Structure of allergens and structure based epitope predictions

Methods

Volumn 66, Issue 1, 2014, Pages 3-21

  Dall'Antonia, Fabio ^a   Pavkov Keller, Tea ^b,c   Zangger, Klaus ^c   Keller, Walter ^c  

^a EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

^b AUSTRIAN CENTRE OF INDUSTRIAL BIOTECHNOLOGY   (Austria)

^c UNIVERSITY OF GRAZ   (Austria)

Author keywords

Allergen structure; IgE epitope; NMR; Protein family; Structure based epitope prediction; X ray

Indexed keywords

ALLERGEN; AMINO ACID; AVENIN; CALCIUM BINDING PROTEIN; CARBON 13; CHITIN; CYCLOPHILIN; CYSTEINE PROTEINASE; EPITOPE; FATTY ACID BINDING PROTEIN; FLAVINE ADENINE NUCLEOTIDE; FOOD ALLERGEN; GLOBULIN; GLYCOSIDASE; HOUSE DUST ALLERGEN; HYALURONIDASE; LIPID TRANSFER PROTEIN; LIPOCALIN; NITROGEN; NITROGEN 15; PAPAIN; PARVALBUMIN; PATULIN; PEPTIDYLPROLYL ISOMERASE; POLLEN ANTIGEN; PROFILIN; PROTEINASE INHIBITOR; RAGWEED ANTIGEN; SEED STORAGE PROTEIN; THAUMATIN;

ANTIGEN ANTIBODY COMPLEX; ANTIGEN STRUCTURE; ARTICLE; CARBON NUCLEAR MAGNETIC RESONANCE; COMPUTER PROGRAM; CROSS REACTION; CRYSTAL STRUCTURE; CRYSTALLIZATION; CRYSTALLOGRAPHY; EPITOPE MAPPING; HUMAN; LIGAND BINDING; MACHINE LEARNING; MOLECULAR DYNAMICS; NITROGEN NUCLEAR MAGNETIC RESONANCE; NONHUMAN; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PHYSICAL CHEMISTRY; PREDICTION; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN EXPRESSION; PROTEIN FOLDING; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; PROTON NUCLEAR MAGNETIC RESONANCE; STRUCTURE ANALYSIS;

ALLERGEN STRUCTURE; IGE EPITOPE; NMR; PROTEIN FAMILY; STRUCTURE BASED EPITOPE PREDICTION; X-RAY;

ALLERGENS; ANIMALS; CRYSTALLOGRAPHY, X-RAY; EPITOPE MAPPING; EPITOPES; HUMANS; HYPERSENSITIVITY; MODELS, MOLECULAR; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; RECOMBINANT FUSION PROTEINS; SOFTWARE;

EID: 84896690627     PISSN: 10462023     EISSN: 10959130     Source Type: Journal    
DOI: 10.1016/j.ymeth.2013.07.024     Document Type: Article

References (263)

