Antibody Structure and Recognition of Antigen

Molecular Biology of B Cells

Volumn , Issue , 2004, Pages 491-509

  Sundberg, Eric J ^a   Mariuzza, Roy A ^a  

^a UNIVERSITY OF MARYLAND BIOTECHNOLOGY INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84866906198     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1016/B978-012053641-2/50032-0     Document Type: Chapter

References (126)

1. Ackers G.K., Smith F.R. Effects of site-specific amino acid modification on protein interactions and biological function. Annu Rev Biochem 1985, 54:597-629.
2. Amzel L.M., Poljak R.J. Three-dimensional structure of immunoglobulins. Annu Rev Biochem 1979, 48:961-997.
3. Arkin M.R., Wells J.A. Probing the importance of second sphere residues in an esterolytic antibody by phage display. J Mol Biol 1998, 284:1083-1094.
4. Barbas C.F., Hu D., Dunlop N., Sawyer L., Cababa D., Hendry R.M., Nara P.L., Burton D.R. In vitro evolution of a neutralizing human antibody to human immunodeficiency virus type 1 to enhance affinity and broaden strain cross-reactivity. Proc Natl Acad Sci U S A 1994, 91:3809-3813.
5. Batista F.D., Neuberger M.S. Affinity dependence of the B cell response to antigen: A threshold, a ceiling and the importance of off-rate. Immunity 1998, 8:751-759.
6. Batista F.D., Neuberger M.S. B cells extract and present immobilized antigen: implications for affinity discrimination. EMBO J 2000, 19:513-520.
7. Berthet-Colominas C., Monaco S., Novelli A., Sibai G., Mallet F., Cusack S. Head-to-tail dimers and interdomain flexibility revealed by the crystal structure of HIV-1 capsid protein (p24) complexed with a monoclonal antibody Fab. EMBO J 1999, 18:1124-1136.
8. Bhat T.N., Bentley G.A., Boulot G., Greene M.I., Tello D., Dall'Acqua W., Souchon H., Schwarz F.P., Mariuzza R.A., Poljak R.J. Bound water molecules and conformational stabilization help mediate an antigen-antibody association. Proc Natl Acad Sci U S A 1994, 91:1089-1093.
9. Boder E.T., Midelfort K.S., Wittrup K.D. Directed evolution of antibody fragments with monovalent femtomolar antigen-binding affinity. Proc Natl Acad Sci U S A 2000, 97:10701-10705.
10. Bogan A.A., Thorn K.S. Anatomy of hot spots in protein interfaces. J Mol Biol 1998, 280:1-9.
11. Braden B.C., Fields B.A., Poljak R.J. Conservation of water molecules in an antibody-antigen interaction. J Mol Recognit 1995, 8:317-325.
12. Braden B.C., Fields B.A., Ysern X., Dall'Acqua W., Goldbaum F.A., Poljak R.J., Mariuzza R.A. Crystal structure of an Fv-Fv idiotope-anti-idiotope complex at 1.9 A resolution. J Mol Biol 1996, 264:137-151.
13. Braden B.C., Fields B.A., Ysern X., Goldbaum F.A., Dall'Acqua W., Schwarz F.P., Poljak R.J., Mariuzza R.A. Crystal structure of the complex of the variable domain of antibody D1.3 and turkey egg white lysozyme: A novel conformational change in antibody CDR-L2 selects for antigen. J Mol Biol 1996, 257:889-894.
14. Braden B.C., Goldman E.R., Mariuzza R.A., Poljak R.J. Anatomy of an antibody molecule: structure, kinetics, thermodynamics and mutational studies of the antilysozyme antibody D1.3. Immunol Rev 1998, 163:45-57.
15. Braden B.C., Souchon H., Eisele J.L., Bentley G.A., Bhat T.N., Navaza J., Poljak R.J. Three-dimensional structures of the free and the antigen-complexed Fab from monoclonal antilysozyme antibody D44.1. J Mol Biol 1994, 243:767-781.
