Modeling and analysis of molecular interaction between Smurf1-WW2 domain and various isoforms of LIM mineralization protein

Proteins: Structure, Function and Genetics

Volumn 68, Issue 3, 2007, Pages 690-701

  Sangadala, Sreedhara ^a,c   Boden, Scott D ^a   Metpally, Raghu Prasad Rao ^b   Reddy, Boojala Vijay B ^b  

^a EMORY UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b CITY UNIVERSITY OF NEW YORK   (United States)

^c ATLANTA VA MEDICAL CENTER   (United States)

Author keywords

Bone morphogenetic proteins; E3 ligase; Homology modeling; LMP; Osteoinduction; Protein protein interaction; Smurf1; WW domain

Indexed keywords

PROTEASOME; PROTEIN; PROTEIN LMP 1; PROTEIN SMURF1; RECOMBINANT PROTEIN; SMAD1 PROTEIN; SMAD5 PROTEIN; UBIQUITIN; UNCLASSIFIED DRUG; COMPLEMENTARY DNA; ISOPROTEIN; LIGAND; PDLIM7 PROTEIN, HUMAN; PRIMER DNA; SIGNAL PEPTIDE; SMURF1 PROTEIN, HUMAN; UBIQUITIN PROTEIN LIGASE;

ARTICLE; MOLECULAR INTERACTION; PREDICTION; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN DOMAIN; PROTEIN INTERACTION; PROTEIN MOTIF; SITE DIRECTED MUTAGENESIS; AMINO ACID SEQUENCE; BINDING SITE; CHEMISTRY; GENE VECTOR; GENETICS; ISOLATION AND PURIFICATION; METABOLISM; MOLECULAR CLONING; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; POLYACRYLAMIDE GEL ELECTROPHORESIS; SEQUENCE HOMOLOGY; WESTERN BLOTTING;

AMINO ACID SEQUENCE; BASE SEQUENCE; BINDING SITES; BLOTTING, WESTERN; CLONING, MOLECULAR; DNA PRIMERS; DNA, COMPLEMENTARY; ELECTROPHORESIS, POLYACRYLAMIDE GEL; GENETIC VECTORS; INTRACELLULAR SIGNALING PEPTIDES AND PROTEINS; LIGANDS; MOLECULAR SEQUENCE DATA; MUTAGENESIS, SITE-DIRECTED; PROTEIN BINDING; PROTEIN ISOFORMS; SEQUENCE HOMOLOGY, AMINO ACID; UBIQUITIN; UBIQUITIN-PROTEIN LIGASES;

EID: 34447519208     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.21429     Document Type: Article

References (35)