1. Greenfield N.J. Nature Protocols 2006, 1:2876-2890.
2. Verdino P., Keller W. Methods 2004, 32:241-248.
3. Whitmore L., Wallace B.A. Biopolymers 2008, 89:392-400.
4. Lindwall G., Chau M., Gardner S.R., Kohlstaedt L.A. Protein Eng. 2000, 13:67-71.
5. Ericsson U.B., Hallberg B.M., Detitta G.T., Dekker N., Nordlund P. Anal. Biochem. 2006, 357:289-298.
6. Derewenda Z.S. Acta Cryst. 2010, D66:604-615.
7. Smialowski P., Schmidt T., Cox J., Kirschner A., Frishman D. Proteins 2006, 62:343-355.
8. Longenecker K.L., Garrard S.M., Sheffield P.J., Derewenda Z.S. Acta Cryst. 2001, D57:679-688.
9. Tan K.W., Jobichen C., Ong T.C., Gao Y.F., Tiong Y.S., Wong K.N., Chew F.T., Sivaraman J., Mok Y.K. PLoS One 2012, 7:e44850.
10. Mueller G.A., Gosavi R.A., Pomes A., Wunschmann S., Moon A.F., London R.E., Pedersen L.C. Allergy 2011, 66:878-885.
11. Metzler W.J., Valentine K., Roebber M., Friedrichs M.S., Marsh D.G., Mueller L. Biochemistry 1992, 31:5117-5127.
12. Metzler W.J., Valentine K., Roebber M., Marsh D.G., Mueller L. Biochemistry 1992, 31:8697-8705.
13. Vidusek D.A., Roberts M.F., Goodfriend L. Biochemistry 1985, 24:2747-2753.
14. Wüthrich K. NMR of Proteins and Nucleic Acids 1986, Wiley, New York.
15. De Marino S., Morelli M.A., Fraternali F., Tamborini E., Musco G., Vrtala S., Dolecek C., Arosio P., Valenta R., Pastore A. Structure 1999, 7:943-952.
16. Cavanagh J., Fairbrother W.J., Palmer A.G., Rance M., Skelton N.J. Protein NMR Spectroscopy 2007, Academic Press, San Diego. second ed.
17. Tjandra N., Bax A. Science 1997, 278:1111-1114.
18. Pervushin K., Riek R., Wider G., Wüthrich K. Proc. Natl. Acad. Sci. USA 1997, 94:12366-12371.
19. Palmer A.G. Chem. Rev. 2004, 104:3623-3640.
20. Madl T., Bermel W., Zangger K. Angew Chem. Int. Ed Engl. 2009, 48:8259-8262.
21. Meyer B., Peters T. Angew Chem. Int. Ed Engl. 2003, 42:864-890.
22. Paterson Y., Englander S.W., Roder H. Science 1990, 249:755-759.
23. Ichikawa S., Takai T., Yashiki T., Takahashi S., Okumura K., Ogawa H., Kohda D., Hatanaka H. Genes Cells 2009, 14:1055-1065.
24. Paterson Y. Nature 1992, 356:456-457.
25. Mayer M., Meyer B. Angew Chem. Int. Ed Engl. 1999, 38:1784-1788.
26. Razzera G., Gadermaier G., De Paula V., Almeida M.S., Egger M., Jahn-Schmid B., Almeida F.C.L., Ferreira F., Valente A.P. Structure 2010, 18:1011-1021.
27. S.L. Chan, T.C. Ong, Y.F. Gao, Y.S. Tiong, Y. Wang de, F.T. Chew, Y.K. Mok, J. Immunol. 181 (2008) 2586-2596.
28. Trevino M.A., Garcia-Mayoral M.F., Barral P., Villalba M., Santoro J., Rico M., Rodriguez R., Bruix M. J. Biol. Chem. 2004, 279:39035-39041.
29. Naik M.T., Chang C.F., Kuo I.C., Kung C.C., Yi F.C., Chua K.Y., Huang T.H. Structure 2008, 16:125-136.
30. Lehmann K., Schweimer K., Reese G., Randow S., Suhr M., Becker W.M., Vieths S., Rosch P. Biochem. J. 2006, 395:463-472.
31. Neudecker P., Nerkamp J., Eisenmann A., Nourse A., Lauber T., Schweimer K., Lehmann K., Schwarzinger S., Ferreira F., Rosch P. J. Mol. Biol. 2004, 336:1141-1157.
32. Aalberse R.C. J Allergy Clin Immunol 2000, 106:228-238.
33. Aalberse R.C., Stapel S.O. Pediatric Allergy Immunol. 2001, 12(Suppl. 14):10-14.
34. Chapman M.D., Pomés A., Aalberse R.C. Allergy Frontiers: Epigenetics 2009, 265-289. Allergens and Risk Factors, Springer Japan. R. Pawankar, S.T. Holgate, L.J. Rosenwasser (Eds.).
35. Chapman M.D., Pomes A., Breiteneder H., Ferreira F. J. Allergy Clin. Immunol. 2007, 119:414-420.
36. Mills E.N., Jenkins J.A., Alcocer M.J., Shewry P.R. Critical Rev. Food Sci. Nutrition 2004, 44:379-407.
37. Pomes A. Curr. Allergy Asthma Rep. 2008, 8:425-432.
38. Radauer C., Bublin M., Wagner S., Mari A., Breiteneder H. J. Allergy Clin. Immunol. 2008, 121(847-852):e847.
39. C. Radauer, H. Breiteneder, in: A. Falus (Ed.), Springer US2009, pp. 127-151.
40. Punta M., Coggill P.C., Eberhardt R.Y., Mistry J., Tate J., Boursnell C., Pang N., Forslund K., Ceric G., Clements J., Heger A., Holm L., Sonnhammer E.L., Eddy S.R., Bateman A., Finn R.D. Nucleic Acids Res. 2012, 40:D290-301.
