Chapter 20: Advancement and Utilization of Biosensors for Protein Interaction Analysis and Proteomics—References
Anderson N.L., Matheson A.D., and Steiner S. 2000. Proteomics: Applications in basic and applied biology. Curr. Opin. Biotechnol. 11: 408–412.
Babcock G.J., Mirzabekov T., Wojtowicz W., and Sodroski J. 2001. Ligand binding characteristics of CXCR4 incorporated into paramagnetic proteoliposomes. J. Biol. Chem. 276: 38433–38440.
Balzarini J., Pannecouque C., De Clercq E., Pavlov A.Y., Printsevskaya S.S., Miroshnikova O.V., Reznikova M.I., and Preobrazhenskaya M.N. 2003. Antiretroviral activity of semisynthetic derivatives of glycopeptide antibiotics. J. Med. Chem. 46: 2755–2764.
Banner D.W., Kokkinidis M., and Tsernoglou D. 1987. Structure of the ColE1 rop protein at 1.7 Å resolution. J. Mol. Biol. 196: 657–675.
Betz S., Fairman R., Fairman R., O'Neil K., Lear J., and Degrado W. 1995. Design of two-stranded and three-stranded coiled-coil peptides. Philos. Trans. R. Soc. Lond. B Biol. Sci. 348: 81–88.
Biorn A.C., Cocklin S., Madani N., Si Z., Ivanovic T., Samanen J., Van Ryk D.I., Pantophlet R., Burton D.R., Freire E., Sodroski J., and Chaiken I. 2004. Mode of action for linear peptide inhibitors of HIV-1 gp120 interactions. Biochemistry 43: 1928–1938.
Brigham-Burke M., Edwards J.R., and O'Shannessy D.J. 1992. Detection of receptor-ligand interactions using surface plasmon resonance: Model studies employing the HIV-1 gp120/CD4 interaction Anal. Biochem. 205: 125–131.
Burkhard P., Ivaninskii S., and Lustig A. 2002. Improving coiled-coil stability by optimizing ionic interactions. J. Mol. Biol. 318: 901–910.
Canziani G., Zhang W., Cines D., Rux A., Willis S., Cohen G., Eisenberg R., and Chaiken I.M. 1999. Exploring biomolecular recognition using optical biosensors. Methods 19: 253–269.
Chaiken I.M. 2001. Revealing and utilizing receptor recognition mechanisms in a high throughput world. J. Cell Biochem. 37: 126–135.
Chaiken I., Wu S.J., Plugariu C., Zhang W., Li C., and Dowd C. 2001. Convergence of recombinant mutagenesis and kinetics interaction analysis for revealing receptor recognition mechanisms and designing receptor ligands. In Drug-receptor thermodynamics: Introduction and applications (ed. R.B. Raffa), pp. 743–781. Wiley, Chichester, United Kingdom.
Clapham P.R. and McKnight A. 2002. Cell surface receptors, virus entry and tropism of primate lentiviruses. J. Gen. Virol. 83: 1809–1829.
Cohen C. and Parry D.A. 1990. Alpha-helical coiled coils and bundles: How to design an alpha-helical protein. Proteins 7: 1–15.
Culp J.S., Johansen H., Hellmig B., Beck J., Matthews T.J., Delers A., and Rosenberg M. 1991. Regulated expression allows high level production and secretion of HIV-1 gp120 envelope glycoprotein in Drosophila Schneider cells. Biotechnology 9: 173–177.
Cusack S., Berthet-Colominas C., Hartlein M., Nassar N., and Leberman R. 1990. A second class of synthetase structure revealed by X-ray analysis of E. coli seryl tRNA synthetase at 2.5 Å. Nature 347: 249.
De Crescenzo G., Pham P.L., Durocher Y., and O'Connor-McCourt M.D. 2003. Transforming growth factor-beta (TGF-β) binding to the extracellular domain of the type II TGF-β receptor: Receptor capture on a biosensor surface using a new coiled-coil capture system demonstrates that avidity contributes significantly to high affinity binding. J. Mol. Biol. 328: 1173.
Dongre A.R., Opiteck G., Cosand W.L., and Hefta S.A. 2001. Proteomics in the post genome age. Biopolymers 60: 206–211.
Dowd C.S., Leavitt S., Babcock G., Godillot A.P., Van Ryk D., Canziani G.A., Sodroski J., Freire E, and Chaiken I.M. 2002. β-turn Phe in HIV-1 Env binding site of CD4 and CD4 mimetic miniprotein enhances Env binding affinity but is not required for activation of co-receptor/17b site. Biochemistry 41: 7038–7046.
Doyle A., Griffiths J.B., and Newell D.G., eds. 1998. Cell and tissue culture: Laboratory procedures. Wiley, Chichester, United Kingdom.
