The structural basis of hyper IgM deficiency - CD40L mutations

Protein Engineering, Design and Selection

Volumn 20, Issue 3, 2007, Pages 133-141

  Thusberg, J ^a   Vihinen, M ^a,b  

^a UNIVERSITY OF TAMPERE   (Finland)

^b TAMPERE UNIVERSITY HOSPITAL   (Finland)

Author keywords

Bioinformatical analysis; Disease causing mutations; Immunodeficiencies; Structural basis of disease; Structure function relationships

Indexed keywords

BIOINFORMATICS; CELLS; ELECTROSTATICS; GENETIC ENGINEERING;

BIOINFORMATICAL ANALYSIS; DISEASE CAUSING MUTATIONS; IMMUNODEFICIENCIES; STRUCTURE-FUNCTION RELATIONSHIPS;

IMMUNOLOGY;

CD40 LIGAND; IMMUNOGLOBULIN M; MUTANT PROTEIN;

ACCURACY; ARTICLE; BIOINFORMATICS; ELECTROCHEMISTRY; HYPERIMMUNOGLOBULIN M DEFICIENCY; IMMUNOGLOBULIN DEFICIENCY; MISSENSE MUTATION; PRIORITY JOURNAL; PROTEIN AGGREGATION; PROTEIN STABILITY; PROTEIN STRUCTURE; RECEPTOR BINDING; SEQUENCE ANALYSIS; STRUCTURE ANALYSIS; THEORETICAL STUDY; X CHROMOSOME LINKED DISORDER;

CD40 LIGAND; HUMANS; HYPER-IGM IMMUNODEFICIENCY SYNDROME; MUTATION;

EID: 34047235797     PISSN: 17410126     EISSN: 17410134     Source Type: Journal    
DOI: 10.1093/protein/gzm004     Document Type: Article

References (81)

