Modeling the surface of campylobacter fetus: Protein surface layer stability and resistance to cationic antimicrobial peptides

Yang, 1992, Reattachment of surface array proteins to Campylobacter fetus cells, J. Bacteriol., 174, 1258, 10.1128/jb.174.4.1258-1267.1992 Dworkin, 1995, A Lipopolysaccharide-binding domain of the Campylobacter fetus S-layer protein resides within the conserved N-terminus of a family of silent and divergent homologs, J. Bacteriol., 177, 1734, 10.1128/jb.177.7.1734-1741.1995 Man, 2011, The clinical importance of emerging Campylobacter species, Nat. Rev. Gastroenterol., 8, 669, 10.1038/nrgastro.2011.191 Blaser, 1998, Campylobacter fetus — emerging infection and model system for bacterial pathogenesis at mucosal surfaces, Clin. Infect. Dis., 27, 256, 10.1086/514655 Penner, 1988, The genus Campylobacter: a decade of progress, Clin. Microbiol. Rev., 1, 157, 10.1128/CMR.1.2.157 Coid, 1983, Campylobacters as placental pathogens, Placenta, 4, 295, 10.1016/S0143-4004(83)80009-5 Moran, 1994, Biochemical characterization of Campylobacter fetus lipopolysaccharides, Infect. Immun., 62, 3922, 10.1128/IAI.62.9.3922-3929.1994 Perez-Perez, 1986, Lipopolysaccharide structures of Campylobacter fetus are related to heat-stable serogroups, Infect. Immun., 51, 209, 10.1128/IAI.51.1.209-212.1986 Brooks, 1996, Electrophoretic and immunoblot analysis of Campylobacter fetus lipopolysaccharides, Vet. Microbiol., 51, 105, 10.1016/0378-1135(96)00015-6 Fujimoto, 1989, Hexagonal surface-layer of Campylobacter fetus isolated from humans, Infect. Immun., 8, 2563, 10.1128/IAI.57.8.2563-2565.1989 Fujimoto, 1991, Correlation between molecular size of the surface array protein and morphology and antigenicity of the Campylobacter fetus S layer, Infect. Immun., 59, 2017, 10.1128/IAI.59.6.2017-2022.1991 Blaser, 1988, Pathogenesis of Campylobacter fetus infections. Failure of encapsulated Campylobacter fetus to bind C3b explains serum and phagocytosis resistance, J. Clin. Invest., 81, 1434, 10.1172/JCI113474 Dubreuil, 1990, Antigenic differences among Campylobacter fetus S-layer proteins, J. Bacteriol., 172, 5035, 10.1128/jb.172.9.5035-5043.1990 Garcia, 1995, Protein shift and antigenic variation in the S-layer of Campylobacter fetus subsp. venerealis during bovine infection accompanied by genomic rearrangement of sapA homologues, J. Bacteriol., 177, 1976, 10.1128/jb.177.8.1976-1980.1995 Wang, 1993, Shift in S-layer protein expression responsible for antigenic variation in Campylobacter fetus, J. Bacteriol., 175, 4979, 10.1128/jb.175.16.4979-4984.1993 Dworkin, 1995, Segmental conservation of sapA sequences in Type B Campylobacter fetus cells, J. Biol. Chem., 270, 15093, 10.1074/jbc.270.25.15093 Stenman, 1978, Distribution of a major connective tissue protein, fibronectin, in normal human tissues, J. Exp. Med., 147, 1054, 10.1084/jem.147.4.1054 Ruoslahti, 1982, Fibronectin: purification, immunochemical properties, and biological activities, Meth. Enzymol., 82, 803, 10.1016/0076-6879(82)82103-4 Graham, 2008, Fibronectin enhances Campylobacter fetus interaction with extracellular matrix components and INT 407 cells, Can. J. Microbiol., 54, 37, 10.1139/W07-115 Koval, 1991, The effect of paracrystalline protein surface layers on predation by Bdellovibrio bacteriovorus, J. Bacteriol., 173, 2244, 10.1128/jb.173.7.2244-2249.1991 Sleytr, 1999, Bacterial S-layers, Trends Microbiol., 7, 253, 10.1016/S0966-842X(99)01513-9 Tremblay, 1998, Antimicrobial susceptibility testing of 59 strains of Campylobacter fetus