41. Gajhede M., Osmark P., Poulsen F.M., Ipsen H., Larsen J.N., Joost van Neerven R.J., Schou C., Lowenstein H., Spangfort M.D. Nat. Struct. Biol. 1996, 3:1040-1045.
42. Kader J.C. Ann. Rev. Plant Physiol. Plant Mol. Biol. 1996, 47:627-654.
43. Pantoja-Uceda D., Bruix M., Gimenez-Gallego G., Rico M., Santoro J. Biochemistry 2003, 42:13839-13847.
44. Shewry P.R., Beaudoin F., Jenkins J., Griffiths-Jones S., Mills E.N. Biochem. Soc. Trans. 2002, 30:906-910.
45. Mills E.N.C., Johnson P.E., Alexeev Y. Food Allergy 2012, W.B. Saunders, Edinburgh, pp. 15-32.
46. Pasquato N., Berni R., Folli C., Folloni S., Cianci M., Pantano S., Helliwell J.R., Zanotti G. J. Mol. Biol. 2006, 356:684-694.
47. Dunwell J.M. Biotechnol. Genetic Eng. Rev. 1998, 15(15):1-32.
48. Shewry P.R., Napier J.A., Tatham A.S. Plant cell 1995, 7:945-956.
49. Wang F., Robotham J.M., Teuber S.S., Tawde P., Sathe S.K., Roux K.H. J. Allergy Clin. Immunol. 2002, 110:160-166.
50. Muntz K. Plant Mol. Biol. 1998, 38:77-99.
51. Staswick P.E., Hermodson M.A., Nielsen N.C. J. Biol. Chem. 1984, 259:13431-13435.
52. Flower D.R., North A.C., Attwood T.K. Protein Sci. 1993, 2:753-761.
53. Flower D.R. Biochem. J. 1996, 318(Pt 1):1-14.
54. Madhurantakam C., Nilsson O.B., Uchtenhagen H., Konradsen J., Saarne T., Hogbom E., Sandalova T., Gronlund H., Achour A. J. Mol. Biol. 2010, 401:68-83.
55. Tan Y.W., Chan S.L., Ong T.C., Yit L.Y., Tiong Y.S., Chew F.T., Sivaraman J., Mok Y.K. J. Biol. Chem. 2009, 284:3148-3157.
56. Kretsinger R.H., Nockolds C.E. J. Biol. Chem. 1973, 248:3313-3326.
57. Valenta R., Hayek B., Seiberler S., Bugajska-Schretter A., Niederberger V., Twardosz A., Natter S., Vangelista L., Pastore A., Spitzauer S., Kraft D. Int. Arch. Allergy Immunol. 1998, 117:160-166.
58. Swain A.L., Kretsinger R.H., Amma E.L. J. Biol. Chem. 1989, 264:16620-16628.
59. Kumar V.D., Lee L., Edwards B.F. Biochemistry 1990, 29:1404-1412.
60. Wild L.G., Lehrer S.B. Curr. Allergy Asthma Rep. 2005, 5:74-79.
61. Verdino P., Westritschnig K., Valenta R., Keller W. Embo J. 2002, 21:5007-5016.
62. Verdino P., Barderas R., Villalba M., Westritschnig K., Valenta R., Rodriguez R., Keller W. J. Immunol. 2008, 180:2313-2321.
63. Henzl M.T., Sirianni A.G., Wycoff W.G., Tan A., Tanner J.J. Proteins 2013, 81:300-315.
64. Rawlings N.D., Barrett A.J., Bateman A. Nucleic Acids Res. 2012, 40:D343-350.
65. Barrett A.J., Rawlings N.D. Persp. Drug Discov. Des. 1996, 6:1-11.
66. Meno K., Thorsted P.B., Ipsen H., Kristensen O., Larsen J.N., Spangfort M.D., Gajhede M., Lund K. J. Immunol. 2005, 175:3835-3845.
67. Radauer C., Willerroider M., Fuchs H., Hoffmann-Sommergruber K., Thalhamer J., Ferreira F., Scheiner O., Breiteneder H. Clin. Immunol. 2006, 36:920-929.
68. van der Wel H., Loeve K. Eur. J. Biochem./FEBS 1972, 31:221-225.
69. Breiteneder H. Allergy 2004, 59:479-481.
70. Ebner C., Hoffmann-Sommergruber K., Breiteneder H. Allergy 2001, 56(Suppl. 67):43-44.
71. Hoffmann-Sommergruber K. Int. Arch. Allergy Immunol. 2000, 122:155-166.
72. Krebitz M., Wagner B., Ferreira F., Peterbauer C., Campillo N., Witty M., Kolarich D., Steinkellner H., Scheiner O., Breiteneder H. J. Mol. Biol. 2003, 329:721-730.
73. Dall'Antonia Y., Pavkov T., Fuchs H., Breiteneder H., Keller W. Communications 2005, 61:186-188.
74. Leone P., Menu-Bouaouiche L., Peumans W.J., Payan F., Barre A., Roussel A., Van Damme E.J., Rouge P. Biochimie 2006, 88:45-52.
75. Ogata C.M., Gordon P.F., De Vos A.M., Kim S.H. J. Mol. Biol. 1992, 228:893-908.
76. Sampedro J., Cosgrove D.J. Genome Biol. 2005, 6:242.
77. Castillo R.M., Mizuguchi K., Dhanaraj V., Albert A., Blundell T.L., Murzin A.G. Struct. Fold. Des. 1999, 7:227-236.
78. Ball T., Edstrom W., Mauch L., Schmitt J., Leistler B., Fiebig H., Sperr W.R., Hauswirth A.W., Valent P., Kraft D., Almo S.C., Valenta R. FEBS J. 2005, 272:217-227.
