards the membrane surface. Support for this idea comes from analysis of published cryo-EM maps of the pneumolysin pore, available crystal structures and molecular dynamics simulations. The latter data in particular reveal that Domains 1, 2 and 4 are able to undergo significant rotational movements with respect to each other. Together, our data provide new and testable insights into the mechanism of pore formation by CDCs.

References

[1]  Hotze EM, Tweten RK (2012) Membrane assembly of the cholesterol-dependent cytolysin pore complex. Biochimica et biophysica acta 1818: 1028–1038. doi: 10.1016/j.bbamem.2011.07.036
[2]  Hotze EM, Le HM, Sieber JR, Bruxvoort C, McInerney MJ, et al. (2013) Identification and characterization of the first cholesterol-dependent cytolysins from Gram-negative bacteria. Infect Immun 81: 216–225. doi: 10.1128/iai.00927-12
[3]  Gaillard JL, Berche P, Mounier J, Richard S, Sansonetti P (1987) In vitro model of penetration and intracellular growth of Listeria monocytogenes in the human enterocyte-like cell line Caco-2. Infect Immun 55: 2822–2829.
[4]  Madden JC, Ruiz N, Caparon M (2001) Cytolysin-mediated translocation (CMT): a functional equivalent of type III secretion in gram-positive bacteria. Cell 104: 143–152. doi: 10.1016/s0092-8674(01)00198-2
[5]  Rossjohn J, Feil SC, McKinstry WJ, Tweten RK, Parker MW (1997) Structure of a cholesterol-binding, thiol-activated cytolysin and a model of its membrane form. Cell 89: 685–692. doi: 10.1016/s0092-8674(00)80251-2
[6]  Rosado CJ, Buckle AM, Law RH, Butcher RE, Kan WT, et al. (2007) A common fold mediates vertebrate defense and bacterial attack. Science 317: 1548–1551. doi: 10.1126/science.1144706
[7]  Soltani CE, Hotze EM, Johnson AE, Tweten RK (2007) Structural elements of the cholesterol-dependent cytolysins that are responsible for their cholesterol-sensitive membrane interactions. Proc Natl Acad Sci U S A 104: 20226–20231. doi: 10.1073/pnas.0708104105
[8]  Tilley SJ, Orlova EV, Gilbert RJ, Andrew PW, Saibil HR (2005) Structural basis of pore formation by the bacterial toxin pneumolysin. Cell 121: 247–256. doi: 10.1016/j.cell.2005.02.033
[9]  Czajkowsky DM, Hotze EM, Shao Z, Tweten RK (2004) Vertical collapse of a cytolysin prepore moves its transmembrane beta-hairpins to the membrane. EMBO J 23: 3206–3215. doi: 10.1038/sj.emboj.7600350
[10]  Ramachandran R, Tweten RK, Johnson AE (2005) The domains of a cholesterol-dependent cytolysin undergo a major FRET-detected rearrangement during pore formation. Proc Natl Acad Sci U S A 102: 7139–7144. doi: 10.1073/pnas.0500556102
[11]  Oloo EO, Yethon JA, Ochs MM, Carpick B, Oomen R (2011) Structure-guided antigen engineering yields pneumolysin mutants suitable for vaccination against pneumococcal disease. J Biol Chem 286: 12133–12140. doi: 10.1074/jbc.m110.191148
[12]  Polekhina G, Giddings KS, Tweten RK, Parker MW (2005) Insights into the action of the superfamily of cholesterol-dependent cytolysins from studies of intermedilysin. Proc Natl Acad Sci U S A 102: 600–605. doi: 10.1073/pnas.0403229101
[13]  Bourdeau RW, Malito E, Chenal A, Bishop BL, Musch MW, et al. (2009) Cellular functions and X-ray structure of anthrolysin O, a cholesterol-dependent cytolysin secreted by Bacillus anthracis. J Biol Chem 284: 14645–14656. doi: 10.1074/jbc.m807631200