16. Budisavljevic M., Geniteau-Legendre M., Boudouin B., Pontillon F., Verroust P.J., Ronco P.M. Angiotensin II (AII)-related idiotypic network. II. Heterogeneity and fine specificity of AII internal images analyzed with monoclonal antibodies. J Immunol 1988, 140:3059-3065.
17. Chacko S., Silverton E., Kam-Morgan L., Smith-Gill S., Cohen G., Davies D. Structure of an antibody-lysozyme complex unexpected effect of conservative mutation. J Mol Biol 1995, 245:261-274.
18. Chen Y., Wiesmann C., Fuh G., Li B., Christinger H.W., McKay P., de Vos A.M., Lowman H.B. Selection and analysis of an optimized anti-VEGF antibody: crystal structure of an affinity-matured Fab in complex with antigen. J Mol Biol 1999, 293:865-881.
19. Chitarra V., Alzari P.M., Bentley G.A., Bhat T.N., Eisele J.L., Houdusse A., Lescar J., Souchon H., Poljak R.J. Three-dimensional structure of a heteroclitic antigen-antibody cross-reaction complex. Proc Natl Acad Sci U S A 1993, 90:7711-7715.
20. Chothia C. The nature of the accessible and buried surfaces in proteins. J Mol Biol 1976, 105:1-12.
21. Chothia C., Lesk A.M., Gherardi E., Tomlinson I.M., Walter G., Marks J.D., Llewelyn M.B., Winter G. Structural repertoire of the human VH segments. J Mol Biol 1992, 227:799-817.
22. Chothia C., Lesk A.M., Tramontano A., Levitt M., Smith-Gill S.J., Air G., Sheriff S., Padlan E.A., Davies D., Tulip W.R., et al. Conformations of immunoglobulin hypervariable regions. Nature 1989, 342:877-883.
23. Clackson T., Wells J.A. A hot spot of binding energy in a hormone-receptor interface. Science 1995, 267:383-386.
24. Conte L.L., Cothia C., Janin J. The atomic structure of protein-protein recognition sites. J Mol Biol 1999, 285:2177-2198.
25. Dall'Acqua W., Goldman E.R., Eisentein E., Mariuzza R.A. A mutational analysis of the binding of two different proteins to the same antibody. Biochemistry 1996, 35:9667-9676.
26. Dall'Acqua W., Goldman E.R., Lin W., Teng C., Tsuchiya D., Li H., Ysern X., Braden B.C., Li Y., Smith-Gill S.J., Mariuzza R.A. A mutational analysis of binding interactions in an antigen-antibody protein-protein complex. Biochemistry 1998, 37:7981-7991.
27. Davies D.R., Cohen G.H. Interactions of protein antigens with antibodies. Proc Natl Acad Sci USA 1996, 93:7-12.
28. De Genst E., Areskoug D., Decanniere K., Muyldermans S., Andersson K. Kinetic and affinity predictions of a protein-protein interaction using multivariate experimental design. J Biol Chem 2002, 277:29897-29907.
29. Decanniere K., Desmyter A., Lauwereys M., Ghahroudi M.A., Muyldermans S., Wyns L. A single-domain antibody fragment in complex with RNase A: Non-canonical loop structures and nanomolar affinity using two CDR loops. Structure Fold Des 1999, 7:361-370.
30. DeLano W.L. Unraveling hot spots in binding interfaces: Progress and challenges. Curr Opin Struct Biol 2002, 12:14-20.
31. Dyson H.J., Wright P.E. Antigenic peptides. FASEB J 1995, 9:37-42.
32. Eisenberg D., McLachlan A.D. Solvation energy in protein folding and binding. Nature 1986, 319:199-203.
33. England P., Bregegere F., Bedouelle H. Energetic and kinetic contributions of contact residues of antibody D1.3 in the interaction with lysozyme. Biochemistry 1997, 36:164-172.
34. England P., Nageotte R., Renard M., Page A.L., Bedouelle H. Functional characterization of the somatic hypermutation process leading to antibody D1.3, a high affinity antibody directed against lysozyme. J Immunol 1999, 162:2129-2136.
35. Eriksson A.E., Baase W.A., Zhang X.J., Heinz D.W., Blaber M., Baldwin E.P., Matthews B.W. Response of a protein structure to cavity-creating mutations and its relation to the hydrophobic effect. Science 1992, 255:178-183.
