Structural and Dynamic Properties of Allergen and Non-Allergen Forms of Tropomyosin

Astwood, 1996, Stability of food allergens to digestion in vitro, Nat. Biotechnol., 14, 1269, 10.1038/nbt1096-1269 Ayuso, 2002, Identification of continuous, allergenic regions of the major shrimp allergen Pen a 1 (tropomyosin), Int. Arch. Allergy Immunol., 127, 27, 10.1159/000048166 Ayuso, 1999, IgE antibody response to vertebrate meat proteins including tropomyosin, Ann. Allergy Asthma Immunol., 83, 399, 10.1016/S1081-1206(10)62837-2 Barua, 2011, Evolutionarily conserved surface residues constitute actin binding sites of tropomyosin, Proc. Natl. Acad. Sci. USA, 108, 10150, 10.1073/pnas.1101221108 Berendsen, 1984, Molecular dynamics with coupling to an external bath, J. Chem. Phys., 81, 3684, 10.1063/1.448118 Brown, 2001, Deciphering the design of the tropomyosin molecule, Proc. Natl. Acad. Sci. USA, 98, 8496, 10.1073/pnas.131219198 Brown, 2005, Structure of the mid-region of tropomyosin: bending and binding sites for actin, Proc. Natl. Acad. Sci. USA, 102, 18878, 10.1073/pnas.0509269102 Camacho, 2008, Structural and thermodynamic approach to peptide immunogenicity, PLoS Comput. Biol., 4, e1000231, 10.1371/journal.pcbi.1000231 Camilleri, 1989, Human gastric emptying and colonic filling of solids characterized by a new method, Am. J. Physiol., 257, G284 Case, 2014 Darden, 1993, Particle mesh Ewald: an N⋅log(N) method for Ewald sums in large systems, J. Chem. Phys., 98, 10089, 10.1063/1.464397 DeWitt, 2004, Recombinant tropomyosin from Penaeus aztecus (rPen a 1) for measurement of specific immunoglobulin E antibodies relevant in food allergy to crustaceans and other invertebrates, Mol. Nutr. Food Res., 48, 370, 10.1002/mnfr.200400015 Finn, 2014, Pfam: the protein families database, Nucleic Acids Res., 42, D222, 10.1093/nar/gkt1223 Fitzsimmons, 2009, Survival of the fittest: allergology or parasitology?, Trends Parasitol., 25, 447, 10.1016/j.pt.2009.07.004 Fu, 2002, Digestibility of food allergens and nonallergenic proteins in simulated gastric fluid and simulated intestinal fluid-a comparative study, J. Agric. Food Chem., 50, 7154, 10.1021/jf020599h Geeves, 2015, A systematic nomenclature for mammalian tropomyosin isoforms, J. Muscle Res. Cell Motil., 36, 147, 10.1007/s10974-014-9389-6 Gonzalez-Fernandez, 2016, Are fish tropomyosins allergens?, Ann. Allergy Asthma Immunol., 116, 74, 10.1016/j.anai.2015.09.017 Greenfield, 2001, Solution NMR structure and folding dynamics of the N terminus of a rat non-muscle alpha-tropomyosin in an engineered chimeric protein, J. Mol. Biol., 312, 833, 10.1006/jmbi.2001.4982 Griswold, 2016, Design and engineering of deimmunized biotherapeutics, Curr. Opin. Struct. Biol., 39, 79, 10.1016/j.sbi.2016.06.003 Harbury, 1993, A switch between two-, three-, and four-stranded coiled coils in GCN4 leucine zipper mutants, Science, 262, 1401, 10.1126/science.8248779 Herman, 2007, Stability of a set of allergens and non-allergens in simulated gastric fluid, Int. J. Food Sci. Nutr., 58, 125, 10.1080/09637480601149640 Hitchcock-DeGregori, 2008, Tropomyosin: function follows structure, Adv. Exp. Med. Biol., 644, 60, 10.1007/978-0-387-85766-4_5 Ishii, 1992, Unfolding domains of recombinant fusion alpha alpha-tropomyosin, Protein Sci., 1, 1319, 10.1002/pro.5560011011 Jameson, 1988, The antigenic index: a novel algorithm