Design and characterization of stabilized derivatives of human CD4D12 and CD4D1

Biochemistry

Volumn 50, Issue 37, 2011, Pages 7891-7900

  Saha, Piyali ^a   Barua, Bipasha ^a   Bhattacharyya, Sanchari ^a   Balamurali, M M ^a   Schief, William R ^b   Baker, David ^b   Varadarajan, Raghavan ^a  

^a INDIAN INSTITUTE OF SCIENCE   (India)

^b UNIVERSITY OF WASHINGTON SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CELLULAR RECEPTORS; CYTOPLASMIC TAIL; EXTRACELLULAR DOMAINS; FIRST DOMAIN; IN-VITRO; MULTI-SITE; T-LYMPHOCYTES; TRANSMEMBRANE REGIONS; TWO DOMAINS; WILD-TYPE PROTEINS;

DISEASES; VIRUSES;

DESIGN;

CD4 ANTIGEN; GLYCOPROTEIN GP 120; HUMAN IMMUNODEFICIENCY VIRUS FUSION INHIBITOR;

ARTICLE; BINDING AFFINITY; CIRCULAR DICHROISM; CONTROLLED STUDY; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS 1; HYDROPHOBICITY; IC 50; IN VITRO STUDY; MUTATION; NONHUMAN; PRIORITY JOURNAL; PROTEIN AGGREGATION; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN DEGRADATION; PROTEIN DOMAIN; PROTEIN PURIFICATION; PROTEIN STABILITY; VIRUS ENTRY; VIRUS INHIBITION; VIRUS NEUTRALIZATION; VIRUS STRAIN;

ANTIGENS, CD4; ANTIVIRAL AGENTS; HIV ENVELOPE PROTEIN GP120; HUMANS; MUTATION; PROTEIN BINDING; PROTEIN FOLDING; PROTEIN STABILITY; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; VIRUS INTERNALIZATION;

HUMAN IMMUNODEFICIENCY VIRUS 1;

EID: 80052778440     PISSN: 00062960     EISSN: 15204995     Source Type: Journal    
DOI: 10.1021/bi200870r     Document Type: Article

References (43)

