Homology modeling and functional analysis of LPG2 protein of leishmania strains

Journal of Proteomics and Bioinformatics

Volumn 2, Issue 1, 2009, Pages 032-050

  Sahoo, Ganesh Chandra ^a   Dikhit, Manas Ranjan ^a   Rani, Mukta ^a   Das, Pradeep ^a  

^a RAJENDRA MEMORIAL RESEARCH INSTITUTE OF MEDICAL SCIENCES   (India)

Author keywords

Comparative (homology) modeling; Leishmaniasis; Ligand binding sites (LBSs); LPG2 protein; Phyre (protein homology analogy recognition engine); SVM (support vector machine)

Indexed keywords

LEISHMANIA BRAZILIENSIS; LEISHMANIA DONOVANI; LEISHMANIA INFANTUM; LEISHMANIA MAJOR; LEISHMANIA MEXICANA; MAMMALIA;

EID: 75649139534     PISSN: None     EISSN: 0974276X     Source Type: Journal    
DOI: 10.4172/jpb.1000059     Document Type: Article

References (52)

1. Abeijon C, Mandon EC, Hirschberg CB (1997) Transporters of nucleotide sugars, nucleotide sulfate and ATP in the Golgi apparatus. Trends Biochem Sci 22: 203-207.
2. Ahn NG, Seger R, Krebs EG (1992) The mitogen-activated protein kinase activator. Curr Opin Cell Biol 4: pp 992-999.
3. Ali A, Hoeflich KP, Woodgett JR (2001) Glycogen synthase kinase-3: properties, functions, and regulation. Chem Rev 101: 2527-2540.
4. Bairoch A, Bucher P, Hofmann K (1997). The PROSITE: database Nucleic Acids Research 25: 217-221.
5. Bedford MT, Reed R, Leder P (1998) 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 95: 10602-10607.
6. Bhattacharyya A, Mukherjee M, Duttagupta S (2002) Studies on Stibanate unresponsive isolates of Leishmania donovani. J Biosci 27: 503-508.
7. Cahill CM, Tzivion G, Nasrin N, Ogg S, Dore J, (2001) Phosphatidylinositol 3-kinase signaling inhibits DAF-16 DNA binding and function via 14-3-3-dependent and 14-3-3-independent pathways. J Biol Chem 276: 13402-13410.
8. Cai CZ, Han LY, Chen X, Cao ZW, Chen YZ (2005) Prediction of Functional Class of the SARS Coronavirus Proteins by a Statistical Learning Method. J Proteome Res 4: 1855-1862.
9. Cai CZ, Han LY, Ji ZL, Chen X, Chen YZ (2003) SVMProt: Web-Based Support Vector Machine Software for Functional Classification of a Protein from Its Primary Sequence. Nucleic Acids Res 31: 3692-3697.
10. Ceroni A, Frasconi P, Passerini A, Vullo A (2004) Disulfide connectivity prediction using recursive neural networks and evolutionary information. Bioinformatics 20: 653-659.
11. Croft SL, Sundar S, Fairlamb AH (2006) Drug resistance in leishmaniasis. Clinical Microbiol Rev 19: 111-126.
12. Descoteaux A, Luo Y, Turco SJ, Beverley SM (1995) A specialized pathway affecting virulence glycoconjugates of Leishmania. Science 269: 1869-1872.
13. Donella DA, Grankowski N, Kudlicki W, Szyszka R, Gasior E (1985) A type-1 casein kinase from yeast phosphorylates both serine and threonine residues of casein. Identification of the phosphorylation sites. Biochim Biophys Acta 829: 180-187.
14. Faust Mand Montenarh M (2000) Subcellular localization of protein kinase CK2. A key to its function. Cell Tissue Res 301: 329-40.
15. Flotow H, Graves PR, Wang A, Fiol CJ, Roeske RW (1990) Phosphate groups as substrate determinants for casein kinase I action. J Biol Chem 265: 14264-14269.
16. Frame S, Cohen P (2001) GSK3 takes centre stage more than 20 years after its discovery. Biochem J 359: 1-16.
17. Hendlich M, Rippmann F, Barnickel G (1997) LIGSITE: automatic and efficient detection of potential small molecule-binding sites in proteins. J Mol Graph Model 15: 359-363.
18. Hirokawa T, Boon CS, Mitaku S (1998) SOSUI: classification and secondary structure prediction system for membrane proteins. Bioinformatics 14: 378-379.
19. Hofmann K and Stoffel W (1993) TMbase -A database of membrane spanning proteins segments. Biol Chem 374: 166-170.
20. Hong K, Ma D, Beverley SM, Turco SJ (2000) The Leishmania GDP-mannose transporter is an autonomous, multi-specific, hexameric complex of LPG2 subunits. Biochemistry 39: 2013-2022.
21. Krogh A, Larsson B, Von HG, Sonnhammer EL (2001) Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol 305: 567-80.
22. Kutay U and Güttinger S (2005) Leucine-rich nuclear-export signals: born to be weak, Trends in Cell Biology. 15: 121-124.
23. Kyte J and Doolittle RF (1982) A simple method for displaying the hydropathic character of a protein. J Mol Biol 157: 105-132.
24. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA (2007) Clustal W and Clustal X version 2.0. Bioinformatics 123: 2947-8.
25. Lu KP, Liou YC, Zhou XZ (2002) Pinning down prolinedirected phosphorrylation signaling. Trends Cell Biol 12: 164-172.
