Virtual Interaction Profiles of Proteins

Journal of Molecular Biology

Volumn 313, Issue 2, 2001, Pages 317-342

  Wollacott, Andrew M ^a   Desjarlais, John R ^a  

^a PENNSYLVANIA STATE UNIVERSITY   (United States)

Author keywords

Mdm2; PDZ; Peptide binding; Protein design; SH3

Indexed keywords

ABELSON KINASE; CALMODULIN DEPENDENT SERINE KINASE; CALMODULIN-DEPENDENT SERINE KINASE; CARRIER PROTEIN; FYN PROTEIN, HUMAN; FYN PROTEIN, MOUSE; HOMER PROTEIN; MDM2 PROTEIN, HUMAN; MDM2 PROTEIN, MOUSE; NERVE PROTEIN; NEUROPEPTIDE; NUCLEAR PROTEIN; NUCLEOSIDE MONOPHOSPHATE KINASE; ONCOPROTEIN; POSTSYNAPTIC DENSITY PROTEINS; PROTEIN; PROTEIN KINASE (CALCIUM,CALMODULIN); PROTEIN KINASE FYN; PROTEIN MDM2;

ALGORITHM; AMINO ACID SEQUENCE; ANIMAL; ARTICLE; BIOLOGY; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; ENZYME SPECIFICITY; HUMAN; METABOLISM; METHODOLOGY; MOLECULAR GENETICS; MOUSE; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN DATABASE; PROTEIN MOTIF; PROTEIN TERTIARY STRUCTURE; SENSITIVITY AND SPECIFICITY; SRC HOMOLOGY DOMAIN; STRUCTURE ACTIVITY RELATION; THERMODYNAMICS;

ALGORITHMS; AMINO ACID MOTIFS; AMINO ACID SEQUENCE; ANIMALS; CA(2+)-CALMODULIN DEPENDENT PROTEIN KINASE; CARRIER PROTEINS; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; DATABASES, PROTEIN; HUMANS; MICE; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NERVE TISSUE PROTEINS; NEUROPEPTIDES; NUCLEAR PROTEINS; NUCLEOSIDE-PHOSPHATE KINASE; PROTEIN BINDING; PROTEIN INTERACTION MAPPING; PROTEIN STRUCTURE, TERTIARY; PROTEINS; PROTO-ONCOGENE PROTEINS; PROTO-ONCOGENE PROTEINS C-ABL; PROTO-ONCOGENE PROTEINS C-FYN; PROTO-ONCOGENE PROTEINS C-MDM2; SENSITIVITY AND SPECIFICITY; SRC HOMOLOGY DOMAINS; STRUCTURE-ACTIVITY RELATIONSHIP; SUBSTRATE SPECIFICITY; THERMODYNAMICS;

EID: 0035914473     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.2001.5035     Document Type: Article

References (51)