Ferrer M. and Harrison S.C. 1999. Peptide ligands to human immunodeficiency virus type 1 gp120 identified from phage display libraries. J. Virol. 73: 5795–5802.
Fredriksson R., Lagerstrom M.C., Lundin L.G., and Schioth H.B. 2003. The G-protein-coupled receptors in the human genome form five main families. Phylogenetic analysis, paralogon groups, and fingerprints. Mol. Pharmacol. 63: 1256–1272.
Gilligan J.J., Schuck P., and Yergey A.L. 2002. Mass spectrometry after capture and small-volume elution of analyte from a surface plasmon resonance biosensor. Anal. Chem. 74: 2041–2047.
Giot L., Bader J.S., Brouwer C., Chaudhuri A., Kuang B., Li Y., Hao Y.L., Ooi C.E., Godwin B., Vitols E., et al. 2003. A protein map of Drosophila melanogaster. Science 302: 1727–1736.
Hodges R.S., Zhou N.E., Kay C.M., and Semchuk P.D. 1990. Synthetic model proteins: Contribution of hydrophobic residues and disulfide bonds to protein stability. Pept. Res. 3: 123–137.
Hong Q., Gutierrez-Aguirre I., Barlic A., Malovrh P., Kristan K., Podlesek Z., Macek P., Turk D., Gonzalez-Manas J.M., Lakey J.H., and Anderluh G. 2002. Two-step membrane binding by Equinatoxin II, a pore-forming toxin from the sea anemone, involves an exposed aromatic cluster and a flexible helix. J. Biol. Chem. 277: 41916–41924.
Howard K. 2000. The bioinformatics gold rush. Sci. Am. 283: 58–63.
Ishino T., Pasut G., Scibek J., and Chaiken I. 2004. Kinetic interaction analysis of human interleukin 5 receptor α mutants reveals a unique binding topology and charge distribution for cytokine recognition. J. Biol. Chem. 279: 9547–9556.
Johnsson B., Lofas S., and Lindquist G. 1991. Immobilization of proteins to a carboxymethyldextran-modified gold surface for biospecific interaction analysis in surface plasmon resonance sensors. Anal. Biochem. 198: 268–277.
Karlsson O.P. and Lofas S. 2002. Flow-mediated on-surface reconstitution of G-protein coupled receptors for applications in surface plasmon resonance biosensors. Anal. Biochem. 300: 132–138.
Kikuchi J., Furukawa Y. and Hayashi N. 2003. Identification of novel p53-binding proteins by biomolecular interaction analysis combined with tandem mass spectrometry. Mol. Biotechnol. 23: 203–212.
Koyanagi Y., Miles S., Mitsuyasu R.T., Merrill J.E., Vinters H.V., and Chen I.S.Y. 1987. Dual infection of the central nervous system by AIDS viruses with distinct cellular tropisms. Science 236: 819–822.
Krone J.R., Nelson R.W., Dogruel D., Williams P., and Granzow R. 1996. Interfacing mass spectrometric immunoassays with BIA. BIA J. 3: 16–17.
Krone J.R., Nelson R.W., Dogruel D., Williams P., and Granzow R. 1997. BIA/MS: Interfacing biomolecular interaction analysis with mass spectrometry. Anal. Biochem. 244: 124–132.
Kwong P.D., Doyle M.L., Casper D.J., Cicala C., Leavitt S.A., Majeed S., Steenbeke T.D., Venturi M., Chaiken I., Fung M. et al. 2002. HIV-1 evades antibody-mediated neutralization through conformational masking of receptor-binding sites. Nature 420: 678–682.
Lopez F., Pichereaux C., Burlet-Schiltz O., Pradayrol L., Monsarrat B., and Esteve J.P. 2003. Improved sensitivity of biomolecular interaction analysis mass spectrometry for the identification of interacting molecules. Proteomics 3: 402–412.
Lovejoy B., Choe S., Cascio D., McRorie D.K., DeGrado W.F., and Eisenberg D. 1993. Crystal structure of a synthetic triple-stranded alpha-helical bundle. Science 259: 1288–1293.
Mirzabekov T., Bannert N., Farzan M., Hofmann W., Kolchinsky P., Wu L., Wyatt R., and Sodroski J. 1999. Enhanced expression, native purification, and characterization of CCR5, a principal HIV-1 coreceptor. J. Biol. Chem. 274: 28745–28750.
Morton T., Li J., Cook R., and Chaiken I. 1995. Mutagenesis in the C-terminal region of human interleukin 5 reveals a central patch for receptor alpha chain recognition. Proc. Natl. Acad. Sci. 92: 10879–10883.
Myszka D.G. 1999. Improving biosensor analysis J. Mol. Recognit. 12: 279–284.
