Crystal structure of a human single domain antibody dimer formed through V H-V H non-covalent interactions

PLoS ONE

Volumn 7, Issue 1, 2012, Pages

  Baral, Toya Nath ^a   Chao, Shi Yu ^b   Li, Shenghua ^a   Tanha, Jamshid ^a   Arbabi Ghahroudi, Mehdi ^a   Zhang, Jianbing ^a   Wang, Shuying ^b,c  

^a NATIONAL RESEARCH COUNCIL CANADA   (Canada)

^b NATIONAL CHENG KUNG UNIVERSITY   (Taiwan)

^c NATIONAL CHENG KUNG UNIVERSITY   (Taiwan)

Author keywords

[No Author keywords available]

Indexed keywords

EPIDERMAL GROWTH FACTOR RECEPTOR 2 SINGLE DOMAIN ANTIBODY GR3; EPIDERMAL GROWTH FACTOR RECEPTOR 2 SINGLE DOMAIN ANTIBODY GR6; EPIDERMAL GROWTH FACTOR RECEPTOR ANTIBODY; HOMODIMER; UNCLASSIFIED DRUG; ANTIBODY; EPIDERMAL GROWTH FACTOR RECEPTOR 2; HER2 PROTEIN, HUMAN;

ARTICLE; CONTROLLED STUDY; COVALENT BOND; CRYSTAL STRUCTURE; DIMERIZATION; GEL PERMEATION CHROMATOGRAPHY; HYDROPHOBICITY; IMMUNOGLOBULIN VARIABLE REGION; MOLECULAR CLONING; MOLECULAR INTERACTION; MOLECULAR LIBRARY; PHAGE DISPLAY; PROTEIN ANALYSIS; PROTEIN ASSEMBLY; PROTEIN ISOLATION; SURFACE PLASMON RESONANCE; THERMOSTABILITY; AMINO ACID SEQUENCE; ANTIBODY SPECIFICITY; CHEMICAL PHENOMENA; CHEMICAL STRUCTURE; CHEMISTRY; HUMAN; IMMUNOLOGY; METABOLISM; MOLECULAR GENETICS; PROTEIN BINDING; PROTEIN MULTIMERIZATION; PROTEIN SECONDARY STRUCTURE; PROTEIN TERTIARY STRUCTURE; SOLUTION AND SOLUBILITY; TRANSITION TEMPERATURE; X RAY CRYSTALLOGRAPHY;

AMINO ACID SEQUENCE; ANTIBODIES; ANTIBODY SPECIFICITY; CRYSTALLOGRAPHY, X-RAY; HUMANS; HYDROPHOBIC AND HYDROPHILIC INTERACTIONS; IMMUNOGLOBULIN VARIABLE REGION; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN BINDING; PROTEIN MULTIMERIZATION; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; RECEPTOR, ERBB-2; SOLUTIONS; TRANSITION TEMPERATURE;

EID: 84855770511     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0030149     Document Type: Article

References (35)