1. van Helden J., Naim A., Mancuso R., Eldridge M., Wernisch L., Gilbert D., Wodak S. J. Representing and analysing molecular and cellular function using the computer. Biol. Chem. 381:2000;921-935.
2. Rudert F., Ge L., Ilag L. L. Functional genomics with protein-protein interactions. Biotechnol. Annu. Rev. 5:2000;45-86.
3. Eisenberg D., Marcotte E. M., Xenarios I., Yeates T. O. Protein function in the post-genomic era. Nature. 405:2000;823-826.
4. Xenarios I., Fernandez E., Salwinski L., Duan X. J., Thompson M. J., Marcotte E. M., Eisenberg D. DIP: the database of interacting proteins: 2001 update. Nucl. Acids Res. 29:2001;239-241.
5. Raha K., Wollocatt A. M., Italia M. J., Desjarlais J. R. Prediction of amino acid sequence from structure. Protein Sci. 9:2000;1106-1119.
6. Koehl P., Levitt M. De novo protein design. II. Plasticity in sequence space. J. Mol. Biol. 293:1999;1183-1193.
7. Kuhlman B., Baker D. Native protein sequences are close to optimal for their structures. Proc. Natl Acad. Sci. USA. 97:2000;10383-10388.
8. Dahiyat B. I., Mayo S. L. De novo protein design: fully automated sequence selection. Science. 278:1997;82-87.
9. Bork P., Schultz J., Ponting C. P. Cytoplasmic signalling domains: the next generation. Trends Biochem. Sci. 22:1997;296-298.
10. Sudol M. From Src homology domains to other signaling modules: proposal of the 'protein recognition code'. Oncogene. 17:1998;1469-1474.
11. Koehl P., Delarue M. Mean-field minimization methods for biological macromolecules. Curr. Opin. Struct. Biol. 6:1996;222-226.
12. Lee C. Predicting protein mutant energetics by self-consistent ensemble optimization. J. Mol. Biol. 236:1994;918-939.
13. Koehl P., Delarue M. Application of a self-consistent mean field theory to predict protein side-chains conformation and estimate their conformational entropy. J. Mol. Biol. 239:1994;249-275.
14. Koehl P., Delarue M. A self consistent mean field approach to simultaneous gap closure and side-chain positioning in homology modelling. Nature Struct. Biol. 2:1995;163-170.
15. Piette J., Neel H., Marechal V. Mdm2: keeping p53 under control. Oncogene. 15:1997;1001-1010.
16. Kussie P. H., Gorina S., Marechal V., Elenbaas B., Moreau J., Levine A. J., Pavletich N. P. Structure of the MDM2 oncoprotein bound to the p53 tumor suppressor transactivation domain. Science. 274:1996;948-953.
17. Bottger V., Bottger A., Howard S. F., Picksley S. M., Chene P., Garcia-Echeverria C. et al. Identification of novel mdm2 binding peptides by phage display. Oncogene. 13:1996;2141-2147.
18. Pawson T., Gish G. D. SH2 and SH3 domains: from structure to function. Cell. 71:1992;359-362.
19. Mayer B. J., Eck M. J. SH3 domains. Minding your p's and q's. Curr. Biol. 5:1995;364-367.
20. Dalgarno D. C., Botfield M. C., Rickles R. J. SH3 domains and drug design: ligands, structure, and biological function. Biopolymers. 43:1997;383-400.
21. Rickles R. J., Botfield M. C., Weng Z., Taylor J. A., Green O. M., Brugge J. S., Zoller M. J. Identification of Src, Fyn, Lyn, PI3 K and Abl SH3 domain ligands using phage display libraries. EMBO J. 13:1994;5598-5604.
22. Sparks A. B., Rider J. E., Hoffman N. G., Fowlkes D. M., Quilliam L. A., Kay B. K. Distinct ligand preferences of Src homology 3 domains from Src, Yes, Abl, Cortactin, p53bp2, PLCy, Crk, and Grb2. Proc. Natl Acad. Sci. USA. 93:1996;1540-1544.
23. Musacchio A., Saraste M., Wilmanns M. High-resolution crystal structures of tyrosine kinase SH3 domains complexed with proline-rich peptides. Nature Struct. Biol. 1:1994;546-551.
24. Pisabarro M. T., Serrano L., Wilmanns M. Crystal structure of the abl-SH3 domain complexed with a designed high- affinity peptide ligand: implications for SH3-ligand interactions. J. Mol. Biol. 281:1998;513-521.
25. Nguyen J. T., Turck C. W., Cohen F. E., Zuckermann R. N., Lim W. A. Exploiting the basis of proline recognition by SH3 and WW domains: design of N-substituted inhibitors. Science. 282:1998;2088-2092.
26. Ren R., Mayer B. J., Cicchetti P., Baltimore D. Identification of a ten-amino acid proline-rich SH3 binding site. Science. 259:1993;1157-1161.