Myszka D.G., Sweet R.W., Hensley P., Brigham-Burke M., Kwong P.D., Hendrickson W.A., Wyatt R., Sodroski J., and Doyle M.L. 2000. Energetics of the HIV gp120-CD4 binding reaction. Proc. Natl. Acad. Sci. 97: 9026–9031.
Natsume T., Taoka M., Manki H., Kume S., Isobe T., and Mikoshiba K. 2002. Rapid analysis of protein interactions: On-chip micropurification of recombinant protein expressed in Escherichia coli. Proteomics 2: 1247–1253.
Nedelkov D. and Nelson R.W. 2000. Exploring the limit of detection in biomolecular interaction analysis mass spectrometry (BIA/MS): Detection of attomole amounts of native proteins present in complex biological mixtures. Anal. Chim. Acta. 423: 1–7.
Nedelkov D. and Nelson R.W. 2001a. Analysis of human urine protein biomarkers via biomolecular interaction analysis mass spectrometry. Am. J. Kidney Dis. 38: 481–487.
Nedelkov D. and Nelson R.W. 2001b. Delineation of in vivo assembled multiprotein complexes via biomolecular interaction analysis mass spectrometry. Proteomics 1: 1441–1446.
Nedelkov D. and Nelson R.W. 2003a. Delineating protein-protein interactions via biomolecular interaction analysis-mass spectrometry. J. Mol. Recognit. 16: 9–14.
Nedelkov D. and Nelson R.W. 2003b. Design and use of multi-affinity surfaces in biomolecular interaction analysis-mass spectrometry (BIA/MS): A step toward the design of SPR/MS arrays. J. Mol. Recognit. 16: 15–19.
Nedelkov D. and Nelson R.W. 2003c. Detection of Staphylococcal enterotoxin B via biomolecular interaction analysis mass spectrometry. Appl. Environ. Microbiol. 69: 5212–5215.
Nedelkov D., Rasooly A., and Nelson R.W. 2000. Multitoxin biosensor-mass spectrometry analysis: A new approach for rapid, real-time, sensitive analysis of Staphylococcal toxins in food. Int. J. Food Microbiol. 60: 1–13.
Nedelkov D., Nelson R.W., Kiernan U.A., Niederkofler E.E., and Tubbs K.A. 2003. Detection of bound and free IGF-1 and IGF-2 in human plasma via biomolecular interaction analysis mass spectrometry. FEBS Lett. 536: 130–134.
Nelson R.W., Krone J.R., and Jansson O. 1997a. Surface plasmon resonance biomolecular interaction analysis mass spectrometry. 1. Chip-based analysis. Anal. Chem. 69: 4363–4368.
Nelson R.W., Jarvik J.W., Taillon B.E., and Tubbs K.A. 1999. BIA/MS of epitope-tagged peptides directly from E. coli lysate: Multiplex detection and protein identification at low-femtomole to subfemtomole levels. Anal. Chem. 71: 2858–2865.
Nelson R.W., Krone J.R., Dogruel D., Tubbs K.A., Granzow R., and Jansson O. 1997b. Interfacing biomolecular interaction with mass spectrometry and the use of bioreactive mass spectrometer probe tips in protein characterization. In Techniques in protein chemistry VIII (ed. D. Marshak), pp. 493–504. Academic Press, San Diego, California.
Nollert P., Kiefer H., and Jahnig F. 1995. Lipid vesicle adsorption versus formation of planar bilayers on solid surfaces. Biophys. J. 69: 1447–1455.
Oas T.G., McIntosh L.P., O'Shea E.K., Dahlquist F.W., and Kim P.S. 1990. Secondary structure of a leucine zipper determined by nuclear magnetic resonance spectroscopy. Biochemistry 29: 2891–2894.
O'Shannessy D.J., Brigham-Burke M., and Peck K. 1992. Immobilization chemistries suitable for use in the BIAcore surface plasmon resonance detector. Anal. Biochem. 205: 132–136.
O'Shea E.K., Klemm J.D., Kim P.S., and Alber T. 1991. X-ray structure of the GCN4 leucine zipper, a two-stranded, parallel coiled coil. Science 254: 539.
Palczewski K., Kumasaka T., Hori T., Behnke C.A., Motoshima H., Fox B.A., Le-Trong I., Teller D.C., Okada T., Stenkamp R.E., Yamamoto M., and Miyano M. 2000. Crystal structure of rhodopsin: A G protein-coupled receptor. Science 289: 739–745.
Sattentau Q.J. and Moore J.P. 1991. Conformational changes induced in the human immunodeficiency virus envelope glycoprotein by soluble CD4 binding. J. Exp. Med. 174: 407–415.