36. Faelber K., Kirchhofer D., Presta L., Kelley R.F., Muller Y.A. The 1.85 A resolution crystal structures of tissue factor in complex with humanized Fab D3h44 and of free humanized Fab D3H44: Revisiting the solvation of antigen combining sites. J Mol Biol 2001, 313:83-97.
37. Fersht A.R. Relationships between apparent binding energies measured in site-directed mutagenesis experiments and energetics of binding and catalysis. Biochemistry 1988, 27:1577-1580.
38. Fields B.A., Goldbaum F.A., Dall'Acqua W., Malchiodi E.L., Cauerhff A., Schwarz F.P., Ysern X., Poljak R.J., Mariuzza R.A. Hydrogen bonding and solvent structure in an antigen-antibody interface. Crystal structures and thermodynamic characterization of three Fv mutants complexed with lysozyme. Biochemistry 1996, 35:15494-15503.
39. Fields B.A., Goldbaum F.A., Ysern X., Poljak R.J., Mariuzza R.A. Molecular basis of antigen mimicry by an anti-idiotope. Nature 1995, 374:739-742.
40. Foote J., Eisen H.N. Kinetic and affinity limits on antibodies produced during immune responses. Proc Natl Acad Sci U S A 1995, 92:1254-1256.
41. Furukawa K., Akasako-Furukawa A., Shirai H., Nakamura H., Azuma T. Junctional amino acids determine the maturation pathway of an antibody. Immunity 1999, 11:329-338.
42. Furukawa K., Shirai H., Azuma T., Nakamura H. A role of the third complementarity-determining region in the affinity maturation of an antibody. J Biol Chem 2001, 276:27622-27628.
43. Garcia K.C., Desiderio S.V., Ronco P.M., Verroust P.J., Amzel L.M. Recognition of angiotensin II: Antibodies at different levels of an idiotypic network are superimposable. Science 1992, 257:528-531.
44. Garcia K.C., Ronco P.M., Verroust P.J., Brunger A.T., Amzel L.M. Three-dimensional structure of an angiotensin II-Fab complex at 3A: Hormone recognition by an anti-idiotypic antibody. Science 1992, 257:502-507.
45. Garman S.C., Wurzburg B.A., Tarchevskaya S.S., Kinet J.P., Jardetzky T.S. Structure of the Fc fragment of human IgE bound to its high-affinity receptor Fc epsilonRI alpha. Nature 2000, 406:259-266.
46. Gerstner R.B., Carter P., Lowman H.B. Sequence plasticity in the antigen-binding site of a therapeutic anti-HER2 antibody. J Mol Biol 2002, 321:851-862.
47. Gibas C.J., Subramaniam S., McCammon J.A., Braden B.C., Poljak R.J. pH dependence of antibody/lysozyme complexation. Biochemistry 1997, 36:15599-15614.
48. Goldbaum F.A., Schwarz F.P., Eisenstein E., Cauerhff A., Mariuzza R.A., Poljak R.J. The effect of water activity on the association constant and the enthalpy of reaction between lysozyme and the specific antibodies D1.3 and D44.1. J Mol Recognit 1996, 9:6-12.
49. Goldman E.R., Dall'Acqua W., Braden B.C., Mariuzza R.A. Analysis of binding interactions in an idiotope-antiidiotope protein-protein complex by double mutant cycles. Biochemistry 1997, 36:49-56.
50. Green S.M., Shortle D. Patterns of nonadditivity between pairs of stability mutations in staphylococcal nuclease. Biochemistry 1993, 32:10131-10139.
51. Guermonprez P., England P., Bedouelle H., Leclerc C. The rate of dissociation between antibody and antigen determines the efficiency of antibody-mediated antigen presentation to T cells. J Immunol 1998, 161:4542-4548.
52. Hahn M., Winkler D., Welfle K., Misselwitz R., Welfle H., Wessner H., Zahn G., Scholz C., Seifert M., Harkins R., et al. Cross-reactive binding of cyclic peptides to an anti-TGFalpha antibody Fab fragment: an X-ray structural and thermodynamic analysis. J Mol Biol 2001, 314:293-309.