1. Sharma, D.; et al. (2005) Biochemistry 44, 16192 - 16202
2. Dalgleish, A. G., Beverley, P. C., Clapham, P. R., Crawford, D. H., Greaves, M. F., and Weiss, R. A. (1984) The CD4 (T4) antigen is an essential component of the receptor for the AIDS retrovirus Nature 312, 763-767 (Pubitemid 15195924)
3. Lasky, L. A., Nakamura, G., Smith, D. H., Fennie, C., Shimasaki, C., Patzer, E., Berman, P., Gregory, T., and Capon, D. J. (1987) Delineation of a region of the human immunodeficiency virus type 1 gp120 glycoprotein critical for interaction with the CD4 receptor Cell 50, 975-985
4. Berger, E. A., Fuerst, T. R., and Moss, B. (1988) A soluble recombinant polypeptide comprising the amino-terminal half of the extracellular region of the CD4 molecule contains an active binding site for human immunodeficiency virus Proc. Natl. Acad. Sci. U. S. A. 85, 2357-2361 (Pubitemid 24315891)
5. Hussey, R. E., Richardson, N. E., Kowalski, M., Brown, N. R., Chang, H. C., Siliciano, R. F., Dorfman, T., Walker, B., Sodroski, J., and Reinherz, E. L. (1988) A soluble CD4 protein selectively inhibits HIV replication and syncytium formation Nature 331, 78-81 (Pubitemid 18053421)
6. Fisher, R. A., Bertonis, J. M., Meier, W., Johnson, V. A., Costopoulos, D. S., Liu, T., Tizard, R., Walker, B. D., Hirsch, M. S., and Schooley, R. T. 1988, HIV infection is blocked in vitro by recombinant soluble CD4 Nature 331, 76-78 (Pubitemid 18053420)
7. Traunecker, A., Luke, W., and Karjalainen, K. (1988) Soluble CD4 molecules neutralize human immunodeficiency virus type 1 Nature 331, 84-86 (Pubitemid 18053423)
8. Deen, K. C., McDougal, J. S., Inacker, R., Folena-Wasserman, G., Arthos, J., Rosenberg, J., Maddon, P. J., Axel, R., and Sweet, R. W. (1988) A soluble form of CD4 (T4) protein inhibits AIDS virus infection Nature 331, 82-84 (Pubitemid 18053422)
9. Daar, E. S., Li, X. L., Moudgil, T., and Ho, D. D. (1990) High concentrations of recombinant soluble CD4 are required to neutralize primary human immunodeficiency virus type 1 isolates Proc. Natl. Acad. Sci. U. S. A. 87, 6574-6578
10. Davis, C. B., Boyle, K. E., Urbanski, J. J., Paradysz, R. T., and Fong, K. L. (1992) Disposition of metabolically labeled recombinant soluble CD4 (sT4) in male Sprague-Dawley rats following intravenous and subcutaneous administration Drug Metab. Dispos. 20, 695-705
11. Cerutti, N., Mendelow, B. V., Napier, G. B., Papathanasopoulos, M. A., Killick, M., Khati, M., Stevens, W., and Capovilla, A. (2010) Stabilization of HIV-1 gp120-CD4 receptor complex through targeted interchain disulfide exchange J. Biol. Chem. 285, 25743-25752
12. Fouts, T., Godfrey, K., Bobb, K., Montefiori, D., Hanson, C. V., Kalyanaraman, V. S., DeVico, A., and Pal, R. (2002) Crosslinked HIV-1 envelope-CD4 receptor complexes elicit broadly cross-reactive neutralizing antibodies in rhesus macaques Proc. Natl. Acad. Sci. U. S. A. 99, 11842-11847 (Pubitemid 34994486)
13. Varadarajan, R., Sharma, D., Chakraborty, K., Patel, M., Citron, M., Sinha, P., Yadav, R., Rashid, U., Kennedy, S., Eckert, D., Geleziunas, R., Bramhill, D., Schleif, W., Liang, X., and Shiver, J. (2005) Characterization of gp120 and its single-chain derivatives, gp120-CD4D12 and gp120-M9: implications for targeting the CD4i epitope in human immunodeficiency virus vaccine design J. Virol. 79, 1713-1723 (Pubitemid 40459117)
14. Sharma, D., Balamurali, M. M., Chakraborty, K., Kumaran, S., Jeganathan, S., Rashid, U., Ingallinella, P., and Varadarajan, R. (2005) Protein minimization of the gp120 binding region of human CD4 Biochemistry 44, 16192-16202 (Pubitemid 41785817)
15. Wilkinson, R. A., Piscitelli, C., Teintze, M., Cavacini, L. A., Posner, M. R., and Lawrence, C. M. (2005) Structure of the Fab fragment of F105, a broadly reactive anti-human immunodeficiency virus (HIV) antibody that recognizes the CD4 binding site of HIV type 1 gp120 J. Virol. 79, 13060-13069 (Pubitemid 41433225)
16. Richards, F. M. (1974) The interpretation of protein structures: total volume, group volume distributions and packing density J. Mol. Biol. 82, 1-14
17. Chothia, C. (1975) Structural invariants in protein folding Nature 254, 304-308
18. Kellis, J. T., Jr., Nyberg, K., Sali, D., and Fersht, A. R. (1988) Contribution of hydrophobic interactions to protein stability Nature 333, 784-786
19. Kellis, J. T., Jr., Nyberg, K., and Fersht, A. R. (1989) Energetics of complementary side-chain packing in a protein hydrophobic core Biochemistry 28, 4914-4922 (Pubitemid 19151074)
20. Varadarajan, R. and Richards, F. M. (1992) Crystallographic structures of ribonuclease S variants with nonpolar substitution at position 13: packing and cavities Biochemistry 31, 12315-12327 (Pubitemid 23163106)
21. Jackson, S. E., Moracci, M., elMasry, N., Johnson, C. M., and Fersht, A. R. (1993) Effect of cavity-creating mutations in the hydrophobic core of chymotrypsin inhibitor 2 Biochemistry 32, 11259-11269 (Pubitemid 23332036)
22. Ratnaparkhi, G. S. and Varadarajan, R. (2000) Thermodynamic and structural studies of cavity formation in proteins suggest that loss of packing interactions rather than the hydrophobic effect dominates the observed energetics Biochemistry 39, 12365-12374