for predicting antigenic determinants, Comput. Appl. Biosci., 4, 181 Jenkins, 2007, Evolutionary distance from human homologs reflects allergenicity of animal food proteins, J. Allergy Clin. Immunol., 120, 1399, 10.1016/j.jaci.2007.08.019 Joint FAO/WHO Codex Alimentarius Commission, 2003 Joung, 2008, Determination of alkali and halide monovalent ion parameters for use in explicitly solvated biomolecular simulations, J. Phys. Chem. B, 112, 9020, 10.1021/jp8001614 Joung, 2009, Molecular dynamics simulations of the dynamic and energetic properties of alkali and halide ions using water-model-specific ion parameters, J. Phys. Chem. B, 113, 13279, 10.1021/jp902584c Khan, 2013, Evaluating pH-induced gastrointestinal aggregation of Arachis hypogaea 1 fragments as potential components of peanut allergy, J. Agric. Food Chem., 61, 8430, 10.1021/jf401701t Ladics, 2011, Bioinformatics and the allergy assessment of agricultural biotechnology products: industry practices and recommendations, Regul. Toxicol. Pharmacol., 60, 46, 10.1016/j.yrtph.2011.02.004 Lehrer, 1998, The stability of tropomyosin at acid pH: effects of anion binding, J. Struct. Biol., 122, 176, 10.1006/jsbi.1998.3973 Li, 2002, The crystal structure of the C-terminal fragment of striated-muscle alpha-tropomyosin reveals a key troponin T recognition site, Proc. Natl. Acad. Sci. USA, 99, 7378, 10.1073/pnas.102179999 Lundgren, 2010, Role of spectral counting in quantitative proteomics, Expert Rev. Proteomics, 7, 39, 10.1586/epr.09.69 Lupas, 2005, The structure of alpha-helical coiled coils, Adv. Protein Chem., 70, 37, 10.1016/S0065-3233(05)70003-6 Ly, 2012, Long-range effects of familial hypertrophic cardiomyopathy mutations E180G and D175N on the properties of tropomyosin, Biochemistry, 51, 6413, 10.1021/bi3006835 Maleki, 2003, The major peanut allergen, Ara h 2, functions as a trypsin inhibitor, and roasting enhances this function, J. Allergy Clin. Immunol., 112, 190, 10.1067/mai.2003.1551 Matyushenko, 2015, Effects of two stabilizing substitutions, D137L and G126R, in the middle part of alpha-tropomyosin on the domain structure of its molecule, Biophys. Chem., 196, 77, 10.1016/j.bpc.2014.10.001 McLachlan, 1975, Sequence repeats in alpha-tropomyosin, J. Mol. Biol., 98, 281, 10.1016/S0022-2836(75)80118-5 Murakami, 2008, Structural basis for tropomyosin overlap in thin (actin) filaments and the generation of a molecular swivel by troponin-T, Proc. Natl. Acad. Sci. USA, 105, 7200, 10.1073/pnas.0801950105 Nevzorov, 2011, Conserved noncanonical residue Gly-126 confers instability to the middle part of the tropomyosin molecule, J. Biol. Chem., 286, 15766, 10.1074/jbc.M110.209353 O'Shea, 1991, X-ray structure of the GCN4 leucine zipper, a two-stranded, parallel coiled coil, Science, 254, 539, 10.1126/science.1948029 Ohgushi, 1983, 'Molten-globule state': a compact form of globular proteins with mobile side-chains, FEBS Lett., 164, 21, 10.1016/0014-5793(83)80010-6 Pali-Scholl, 2011, Anti-acid medication as a risk factor for food allergy, Allergy, 66, 469, 10.1111/j.1398-9995.2010.02511.x Park, 2004, Probing the high energy states in proteins by proteolysis, J. Mol. Biol., 343, 1467, 10.1016/j.jmb.2004.08.085 Pike, 2015, Empirical estimation of local dielectric constants: toward atomistic design of collagen mimetic peptides, Pept. Sci., 104, 360, 10.1002/bip.22644 Potekhin, 