27. Morais Cabral J. H., Petosa C., Sutcliffe M. J., Raza S., Byron O., Poy F. et al. Crystal structure of a PDZ domain. Nature. 382:1996;649-652.
28. Saras J., Heldin C. H. PDZ domains bind carboxy-terminal sequences of target proteins. Trends Biochem. Sci. 21:1996;455-458.
29. Fanning A. S., Anderson J. M. Protein modules as organizers of membrane structure. Curr. Opin. Cell Biol. 11:1999;432-439.
30. Songyang Z., Fanning A. S., Fu C., Xu J., Marfatia S. M., Chishti A. H. et al. Recognition of unique carboxyl-terminal motifs by distinct PDZ domains. Science. 275:1997;73-77.
31. Doyle D. A., Lee A., Lewis J., Kim E., Sheng M., MacKinnon R. Crystal structures of a complexed and peptide-free membrane protein-binding domain: molecular basis of peptide recognition by PDZ. Cell. 85:1996;1067-1076.
32. Daniels D. L., Cohen A. R., Anderson J. M., Brunger A. T. Crystal structure of the hCASK PDZ domain reveals the structural basis of class II PDZ domain target recognition. Nature Struct. Biol. 5:1998;317-325.
33. Niethammer M., Valtschanoff J. G., Kapoor T. M., Allison D. W., Weinberg T. M., Craig A. M., Sheng M. CRIPT, a novel postsynaptic protein that binds to the third PDZ domain of PSD-95/SAP90. Neuron. 20:1998;693-707.
34. Brakeman P. R., Lanahan A. A., O'Brien R., Roche K., Barnes C. A., Huganir R. L., Worley P. F. Homer: a protein that selectively binds metabotropic glutamate receptors. Nature. 386:1997;284-288.
35. Tu J. C., Xiao B., Yuan J. P., Lanahan A. A., Leoffert K., Li M. et al. Homer binds a novel proline-rich motif and links group 1 metabotropic glutamate receptors with IP3 receptors. Neuron. 21:1998;717-726.
36. Beneken J., Tu J. C., Xiao B., Nuriya M., Yuan J. P., Worley P. F., Leahy D. J. Structure of the Homer EVH1 domain-peptide complex reveals a new twist in polyproline recognition. Neuron. 26:2000;143-154.
37. Niebuhr ?. Title. Sertitle. 00:1997;000-000.
38. Buckbinder L., Velasco-Miguel S., Chen Y., Xu N., Talbott R., Gelbert L. et al. The p53 tumor suppressor targets a novel regulator of G protein signaling. Proc. Natl Acad. Sci. USA. 94:1997;7868-7872.
39. Snow B. E., Hall R. A., Krumins A. M., Brothers G. M., Bouchard D., Brothers C. A. et al. GTPase activating specificity of RGS12 and binding specificity of an alternatively spliced PDZ (PSD-95/Dlg/ZO-1) domain. J. Biol. Chem. 273:1998;17749-17755.
40. Itoh M., Furuse M., Morita K., Kubota K., Saitou M., Tsukita S. Direct binding of three tight junction-associated MAGUKs, ZO-1, ZO-2, and ZO-3, with the COOH termini of claudins. J. Cell Biol. 147:1999;1351-1363.
41. Ebnet K., Schulz C. U., Meyer Zu, Brickwedde M. K., Pendl G. G., Vestweber D. Junctional adhesion molecule interacts with the PDZ domain-containing proteins AF-6 and ZO-1. J. Biol. Chem. 275:2000;27979-27988.
42. Kreienkamp H., Zitzer H., Richter D. Identification of proteins interacting with the rat somatostatin receptor subtype 2. J. Physiol. Paris. 94:2000;193-198.
43. Bockaert J., Pin J. P. Molecular tinkering of G protein-coupled receptors: an evolutionary success. EMBO J. 18:1999;1723-1729.
44. Brannetti B., Via A., Cestra G., Cesareni G., Citterich M. H. SH3-SPOT: an algorithm to predict preferred ligands to different members of the SH3 gene family. J. Mol. Biol. 298:2000;313-328.
45. Marcotte E. M., Pellegrini M., Ng H. L., Rice D. W., Yeates T. O., Eisenberg D. Detecting protein function and protein-protein interactions from genome sequences. Science. 285:1999;751-753.
46. Marcotte E. M., Xenarios I., Eisenberg D. Mining literature for protein-protein interactions. Bioinformatics. 17:2001;359-363.
47. Yaffe M. B., Leparc G. G., Lai J., Obata T., Volinia S., Cantley L. C. A motif-based profile scanning approach for genome-wide prediction of signaling pathways. Nature Biotechnol. 19:2001;348-353.
48. Creamer T. P. Side-chain conformational entropy in protein unfolded states. Proteins: Struct. Funct. Genet. 40:2000;443-450.
49. Bairoch A., Apweiler R. The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucl. Acids Res. 28:2000;45-48.
50. Kraulis P. J. MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallog. 24:1991;946-950.
51. Merrit E. A., Bacon D. J. Raster3D: photorealistic molecular graphics. Methods Enzymol. 277:1997;505-524.