Homology modeling and molecular dynamics study of GSK3/SHAGGY-like kinase

Computational Biology and Chemistry

Volumn 28, Issue 3, 2004, Pages 179-188

  Xiao, Jing Fa ^a   Li, Ze Sheng ^a   Sun, Miao ^a   Zhang, Yuan ^a   Sun, Chia Chung ^a  

^a JILIN UNIVERSITY   (China)

Author keywords

ATP; Docking; GSK3 SHAGGY like kinase; Homology modeling; Molecular dynamics

Indexed keywords

ADENOSINETRIPHOSPHATE; COMPUTER SIMULATION; CONFORMATIONS; ENZYMES; FUNCTIONS; SIGNAL THEORY; X RAY DIFFRACTION;

GSK3/SHAGGY-LIKE KINASE; HOMOLOGY MODELING; MOLECULAR INTERACTIONS; SIGNALING PATHWAYS;

MOLECULAR DYNAMICS;

EUKARYOTA;

ADENOSINE TRIPHOSPHATE; AMINO ACID; CDK2 PROTEIN, HUMAN; CYCLIN DEPENDENT KINASE; CYCLIN DEPENDENT KINASE 2; GLYCOGEN SYNTHASE KINASE 3; GLYCOGEN SYNTHASE KINASE 3 BETA; VEGETABLE PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; BINDING SITE; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; ELECTRICITY; GENETICS; HUMAN; HYDROGEN BOND; HYDROPHOBICITY; METABOLISM; MOLECULAR GENETICS; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN SECONDARY STRUCTURE; PROTEIN TERTIARY STRUCTURE; SEQUENCE HOMOLOGY; STRUCTURAL HOMOLOGY; SURFACE PROPERTY; THERMODYNAMICS;

ADENOSINE TRIPHOSPHATE; AMINO ACID SEQUENCE; AMINO ACIDS; BINDING SITES; CDC2-CDC28 KINASES; COMPUTER SIMULATION; CYCLIN-DEPENDENT KINASE 2; ELECTROSTATICS; GLYCOGEN SYNTHASE KINASE 3; HUMANS; HYDROGEN BONDING; HYDROPHOBICITY; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PLANT PROTEINS; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; SEQUENCE HOMOLOGY, AMINO ACID; STRUCTURAL HOMOLOGY, PROTEIN; SURFACE PROPERTIES; THERMODYNAMICS;

EID: 3142537294     PISSN: 14769271     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.compbiolchem.2004.02.003     Document Type: Article

References (23)

1. Bourne Y., Watson M.H., Hickey M.J., Holmes W., Rocque W., Reed S.I., Tainer J.A. Crystal structure and mutational analysis of the human CDK2 kinase complex with cell cycle-regulatory protein CksHsl. Cell. 84:1996;863-874.
2. Cavalli A., Dezi C., Folkers G., Scapozza L., Recanatini M. Three-dimensional model of the cyclin-dependent kinase 1 (CDK1): ab initio active site parameters for molecular dynamics studies of CDKs. Proteins. 45:2001;478-485.
3. Clouse S.D., Sasse J.M. Brassinosteroids: essential regulators of plant growth and development. Annu. Rev. Plant Mol. Biol. Plant Physiol. 49:1998;427-451.
4. Dauber-Osguthorpe P., Roberts V.A., Osguthorpe D.J., Wolff J., Genest M., Hagler A.T. Structure and energetics of ligand binding to protein: E. coli dihydreofolate reductase-trimethoprim, a drug-receptor system. Proteins. 4:1988;31-47.
5. Denessiouk K.A., Johnson M.S. When fold is not important: a common structural framework for adenine and AMP binding in 12 unrelated protein families. Proteins. 38:2000;310-326.
6. Denessiouk K.A., Rantanen V.V., Johnson M.S. Adenine recognition: a motif present in ATP-, CoA-, NAD-, NADP-, and FAD-dependent proteins. Proteins. 44:2001;282-291.
7. Dornelas M.C., van Lammeren A.A., Kreis M. Arabidopsis thaliana SHAGGY-related protein kinase (AtSK11 and 12) function in perianth and gynoecium development. Plant J. 21:2000;419-429.
8. Eisenhaber F., Persson B., Argos P. Protein structure prediction: recognition of primary, secondary, and tertiary structural features from amino acid sequence. Crit. Rev. Biochem. Mol. Biol. 30:1995;1-94.
9. Jonak C., Beisteiner D., Beyerly J., Hirt H. Wound-induced expression and activation of WIG, a novel Glycogen synthase kinase 3. Plant Cell. 12:2000;1467-1475.
10. Kabsch W., Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen bonded and geometrical features. Biopolymers. 22:1983;2577-2637.
11. Lai, L.H., 1993. Protein Structural Prediction and Molecular Design. Beijing University Press, pp. 1-15.
12. Li J.M., Nam K.H. Regulation of brassinosteroid signaling by a GSK3/SHAGGY-like kinase. Science. 295:2002;1299-1301.
13. Luthy R., Bowie J.U., Eisenberg D. Assessment of protein models with three-dimensional profiles. Nature. 356:1992;83-85.
14. Murray, R.K., Granner, D.K., Mayes, P.A., Rodwell, V.W., 2000. Harper's Biochemistry, 25th ed. McGraw-Hill, p. 119.
15. Piao H.L., Pih K.T., Lim J.H., Kang S.G., Jin J.B., Kim S.H., Hwang I. An arabidopsis GSK3/SHAGGY-like gene that complements yeast salt stress-sensitive mutants is induced by NaCl and abscisic acid. Plant Physiol. 119:1999;1527-1534.
16. Pierce S.B., Kimelman D. Regulation of Spemann organizer formation by the intracellular kinase Xgsk-3. Development. 121:1995;755-765.
17. Russo A.A., Jeffrey P.D., Patten A.K., Massague J., Pavletich N.P. Crystal structure of the p27Kip1 cyclin-dependent-kinase inhibitor bound to the cyclin A-Cdk2 complex. Nature. 382:1996;325-331.
18. Schulz G.E., Schirmer R.H. Topological comparision of adenylate kinase with other proteins. Nature. 250:1974;142-144.
19. Schulz G.E., Schiltz E., Tomasselli A.G., Frank R., Brune M., Witting-hofer A., Schirmer R.H. Structural relationships in the adenylate kinase family. Eur. J. Biochem. 161:1986;127-132.
20. Siegfried E., Perkins L.A., Capaci T.M., Perrimon N. Putative protein kinase product of the Drosophila segment-polarity gene zeste-white 3. Nature. 345:1990;825-829.
21. Ter Haar E., Coll J.T., Austen D.A., Hsiao H.M., Swenson L., Jain J. Structure of Gsk3 beta reveals a primed phosphorylation mechanism. Nat. Struct. Biol. 8:2001;593-596.
22. Woodgett J.R. Molecular cloning and expression of Glycogen synthasekinase-3/factor A. EMBO J. 9:1990;2431-2438.
23. Vonrhein C., Schlauderer G.J., Schulz G.E. Movie of the structural changes during a catalytic cycle of nucleoside monophosphate kinase. Structure. 3:1995;483-490.