1982, Co-operative blocks in tropomyosin, J. Mol. Biol., 159, 519, 10.1016/0022-2836(82)90299-6 Reese, 1999, Tropomyosin: an invertebrate pan-allergen, Int. Arch. Allergy Immunol., 119, 247, 10.1159/000024201 Reese, 2001, The IgE-binding regions of the major allergen Pen a 1: multiple epitopes or intramolecular cross-reactivity?, Int. Arch. Allergy Immunol., 124, 103, 10.1159/000053683 Reese, 2005, Reduced allergenic potency of VR9-1, a mutant of the major shrimp allergen Pen a 1 (tropomyosin), J. Immunol., 175, 8354, 10.4049/jimmunol.175.12.8354 Roe, 2013, PTRAJ and CPPTRAJ: software for processing and analysis of molecular dynamics trajectory data, J. Chem. Theory Comput., 9, 3084, 10.1021/ct400341p Sampson, 1999, Food allergy. Part 1: immunopathogenesis and clinical disorders, J. Allergy Clin. Immunol., 103, 717, 10.1016/S0091-6749(99)70411-2 Schubert, 2018, Population-specific design of de-immunized protein biotherapeutics, PLoS Comput. Biol., 14, e1005983, 10.1371/journal.pcbi.1005983 Sicherer, 2004, Prevalence of seafood allergy in the United States determined by a random telephone survey, J. Allergy Clin. Immunol., 114, 159, 10.1016/j.jaci.2004.04.018 Sicherer, 2010, Food allergy, J. Allergy Clin. Immunol., 125, S116, 10.1016/j.jaci.2009.08.028 Singh, 2003, Local destabilization of the tropomyosin coiled coil gives the molecular flexibility required for actin binding, Biochemistry, 42, 14114, 10.1021/bi0348462 Singh, 2006, Dual requirement for flexibility and specificity for binding of the coiled-coil tropomyosin to its target, actin, Structure, 14, 43, 10.1016/j.str.2005.09.016 Sumida, 2008, Conserved Asp-137 imparts flexibility to tropomyosin and affects function, J. Biol. Chem., 283, 6728, 10.1074/jbc.M707485200 Summa, 2002 Talley, 2010, On the pH-optimum of activity and stability of proteins, Proteins, 78, 2699 Taylor, 1997, Food from genetically modified organisms and potential for food allergy, Environ. Toxicol. Pharmacol., 4, 121, 10.1016/S1382-6689(97)10052-7 Taylor, 2002, Protein allergenicity assessment of foods produced through agricultural biotechnology, Annu. Rev. Pharmacol., 42, 99, 10.1146/annurev.pharmtox.42.082401.130208 Tyagi, 2015, Comparisons of allergenic and metazoan parasite proteins: allergy the price of immunity, PLoS Comput. Biol., 11, e1004546, 10.1371/journal.pcbi.1004546 Untersmayr, 2003, Antacid medication inhibits digestion of dietary proteins and causes food allergy: a fish allergy model in BALB/c mice, J. Allergy Clin. Immunol., 112, 616, 10.1016/S0091-6749(03)01719-6 Whitby, 2000, Crystal structure of tropomyosin at 7 Angstroms resolution, Proteins, 38, 49, 10.1002/(SICI)1097-0134(20000101)38:1<49::AID-PROT6>3.0.CO;2-B Williams, 1981, Tropomyosin stability: assignment of thermally induced conformational transitions to separate regions of the molecule, Biochemistry, 20, 3856, 10.1021/bi00516a029 Woods, 1977, Stability of segments of rabbit alpha-tropomyosin, Aust. J. Biol. Sci., 30, 527, 10.1071/BI9770527 Zeng, 1997, Buried asparagines determine the dimerization specificities of leucine zipper mutants, Proc. Natl. Acad. Sci. USA, 94, 3673, 10.1073/pnas.94.8.3673 Zheng, 2016, Investigating the effects of tropomyosin mutations on its flexibility and interactions with filamentous actin using molecular dynamics simulation, J. Muscle Res. Cell Motil., 37, 131, 10.1007/s10974-016-9447-3