79. Yennawar N.H., Li L.C., Dudzinski D.M., Tabuchi A., Cosgrove D.J. Proc. Natl. Acad. Sci. USA 2006, 103:14664-14671.
80. Schweimer K., Petersen A., Suck R., Becker W.M., Rosch P., Matecko I. Biol. Chem. 2008, 389:919-923.
81. Padavattan S., Flicker S., Schirmer T., Madritsch C., Randow S., Reese G., Vieths S., Lupinek C., Ebner C., Valenta R., Markovic-Housley Z. J. Immunol. 2009, 182:2141-2151.
82. Bufe A., Betzel C., Schramm G., Petersen A., Becker W.M., Schlaak M., Perbandt M., Dauter Z., Weber W. J. Biol. Chem. 1996, 271:27193-27196.
83. Rajashankar K., Bufe A., Weber W., Eschenburg S., Lindner B., Betzel C. Section D, Biol. Cryst. 2002, 58:1175-1181.
84. Mueller G.A., Gosavi R.A., Krahn J.M., Edwards L.L., Cuneo M.J., Glesner J., Pomes A., Chapman M.D., London R.E., Pedersen L.C. J. Biol. Chem. 2010, 285:25394-25401.
85. King T.P., Spangfort M.D. Int. Arch. Allergy Immun. 2000, 123:99-106.
86. Gibbs G.M., Roelants K., O'Bryan M.K. Endocrine Rev. 2008, 29:865-897.
87. Henriksen A., King T.P., Mirza O., Monsalve R.I., Meno K., Ipsen H., Larsen J.N., Gajhede M., Spangfort M.D. Proteins 2001, 45:438-448.
88. Wright H.T., Sandrasegaram G., Wright C.S. J. Mol. Evol. 1991, 33:283-294.
89. Reyes-Lopez C.A., Hernandez-Santoyo A., Pedraza-Escalona M., Mendoza G., Hernandez-Arana A., Rodriguez-Romero A. Biochem. Biophys. Res. Co. 2004, 314:123-130.
90. Mueller G.A., Benjamin D.C., Rule G.S. Biochemistry 1998, 37:12707-12714.
91. Bork P., Holm L., Sander C. J. Mol. Biol. 1994, 242:309-320.
92. Derewenda U., Li J., Derewenda Z., Dauter Z., Mueller G.A., Rule G.S., Benjamin D.C. J. Mol. Biol. 2002, 318:189-197.
93. Ichikawa S., Takai T., Inoue T., Yuuki T., Okumura Y., Ogura K., Inagaki F., Hatanaka H. J. Biochem. 2005, 137:255-263.
94. Suzuki M., Tanaka Y., Korematsu S., Mikami B., Minato N. Biochem. Biophys. Res. Co. 2006, 339:679-686.
95. Cantarel B.L., Coutinho P.M., Rancurel C., Bernard T., Lombard V., Henrissat B. Nucleic Acids Res. 2009, 37:D233-238.
96. Receveur-Brechot V., Czjzek M., Barre A., Roussel A., Peumans W.J., Van Damme E.J., Rouge P. Proteins 2006, 63:235-242.
97. Kreil G. Protein Sci. 1995, 4:1666-1669.
98. Markovic-Housley Z., Miglierini G., Soldatova L., Rizkallah P.J., Muller U., Schirmer T. Structure 2000, 8:1025-1035.
99. Skov L.K., Seppala U., Coen J.J.F., Crickmore N., King T.P., Monsalve R., Kastrup J.S., Spangfort M.D., Gajhede M. Acta Cryst. D 2006, 62:595-604.
100. Hemmer W., Focke M., Kolarich D., Wilson I.B., Altmann F., Wohrl S., Gotz M., Jarisch R. J. Allergy Clin. Immunol. 2001, 108:1045-1052.
101. Soldatova L.N., Tsai C., Dobrovolskaia E., Markovic-Housley Z., Slater J.E. Allergy Asthma Proc. Offic. J. Reg. State Allergy Soc. 2007, 28:210-215.
102. Kolarich D., Leonard R., Hemmer W., Altmann F. FEBS J. 2005, 272:5182-5190.
103. Wang P., Heitman J. Genome Biol. 2005, 6:226.
104. Glaser A.G., Limacher A., Fluckiger S., Scheynius A., Scapozza L., Crameri R. Biochem. J. 2006, 396:41-49.
105. Limacher A., Kloer D.P., Fluckiger S., Folkers G., Crameri R., Scapozza L. Structure 2006, 14:185-195.
106. Huang T.-H., Peng H.-J., Su S.-N., Liaw S.-H. Acta Cryst. Section D 2012, 68:1303-1310.
107. D. Zafred, A. Nandy, H. Kahlert, L. Pump, W. Keller, J. Allergy Clin. Immunol. In press (2013).
108. Garcia K.C., Teyton L., Wilson I.A. Ann. Rev. Immunol. 1999, 17:369-397.
109. Reth M. Ann. Rev. Immunol. 1992, 10:97-121.
110. Lo Conte L., Chothia C., Janin J. J. Mol. Biol. 1999, 285:2177-2198.
111. Benjamin D.C., Berzofsky J.A., East I.J., Gurd F.R., Hannum C., Leach S.J., Margoliash E., Michael J.G., Miller A., Prager E.M., et al. Ann. Rev. Immunol. 1984, 2:67-101.
112. Atassi M.Z., Smith J.A. Immunochemistry 1978, 15:609-610.
113. East I.J., Todd P.E., Leach S.J. Mol. Immunol. 1980, 17:519-525.
114. Lando G., Reichlin M. J. Immunol. 1982, 129:212-216.
115. Chruszcz M., Pomes A., Glesner J., Vailes L.D., Osinski T., Porebski P.J., Majorek K.A., Heymann P.W., Platts-Mills T.A., Minor W., Chapman M.D. J. Biol. Chem. 2012, 287:7388-7398.