[14]  Xu L, Huang B, Du H, Zhang XC, Xu J, et al. (2010) Crystal structure of cytotoxin protein suilysin from Streptococcus suis. Protein Cell 1: 96–105. doi: 10.1007/s13238-010-0012-3
[15]  Whisstock JC, Skinner R, Carrell RW, Lesk AM (2000) Conformational changes in serpins: I. The native and cleaved conformations of alpha(1)-antitrypsin. J Mol Biol 296: 685–699. doi: 10.1006/jmbi.1999.3520
[16]  Rossjohn J, Polekhina G, Feil SC, Morton CJ, Tweten RK, et al. (2007) Structures of perfringolysin O suggest a pathway for activation of cholesterol-dependent cytolysins. J Mol Biol 367: 1227–1236. doi: 10.1016/j.jmb.2007.01.042
[17]  Schuerch DW, Wilson-Kubalek EM, Tweten RK (2005) Molecular basis of listeriolysin O pH dependence. Proc Natl Acad Sci U S A 102: 12537–12542. doi: 10.1073/pnas.0500558102
[18]  Hotze EM, Wilson-Kubalek EM, Rossjohn J, Parker MW, Johnson AE, et al. (2001) Arresting pore formation of a cholesterol-dependent cytolysin by disulfide trapping synchronizes the insertion of the transmembrane beta-sheet from a prepore intermediate. J Biol Chem 276: 8261–8268. doi: 10.1074/jbc.m009865200
[19]  Salemme FR, Weatherford DW (1981) Conformational and geometrical properties of beta-sheets in proteins. II. Antiparallel and mixed beta-sheets. J Mol Biol 146: 119–141. doi: 10.1016/0022-2836(81)90369-7
[20]  Ramachandran R, Tweten RK, Johnson AE (2004) Membrane-dependent conformational changes initiate cholesterol-dependent cytolysin oligomerization and intersubunit beta-strand alignment. Nature structural & molecular biology 11: 697–705. doi: 10.1038/nsmb793
[21]  Aleshin AE, Schraufstatter IU, Stec B, Bankston LA, Liddington RC, et al. (2012) Structure of complement C6 suggests a mechanism for initiation and unidirectional, sequential assembly of membrane attack complex (MAC). J Biol Chem 287: 10210–10222. doi: 10.1074/jbc.m111.327809
[22]  Rosado CJ, Kondos S, Bull TE, Kuiper MJ, Law RH, et al. (2008) The MACPF/CDC family of pore-forming toxins. Cell Microbiol 10: 1765–1774. doi: 10.1111/j.1462-5822.2008.01191.x
[23]  Hotze EM, Wilson-Kubalek E, Farrand AJ, Bentsen L, Parker MW, et al. (2012) Monomer-monomer interactions propagate structural transitions necessary for pore formation by the cholesterol-dependent cytolysins. J Biol Chem 287: 24534–24543. doi: 10.1074/jbc.m112.380139
[24]  Sato TK, Tweten RK, Johnson AE (2013) Disulfide-bond scanning reveals assembly state and beta-strand tilt angle of the PFO beta-barrel. Nat Chem Biol 9: 383–389. doi: 10.1038/nchembio.1228
[25]  Reboul CF, Mahmood K, Whisstock JC, Dunstone MA (2012) Predicting giant transmembrane beta-barrel architecture. Bioinformatics 28: 1299–1302. doi: 10.1093/bioinformatics/bts152
[26]  Shatursky O, Heuck AP, Shepard LA, Rossjohn J, Parker MW, et al. (1999) The mechanism of membrane insertion for a cholesterol-dependent cytolysin: a novel paradigm for pore-forming toxins. Cell 99: 293–299. doi: 10.1016/s0092-8674(00)81660-8