1. Boden SD, Liu Y, Hair GA, Helms JA, Hu D, Racine M, Nanes MS, Titus L. LMP-1, a LIM-domain protein, mediates BMP-6 effects on bone formation. Endocrinology 1998;139:5125-5134.
2. Boden SD, Titus L, Hair G, Liu Y, Viggeswarapu M, Nanes MS, Baranowski C. Lumbar spine fusion by local gene therapy with a cDNA encoding a novel osteoinductive protein (LMP-1). Spine 1998;23:2486-2492.
3. Liu Y, Hair GA, Boden SD, Viggeswarapu M, Titus L. Overexpressed LIM mineralization proteins do not require LIM domains to induce bone. J Bone Miner Res 2002;17:406-414.
4. Sangadala S, Boden SD, Viggeswarapu M, Liu Y, Titus L. LIM mineralization protein-1 potentiates bone morphogenetic protein responsiveness via a novel interaction with Smurf1 resulting in decreased ubiquitination of Smads. J Biol Chem 2006;281:17212-17219.
5. Shi W, Chen H, Sun J, Chen C, Zhao J, Wang YL, Anderson KD, Warburton D. Overexpression of Smurf1 negatively regulates mouse embryonic lung branching morphogenesis by specifically reducing Smad1 and Smad5 proteins. Am J Physiol Lung Cell Mol Physiol 2004;286:L293-L300.
6. Zhao M, Qiao M, Harris SE, Oyajobi BO, Mundy GR, Chen D. Smurfl inhibits osteoblast differentiation and bone formation in vitro and in vivo. J Biol Chem 2004;279:12854-12859.
7. Zhao M, Qiao M, Oyajobi BO, Mundy GR, Chen D. E3 ubiquitin ligase Smurf1 mediates core-binding factor alpha1/Runx2 degradation and plays a specific role in osteoblast differentiation. J Biol Chem 2003;278:27939-27944.
8. Ying SX, Hussain ZJ, Zhang YE. Smurf1 facilitates myogenic differentiation and antagonizes the bone morphogenetic protein-2-induced osteoblast conversion by targeting Smad5 for degradation. J Biol Chem 2003;278:39029-39036.
9. Brannetti B, Helmer-Citterich M. iSPOT: A web tool to infer the interaction specificity of families of protein modules. Nucleic Acids Res 2003;31:3709-3711.
10. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997;25:3389-3402.
11. Schaffer AA, Aravind L, Madden TL, Shavirin S, Spouge JL, Wolf YI, Koonin EV, Altschul SF. Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. Nucleic Acids Res 2001;29:2994-3005.
12. Sali A, Blundell TL. Comparative protein modeling by satisfaction of spatial restraints. J Mol Biol 1993;234:779-815.
13. Fiser A, Sali A. Modeller: generation and refinement of homology-based protein structure models. Methods Enzymol 2003;374:461-491.
14. Laskowski RA, MacArthur MW, Moss DS, Thornton JM. PRO-CHECK: a program to check the stereochemical quality of protein structures. J Appl Cryst 1993;26:283-291.
15. Guex N, Peitsch MC. SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling. Electrophoresis 1997; 18:2714-2723.
16. Schwede T, Kopp J, Guex N, Peitsch MC. SWISS-MODEL: an automated protein homology-modeling server. Nucleic Acids Res 2003;31: 3381-3385.
17. Sasin JM, Bujnicki JM. COLORADO3D, a web server for the visual analysis of protein structures. Nucleic Acids Res 2004;32:W586-W589 (Web Server issue).
18. Eisenberg D, Luthy R, Bowie JU. VERIFY3D: assessment of protein models with three-dimensional profiles. Methods Enzymol 1997;277: 396-404.
19. Sippl MJ. Recognition of errors in three-dimensional structures of proteins. Proteins 1993;17:355-362.
20. Melo F, Devos D, Depiereux E, Feytmans E. ANOLEA: a www server to assess protein structures. Proc Int Conf Intell Syst Mol Biol 1997;5:187-190.
21. Pontius J, Richelle J, Wodak SJ. Deviations from standard atomic volumes as a quality measure for protein crystal structures. J Mol Biol 1996;264:121-136.
22. Sayle RA, Milner-White EJ. RASMOL: biomolecular graphics for all. Trends Biochem Sci 1995;20:374.
23. Verkhivker GM, Bouzida D, Gehlhaar DK, Rejto PA, Arthurs S, Colson AB, Freer ST, Larson V, Luty BA, Marrone T, Rose PW. Deciphering common failures in molecular docking of ligand-protein complexes. J Comput Aided Mol Des 2000;14:731-751.
24. Muegge I, Martin YC. A general and fast scoring function for protein-ligand interactions: a simplified potential approach. J Med Chem 1999;42:791-804.
25. Reddy BVB, Kaznessis Y. A quantitative analysis of amino acid position conservation in interface regions of protein-protein heterocomplexes. J Bioinformatics and Computational Biol 2005;3:1137-1150.
26. Otte L, Wiedemann U, Schlegel B, Pires JR, Beyermann M, Schmieder P, Krause G, Volkmer-Engert R, Schneider-Mergener J, Oschkinat H. WW domain sequence activity relationships identified using ligand recognition propensities of 42 WW domains. Protein Sci 2003;12:491-500.
27. Boden SD, Schimandle JH, Hutton WC. 1995 Volvo Award in basic sciences. The use of an osteoinductive growth factor for lumbar spinal fusion, Part 2: Study of dose, carrier, and species. Spine 1995; 20:2633-2644.
28. Kusumoto K, Bessho K, Fujimura K, Akioka J, Okubo Y, Wang Y, Iizuka T, Ogawa Y. Osteoinduction by recombinant human bone morphogenetic protein-2 in muscles of non-human primates. J Int Med Res 2002;30:251-259.
29. Wang G, Yang J, Huibregtse JM. Functional domains of the Rsp5 ubiquitin-protein ligase. Mol Cell Biol 1999;19:342-352.
30. Bedford MT, Reed R, Leder P. WW domain-mediated interactions reveal a spliceosome-associated protein that binds a third class of proline-rich motif: the proline glycine and methionine-rich motif. Proc Natl Acad Sci USA 1998;95:10602-10607.
31. Yagi R, Chen LF, Shigesada K, Murakami Y, Ito Y. A WW domain-containing yes-associated protein (YAP) is a novel transcriptional co-activator. EMBO J 1999;18:2551-2562.
32. Shen M, Stukenberg PT, Kirschner MW, Lu KP. The essential mitotic peptidyl-prolyl isomerase Pin1 binds and regulates mitosis-specific phosphoproteins. Genes Dev 1998;12:706-720.
33. Yaffe MB, Schutkowski M, Shen M, Zhou XZ, Stukenberg PT, Rahfeld JU, Xu J, Kuang J, Kirschner MW, Fischer G, Cantley LC, Lu KP. Sequence-specific and phosphorylation-dependent proline isomerization: a potential mitotic regulatory mechanism. Science 1997;278: 1957-1960.
34. Garrett IR, Chen D, Gutierrez G, Zhao M, Escobedo A, Rossini G, Harris SE, Gallwitz W, Kim KB, Hu S, Crews CM, Mundy GR. Selective inhibitors of the osteoblast proteasome stimulate bone formation in vivo and in vitro. J Clin Invest 2003;111:1771-1782.
35. Liu Z, Shi W, Ji X, Sun C, Jee WS, Wu Y, Mao Z, Nagy TR, Li Q, Cao X. Molecules mimicking Smad1 interacting with Hox stimulate bone formation. J Biol Chem 2004;279:11313-11319.