116. Niemi M., Janis J., Jylha S., Kallio J.M., Hakulinen N., Laukkanen M.L., Takkinen K., Rouvinen J. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 2008, 64:25-28.
117. Li Y., Li H., Yang F., Smith-Gill S.J., Mariuzza R.A. Nat. Struct. Biol. 2003, 10:482-488.
118. Ponomarenko J., Van Regenmortel M.H. Structural Bioinformatics 2009, 849-879. John Wiley & Sons, New York. J. Gu, P.E. Bourne (Eds.).
119. Li M., Gustchina A., Alexandratos J., Wlodawer A., Wunschmann S., Kepley C.L., Chapman M.D., Pomes A. J. Biol. Chem. 2008, 283:22806-22814.
120. Padavattan S., Schirmer T., Schmidt M., Akdis C., Valenta R., Mittermann I., Soldatova L., Slater J., Mueller U., Markovic-Housley Z. J. Mol. Biol. 2007, 368:742-752.
121. Kabat E.A., Wu T.T., Bilofsky H. J. Biol. Chem. 1977, 252:6609-6616.
122. Chothia C., Lesk A.M., Tramontano A., Levitt M., Smithgill S.J., Air G., Sheriff S., Padlan E.A., Davies D., Tulip W.R., Colman P.M., Spinelli S., Alzari P.M., Poljak R.J. Nature 1989, 342:877-883.
123. Mogensen J.E., Wimmer R., Larsen J.N., Spangfort M.D., Otzen D.E. J. Biol. Chem. 2002, 277:23684-23692.
124. Mueller G.A., Smith A.M., Chapman M.D., Rule G.S., Benjamin D.C. J. Biol. Chem. 2001, 276:9359-9365.
125. Meenan N.A., Ball G., Bromek K., Uhrin D., Cooper A., Kennedy M.W., Smith B.O. PLoS Neglected Tropical Dis. 2011, 5:e1040.
126. Neudecker P., Schweimer K., Nerkamp J., Scheurer S., Vieths S., Sticht H., Rosch P. J. Biol. Chem. 2001, 276:22756-22763.
127. Sollner J., Mayer B. J. Mol. Recog. 2006, 19:200-208.
128. Hopp T.P., Woods K.R. Proc. Natl. Acad. Sci. USA 1981, 78:3824-3828.
129. Westhof E., Altschuh D., Moras D., Bloomer A.C., Mondragon A., Klug A., Van Regenmortel M.H. Nature 1984, 311:123-126.
130. Karplus P.A., Schulz G.E. Naturwissenschaften 1985, 72:212-213.
131. Emini E.A., Hughes J.V., Perlow D.S., Boger J. J. Virol. 1985, 55:836-839.
132. Janin J., Wodak S. J. Mol. Biol. 1978, 125:357-386.
133. Blythe M.J., Flower D.R. Protein Sci. 2005, 14:246-248.
134. Gammermann A. Comput. Statistics 2000, 15:31-39.
135. Chen J., Liu H., Yang J., Chou K.C. Amino Acids 2007, 33:423-428.
136. Saha S., Bhasin M., Raghava G.P. BMC Genomics 2005, 6:79.
137. Odorico M., Pellequer J.L. J. Mol. Recog. 2003, 16:20-22.
138. Saha S., Raghava G.P. Proteins 2006, 65:40-48.
139. El-Manzalawy Y., Dobbs D., Honavar V. J. Mol. Recog. 2008, 21:243-255.
140. Larsen J.E., Lund O., Nielsen M. Immunome Res. 2006, 2:2.
141. Parker J.M., Guo D., Hodges R.S. Biochemistry 1986, 25:5425-5432.
142. Ansari H.R., Raghava G.P. Immunome Res. 2010, 6:6.
143. Giaco L., Amicosante M., Fraziano M., Gherardini P.F., Ausiello G., Helmer-Citterich M., Colizzi V., Cabibbo A. Adv. Appl. Bioinform Chem. 2012, 5:11-21.
144. Van Regenmortel M.H.V. Methods 1996, 9:465-472.
145. Van Regenmortel M.H. J. Mol. Recog. 2006, 19:183-187.
146. Berman H.M., Westbrook J., Feng Z., Gilliland G., Bhat T.N., Weissig H., Shindyalov I.N., Bourne P.E. Nucleic Acids Res. 2000, 28:235-242.
147. Huang J., Honda W. BMC Immunol. 2006, 7:7.
148. Schlessinger A., Ofran Y., Yachdav G., Rost B. Nucleic Acids Res. 2006, 34:D777-780.
149. Thornton J.M., Edwards M.S., Taylor W.R., Barlow D.J. EMBO J. 1986, 5:409-413.
150. Rapberger R., Lukas A., Mayer B. J. Mol. Recog. 2007, 20:113-121.
151. Rubinstein N.D., Mayrose I., Halperin D., Yekutieli D., Gershoni J.M., Pupko T. Mol. Immunol. 2008, 45:3477-3489.
152. Novotny J., Handschumacher M., Haber E., Bruccoleri R.E., Carlson W.B., Fanning D.W., Smith J.A., Rose G.D. Proc. Natl. Acad. Sci. USA 1986, 83:226-230.
153. Haste Andersen P., Nielsen M., Lund O. Protein Sci. 2006, 15:2558-2567.
154. Liu R., Hi J. J. Proteomics Bioinform. 2011, 4:10-15.
155. Zhang W., Xiong Y., Zhao M., Zou H., Ye X., Liu J. BMC Bioinform. 2011, 12:341.
156. Aalberse R.C., Akkerdaas J., van Ree R. Allergy 2001, 56:478-490.
157. Pomes A. Int. Arch. Allergy Imm. 2010, 152:1-11.