23. Karpusas, M., Baase, W. A., Matsumura, M., and Matthews, B. W. (1989) Hydrophobic packing in T4 lysozyme probed by cavity-filling mutants Proc. Natl. Acad. Sci. U. S. A. 86, 8237-8241 (Pubitemid 19286034)
24. Ohmura, T., Ueda, T., Ootsuka, K., Saito, M., and Imoto, T. (2001) Stabilization of hen egg white lysozyme by a cavity-filling mutation Protein Sci. 10, 313-320 (Pubitemid 32225651)
25. Yoshida, Y., Ohkuri, T., Kino, S., Ueda, T., and Imoto, T. (2005) Elucidation of the relationship between enzyme activity and internal motion using a lysozyme stabilized by cavity-filling mutations Cell. Mol. Life Sci. 62, 1047-1055 (Pubitemid 40655620)
26. Eijsink, V. G., Dijkstra, B. W., Vriend, G., van der Zee, J. R., Veltman, O. R., van der Vinne, B., van den Burg, B., Kempe, S., and Venema, G. (1992) The effect of cavity-filling mutations on the thermostability of Bacillus stearothermophilus neutral protease Protein Eng. 5, 421-426
27. Ishikawa, K., Nakamura, H., Morikawa, K., and Kanaya, S. (1993) Stabilization of Escherichia coli ribonuclease HI by cavity-filling mutations within a hydrophobic core Biochemistry 32, 6171-6178 (Pubitemid 23196872)
28. Morii, H., Uedaira, H., Ogata, K., Ishii, S., and Sarai, A. (1999) Shape and energetics of a cavity in c-Myb probed by natural and non-natural amino acid mutations J. Mol. Biol. 292, 909-920 (Pubitemid 29465483)
29. Lassalle, M. W., Yamada, H., Morii, H., Ogata, K., Sarai, A., and Akasaka, K. (2001) Filling a cavity dramatically increases pressure stability of the c-Myb R2 subdomain Proteins 45, 96-101
30. Kono, H., Saito, M., and Sarai, A. (2000) Stability analysis for the cavity-filling mutations of the Myb DNA-binding domain utilizing free-energy calculations Proteins 38, 197-209 (Pubitemid 30051419)
31. Lee, C., Park, S. H., Lee, M. Y., and Yu, M. H. (2000) Regulation of protein function by native metastability Proc. Natl. Acad. Sci. U. S. A. 97, 7727-7731 (Pubitemid 30460715)
32. Sengupta, T., Tsutsui, Y., and Wintrode, P. L. (2009) Local and global effects of a cavity filling mutation in a metastable serpin Biochemistry 48, 8233-8240
33. Kuhlman, B., Dantas, G., Ireton, G. C., Varani, G., Stoddard, B. L., and Baker, D. (2003) Design of a novel globular protein fold with atomic-level accuracy Science 302, 1364-1368 (Pubitemid 37452172)
34. Chakravarty, S., Bhinge, A., and Varadarajan, R. (2002) A procedure for detection and quantitation of cavity volumes proteins. Application to measure the strength of the hydrophobic driving force in protein folding J. Biol. Chem. 277, 31345-31353 (Pubitemid 34968933)
35. Murzin, A. G., Brenner, S. E., Hubbard, T., and Chothia, C. (1995) SCOP: a structural classification of proteins database for the investigation of sequences and structures J. Mol. Biol. 247, 536-540
36. Dantas, G., Kuhlman, B., Callender, D., Wong, M., and Baker, D. (2003) A large scale test of computational protein design: folding and stability of nine completely redesigned globular proteins J. Mol. Biol. 332, 449-460 (Pubitemid 37013512)
37. Pace, C. N., Vajdos, F., Fee, L., Grimsley, G., and Gray, T. (1995) How to measure and predict the molar absorption coefficient of a protein Protein Sci. 4, 2411-2423
38. Beena, K., Udgaonkar, J. B., and Varadarajan, R. (2004) Effect of signal peptide on the stability and folding kinetics of maltose binding protein Biochemistry 43, 3608-3619 (Pubitemid 38391716)
39. Richman, D. D., Wrin, T., Little, S. J., and Petropoulos, C. J. (2003) Rapid evolution of the neutralizing antibody response to HIV type 1 infection Proc. Natl. Acad. Sci. U. S. A. 100, 4144-4149 (Pubitemid 36418171)
40. Zolla-Pazner, S., Cohen, S., Pinter, A., Krachmarov, C., Wrin, T., Wang, S., and Lu, S. (2009) Cross-clade neutralizing antibodies against HIV-1 induced in rabbits by focusing the immune response on a neutralizing epitope Virology 392, 82-93
41. Li, M., Gao, F., Mascola, J. R., Stamatatos, L., Polonis, V. R., Koutsoukos, M., Voss, G., Goepfert, P., Gilbert, P., Greene, K. M., Bilska, M., Kothe, D. L., Salazar-Gonzalez, J. F., Wei, X., Decker, J. M., Hahn, B. H., and Montefiori, D. C. (2005) Human immunodeficiency virus type 1 env clones from acute and early subtype B infections for standardized assessments of vaccine-elicited neutralizing antibodies J. Virol. 79, 10108-10125 (Pubitemid 41098552)
42. Huang, C. C., Stricher, F., Martin, L., Decker, J. M., Majeed, S., Barthe, P., Hendrickson, W. A., Robinson, J., Roumestand, C., Sodroski, J., Wyatt, R., Shaw, G. M., Vita, C., and Kwong, P. D. (2005) Scorpion-toxin mimics of CD4 in complex with human immunodeficiency virus gp120 crystal structures, molecular mimicry, and neutralization breadth Structure 13, 755-768 (Pubitemid 40704664)
43. Chen, W., Feng, Y., Gong, R., Zhu, Z., Wang, Y., Zhao, Q., and Dimitrov, D. S. Engineered single human CD4 domains as potent HIV-1 inhibitors and components of vaccine immunogens.. J. Virol. 2011, in press.