26. Ma DQ, Russell DG, Beverley SM, Turco SJ (2004) Reconstitution of GDP-Man Transport Activity with Purified. J Biol Chem 280: 2018-2035.
27. Marshall CJ (1995) Specificity of receptor tyrosine kinase signaling: transient versus sustained extracellular signal-regulated kinase activation. Cell 80: pp179-185.
28. Meggio F, Donella DA, Pinna LA (1979) Studies on the structural requirements of a microsomal cAMP-independent protein kinase. FEBS Lett 106: 76-80.
29. Muller S, Hoege C, Pyrowolakis G, Jentsch S (2001) SUMO, ubiquitin's mysterious cousin. Nat Rev Mol Cell Biol 2: 202-10.
30. Ng K, Handman E, Bacic A (1994) Biosynthesis of lipophosphoglycan from Leishmania major: characterization of (ß1-3)-galactosyltransferase(s). Glycobiology 4: 845-853.
31. Nishida E and Gotoh Y (1993) The MAP kinase cascade is essential for diverse signal transduction pathways. Trends Biochem Sci 18: pp128-131.
32. Paris C, Loiseau PM, Bories C, Bréard J (2004) Miltefosine Induces Apoptosis-Like Death in Leishmania donovani Promastigotes. Antimicrobial Agents and Chemotherapy 48: pp 852-859.
33. Pinna LA and Ruzzene M (1996) How do protein kinases recognize their substrates. Biochim Biophys Acta 1314: 191-225.
34. Puntervoll P, Linding R, Gemünd C, Chabanis DS, Mattingsdal M (2003) ELM server: a new resource for investigating short functional sites in modular eukaryotic proteins. Nucleic Acids Res 31: 3625-3630.
35. Rena G, Bain J, Elliott M, Cohen P (2004) D4476, a cell-permeant inhibitor of CK1, suppresses the site-specific phosphorylation and nuclear exclusion of FOXO1a. EMBO reports 5: 60-65.
36. Roach PJ (1991) Multisite and hierarchal protein phosphorylation. J Biol Chem 266: 14139-14142.
37. Rost B, Yachdav G, Liu J (2004) The PredictProtein Server. Nucleic Acids Research 32: W321-W326.
38. Ruppert J, Welch W, Jain AN (1997) Automatic identification and representation of protein binding sites for molecular docking. Protein Science 6: 524-533.
39. Sahoo GC, Dikhit MR, Das P (2008) Functional assignment to JEV proteins using SVM. Bioinformation 3: 1-7.
40. Saridakis V, Sheng Y, Sarkari F, Holowaty MN, Shire K (2005) Structure of the p53 Binding Domain of HAUSP/USP7 Bound to Epstein-Barr Nuclear Antigen 1 Implications for EBV-Mediated Immortalization. Molecular Cell 18: 25-36.
41. Songyang Z, Lu KP, Kwon YT, Tsai LH, Filhol O (1996) A structural basis for substrate specificities of protein Ser/Thr kinases: Primary sequence preference of casein kinases I and II, NIMA, phosphorylase kinase, calmodulin-dependent kinase II, CDK5, and Erk1. Mol Cell Biol 16: 6486-6493.
42. Stephens DJ and Banting G (1998) Specificity of interaction between adaptor-complex medium chains and the tyrosine-based sorting motifs of TGN38 and lgp120. Biochem J 335: 567-572.
43. Sturgill TW and Wu J (1991) Recent progress in characterization of protein kinase cascades for phosphorylation of ribosomal protein S6. Biochim, Biophys, Acta 1092: pp 350-357.
44. Takeda DY, Wohlschlegel JA, Dutta A (2001) A Bipartite Substrate Recognition Motif for Cyclin-Dependent Kinases. J Biol Chem 276: 1993-1997.
45. Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positionspecific gap penalties and weight matrix choice. Nucleic Acids Res 22: 4673-4680.
46. TusnaÂdy GE, Simon I (1998) Principles Governing Amino Acid Composition of Integral Membrane Proteins: Application to Topology Prediction. J Mol Biol 283: 489-506.
47. Tzivion G, Luo Z, Avruch J (1998) A dimeric 14-3-3 protein is an essential cofactor for Raf kinase activity. Nature 394: 88-92.
48. Vergnes B, Gourbal B, Girard I, Sundar S (2007) Jolyne Drummelsmith, and Marc Ouellette; A Proteomics Screen Implicates HSP83 and a Small Kinetoplastid Calpain-related Protein in Drug Resistance in Leishmania donovani Clinical Field Isolates by Modulating Druginduced Programmed Cell Death. The American Society for Biochemistry 6: 88-101.
49. Vijay IK (1998) Developmental and Hormonal Regulation of Protein N Glycosylation in the Mammary Gland. Journal of Mammary Gland Biology and Neoplasia 3: 325-336.
50. Waterman MJ, Stavridi ES, Waterman JL, Halazonetis TD (1998) ATM-dependent activation of p53 involves dephosphorylation and association with 14-3-3 proteins. Nat Genet 19: 175-178.
51. Winberg ME, Rasmussona B, Sundqvista T (2007) Leishmania donovani: Inhibition of phagosomal maturation is rescued by nitric oxide in macrophages. Experimental Parasitology 117: 165-170.
52. Zhou XZ, Lu PJ, Wulf G, Lu KP (1999) Phosphorylation-dependent prolyl isomerization: A novel signaling regulatory mechanism. Cell Mol Life Sci 56: 788-806.