53. Hamers-Casterman C., Atarhouch T., Muyldermans S., Robinson G., Hamers C., Songa E.B., Bendahman N., Hamers R. Naturally occurring antibodies devoid of light chains. Nature 1993, 363:446-448.
54. Harata K. X-ray structure of a monoclinic form of hen egg-white lysozyme crystallized at 313 K. Comparison of two independent molecules. Acta Crystallogr 1994, D50:250-257.
55. Harris L.J., Larson S.B., Hasel K.W., Day J., Greenwood A., McPherson A. The three-dimensional structure of an intact monoclonal antibody for canine lymphoma. Nature 1992, 360:369-372.
56. Harris L.J., Larson S.B., Hasel K.W., McPherson A. Refined structure of an intact IgG2a monoclonal antibody. Biochemistry 1997, 36:1581-1597.
57. Harris L.J., Skaletsky E., McPherson A. Crystallographic structure of an intact IgG1 monoclonal antibody. J Mol Biol 1998, 275:861-872.
58. Herron J.N., He X.M., Ballard D.W., Blier P.R., Pace P.E., Bothwell A.L., Voss E.W., Edmundson A.B. An autoantibody to single-stranded DNA: Comparison of the three-dimensional structures of the unliganded Fab and a deoxynucleotide-Fab complex. Proteins 1991, 11:159-175.
59. Herron J.N., Terry A.H., Johnston S., He X.M., Guddat L.W., Voss E.W., Edmundson A.B. High resolution structures of the 4-4-20 Fab-fluorescein complex in two solvent systems: Effects of solvent on structure and antigen-binding affinity. Biophys J 1994, 67:2167-2183.
60. Janin J., Chothia C. The structure of protein-protein recognition sites. J Biol Chem 1990, 265:16027-16030.
61. Jin L., Wells J.A. Dissecting the energetics of an antibody-antigen interface by alanine shaving and molecular grafting. Protein Sci 1994, 3:2351-2357.
62. Jones S., Thornton J.M. Principles of protein-protein interactions. Proc Natl Acad Sci U S A 1996, 93:13-20.
63. Kabat E.A., Wu T.T., Bilofsky H. Unusual distributions of amino acids in complementarity-determining (hypervariable) segments of heavy and light chains of immunoglobulins and their possible roles in specificity of antibody-combining sites. J Biol Chem 1977, 252:6609-6616.
64. Kelley R.F., O'Connell M.P., Carter P., Presta L., Eigenbrot C., Covarrubias M., Snedecor B., Bourell J.H., Vetterlein D. Antigen binding thermodynamics and antiproliferative effects of chimeric and humanized anti-p185HER2 antibody Fab fragments. Biochemistry 1992, 31:5434-5441.
65. Kellis J.T., Nyberg K., Fersht A.R. Energetics of complementary side-chain packing in a protein hydrophobic core. Biochemistry 1989, 28:4914-4922.
66. Kondo H., Shiroishi M., Matsushima M., Tsumoto K., Kumagai I. Crystal structure of anti-Hen egg white lysozyme antibody (HyHEL-10) Fv-antigen complex. Local structural changes in the protein antigen and water-mediated interactions of Fv-antigen and light chain-heavy chain interfaces. J Biol Chem 1999, 274:27623-27631.
67. Kouskoff V., Famiglietti S., Lacaud G., Lang P., Rider J.E., Kay B.K., Cambier J.C., Nemazee D. Antigens varying in affinity for the B cell receptor induce differential B lymphocyte responses. J Exp Med 1998, 188:1453-1464.
68. Kurinov I.V., Harrison R.W. The influence of temperature on lysozyme crystals. Structure and dynamics of protein and water. Acta Crystallogr 1995, D51:98-109.
69. Lang S., Xu J., Stuart F., Thomas R.M., Vrijbloed J.W., Robinson J.A. Analysis of antibody A6 binding to the extracellular interferon gamma receptor alpha-chain by alanine-scanning mutagenesis and random mutagenesis with phage display. Biochemistry 2000, 39:15674-15685.