158. Dall'Antonia F., Gieras A., Devanaboyina S.C., Valenta R., Keller W. J. Allergy Clin. Immunol. 2011, 128(872-879):e878.
159. Kulkarni-Kale U., Bhosle S., Kolaskar A.S. Nucleic Acids Res. 2005, 33:W168-171.
160. Sweredoski M.J., Baldi P. Bioinformatics 2008, 24:1459-1460.
161. Hamelryck T. Proteins 2005, 59:38-48.
162. Ponomarenko J., Bui H.H., Li W., Fusseder N., Bourne P.E., Sette A., Peters B. BMC Bioinform. 2008, 9:514.
163. Rubinstein N.D., Mayrose I., Martz E., Pupko T. BMC Bioinform. 2009, 10:287.
164. Sun J., Wu D., Xu T., Wang X., Xu X., Tao L., Li Y.X., Cao Z.W. Nucleic Acids Res. 2009, 37:W612-616.
165. Liang S., Zheng D., Standley D.M., Yao B., Zacharias M., Zhang C. BMC Bioinform. 2010, 11:381.
166. Aas K. Allergy 1978, 33:3-14.
167. Mari A., Scala E., Palazzo P., Ridolfi S., Zennaro D., Carabella G. Cellular Immunol. 2006, 244:97-100.
168. Ivanciuc O., Schein C.H., Braun W. Nucleic Acids Res. 2003, 31:359-362.
169. Bannon G.A., Ogawa T. Mol. Nutr. Food Res. 2006, 50:638-644.
170. Jenkins J.A., Griffiths-Jones S., Shewry P.R., Breiteneder H., Mills E.N. J. Allergy Clin. Immunol. 2005, 115:163-170.
171. Glaser F., Pupko T., Paz I., Bell R.E., Bechor-Shental D., Martz E., Ben-Tal N. Bioinformatics 2003, 19:163-164.
172. Furmonaviciene R., Sutton B.J., Glaser F., Laughton C.A., Jones N., Sewell H.F., Shakib F. Bioinformatics 2005, 21:4201-4204.
173. Nair S., Kukreja N., Singh B.P., Arora N. PLoS One 2011, 6:e20020.
174. Miller S., Janin J., Lesk A.M., Chothia C. J. Mol. Biol. 1987, 196:641-656.
175. Ghose A.K., Viswanadhan V.N., Wendoloski J.J. J. Phys. Chem. A 1998, 102:3762-3772.
176. Heiden W., Moeckel G., Brickmann J. J. Comput.-Aided Mol. Des. 1993, 7:503-514.
177. Baker N.A., Sept D., Joseph S., Holst M.J., McCammon J.A. Proc. Natl. Acad. Sci. USA 2001, 98:10037-10041.
178. Schirmer T., Hoffimann-Sommergrube K., Susani M., Breiteneder H., Markovic-Housley Z. J. Mol. Biol. 2005, 351:1101-1109.
179. Holm J., Gajhede M., Ferreras M., Henriksen A., Ipsen H., Larsen J.N., Lund L., Jacobi H., Millner A., Wurtzen P.A., Spangfort M.D. J. Immunol. 2004, 173:5258-5267.
180. Kofler S., Asam C., Eckhard U., Wallner M., Ferreira F., Brandstetter H. J. Mol. Biol. 2012, 422:109-123.
181. Markovic-Housley Z., Degano M., Lamba D., von Roepenack-Lahaye E., Clemens S., Susani M., Ferreira F., Scheiner O., Breiteneder H. J. Mol. Biol. 2003, 325:123-133.
182. Mirza O., Henriksen A., Ipsen H., Larsen J.N., Wissenbach M., Spangfort M.D., Gajhede M. J. Immunol. 2000, 165:331-338.
183. Schweimer K., Sticht H., Nerkamp J., Boehm M., Breitenbach M., Vieths S., Rösch P. Appl. Mag. Reson. 1999, 17:449-464.
184. Spangfort M.D., Mirza O., Ipsen H., Van Neerven R.J., Gajhede M., Larsen J.N. J. Immunol. 2003, 171:3084-3090.
185. Markovic-Housley Z., Basle A., Padavattan S., Maderegger B., Schirmer T., Hoffmann-Sommergruber K. Section D, Biol. Crystallogr. 2009, 65:1206-1212.
186. Berkner H., Neudecker P., Mittag D., Ballmer-Weber B.K., Schweimer K., Vieths S., Rosch P. Biosci. Rep. 2009, 29:183-192.
187. Pasternak O., Bujacz G.D., Fujimoto Y., Hashimoto Y., Jelen F., Otlewski J., Sikorski M.M., Jaskolski M. Plant Cell 2006, 18:2622-2634.
188. Biesiadka J., Bujacz G., Sikorski M.M., Jaskolski M. J. Mol. Biol. 2002, 319:1223-1234.
189. Fernandes H., Pasternak O., Bujacz G., Bujacz A., Sikorski M.M., Jaskolski M. J. Mol. Biol. 2008, 378:1040-1051.
190. Rundqvist L., Tengel T., Zdunek J., Bjorn E., Schleucher J., Alcocer M.J., Larsson G. PLoS One 2012, 7:e46435.
191. Rico M., Bruix M., Gonzalez C., Monsalve R.I., Rodriguez R. Biochemistry 1996, 35:15672-15682.
192. Lerche M.H., Kragelund B.B., Bech L.M., Poulsen F.M. Structure 1997, 5:291-306.
193. Lerche M.H., Poulsen F.M. Protein Sci. 1998, 7:2490-2498.
194. Gomar J., Petit M.C., Sodano P., Sy D., Marion D., Kader J.C., Vovelle F., Ptak M. Protein Sci. 1996, 5:565-577.