1. Allen,R.C. et al. (1993) Science, 259, 990-993.
2. Altschul,S.F., Madden,T.L., Schaffer,A.A., Zhang,J., Zhang,Z., Miller,W. and Lipman,D.J. (1997) Nucleic Acids Res., 25, 3389-3402.
3. Armitage,R.J. et al. (1992) Nature, 357, 80-82.
4. Aruffo,A. et al. (1993) Cell, 72, 291-300.
5. Bateman,A. et al. (2004) Nucleic Acids Res., 32, D138-D141.
6. Berberich,I., Shu,G., Siebelt,F., Woodgett,J.R., Kyriakis,J.M. and Clark,E.A. (1996) EMBO J., 15, 92-101.
7. Berberich,I., Shu,G.L. and Clark,E.A. (1994) J. Immunol., 153, 4357-4366.
8. Berezin,C., Glaser,F., Rosenberg,J., Paz,I., Pupko,T., Fariselli,P., Casadio,R. and Ben-Tal,N. (2004) Bioinformatics, 20, 1322-1324.
9. Bodmer,J.L., Schneider,P. and Tschopp,J. (2002) Trends Biochem. Sci., 27, 19-26.
10. Bonifacino,J.S., Cosson,P., Shah,N. and Klausner,R.D. (1991) EMBO J., 10, 2783-2793.
11. Burdin,N., Peronne,C., Banchereau,J. and Rousset,F. (1993) J. Exp. Med., 177, 295-304.
12. Chasman,D. and Adams,R.M. (2001) J. Mol. Biol., 307, 683-706.
13. Chiti,F., Stefani,M., Taddei,N., Ramponi,G. and Dobson,C.M. (2003) Nature, 424, 805-808.
14. Clark,E.A. and Ledbetter,J.A. (1986) Proc. Natl Acad. Sci. USA, 83, 4494-4498.
15. Clark,E.A. and Shu,G. (1990) J. Immunol., 145, 1400-1406.
16. Coffman,R.L., Lebman,D.A. and Rothman,P. (1993) Adv. Immunol., 54, 229-270.
17. Dadgostar,H., Zarnegar,B., Hoffmann,A., Qin,X.F., Truong,U., Rao,G., Baltimore,D. and Cheng,G. (2002) Proc. Natl Acad. Sci. USA, 99, 1497-1502.
18. DeLano,W.L. (2002) DeLano Scientific, San Carlos, CA, USA. http://www.pymol.org
19. Fernandez-Escamilla,A.M., Rousseau,F., Schymkowitz,J. and Serrano,L. (2004) Nat. Biotechnol., 22, 1302-1306.
20. Ferrer-Costa,C., Gelpi,J.L., Zamakola,L., Parraga,I., de la Cruz,X. and Orozco,M. (2005) Bioinformatics, 21, 3176-3178.
21. Finkelman,F.D., Holmes,J., Katona,I.M., Urban,J.F., Beckmann,M.P., Park,L.S., Schooley,K.A., Coffman,R.L., Mosmann,T.R. and Paul,W.E. (1990) Annu. Rev. Immunol., 8, 303-333.
22. Fuleihan,R., Ramesh,N., Loh,R., Jabara,H., Rosen,R.S., Chatila,T., Fu,S.M., Stamenkovic,I. and Geha,R.S. (1993) Proc. Natl Acad. Sci. USA, 90, 2170-2173.
23. Garber,E., Su,L., Ehrenfels,B., Karpusas,M. and Hsu,Y.M. (1999) J. Biol. Chem., 274, 33545-33550.
24. Gilis,D. and Rooman,M. (2000) Protein Eng., 13, 849-856.
25. Glaser,F., Pupko,T., Paz,I., Bell,R.E., Bechor-Shental,D., Martz,E. and Ben-Tal,N. (2003) Bioinformatics, 19, 163-164.
26. Harigai,M. et al. (2004) Arthritis Rheum., 50, 2167-2177.
27. Hostager,B.S., Catlett,I.M. and Bishop,G.A. (2000) J. Biol. Chem., 275, 15392-15398.
28. Karpusas,M., Hsu,Y.M., Wang,J.H., Thompson,J., Lederman,S., Chess,L. and Thomas,D. (1995) Structure, 3, 1031-1039.
29. Karpusas,M., Lucci,J., Ferrant,J., Benjamin,C., Taylor,F.R., Strauch,K., Garber,E. and Hsu,Y.M. (2001) Structure, 9, 321-329.
30. Kindler,V., Matthes,T., Jeannin,P. and Zubler,R.H. (1995) Eur. J. Immunol., 25, 1239-1243.
31. Klaus,S.J., Berberich,I., Shu,G. and Clark,E.A. (1994) Semin. Immunol., 6, 279-286.
32. Kroczek,R.A., Graf,D., Brugnoni,D., Giliani,S., Korthuer,U., Ugazio,A., Senger,G., Mages,H.W., Villa,A. and Notarangelo,L.D. (1994) Immunol. Rev., 138, 39-59.
33. Kwasigroch,J.M., Gilis,D., Dehouck,Y. and Rooman,M. (2002) Bioinformatics, 18, 1701-1702.
34. Lappalainen,I., Giliani,S., Franceschini,R., Bonnefoy,J.Y., Duckett,C., Notarangelo,L.D. and Vihinen,M. (2000) Biochem. Biophys. Res. Commun., 269, 124-130.
35. Lappalainen,I. and Vihinen,M. (2002) Protein Eng., 15, 1005-1014.
36. Levy,J. et al. (1997) J. Pediatr., 131, 47-54.
37. Li,X., Romero,P., Rani,M., Dunker,A.K. and Obradovic,Z. (1999) Genome Inform. Ser. Workshop Genome Inform., 10, 30-40.
38. Li,Y.Y., Baccam,M., Waters,S.B., Pessin,J.E., Bishop,G.A. and Koretzky,G.A. (1996) J. Immunol., 157, 1440-1447.
39. Linding,R., Jensen,L.J., Diella,F., Bork,P., Gibson,T.J. and Russell,R.B. (2003a) Structure, 11, 1453-1459.