70. Lawrence M.C., Colman P.M. Shape complementarity at protein/protein interfaces. J Mol Biol 1993, 234:946-950.
71. Lea S., Stuart D. Analysis of antigenic surfaces of proteins. FASEB J 1995, 9:87-93.
72. Li Y., Li H., Smith-Gill S.J., Mariuzza R.A. Three-dimensional structures of the free and antigen-bound Fab from monoclonal antilysozyme antibody HyHEL-63. Biochemistry 2000, 39:6296-6309.
73. Li Y., Li H., Yang F., Smith-Gill S.J., Mariuzza R.A. X-ray snapshots of the maturation of an antibody response to a protein antigen. Nat Struct Biol 2003, 10:482-488.
74. Li Y., Lipschultz C.A., Mohan S., Smith-Gill S.J. Mutations of an epitope hot-spot residue alter rate limiting steps of antigen-antibody protein-protein associations. Biochemistry 2001, 40:2011-2022.
75. LiCata V.J., Ackers G.K. Long-range, small magnitude nonadditivity of mutational effects in proteins. Biochemistry 1995, 34:3133-3139.
76. Lipschultz C.A., Li Y., Smith-Gill S. Experimental design for analysis of complex kinetics using surface plasmon resonance. Methods 2000, 20:310-318.
77. MacCallum R.M., Martin A.C., Thornton J.M. Antibody-antigen interactions: Contact analysis and binding site topography. J Mol Biol 1996, 262:732-745.
78. Manivel V., Sahoo N.C., Salunke D.M., Rao K.V. Maturation of an antibody response is governed by modulations in flexibility of the antigen-combining site. Immunity 2000, 13:611-620.
79. Matsumura M., Becktel W.J., Matthews B.W. Hydrophobic stabilization in T4 lysozyme determined directly by multiple substitutions of Ile 3. Nature 1988, 334:406-410.
80. Monaco-Malbet S., Berthet-Colominas C., Novelli A., Battai N., Piga N., Cheynet V., Mallet F., Cusack S. Mutual conformational adaptations in antigen and antibody upon complex formation between an Fab and HIV-1 capsid protein p24. Structure Fold Des 2000, 8:1069-1077.
81. Mylvaganam S.E., Paterson Y., Getzoff E.D. Structural basis for the binding of an anti-cytochrome c antibody to its antigen: Crystal structures of FabE8-cytochrome c complex to 1.8A resolution and FabE8 to 2.26A resolution. J Mol Biol 1998, 281:301-322.
82. Nicholls A., Sharp K.A., Honig B. Protein folding and association: Insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins 1991, 11:281-296.
83. Omelyanenko V.G., Jiskoot W., Herron J.N. Role of electrostatic interactions in the binding of fluorescein by anti-fluorescein antibody 4-4-20. Biochemistry 1993, 32:10423-10429.
84. Ooi T., Oobatake M., Nemethy G., Scheraga H.A. Accessible surface areas as a measure of the thermodynamic parameters of hydration of peptides. Proc Natl Acad Sci U S A 1987, 84:3086-3090.
85. Padlan E.A. On the nature of antibody combining sites: Unusual structural features that may confer on these sites an enhanced capacity for binding ligands. Proteins 1990, 7:112-124.
86. Padlan E.A., Silverton E.W., Sheriff S., Cohen G.H., Smith-Gill S.J., Davies D.R. Structure of an antibody-antigen complex: Crystal structure of the HyHEL-10 Fab-lysozyme complex. Proc Natl Acad Sci U S A 1989, 86:5938-5942.
87. Pan Y., Yuhasz S.C., Amzel L.M. Anti-idiotypic antibodies: biological function and structural studies. FASEB J 1995, 9:43-49.
88. Patten P.A., Gray N.S., Yang P.L., Marks C.B., Wedemayer G.J., Boniface J.J., Stevens R.C., Schultz P.G. The immunological evolution of catalysis. Science 1996, 271:1086-1091.
89. Poljak R.J. An idiotope-anti-idiotope complex and the structural basis of molecular mimicking. Proc Natl Acad Sci U S A 1994, 91:1599-1600.
