Improved isolation of anti-rhTNF-α scFvs from phage display library by bioinformatics

Molecular Biotechnology

Volumn 43, Issue 1, 2009, Pages 20-28

  Chen, Wei ^a   Zhang, Juan ^a   Zhang, Tao ^a   Li, Haixin ^a   Wang, Wenyi ^a   Xia, Zhinan ^b   Wang, Min ^a  

^a CHINA PHARMACEUTICAL UNIVERSITY   (China)

^b HARVARD MEDICAL SCHOOL   (United States)

Author keywords

Bioinformatics; Docking; Homology modeling; Phage display; ScFv; TNF

Indexed keywords

BIOLOGICAL ASSAYS; ELISA ASSAY; EXPERIMENTAL DATA; HOMOLOGY MODELING; PHAGE DISPLAY; PHAGE DISPLAY LIBRARIES; PHAGE DISPLAY TECHNOLOGY; SCFV; SEQUENCE IDENTITY; WESTERN-BLOT ANALYSIS;

BACTERIOPHAGES; DOCKING;

BIOINFORMATICS;

SINGLE CHAIN FRAGMENT VARIABLE ANTIBODY; TUMOR NECROSIS FACTOR ALPHA ANTIBODY; PEPTIDE LIBRARY; TUMOR NECROSIS FACTOR ALPHA;

ANIMAL CELL; ANIMAL EXPERIMENT; ANTIBODY ISOLATION; ARTICLE; BIOASSAY; BIOINFORMATICS; BIOPANNING; CELL STRAIN L 929; CYTOTOXICITY; DNA SEQUENCE; ENZYME LINKED IMMUNOSORBENT ASSAY; GENE INSERTION; IC 50; MOUSE; NONHUMAN; PHAGE DISPLAY; POLYMERASE CHAIN REACTION; SEQUENCE ALIGNMENT; WESTERN BLOTTING; BIOLOGY; GENETIC ENHANCEMENT; GENETICS; IMMUNOGLOBULIN VARIABLE REGION; IMMUNOLOGY; METHODOLOGY; MOLECULAR CLONING; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PROTEIN ENGINEERING;

BASE SEQUENCE; CLONING, MOLECULAR; COMPUTATIONAL BIOLOGY; GENETIC ENHANCEMENT; IMMUNOGLOBULIN VARIABLE REGION; MOLECULAR SEQUENCE DATA; PEPTIDE LIBRARY; PROTEIN ENGINEERING; TUMOR NECROSIS FACTOR-ALPHA;

EID: 70350489498     PISSN: 10736085     EISSN: None     Source Type: Journal    
DOI: 10.1007/s12033-009-9172-x     Document Type: Article

References (28)