195. Han G.W., Lee J.Y., Song H.K., Chang C., Min K., Moon J., Shin D.H., Kopka M.L., Sawaya M.R., Yuan H.S., Kim T.D., Choe J., Lim D., Moon H.J., Suh S.W. J. Mol. Biol. 2001, 308:263-278.
196. Shin D.H., Lee J.Y., Hwang K.Y., Kim K.K., Suh S.W. Structure 1995, 3:189-199.
197. Cabanos C., Urabe H., Masuda T., Tandang-Silvas M.R., Utsumi S., Mikami B., Maruyama N. Acta Cryst. F 2010, 66:1071-1073.
198. Cabanos C., Urabe H., Tandang-Silvas M.R., Utsumi S., Mikami B., Maruyama N. Mol. Immunol. 2011, 49:115-123.
199. Chruszcz M., Maleki S.J., Majorek K.A., Demas M., Bublin M., Solberg R., Hurlburt B.K., Ruan S., Mattison C.P., Breiteneder H., Minor W. J. Biol. Chem. 2011, 286:39318-39327.
200. Jin T., Howard A., Zhang Y.Z. Acta Cryst. F 2007, 63:848-851.
201. Jin T., Guo F., Chen Y.W., Howard A., Zhang Y.Z. Mol. Immunol. 2009, 46:1796-1804.
202. Adachi M., Takenaka Y., Gidamis A.B., Mikami B., Utsumi S. J. Mol. Biol. 2001, 305:291-305.
203. Adachi M., Kanamori J., Masuda T., Yagasaki K., Kitamura K., Mikami B., Utsumi S. Proc. Natl. Acad. Sci. USA 2003, 100:7395-7400.
204. Tandang-Silvas M.R., Fukuda T., Fukuda C., Prak K., Cabanos C., Kimura A., Itoh T., Mikami B., Utsumi S., Maruyama N. Biochimica et Biophysica Acta 2010, 1804:1432-1442.
205. Maruyama N., Adachi M., Takahashi K., Yagasaki K., Kohno M., Takenaka Y., Okuda E., Nakagawa S., Mikami B., Utsumi S. Eur. J. Biochem./FEBS 2001, 268:3595-3604.
206. Albillos S.M., Jin T., Howard A., Zhang Y., Kothary M.H., Fu T.J. J. Agric. Food Chem. 2008, 56:5352-5358.
207. Jin T., Albillos S.M., Guo F., Howard A., Fu T.J., Kothary M.H., Zhang Y.Z. J. Agric. Food Chem. 2009, 57:8643-8651.
208. Rouvinen J., Rautiainen J., Virtanen T., Zeiler T., Kauppinen J., Taivainen A., Mantyjarvi R. J. Biol. Chem. 1999, 274:2337-2343.
209. Qin B.Y., Creamer L.K., Baker E.N., Jameson G.B. FEBS Lett. 1998, 438:272-278.
210. Chan S.L., Ong S.T., Ong S.Y., Chew F.T., Mok Y.K. J. Immunol. 2006, 176:7132.
211. Gregoire C., Tavares G.A., Lorenzo H.K., Dandeu J.P., David B., Alzari P.M. Section D, Biol. Crystallogr. 1999, 55:880-882.
212. Lascombe M.B., Gregoire C., Poncet P., Tavares G.A., Rosinski-Chupin I., Rabillon J., Goubran-Botros H., Mazie J.C., David B., Alzari P.M. J. Biol. Chem. 2000, 275:21572-21577.
213. Bocskei Z., Groom C.R., Flower D.R., Wright C.E., Phillips S.E., Cavaggioni A., Findlay J.B., North A.C. Nature 1992, 360:186-188.
214. Kuser P.R., Franzoni L., Ferrari E., Spisni A., Polikarpov I. Acta Cryst. D 2001, 57:1863-1869.
215. Lucke C., Franzoni L., Abbate F., Lohr F., Ferrari E., Sorbi R.T., Ruterjans H., Spisni A. Eur. J. Biochem./FEBS 1999, 266:1210-1218.
216. Chaudhuri B.N., Kleywegt G.J., Bjorkman J., Lehman-McKeeman L.D., Oliver J.D., Jones T.A. Section D, Biol. Crystallogr. 1999, 55:753-762.
217. Baker E.N. J. Mol. Biol. 1977, 115:263-277.
218. Baker E.N. J. Mol. Biol. 1980, 141:441-484.
219. Varughese K.I., Su Y., Cromwell D., Hasnain S., Xuong N.H. Biochemistry 1992, 31:5172-5176.
220. Kamphuis I.G., Kalk K.H., Swarte M.B., Drenth J. J. Mol. Biol. 1984, 179:233-256.
221. Pickersgill R.W., Harris G.W., Garman E. Acta Crystallogr. Section B-Struct. Sci. 1992, 48:59-67.
222. De Halleux S., Stura E., VanderElst L., Carlier V., Jacquemin M., Saint-Remy J.M. J. Allergy Clin. Immunol. 2006, 117:571-576.
223. Chruszcz M., Chapman M.D., Vailes L.D., Stura E.A., Saint-Remy J.M., Minor W., Pomes A. J. Mol. Biol. 2009, 386:520-530.
224. Wang Y., Fu T.J., Howard A., Kothary M.H., McHugh T.H., Zhang Y. J. Agric. Food Chem. 2013, 61:1573-1578.
225. Thorn K.S., Christensen H.E., Shigeta R., Huddler D., Shalaby L., Lindberg U., Chua N.H., Schutt C.E. Structure 1997, 5:19-32.
226. Fedorov A.A., Ball T., Mahoney N.M., Valenta R., Almo S.C. Structure 1997, 5:33-45.
227. Liaw S.H., Chen H.Z., Kuo I.C., Chua K.Y. J. Struct. Biol. 1998, 123:265-268.
228. Tan K.W., Ong T.C., Gao Y.F., Tiong Y.S., Wong K.N., Chew F.T., Mok Y.K. J. Biol. Chem. 2012, 287:34776-34785.