90. Pons J., Rajpal A., Kirsch J.F. Energetic analysis of an antigen/antibody interface: Alanine scanning mutagenesis and double mutant cycles on the HyHEL-10/lysozyme interaction. Protein Sci 1999, 8:958-968.
91. Prasad G.S., Earhart C.A., Murray D.L., Novick R.P., Schlievert P.M., Ohlendorf D.H. Structure of toxic shock syndrome toxin 1. Biochemistry 1993, 32:13761-13766.
92. Rajewsky K. Clonal selection and learning in the antibody system. Nature 1996, 381:751-758.
93. Rajpal A., Kirsch J.F. Role of the minor energetic determinants of chicken egg white lysozyme (HEWL) to the stability of the HEWL antibody scFv-10 complex. Proteins 2000, 40:49-57.
94. Ramanadham M., Sieker L.C., Jensen L.H. Refinement of triclinic lysozyme: II. The method of stereochemically restrained least squares. Acta Crystallogr B 1990, 46(Pt 1):63-69.
95. Rini J.M., Schulze-Gahmen U., Wilson I.A. Structural evidence for induced fit as a mechanism for antibody-antigen recognition. Science 1992, 255:959-965.
96. Rini J.M., Stanfield R.L., Stura E.A., Salinas P.A., Profy A.T., Wilson I.A. Crystal structure of a human immunodeficiency virus type 1 neutralizing antibody, 50.1, in complex with its V3 loop peptide antigen. Proc Natl Acad Sci U S A 1993, 90:6325-6329.
97. Romesberg F.E., Spiller B., Schultz P.G., Stevens R.C. Immunological origins of binding and catalysis in a Diels-Alderase antibody. Science 1998, 279:1929-1933.
98. Roost H.P., Bachmann M.F., Haag A., Kalinke U., Pliska V., Hengartner H., Zinkernagel R.M. Early high-affinity neutralizing anti-viral IgG responses without further overall improvements of affinity. Proc Natl Acad Sci U S A 1995, 92:1257-1261.
99. Saphire E.O., Stanfield R.L., Crispin M.D., Parren P.W., Rudd P.M., Dwek R.A., Burton D.R., Wilson I.A. Contrasting IgG structures reveal extreme asymmetry and flexibility. J Mol Biol 2002, 319:9-18.
100. Schier R., McCall A., Adams G.P., Marshall K.W., Merritt H., Yim M., Crawford R.S., Weiner L.M., Marks C., Marks J.D. Isolation of picomolar affinity anti-c-erbB-2 single-chain Fv by molecular evolution of the complementarity determining regions in the center of the antibody binding site. J Mol Biol 1996, 263:551-567.
101. Schreiber G., Fersht A.R. Energetics of protein-protein interactions: Analysis of the barnase-barstar interface by single mutations and double mutant cycles. J Mol Biol 1995, 248:478-486.
102. Serrano L., Horovitz A., Avron B., Bycroft M., Fersht A.R. Estimating the contribution of engineered surface electrostatic interactions to protein stability by using double-mutant cycles. Biochemistry 1990, 29:9343-9352.
103. Sharp K.A., Nicholls A., Fine R.F., Honig B. Reconciling the magnitude of the microscopic and macroscopic hydrophobic effects. Science 1991, 252:106-109.
104. Shortle D., Stites W.E., Meeker A.K. Contributions of the large hydrophobic amino acids to the stability of staphylococcal nuclease. Biochemistry 1990, 29:8033-8041.
105. Sigurskjold B.W., Altman E., Bundle D.R. Sensitive titration microcalorimetric study of the binding of Salmonella O-antigenic oligosaccharides by a monoclonal antibody. Eur J Biochem 1991, 197:239-246.
106. Sondermann P., Huber R., Oosthuizen V., Jacob U. The 3.2-A crystal structure of the human IgG1 Fc fragment-Fc gammaRIll complex. Nature 2000, 406:267-273.
107. Stanfield R.L., Fieser T.M., Lerner R.A., Wilson I.A. Crystal structures of an antibody to a peptide and its complex with peptide antigen at 2.8A. Science 1990, 248:712-719.