1. GP Smith 1985 Filamentous fusion phage: Novel expression vectors that display cloned antigens on the virion surface Science 228 1315 1317 10.1126/science.4001944 1:STN:280:DyaL2M3hvVOquw%3D%3D
2. J McCafferty AD Griffiths G Winter DJ Chiswell 1990 Phage antibodies: Filamentous phage displaying antibody variable domains Nature 348 552 554 10.1038/348552a0 10.1038/348552a0 1:CAS:528:DyaK3MXktVKruw%3D%3D
3. DR Buckler A Park M Viswanathan RM Hoet RC Ladner 2008 Screening isolates from antibody phage-display libraries Drug Discovery Today 13 318 324 10.1016/j.drudis.2007.10.012 10.1016/j.drudis.2007.10.012 1:CAS:528: DC%2BD1cXkslartL4%3D
4. G Kollias E Douni G Kassiotis D Kontoyiannis 1999 On the role of tumor necrosis factor and receptors in models of multiorgan failure, rheumatoid arthritis, multiple sclerosis and inflammatory bowel disease Immunological Reviews 169 175 194 10.1111/j.1600-065X.1999.tb01315.x 10.1111/j.1600-065X.1999. tb01315.x 1:CAS:528:DyaK1MXltlOgsLo%3D
5. MA Palladino FR Bahjat EA Theodorakis LL Moldawer 2003 Anti-TNF-alpha therapies: The next generation. Nature Reviews Drug Discovery 2 736 746 10.1038/nrd1175 10.1038/nrd1175 1:CAS:528:DC%2BD3sXmvVWlsLc%3D
6. H Chang W Qin Y Li J Zhang Z Lin M Lv, et al. 2007 A novel human scFv fragment against TNF-alpha from de novo design method Molecular Immunology 44 3789 3796 10.1016/j.molimm.2007.03.020 10.1016/j.molimm.2007.03.020 1:CAS:528:DC%2BD2sXmtVSksLc%3D
7. SU Eisenhardt M Schwarz N Bassler K Peter 2007 Subtractive single-chain antibody (scFv) phage-display: Tailoring phage-display for high specificity against function-specific conformations of cell membrane molecules Nature Protocols 2 3063 3073 10.1038/nprot.2007.455 10.1038/nprot.2007.455 1:CAS:528:DC%2BD2sXhsVejtrfL
8. R de Bruin K Spelt J Mol R Koes F Quattrocchio 1999 Selection of high-affinity phage antibodies from phage display libraries Nature Biotechnology 17 397 399 10.1038/7959 10.1038/7959
9. JW Kehoe N Velappan M Walbolt J Rasmussen D King J Lou, et al. 2006 Using phage display to select antibodies recognizing post-translational modifications independently of sequence context Molecular & Cellular Proteomics 5 2350 2363 10.1074/mcp.M600314-MCP200 10.1074/mcp.M600314-MCP200 1:CAS:528: DC%2BD28XhtlCgu7zK
10. AD Griffiths SC Williams O Hartley IM Tomlinson P Waterhouse WL Crosby, et al. 1994 Isolation of high affinity human antibodies directly from large synthetic repertoires The EMBO Journal 13 3245 3260 1:CAS:528:DyaK2cXlslOjt78%3D
11. HR Hoogenboom AD Griffiths KS Johnson DJ Chiswell P Hudson G Winter 1991 Multi-subunit proteins on the surface of filamentous phage: Methodologies for displaying antibody (Fab) heavy and light chains Nucleic Acids Research 19 4133 4137 10.1093/nar/19.15.4133 10.1093/nar/19.15.4133 1:CAS:528:DyaK3MXlvVSru7g%3D
12. JD Marks HR Hoogenboom TP Bonnert J McCafferty AD Griffiths G Winter 1991 By-passing immunization. Human antibodies from V-gene libraries displayed on phage Journal of Molecular Biology 222 581 597 10.1016/0022-2836(91)90498-U 10.1016/0022-2836(91)90498-U 1:CAS:528:DyaK38XhslWksbY%3D
13. Sambrook, J., & Russell, D. (2001). Molecular cloning: A laboratory manual (3rd ed.). Cold Spring Harbour, New York: Cold Spring Harbour Laboratory Press.
14. JD Thompson DG Higgins TJ Gibson 1994 CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice Nucleic Acids Research 22 4673 4680 10.1093/nar/22.22.4673 10.1093/nar/22.22.4673 1:CAS:528:DyaK2MXitlSgu74%3D
15. J Westbrook Z Feng L Chen H Yang HM Berman 2003 The protein data bank and structural genomics Nucleic Acids Research 31 489 491 10.1093/nar/gkg068 10.1093/nar/gkg068 1:CAS:528:DC%2BD3sXhvFSltr4%3D
16. K Arnold L Bordoli J Kopp T Schwede 2006 The SWISS-MODEL workspace: A web-based environment for protein structure homology modelling Bioinformatics 22 195 201 10.1093/bioinformatics/bti770 10.1093/bioinformatics/bti770 1:CAS:528:DC%2BD28XovVCltw%3D%3D
17. C Arcangeli C Cantale P Galeffi V Rosato 2008 Structure and dynamics of the anti-AMCV scFv(F8): Effects of selected mutations on the antigen combining site Journal of Structural Biology 164 119 133 10.1016/j.jsb.2008.06.013 10.1016/j.jsb.2008.06.013 1:CAS:528:DC%2BD1cXhtFCgu7zN
18. SR Comeau DW Gatchell S Vajda CJ Camacho 2004 ClusPro: A fully automated algorithm for protein-protein docking Nucleic Acids Research 32 W96 W99 10.1093/nar/gkh354 10.1093/nar/gkh354 1:CAS:528:DC%2BD2cXlvFKnsLo%3D
19. R Chen L Li Z Weng 2003 ZDOCK: An initial-stage protein-docking algorithm Proteins 52 80 87 10.1002/prot.10389 10.1002/prot.10389 1:CAS:528: DC%2BD3sXkslahs7w%3D
20. Salfeld, J. G., Allen, D. J., Hoogenboom, H. R. J. M., Kaymakcalan, Z., Labkovsky, B., Mankovich, J. A., et al. (2000). Human antibodies that bind human TNFα. US patent no. 6,090,382.
21. AL Morris MW MacArthur EG Hutchinson JM Thornton 1992 Stereochemical quality of protein structure coordinates Proteins 12 345 364 10.1002/prot.340120407 10.1002/prot.340120407 1:CAS:528:DyaK38XisFWls7o%3D
22. M Wiederstein MJ Sippl 2007 ProSA-web: Interactive web service for the recognition of errors in three-dimensional structures of proteins Nucleic Acids Research 35 W407 W410 10.1093/nar/gkm290 10.1093/nar/gkm290
23. L Lo Conte C Chothia J Janin 1999 The atomic structure of protein-protein recognition sites Journal of Molecular Biology 285 2177 2198 10.1006/jmbi.1998.2439 10.1006/jmbi.1998.2439 1:STN:280:DyaK1M7is1Gntg%3D%3D
24. B Lee FM Richards 1971 The interpretation of protein structures: Estimation of static accessibility Journal of Molecular Biology 55 379 400 10.1016/0022-2836(71)90324-X 10.1016/0022-2836(71)90324-X 1:CAS:528: DyaE3MXht1Shtrk%3D
25. R Mutuberria HR Hoogenboom E van der Linden AP de Bruine RC Roovers 1999 Model systems to study the parameters determining the success of phage antibody selections on complex antigens Journal of Immunological Methods 231 65 81 10.1016/S0022-1759(99)00141-6 10.1016/S0022-1759(99)00141-6 1:CAS:528: DC%2BD3cXmtVKktA%3D%3D
26. T Kretzschmar T von Ruden 2002 Antibody discovery: Phage display Current Opinion in Biotechnology 13 598 602 10.1016/S0958-1669(02)00380-4 10.1016/S0958-1669(02)00380-4 1:CAS:528:DC%2BD38XptlWlsbo%3D
27. AD Griffiths M Malmqvist JD Marks JM Bye MJ Embleton J McCafferty, et al. 1993 Human anti-self antibodies with high specificity from phage display libraries The EMBO Journal 12 725 734 1:CAS:528:DyaK3sXhsVGlsro%3D
28. SG Hymowitz MP O'Connell MH Ultsch A Hurst K Totpal A Ashkenazi, et al. 2000 A unique zinc-binding site revealed by a high-resolution X-ray structure of homotrimeric Apo2L/TRAIL Biochemistry 39 633 640 10.1021/bi992242l 10.1021/bi992242l 1:CAS:528:DC%2BD3cXjsVKq