1. Padlan EA, (1994) Anatomy of the antibody molecule. Mol Immunol 31: 169-217.
2. Williamson AR, (1976) The biological origin of antibody diversity. Annu Rev Biochem 45: 467-500.
3. Schroeder HW Jr, Cavacini L, (2010) Structure and function of immunoglobulins. J Allergy Clin Immunol 125: S41-52.
4. Hamers-Casterman C, Atarhouch T, Muyldermans S, Robinson G, Hamers C, et al. (1993) Naturally occurring antibodies devoid of light chains. Nature 363: 446-448.
5. Wesolowski J, Alzogaray V, Reyelt J, Unger M, Juarez K, et al. (2009) Single domain antibodies: promising experimental and therapeutic tools in infection and immunity. Med Microbiol Immunol 198: 157-174.
6. Arbabi Ghahroudi M, Desmyter A, Wyns L, Hamers R, Muyldermans S, (1997) Selection and identification of single domain antibody fragments from camel heavy-chain antibodies. FEBS Lett 414: 521-526.
7. Behar G, Siberil S, Groulet A, Chames P, Pugniere M, et al. (2008) Isolation and characterization of anti-FcgammaRIII (CD16) llama single-domain antibodies that activate natural killer cells. Protein Eng Des Sel 21: 1-10.
8. Dumoulin M, Conrath K, Van Meirhaeghe A, Meersman F, Heremans K, et al. (2002) Single-domain antibody fragments with high conformational stability. Protein Sci 11: 500-515.
9. Stijlemans B, Conrath K, Cortez-Retamozo V, Van Xong H, Wyns L, et al. (2004) Efficient targeting of conserved cryptic epitopes of infectious agents by single domain antibodies. African trypanosomes as paradigm. J Biol Chem 279: 1256-1261.
10. Behar G, Chames P, Teulon I, Cornillon A, Alshoukr F, et al. (2009) Llama single-domain antibodies directed against nonconventional epitopes of tumor-associated carcinoembryonic antigen absent from nonspecific cross-reacting antigen. FEBS J 276: 3881-93.
11. Baral TN, Magez S, Stijlemans B, Conrath K, Vanhollebeke B, et al. (2006) Experimental therapy of African trypanosomiasis with a nanobody-conjugated human trypanolytic factor. Nat Med 12: 580-584.
12. Cortez-Retamozo V, Lauwereys M, Hassanzadeh Gh G, Gobert M, Conrath K, et al. (2002) Efficient tumor targeting by single-domain antibody fragments of camels. Int J Cancer 98: 456-462.
13. To R, Hirama T, Arbabi-Ghahroudi M, MacKenzie R, Wang P, et al. (2005) Isolation of monomeric human V(H)s by a phage selection. J Biol Chem 280: 41395-41403.
14. Jespers L, Schon O, James LC, Veprintsev D, Winter G, (2004) Crystal structure of HEL4, a soluble, refoldable human V(H) single domain with a germ-line scaffold. J Mol Biol 337: 893-903.
15. Arbabi-Ghahroudi M, MacKenzie R, Tanha J, (2009) Selection of non-aggregating VH binders from synthetic VH phage-display libraries. Methods Mol Biol 525: 187-216, xiii.
16. Barthelemy PA, Raab H, Appleton BA, Bond CJ, Wu P, et al. (2008) Comprehensive analysis of the factors contributing to the stability and solubility of autonomous human VH domains. J Biol Chem 283: 3639-3654.
17. Arbabi-Ghahroudi M, To R, Gaudette N, Hirama T, Ding W, et al. (2009) Aggregation-resistant VHs selected by in vitro evolution tend to have disulfide-bonded loops and acidic isoelectric points. Protein Eng Des Sel 22: 59-66.
18. Els Conrath K, Lauwereys M, Wyns L, Muyldermans S, (2001) Camel single-domain antibodies as modular building units in bispecific and bivalent antibody constructs. J Biol Chem 276: 7346-7350.
19. Kabat EA, Wu TT, (1991) Identical V region amino acid sequences and segments of sequences in antibodies of different specificities. Relative contributions of VH and VL genes, minigenes, and complementarity-determining regions to binding of antibody-combining sites. J Immunol 147: 1709-1719.
20. Vaguine AA, Richelle J, Wodak SJ, (1999) SFCHECK: a unified set of procedures for evaluating the quality of macromolecular structure-factor data and their agreement with the atomic model. Acta Crystallographica Section D 55: 191-205.
21. Dottorini T, Vaughan CK, Walsh MA, LoSurdo P, Sollazzo M, (2004) Crystal structure of a human VH: requirements for maintaining a monomeric fragment. Biochemistry 43: 622-628.
22. Fan Z-c, Shan L, Guddat LW, He X-m, Gray WR, et al. (1992) Three-dimensional structure of an Fv from a human IgM immunoglobulin. Journal of Molecular Biology 228: 188-207.
23. Collaborative, (1994) The CCP4 suite: programs for protein crystallography. Acta Crystallographica Section D 50: 760-763.
24. Tina K, Bhadra R, Srinivasan N, (2007) PIC: Protein interactions calculator. Nucleic Acids Research 35: W473.
25. Willuda J, Honegger A, Waibel R, Schubiger PA, Stahel R, et al. (1999) High thermal stability is essential for tumor targeting of antibody fragments: engineering of a humanized anti-epithelial glycoprotein-2 (epithelial cell adhesion molecule) single-chain Fv fragment. Cancer Res 59: 5758-5767.
26. Chatellier J, Van Regenmortel MH, Vernet T, Altschuh D, (1996) Functional mapping of conserved residues located at the VL and VH domain interface of a Fab. J Mol Biol 264: 1-6.
27. Vargas-Madrazo E, Paz-Garcia E, (2003) An improved model of association for VH-VL immunoglobulin domains: asymmetries between VH and VL in the packing of some interface residues. J Mol Recognit 16: 113-120.
28. Van Bockstaele F, Holz JB, Revets H, (2009) The development of nanobodies for therapeutic applications. Curr Opin Investig Drugs 10: 1212-1224.
29. Muyldermans S, (2001) Single domain camel antibodies: current status. J Biotechnol 74: 277-302.
30. Nahta R, Esteva FJ, (2007) Trastuzumab: triumphs and tribulations. Oncogene 26: 3637-3643.
31. Bell A, Wang ZJ, Arbabi-Ghahroudi M, Chang TA, Durocher Y, et al. (2009) Differential tumor-targeting abilities of three single-domain antibody formats. Cancer Lett.
32. Otwinowski Z, Minor W, (1997) Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol 276: 307-326.
33. McCoy AJ, Grosse-Kunstleve RW, Adams PD, Winn MD, Storoni LC, et al. (2007) Phaser crystallographic software. Journal of Applied Crystallography 40: 658-674.
34. Emsley P, Cowtan K, (2004) Coot: model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr 60: 2126-2132.
35. Brunger A, Adams P, Clore G, DeLano W, Gros P, et al. (1998) Crystallography & NMR system: a new software suite for macromolecular structure determination. Acta Crystallographica Section D: Biological Crystallography 54: 905-921.