[27]  Shepard LA, Heuck AP, Hamman BD, Rossjohn J, Parker MW, et al. (1998) Identification of a membrane-spanning domain of the thiol-activated pore-forming toxin Clostridium perfringens perfringolysin O: an alpha-helical to beta-sheet transition identified by fluorescence spectroscopy. Biochemistry 37: 14563–14574. doi: 10.1021/bi981452f
[28]  Heuck AP, Hotze EM, Tweten RK, Johnson AE (2000) Mechanism of membrane insertion of a multimeric beta-barrel protein: perfringolysin O creates a pore using ordered and coupled conformational changes. Mol Cell 6: 1233–1242. doi: 10.1016/s1097-2765(00)00119-2
[29]  Ramachandran R, Heuck AP, Tweten RK, Johnson AE (2002) Structural insights into the membrane-anchoring mechanism of a cholesterol-dependent cytolysin. Nature Structural Biology 9: 823–827. doi: 10.1038/nsb855
[30]  Degiacomi MT, Iacovache I, Pernot L, Chami M, Kudryashev M, et al. (2013) Molecular assembly of the aerolysin pore reveals a swirling membrane-insertion mechanism. Nat Chem Biol 9: 623–629. doi: 10.1038/nchembio.1312
[31]  Perica T, Chothia C, Teichmann SA (2012) Evolution of oligomeric state through geometric coupling of protein interfaces. Proc Natl Acad Sci U S A 109: 8127–8132. doi: 10.1073/pnas.1120028109
[32]  Irving JA, Whisstock JC, Lesk AM (2001) Protein structural alignments and functional genomics. Proteins 42: 378–382. doi: 10.1002/1097-0134(20010215)42:3<378::aid-prot70>3.0.co;2-3
[33]  McPhalen CA, Vincent MG, Picot D, Jansonius JN, Lesk AM, et al. (1992) Domain closure in mitochondrial aspartate aminotransferase. J Mol Biol 227: 197–213. doi: 10.1016/0022-2836(92)90691-c
[34]  Best RB, Lindorff-Larsen K, DePristo MA, Vendruscolo M (2006) Relation between native ensembles and experimental structures of proteins. Proc Natl Acad Sci U S A 103: 10901–10906. doi: 10.1073/pnas.0511156103
[35]  Whisstock JC, Pike RN, Jin L, Skinner R, Pei XY, et al. (2000) Conformational changes in serpins: II. The mechanism of activation of antithrombin by heparindagger. J Mol Biol 301: 1287–1305. doi: 10.1006/jmbi.2000.3982
[36]  Friedland GD, Lakomek NA, Griesinger C, Meiler J, Kortemme T (2009) A correspondence between solution-state dynamics of an individual protein and the sequence and conformational diversity of its family. PLoS Comput Biol 5: e1000393. doi: 10.1371/journal.pcbi.1000393
[37]  Konagurthu AS, Reboul CF, Schmidberger JW, Irving JA, Lesk AM, et al. (2010) MUSTANG-MR structural sieving server: applications in protein structural analysis and crystallography. PLoS One 5: e10048. doi: 10.1371/journal.pone.0010048
[38]  Bakan A, Meireles LM, Bahar I (2011) ProDy: protein dynamics inferred from theory and experiments. Bioinformatics 27: 1575–1577. doi: 10.1093/bioinformatics/btr168
[39]  Schrodinger LLC (2010) The PyMOL Molecular Graphics System, Version 1.3r1.
[40]  Humphrey W, Dalke A, Schulten K (1996) VMD: visual molecular dynamics. J Mol Graph 14: 33–38, 27–38. doi: 10.1016/0263-7855(96)00018-5
[41]  Ho BK, Curmi PM (2002) Twist and shear in beta-sheets and beta-ribbons. J Mol Biol 317: 291–308. doi: 10.1006/jmbi.2001.5385
[42]  Krissinel E, Henrick K (2007) Inference of macromolecular assemblies from crystalline state. J Mol Biol 372: 774–797. doi: 10.1016/j.jmb.2007.05.022
[43]  Case DA, Darden TA, Cheatham ITE, Simmerling CL, Wang J, et al.. (2012) AMBER 13. University of California, San Francisco.