40. Linding,R., Russell,R.B., Neduva,V. and Gibson,T.J. (2003b) Nucleic Acids Res., 31, 3701-3708.
41. Linding,R., Schymkowitz,J., Rousseau,F., Diella,F. and Serrano,L. (2004) J. Mol. Biol., 342, 345-353.
42. Lovell,S.C., Davis,I.W., Arendall,W.B., 3rd, de Bakker,P.I., Word,J.M., Prisant,M.G., Richardson,J.S. and Richardson,D.C. (2003) Proteins, 50, 437-450.
43. Lovell,S.C., Word,J.M., Richardson,J.S. and Richardson,D.C. (2000) Proteins, 40, 389-408.
44. Miller,M.P. and Kumar,S. (2001) Hum. Mol. Genet., 10, 2319-2328.
45. Mooney,S.D. and Klein,T.E. (2002) BMC Bioinformatics, 3, 24.
46. Morris,A.E., Remmele,R.L. Jr, Klinke,R., Macduff,B.M., Fanslow,W.C. and Armitage,R.J. (1999) J. Biol. Chem., 274, 418-423.
47. Muñoz,V. and Serrano,L. (1997) Biopolymers, 41, 495-509.
48. Ng,P.C. and Henikoff,S. (2001) Genome Res., 11, 863-874.
49. Noelle,R.J., Roy,M., Shepherd,D.M., Stamenkovic,I., Ledbetter,J.A. and Aruffo,A. (1992) Proc. Natl Acad. Sci. USA, 89, 6550-6554.
50. Notarangelo,L.D., Duse,M. and Ugazio,A.G. (1992) Immunodefic. Rev., 3, 101-121.
51. Notarangelo,L.D. and Peitsch,M.C. (1996) Immunol. Today, 17, 511-516.
52. Park,J.H. and Levitt,L. (1993) Blood, 82, 2470-2477.
53. Pei,J. and Grishin,N.V. (2001) Bioinformatics, 17, 700-712.
54. Peitsch,M.C. and Jongeneel,C.V. (1993) Int. Immunol., 5, 233-238.
55. Piirilä,H., Väliaho,J. and Vihinen,M. (2006) Hum. Mutat., 27, 1200-1208.
56. Pinchuk,L.M., Klaus,S.J., Magaletti,D.M., Pinchuk,G.V., Norsen,J.P. and Clark,E.A. (1996) J. Immunol., 157, 4363-4370.
57. Raingeaud,J., Whitmarsh,A.J., Barrett,T., Derijard,B. and Davis,R.J. (1996) Mol. Cell Biol., 16, 1247-1255.
58. Romero,P., Obradovic,Z. and Dunker,A.K. (1997) Genome Inform. Ser. Workshop Genome Inform., 8, 110-124.
59. Rong,S.B., Väliaho,J. and Vihinen,M. (2000) Mol. Med., 6, 155-164.
60. Rong,S.B. and Vihinen,M. (2000) J. Mol. Med., 78, 530-537.
61. Shen,B. and Vihinen,M. (2003) Bioinformatics, 19, 2161-2162.
62. Shen,B. and Vihinen,M. (2004) Protein Eng. Des. Sel., 17, 267-276.
63. Singh,J., Garber,E., Van Vlijmen,H., Karpusas,M., Hsu,Y.M., Zheng,Z., Naismith,J.H. and Thomas,D. (1998) Protein Sci., 7, 1124-1135.
64. Sobolev,V., Sorokine,A., Prilusky,J., Abola,E.E. and Edelman,M. (1999) Bioinformatics, 15, 327-332.
65. Steward,R.E., MacArthur,M.W., Laskowski,R.A. and Thornton,J.M. (2003) Trends Genet. 19, 505-513.
66. Sunyaev,S., Ramensky,V., Koch,I., Lathe,W., 3rd, Kondrashov,A.S. and Bork,P. (2001) Hum. Mol. Genet., 10, 591-597.
67. Sutherland,C.L., Heath,A.W., Pelech,S.L., Young,P.R. and Gold,M.R. (1996) J. Immunol., 157, 3381-3390.
68. Thompson,J.D., Higgins,D.G. and Gibson,T.J. (1994) Nucleic Acids Res., 22, 4673-4680.
69. Thusberg,J. and Vihinen,M. (2006) Hum. Mutat., 27, 1230-1243.
70. Väliaho,J., Smith,C.I.E. and Vihinen,M. (2006) Hum. Mutat., 27, 1209-1217.
71. Vihinen,M., Nilsson,L. and Smith,C.I.E. (1994a) Biochem. Biophys. Res. Commun., 205, 1270-1277.
72. Vihinen,M. et al. (1994b) Proc. Natl Acad. Sci. USA, 91, 12803-12807.
73. Vitkup,D., Sander,C. and Church,G.M. (2003) Genome Biol., 4, R72.
74. Wang,Z. and Moult,J. (2001) Hum. Mutat., 17, 263-270.
75. Ward,J.J., McGuffin,L.J., Bryson,K., Buxton,B.F. and Jones,D.T. (2004) Bioinformatics, 20, 2138-2139.
76. Word,J.M., Bateman,R.C., Jr, Presley,B.K., Lovell,S.C. and Richardson,D.C. (2000) Protein Sci., 9, 2251-2259.
77. Word,J.M., Lovell,S.C., LaBean,T.H., Taylor,H.C., Zalis,M.E., Presley,B.K., Richardson,J.S. and Richardson,D.C. (1999a) J. Mol. Biol., 285, 1711-1733.
78. Word,J.M., Lovell,S.C., Richardson,J.S. and Richardson,D.C. (1999b) J. Mol. Biol., 285, 1735-1747.
79. Worm,M., Ebermayer,K. and Henz,B. (1998) Immunology, 94, 395-402.
80. Worm,M. and Geha,R.S. (1995) Int. Arch. Allergy Immunol., 107, 368-369.
81. Yue,P., Melamud,E. and Moult,J. (2006) BMC Bioinform., 7, 166.