108. Stanfield R.L., Takimoto-Kamimura M., Rini J.M., Profy A.T., Wilson I.A. Major antigen-induced domain rearrangements in an antibody. Structure 1993, 1:83-93.
109. Sundberg E.J., Urrutia M., Braden B.C., Isern J., Tsuchiya D., Fields B.A., Malchiodi E.L., Tormo J., Schwarz F.P., Mariuzza R.A. Estimation of the hydrophobic effect in an antigen-antibody protein-protein interface. Biochemistry 2000, 39:15375-15387.
110. Tomlinson I.M., Cox J.P., Gherardi E., Lesk A.M., Chothia C. The structural repertoire of the human V kappa domain. EMBO J 1995, 14:4628-4638.
111. Tomlinson I.M., Walter G., Jones P.T., Dear P.H., Sonnhammer E.L., Winter G. The imprint of somatic hypermutation on the repertoire of human germline V genes. J Mol Biol 1996, 256:813-817.
112. Tonegawa S. Somatic generation of antibody diversity. Nature 1983, 302:575-581.
113. Tormo J., Blaas D., Parry N.R., Rowlands D., Stuart D., Fita I. Crystal structure of a human rhinovirus neutralizing antibody complexed with a peptide derived from viral capsid protein VP2. EMBO J 1994, 13:2247-2256.
114. Ulrich H.D., Mundorff E., Santarsiero B.D., Driggers E.M., Stevens R.C., Schultz P.G. The interplay between binding energy and catalysis in the evolution of a catalytic antibody. Nature 1997, 389:271-275.
115. Vajdos F.F., Adams C.W., Breece T.N., Presta L.G., de Vos A.M., Sidhu S.S. Comprehensive functional maps of the antigen-binding site of an anti-ErbB2 antibody obtained with shotgun scanning mutagenesis. J Mol Biol 2002, 320:415-428.
116. Webster D.M., Henry A.H., Rees A.R. Antibody-antigen interactions. Curr Opin Struct Biol 1994, 4:123-129.
117. Wedemayer G.J., Patten P.A., Wang L.H., Schultz P.G., Stevens R.C. Structural insights into the evolution of an antibody combining site. Science 1997, 276:1665-1669.
118. Wedemayer G.J., Wang L.H., Patten P.A., Schultz P.G., Stevens R.C. Crystal structures of the free and liganded form of an esterolytic catalytic antibody. J Mol Biol 1997, 268:390-400.
119. Wilson I.A., Stanfield R.L. Antibody-antigen interactions. Curr. Opin Struct Biol 1993, 3:113-118.
120. Wilson I.A., Stanfield R.L. Antibody-antigen interactions: new structures and new conformational changes. Curr Opin Struct Biol 1994, 4:857-867.
121. Wu T.T., Kabat E.A. An analysis of the sequences of the variable regions of Bence Jones proteins and myeloma light chains and their implications for antibody complementarity. J Exp Med 1970, 132:211-250.
122. Xavier K.A., McDonald S.M., McCammon J.A., Willson R.C. Association and dissociation kinetics of bobwhite quail lysozyme with monoclonal antibody HyHEL-5. Protein Eng 1999, 12:79-83.
123. Xu J., Baase W.A., Baldwin E., Matthews B.W. The response of T4 lysozyme to large-to-small substitutions within the core and its relation to the hydrophobic effect. Protein Sci 1998, 7:158-177.
124. Yang P.L., Schultz P.G. Mutational analysis of the affinity maturation of antibody 48G7. J Mol Biol 1999, 294:1191-1201.
125. Ysern X., Fields B.A., Bhat T.N., Goldbaum F.A., Dall'Acqua W., Schwarz F.P., Poljak R.J., Mariuzza R.A. Solvent rearrangement in an antigen-antibody interface introduced by sitedirected mutagenesis of the antibody combining site. J Mol Biol 1994, 238:496-500.
126. Yutani K., Ogasahara K., Tsujita T., Sugino Y. Dependence of conformational stability on hydrophobicity of the amino acid residue in a series of variant proteins substituted at a unique position of tryptophan synthase alpha subunit. Proc Natl Acad Sci U S A 1987, 84:4441-4444.