In vitro selection and prediction of TIP47 protein-interaction interfaces

Nature Methods

Volumn 1, Issue 1, 2004, Pages 55-60

  Burguete, Alondra Schweizer ^a   Harbury, Pehr B ^a   Pfeffer, Suzanne R ^a  

^a STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CYSTEINE; DNA BINDING PROTEIN; M6PRBP1 PROTEIN, HUMAN; PLACENTA PROTEIN; RECOMBINANT PROTEIN; SIGNAL PEPTIDE;

AMINO ACID SUBSTITUTION; ARTICLE; BINDING SITE; CHEMISTRY; ESCHERICHIA COLI; EVALUATION; GENETICS; HUMAN; METABOLISM; METHODOLOGY; MOLECULAR CLONING; PROTEIN ANALYSIS; PROTEIN BINDING; SITE DIRECTED MUTAGENESIS;

AMINO ACID SUBSTITUTION; BINDING SITES; CLONING, MOLECULAR; CYSTEINE; DNA-BINDING PROTEINS; ESCHERICHIA COLI; HUMANS; INTRACELLULAR SIGNALING PEPTIDES AND PROTEINS; MUTAGENESIS, SITE-DIRECTED; PREGNANCY PROTEINS; PROTEIN BINDING; PROTEIN INTERACTION MAPPING; RECOMBINANT PROTEINS;

EID: 18744380695     PISSN: 15487091     EISSN: 15487105     Source Type: Journal    
DOI: 10.1038/nmeth702     Document Type: Article

References (15)

1. Silverman, J.A. & Harbury, P.B. Rapid mapping of protein structure, interactions, and ligand binding by misincorporation proton-alkyl exchange. J. Biol. Chem. 277, 30968-30975 (2002).
2. Diaz, E. & Pfeffer, S.R. TIP47: A cargo selection device for mannose 6-phosphate receptor trafficking. Cell 93, 433-443 (1998).
3. Krise, J.P., Sincock, P.M., Orsel, J.G. & Pfeffer, S.R. Quantitative analysis of TIP47-receptor cytoplasmic domain interactions: Implications for endosome-to-trans Golgi network trafficking. J. Biol. Chem. 275, 25188-25193 (2000).
4. Orsel, J.G., Sincock, P.M., Krise, J.P. & Pfeffer, S.R. Recognition of the 300-kDa mannose 6-phosphate receptor cytoplasmic domain by 47-kDa tail-interacting protein. Proc. Natl. Acad. Sci. USA 97, 9047-9051 (2000).
5. Carroll, K.S. et al. Role of Rab9 GTPase in facilitating receptor recruitment by TIP47. Science 292, 1373-1377 (2001).
6. Hanna, J., Carroll, K. & Pfeffer, S.R. Identification of residues in TIP47 essential for Rab9 binding. Proc. Natl. Acad. Sci. USA 99, 7450-7454 (2002).
7. Hickenbottom, S.J., Kimmel, A.R., Londos, C. & Hurley, J.H. Structure of a Lipid-droplet protein: The PAT family member TIP47. Structure 12, 1199-1207 (2004).
8. Jacobson, G.R., Schaffer, M.H., Stark, G.R. & Vanaman, T.C. Specific chemical cleavage in high yield at the amino peptide bonds of cysteine and cystine residues. J. Biol. Chem. 248, 6583-6591 (1973).
9. Wu, J. & Watson, J.T. Optimization of the cleavage reaction for cyanylated cysteinyl proteins for efficient and simplified mass mapping. Anal. Biochem. 258, 268-276 (1998).
10. Janin, J. Surface and inside volumes in globular proteins. Nature 277, 491-492 (1979).
11. Rost, B. Ph.D.: Predicting one-dimensional protein structure by profile based neural networks. Methods Enzymol. 266, 525-539 (1996).
12. Lo Conte, L., Chothia, C. & Janin, J. The atomic structure of protein-protein recognition sites. J. Mol. Biol. 285, 2177-2198 (1999).
13. Stemmer, W.P., Crameri, A., Ha, K.D., Brennan, T.M. & Heyneker, H.L. Single-step assembly of a gene and entire plasmid from large numbers of oligodeoxy- ribonucleotides. Gene 164, 49-53 (1995).
14. Janin, J. & Wodak, S. Conformation of amino acid side-chains in proteins. J. Mol. Biol. 125, 357-386 (1978).
15. Fraczkiewicz, R. & Braun, W. Exact and efficient analytical calculation of the accessible surface areas and their gradients for macromolecules. J. Comp. Chem. 19, 319-333 (1998).