[44]  Hornak V, Abel R, Okur A, Strockbine B, Roitberg A, et al. (2006) Comparison of multiple Amber force fields and development of improved protein backbone parameters. Proteins 65: 712–725. doi: 10.1002/prot.21123
[45]  Phillips JC, Braun R, Wang W, Gumbart J, Tajkhorshid E, et al. (2005) Scalable molecular dynamics with NAMD. J Comput Chem 26: 1781–1802. doi: 10.1002/jcc.20289
[46]  Eswar N, Webb B, Marti-Renom MA, Madhusudhan MS, Eramian D, et al. (2006) Comparative protein structure modeling using Modeller. Current protocols in bioinformatics/editoral board, Andreas D Baxevanis [et al] Chapter 5: Unit 5 6. doi: 10.1002/0471250953.bi0506s15
[47]  Wriggers W (2010) Using Situs for the integration of multi-resolution structures. Biophys Rev 2: 21–27. doi: 10.1007/s12551-009-0026-3
[48]  Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, et al. (2004) UCSF Chimera–a visualization system for exploratory research and analysis. J Comput Chem 25: 1605–1612. doi: 10.1002/jcc.20084
[49]  Trabuco LG, Villa E, Mitra K, Frank J, Schulten K (2008) Flexible fitting of atomic structures into electron microscopy maps using molecular dynamics. Structure 16: 673–683. doi: 10.1016/j.str.2008.03.005
[50]  Chan KY, Gumbart J, McGreevy R, Watermeyer JM, Sewell BT, et al. (2011) Symmetry-restrained flexible fitting for symmetric EM maps. Structure 19: 1211–1218. doi: 10.1016/j.str.2011.07.017
[51]  Huang J, MacKerell AD Jr (2013) CHARMM36 all-atom additive protein force field: validation based on comparison to NMR data. J Comput Chem 34: 2135–2145. doi: 10.1002/jcc.23354
[52]  Schreiner E, Trabuco LG, Freddolino PL, Schulten K (2011) Stereochemical errors and their implications for molecular dynamics simulations. BMC Bioinformatics 12: 190. doi: 10.1186/1471-2105-12-190
[53]  Jo S, Kim T, Iyer VG, Im W (2008) CHARMM-GUI: a web-based graphical user interface for CHARMM. J Comput Chem 29: 1859–1865. doi: 10.1002/jcc.20945
[54]  Jo S, Lim JB, Klauda JB, Im W (2009) CHARMM-GUI Membrane Builder for mixed bilayers and its application to yeast membranes. Biophys J 97: 50–58. doi: 10.1016/j.bpj.2009.04.013
[55]  Klauda JB, Venable RM, Freites JA, O'Connor JW, Tobias DJ, et al. (2010) Update of the CHARMM all-atom additive force field for lipids: validation on six lipid types. J Phys Chem B 114: 7830–7843. doi: 10.1021/jp101759q
[56]  Sitkoff D, Sharp KA, Honig B (1994) Accurate Calculation of Hydration Free Energies Using Macroscopic Solvent Models. The Journal of Physical Chemistry 98: 1978–1988. doi: 10.1021/j100058a043
[57]  Goscinski WJ, McIntosh P, Felzmann U, Maksimenko A, Hall CJ, et al. (2014) The multi-modal Australian ScienceS Imaging and Visualization Environment (MASSIVE) high performance computing infrastructure: applications in neuroscience and neuroinformatics research. Front Neuroinform 8: 30. doi: 10.3389/fninf.2014.00030
[58]  Dunstone MA, Tweten RK (2012) Packing a punch: the mechanism of pore formation by cholesterol dependent cytolysins and membrane attack complex/perforin-like proteins. Curr Opin Struct Biol 22: 342–349. doi: 10.1016/j.sbi.2012.04.008
[59]  Chen VB, Arendall WB 3rd, Headd JJ, Keedy DA, Immormino RM, et al. (2010) MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr D Biol Crystallogr 66: 12–21. doi: 10.1107/s0907444909042073

Full-Text

comments powered by Disqus