229. Padavattan S., Schmidt M., Hoffman D.R., Markovic-Housley Z. J. Mol. Biol. 2008, 383:178-185.
230. Andersen N.H., Cao B., Rodriguez-Romero A., Arreguin B. Biochemistry 1993, 32:1407-1422.
231. Schwefel D., Maierhofer C., Beck J.G., Seeberger S., Diederichs K., Moller H.M., Welte W., Wittmann V. J. Am. Chem. Soc. 2010, 132:8704-8719.
232. Wright C.S. J. Mol. Biol. 1990, 215:635-651.
233. Wright C.S., Jaeger J. J. Mol. Biol. 1993, 232:620-638.
234. Ichikawa S., Hatanaka H., Yuuki T., Iwamoto N., Kojima S., Nishiyama C., Ogura K., Okumura Y., Inagaki F. J. Biol. Chem. 1998, 273:356-360.
235. Johannessen B.R., Skov L.K., Kastrup J.S., Kristensen O., Bolwig C., Larsen J.N., Spangfort M., Lund K., Gajhede M. FEBS Lett. 2005, 579:1208-1212.
236. Calvo E., Mans B.J., Ribeiro J.M., Andersen J.F. Proc. Natl. Acad. Sci. USA 2009, 106:3728-3733.
237. Chruszcz M., Chapman M.D., Osinski T., Solberg R., Demas M., Porebski P.J., Majorek K.A., Pomes A., Minor W. J. Allergy Clin. Immunol. 2012, 130(241-247):e249.
238. Scott D.L., Otwinowski Z., Gelb M.H., Sigler P.B. Science 1990, 250:1563-1566.
239. Hewish D.R., Barnham K.J., Werkmeister J.A., Kirkpatrick A., Bartone N., Liu S.T., Norton R.S., Curtain C., Rivetta D.E. J. Protein Chem. 2002, 21:243-253.
240. Terwilliger T.C., Eisenberg D. J. Biol. Chem. 1982, 257:6010-6015.
241. Terwilliger T.C., Eisenberg D. J. Biol. Chem. 1982, 257:6016-6022.
242. Razzera G., Gadermaier G., Almeida M.S., Ferreira F., Almeida F.C., Valente A.P. Biomol. NMR Assign 2009, 3:103-106.
243. Yang X., Moffat K. Structure 1996, 4:837-852.
244. Fluckiger S., Mittl P.R., Scapozza L., Fijten H., Folkers G., Grutter M.G., Blaser K., Crameri R. J. Immunol. 2002, 168:1267-1272.
245. Brzozowski A.M., Davies G.J. Biochemistry 1997, 36:10837-10845.
246. Gustchina A., Li M., Wunschmann S., Chapman M.D., Pomes A., Wlodawer A. J. Mol. Biol. 2005, 348:433-444.
247. Li M., Gustchina A., Glesner J., Wunschmann S., Vailes L.D., Chapman M.D., Pomes A., Wlodawer A. J. Immunol. 2011, 186:333-340.
248. Chrysina E.D., Brew K., Acharya K.R. J. Biol. Chem. 2000, 275:37021-37029.
249. Mueller-Dieckmann C., Panjikar S., Schmidt A., Mueller S., Kuper J., Geerlof A., Wilmanns M., Singh R.K., Tucker P.A., Weiss M.S. Acta Cryst. D 2007, 63:366-380.
250. Steigemann W., Weber E. J. Mol. Biol. 1979, 127:309-338.
251. Nuss D., Goettig P., Magler I., Denk U., Breitenbach M., Schneider P.B., Brandstetter H., Simon-Nobbe B. Biochimie 2010, 92:985-993.
252. Mueller G.A., Edwards L.L., Aloor J.J., Fessler M.B., Glesner J., Pomes A., Chapman M.D., London R.E., Pedersen L.C. J. Allergy Clin. Immunol. 2010, 125(909-917):e904.
253. Kaiser L., Gronlund H., Sandalova T., Ljunggren H.G., van Hage-Hamsten M., Achour A., Schneider G. J. Biol. Chem. 2003, 278:37730-37735.
254. Kaiser L., Velickovic T.C., Badia-Martinez D., Adedoyin J., Thunberg S., Hallen D., Berndt K., Gronlund H., Gafvelin G., van Hage M., Achour A. J. Mol. Biol. 2007, 370:714-727.
255. Olsen L.R., Dessen A., Gupta D., Sabesan S., Sacchettini J.C., Brewer C.F. Biochemistry 1997, 36:15073-15080.
256. Czerwinski E.W., Midoro-Horiuti T., White M.A., Brooks E.G., Goldblum R.M. J. Biol. Chem. 2005, 280:3740-3746.
257. Vilhelmsson M., Zargari A., Crameri R., Rasool O., Achour A., Scheynius A., Hallberg B.M. J. Mol. Biol. 2007, 369:1079-1086.
258. Limacher A., Glaser A.G., Meier C., Schmid-Grendelmeier P., Zeller S., Scapozza L., Crameri R. J. Immunol. 2007, 178:389-396.
259. Trevino M.A., Palomares O., Castrillo I., Villalba M., Rodriguez R., Rico M., Santoro J., Bruix M. Protein Sci. 2008, 17:371-376.
260. Yamasaki M., Arii Y., Mikami B., Hirose M. J. Mol. Biol. 2002, 315:113-120.
261. Yamasaki M., Takahashi N., Hirose M. J. Biol. Chem. 2003, 278:35524-35530.
262. Borer A.S., Wassmann P., Schmidt M., Hoffman D.R., Zhou J.J., Wright C., Schirmer T., Markovic-Housley Z. J. Mol. Biol. 2012, 415:635-648.
263. Fraczkiewicz R., Braun W. J. Comput. Chem. 1998, 19:319-333.