Sattentau Q.J., Moore J.P., Vignaux F., Traincard F., and Poignard P. 1993. Conformational changes induced in the envelope glycoproteins of the human and simian immunodeficiency viruses by soluble receptor binding. J. Virol. 67: 7383–7393.
Scibek J.J., Evergren E., Zahn S., Canziani G.A., Van Ryk D., and Chaiken I.M. 2002. Biosensor analysis of dynamics of interleukin 5 receptor subunit βc interaction with IL5:IL5Rα complexes. Anal. Biochem. 307: 258–265.
Sergi M., Zurawski J., Cocklin S., and Chaiken I. 2004. Proteins, recognition networks and developing interfaces for macromolecular biosensing. J. Mol. Recognit. 17: 198–208.
Si Z., Madani N., Cox J.M., Chruma J.J., Klein J.C., Schon A., Phan N., Wang L., Biorn A.C., Cocklin S., Chaiken I., Freire E., Smith A.B., III, and Sodroski J.G. 2004. Small-molecule inhibitors of HIV-1 entry block receptor-induced conformational changes in the viral envelope glycoproteins Proc. Natl. Acad. Sci. 101: 5036–5041.
Sonksen C.P., Nordhoff E., Jansson O., Malmqvist M., and Roepstorff P. 1998. Combining MALDI mass spectrometry and biomolecular interaction analysis using a biomolecular interaction analysis instrument. Anal. Chem. 70: 2731–2736.
Sonksen C.P., Roepstorff P., Markgren P.O., Danielson U.H., Hamalainen M.D., and Jansson O. 2001. Capture and analysis of low molecular weight ligands by surface plasmon resonance combined with mass spectrometry. Eur. J. Mass Spectrom. 7: 385–391.
Stenlund P., Babcock G.J., Sodroski J., and Myszka D.G. 2003. Capture and reconstitution of G protein-coupled receptors on a biosensor surface. Anal. Biochem. 316: 243–250.
Thali M., Moore J.P., Furman C., Charles M., Ho D.D., Robinson J., and Sodroski J. 1993. Characterization of conserved human immunodeficiency virus type 1 gp120 neutralization epitopes exposed upon gp120-CD4 binding. J. Virol. 67: 3978–3988.
Trkola A., Dragic T., Arthos J., Binley J.M., Olson W.C., Allaway G.P., Cheng-Mayer C., Robinson J., Maddon P.J., and Moore J.P. 1996. CD4-dependent, antibody-sensitive interactions between HIV-1 and its coreceptor CCR5. Nature 384: 184–187.
Wilchek M. and Miron T. 2003. Oriented versus random protein immobilization. J. Biochem. Biophys. Methods 55: 67–70.
Vita C., Drakopoulou E., Vizzanova J., Rochette S., Martru L., Menez A., Roumestand C., Yarg Y.S., Ylisastigui L., Benjinad A., and Gluchman J.C. 1999. Rational engineering of a miniprotein that reproduces the core of the CD4 site interacting with HIV-1 envelope glycoprotein. Proc. Natl. Acad. Sci. 96: 13091–13096.
Wu L., Gerard N.P., Wyatt R., Choe H, Parolin C., Ruffing N., Borsetti A., Cardoso A.A., Desjardin E., Newman W., Gerard C., and Sodroski J. 1996. CD4-induced interaction of primary HIV-1 gp120 glycoproteins with the chemokine receptor CCR-5. Nature 384: 179–183.
Wu S.-J. and Chaiken I. 2003. Biosensor analysis of receptor-ligand interactions. Methods Mol. Biol. 249: 93–110.
Xiang S.H., Kwong P.D., Gupta R., Rizzuto C.D., Casper D.J., Wyatt R., Wang L., Hendrickson W.A., Doyle M.L., and Sodroski J. 2002. Mutagenic stabilization and/or disruption of a CD4-bound state reveals distinct conformations of the human immunodeficiency virus type 1 gp120 envelope glycoprotein. J. Virol. 76: 9888–9899.
Zhang W., Canziani G., Plugariu C., Wyatt R., Sodroski J., Sweet R., Kwong P., Hendrickson W., and Chaiken I. 1999. Conformational changes of gp120 in epitopes near the CCR5 binding site are induced by CD4 and a CD4 miniprotein mimetic. Biochemistry 38: 9405–9416.
Zhukov A., Suckau D., and Buijs J. 2002. From isolation to identification: Using surface plasmon resonance-mass spectrometry in proteomics. PharmaGenomics March/April, 18–28.
Zimmerman M.A., Selzman C.H., Cothren C., Sorensen A.C., Raeburn C.D., and Harken A.H. 2003. Diagnostic implications of C-reactive protein. Arch. Surgery 138: 220–224.
<<< Chapter 19 References
Chapter 21 References >>>
|
