The 1.85 Å 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

Journal of Molecular Biology

Volumn 313, Issue 1, 2001, Pages 83-97

  Faelber, Katja ^a,b   Kirchhofer, Daniel ^c   Presta, Leonard ^d   Kelley, Robert F ^e   Muller, Yves A ^a  

^a MAX DELBRÜCK CENTER FOR MOLECULAR MEDICINE   (Germany)

^b FREIE UNIVERSITÄT BERLIN   (Germany)

^c Genentech   (United States)

^d Immunology   (United States)

^e GENENTECH INC   (United States)

Author keywords

Antigen antibody recognition; Blood coagulation; Crystal structures; Humanised antibody; Interface water molecules

Indexed keywords

EPITOPE; IMMUNOGLOBULIN F(AB) FRAGMENT; THROMBOPLASTIN; WATER; SOLVENT;

ANTIGEN ANTIBODY COMPLEX; ANTIGEN BINDING; ANTIGEN RECOGNITION; ARTICLE; BLOOD CLOTTING; CONFORMATIONAL TRANSITION; CONTROLLED STUDY; CRYSTAL STRUCTURE; HUMAN; MOLECULAR RECOGNITION; MUTAGENESIS; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN STRUCTURE; SOLVATION; STRUCTURE ANALYSIS; AMINO ACID SEQUENCE; ANTIBODY COMBINING SITE; CHEMICAL STRUCTURE; CHEMISTRY; IMMUNOLOGY; METABOLISM; MOLECULAR GENETICS; PROTEIN TERTIARY STRUCTURE; X RAY CRYSTALLOGRAPHY;

AMINO ACID SEQUENCE; BINDING SITES, ANTIBODY; CRYSTALLOGRAPHY, X-RAY; HUMANS; IMMUNOGLOBULIN FAB FRAGMENTS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN STRUCTURE, TERTIARY; SOLVENTS; THROMBOPLASTIN; WATER;

EID: 0035850666     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.2001.5036     Document Type: Article

References (61)

1. Antibody-antigen interactions: New structures and new conformational changes
2. Interactions of protein antigens with antibodies
3. The atomic structure of protein-protein recognition sites
4. Principles of protein-protein interactions
5. Bound water molecules and conformational stabilization help mediate an antigen-antibody association
6. Structural basis for the binding of an anti-cytochrome c antibody to its antigen: Crystal structures of FabE8-cytochrome c complex to 1.8 Å resolution and FabE8 to 2.26 Å resolution
7. Three-dimensional structures of the free and antigen-bound Fab from monoclonal antilysozyme antibody HyHEL-63
8. Biochemistry and physiology of blood coagulation
9. The tissue factor pathway: How it has become a "prima ballerina"
10. Epitope location on tissue factor determines the anticoagulant potency of monoclonal anti-tissue factor antibodies
11. Antibody mapping of tissue factor implicates two different exon-encoded regions in function
12. An anti-tissue factor monoclonal antibody which inhibits TF. VIIa complex is a potent anticoagulant in plasma
13. The crystal structure of the complex of blood coagulation factor VIIa with soluble tissue factor
14. The mechanism of an inhibitory antibody on TF-initiated blood coagulation revealed by the crystal structures of human tissue factor, Fab 5G9 and TF. G9 complex
15. The tissue factor region that interacts with substrates factor IX and factor X
16. Lysine residues 165 and 166 are essential for the cofactor function of tissue factor
17. Cofactor residues lysine 165 and 166 are critical for protein substrate recognition by the tissue factor-factor VIIa protease complex
18. The tissue factor region that interacts with factor Xa in the activation of factor VII
19. Influence of mutations in tissue factor on the fine specificity of macromolecular substrate activation
20. Generation of a humanized, high affinity anti-tissue factor antibody for use as a novel antithrombotic therapeutic
21. An unusual antibody that blocks tissue factor/factor VIIa function by inhibiting cleavage only of macromolecular substrates
22. Mammalian cell transient expression of tissue factor for the production of antigen
23. The crystal structure of the extracellular domain of human tissue factor refined to 1.7 Å resolution
24. Small rearrangements in structures of Fv and Fab fragments of antibody D1. 3 on antigen binding
25. Procheck: A program to check the stereochemical quality of protein structures
26. Refined structures of bobwhite quail lysozyme uncomplexed and complexed with the HyHEL-5 Fab fragment
27. VEGF and the Fab fragment of a humanized neutralizing antibody: Crystal structure of the complex at 2.4 Å resolution and mutational analysis of the interface
28. A revised set of potentials for beta-turn formation in proteins
29. Crystal structure of the extracellular region of human tissue factor
30. Hinge bending within the cytokine receptor super-family revealed by the 2.4 Å crystal structure of the extracellular domain of rabbit tissue factor
31. Monoclonal antibody analysis of purified and cell-associated tissue factor
32. Major antigen-induced domain rearrangements in an antibody
33. The immunoglobulin superfamily-domains for cell surface recognition
34. The molecular structure of cell adhesion molecules
35. Antibody-antigen interactions
36. Hydrogen bonds with pi-acceptors in proteins: Frequencies and role in stabilizing local 3D structures
37. A hot spot of binding energy in a hormone-receptor interface
38. Systematic mutational analyses of protein-protein interfaces
39. Water molecules participate in proteinase-inhibitor interactions: Crystal structures of Leu18, Ala18, and Gly18 variants of turkey ovomucoid inhibitor third domain complexed with Streptomyces griseus proteinase
40. Analysis of protein-protein interactions and the effects of amino acid mutations on their energetics. The importance of water molecules in the binding epitope
41. Anatomy of an antibody molecule: Structure, kinetics, thermodynamics and mutational studies of the antilysozyme antibody D1. 3
42. A mutational analysis of binding interactions in an antigen-antibody protein-protein complex
43. The protein data bank
44. Analysis of the factor VIIa binding site on human tissue factor: Effects of tissue factor mutations on the kinetics and thermodynamics of binding
45. Crystal structure of the interleukin-4/receptor alpha chain complex reveals a mosaic binding interface
46. On the nature of antibody combining sites: Unusual structural features that may confer on these sites an enhanced capacity for binding ligands
47. Structure, function and properties of antibody binding sites
48. 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
49. The 2.5 Å resolution structure of the je142 Fab fragment/HPr complex
50. Rational design of potent, bioavailable, nonpeptide cyclic ureas as HIV protease inhibitors
51. Selection and analysis of an optimized anti-VEGF antibody: Crystal structure of an affinity-matured Fab in complex with antigen
52. Structure of the extracellular domain of human tissue factor: Location of the factor VIIa binding site
53. Evaluation of single crystal X-ray diffraction data from a position sensitive detector
54. The CCP4 suite: Programs for protein crystallography
55. Crystallography & NMR system: A new software suite for macromolecular structure determination
56. Improved Fourier coefficients for maps using partial structures with errors
57. Improved methods for building protein models in electron density maps and the location of errors in these models
58. WHAT IF: A molecular modeling and drug design program
59. Structural superposition of proteins with unknown alignment and detection of topological similarity using a six-dimensional search algorithm
60. Molmol: A program for display and analysis of macromolecular structures