subsp. fetus, Antimicrob. Agents Chemother., 42, 1847, 10.1128/AAC.42.7.1847 Pink, 2003, Divalent calcium ions inhibit the penetration of protamine through the polysaccharide brush of the outer membrane of Gram-negative bacteria, Langmuir, 19, 8852, 10.1021/la030193e Ando, 1973, Protamines; isolation, characterization, structure and function, 1, 10.1007/978-3-642-46294-8_1 Salloway, 1996, Miller–Fisher syndrome associated with Campylobacter jejuni bearing lipopolysaccharide molecules that mimic human ganglioside GD3, Infect. Immun., 64, 2945, 10.1128/IAI.64.8.2945-2949.1996 Senchenkova, 1997, The O-specific polysaccharide chain of Campylobacter fetus serotype A lipopolysaccharide is a partial O-acetylated 1,3-linked α-D-mannan, Eur. J. Biochem., 245, 637, 10.1111/j.1432-1033.1997.00637.x Senchenkova, 1996, The O-specific polysaccharide chain of Campylobacter fetus serotype B lipopolysaccharide is a D-rhamnan terminated with 3-0-methyl-D-rhamnose (D-acofriose), Eur. J. Biochem., 239, 434, 10.1111/j.1432-1033.1996.0434u.x Oliveira, 2010, Crucial roles of calcium and charged saccharide moieties in survival of gram-negative bacteria revealed by combination of grazing-incidence X-ray structural characterizations and Monte Carlo simulations, Phys. Rev. E, 81, 041901, 10.1103/PhysRevE.81.041901 Kelley, 2009, Protein structure prediction on the web: a case study using the Phyre server, Nat. Protoc., 4, 363, 10.1038/nprot.2009.2 Parsegian, 2005 Israelachvili, 2006 Binder, 1997, Applications of Monte Carlo methods to statistical physics, Rep. Prog. Phys., 60, 487, 10.1088/0034-4885/60/5/001 Binder, 2010 Dzyaloshinskii, 1961, General theory of van der Waal's forces, Sov. Phys. Usp., 73, 153, 10.1070/PU1961v004n02ABEH003330 French, 2010, Long range interactions in nanoscale science, Rev. Mod. Phys., 82, 1887, 10.1103/RevModPhys.82.1887 Hamaker, 1937, The London — van der Waals attraction between spherical particles, Physica, 4, 1058, 10.1016/S0031-8914(37)80203-7 Berendsen, 1995, GROMACS: a message-passing parallel molecular dynamics implementation, Comput. Phys. Commun., 91, 43, 10.1016/0010-4655(95)00042-E Kutzner, 2007, Speeding up parallel GROMACS on high-latency networks, J. Comput. Chem., 28, 2075, 10.1002/jcc.20703 van der Spoel Netz, 1999, Debye–Hückel theory for interfacial geometries, Phys. Rev. E., 60, 3174, 10.1103/PhysRevE.60.3174 Netz, 2003, Neutral and charged polymers at interfaces, Phys. Rep., 380, 1, 10.1016/S0370-1573(03)00118-2 Shafir, 2003, Adsorption and depletion of polyelectrolytes from charged surfaces, J. Chem. Phys., 119, 2355, 10.1063/1.1580798 Lai, 1992, Structure and dynamics of polymer brushes near the Θ point: a Monte Carlo simulation, J. Chem. Phys., 97, 586, 10.1063/1.463554 Carmesin, 1988, The bond fluctuation method: a new effective algorithm for the dynamics of polymers in all spatial dimensions, Macromolecules, 21, 2819, 10.1021/ma00187a030 NCCLS, 2003 Graham, 1998, The Campylobacter fetus S-layer is not essential for initial interaction with HEp-2 cells, Can. J. Microbiol., 44, 244, 10.1139/cjm-44-3-244 Rosenberg, 1980, Adherence of bacteria to hydrocarbons: a simple method for measuring cell surface hydrophobicity, FEMS Microbiol. Lett., 9, 29, 10.1111/j.1574-6968.1980.tb05599.x Sára, 1987, Molecular sieving through S-layers of Bacillus stearothermophilus strains, J. Bacteriol., 169, 4092, 10.1128/jb.169.9.4092-4098.1987 Arbing, 2012, Structure of the surface layer of the methanogenic archaean Methanosarcina acetivorans, Proc. Natl. Acad. Sci. U. S. A., 109, 11812, 10.1073/pnas.1120595109