Modeling of three dimensional structure of human alpha-fetoprotein complexed with diethylstilbestrol: Docking and molecular dynamics simulation study

Journal of Bioinformatics and Computational Biology

Volumn 10, Issue 2, 2012, Pages

  Terentiev, Alexander A ^a   Moldogazieva, Nurbubu T ^a   Levtsova, Olga V ^b   Maximenko, Dmitry M ^a   Borozdenko, Denis A ^a   Shaitan, Konstantin V ^b  

^a PIROGOV RUSSIAN NATIONAL RESEARCH MEDICAL UNIVERSITY   (Russian Federation)

^b MOSCOW STATE UNIVERSITY   (Russian Federation)

Author keywords

alpha fetoprotein; complex with diethylstilbestrol; estrogens; Homology based modeling; molecular docking; molecular dynamics; serum albumin; Vitamin Dbinding protein

Indexed keywords

RODENTIA;

AFP PROTEIN, HUMAN; ALPHA FETOPROTEIN; DIETHYLSTILBESTROL;

ARTICLE; BINDING SITE; CHEMICAL STRUCTURE; CHEMISTRY; HUMAN; HYDROGEN BOND; METABOLISM; MOLECULAR DYNAMICS; PROTEIN SECONDARY STRUCTURE;

ALPHA-FETOPROTEINS; BINDING SITES; DIETHYLSTILBESTROL; HUMANS; HYDROGEN BONDING; MODELS, MOLECULAR; MOLECULAR DYNAMICS SIMULATION; PROTEIN STRUCTURE, SECONDARY;

EID: 84859756170     PISSN: 02197200     EISSN: None     Source Type: Journal    
DOI: 10.1142/S0219720012410120     Document Type: Article

References (48)

1. Deutsch HF, Chemistry and biology of alpha-fetoprotein, Adv Cancer Res 56:253-312, 1991.
2. Terentiev AA, Moldogazieva NT, Structural and functional mapping of alpha-fetoprotein, Biochemistry (Mosc.) 71:120-132, 2006.
3. Mizejewski GJ, Biological role of alpha-fetoprotein in cancer: Prospects for anticancer therapy, Expert Rev Anticancer Ther 2:709-735, 2002. (Pubitemid 35469493)
4. Morinaga T, Sakai M, Wegmann TG, Tamaoki T, Primary structure of human alphafetoprotein and its mRNA, Proc Natl Acad Sci USA 80:4604-4608, 1983. (Pubitemid 13030973)
5. Pucci P, Siliciano R,Malorni A, Marino G, TecceMF, Ceccarini C, Terrana B, Human alphafetoprotein primary structure: A mass spectrometric study, Biochemistry 30:5061-5066, 1991.
6. Song Y-H, Naumova AK, Liebhaber SA, Cooke NE, Physical and meiotic mapping of the region of human chromosome 4q11-q13 encompassing the Vitamin D-binding protein DBP/Gc-globulin and albumin multigene cluster, Genome Res 9:581-587, 1999. (Pubitemid 29361275)
7. Beatie WG, Dugaiczyk A, Structure and evolution of human alpha-fetoprotein deduced from partial sequence of cloned cDNA, Gene 20:415-422, 1982. (Pubitemid 13146376)
8. Luft AJ, Loscheider FL, Structural analysis of human and bovine α-fetoprotein by electron microscopy, image processing and circular dichroism, Biochemistry 22:5971-5978, 1983.
9. He XM, Carter DC, Atomic structure and chemistry of human serum albumin, Nature 358:209-315, 1992.
10. Petitpas I, Gruene T, Bhattacharya AA, Curry S, Crystal structures of human serum albumin complexed with monounsaturated and polyunsaturated fatty acids, J Mol Biol 314:955-960, 2001. (Pubitemid 34073060)
11. Zunszain PA, Ghuman J, Komatsu T, Tsuchida E, Curry S, Crystal structure analysis of human serum albumin complexed with hemin and fatty acids, BMC Struct Biol 3:6, 2003.
12. Petitpas I, Petersen CE, Ha CE, Bhattacharya AA, Zunszain PA, Ghuman J, Bhagavan NV, Curry S, Structural basis of albumin-thyroxine interactions and familial dysalbuminemic hyperthyroxinemia, Proc Natl Acad Sci USA 100:6440-6445, 2003. (Pubitemid 36666600)
13. Ghuman J, Zunszain PA, Petitpas I, Bhattacharya AA, Otagiri M, Curry S, Structural basis of the drug-binding specificity of human serum albumin, J Mol Biol 353:38-52, 2005. (Pubitemid 41338838)
14. Zunszain PA, Ghuman J, McDonagh AF, Curry S, Crystallographic analysis of human serum albumin complexed with 4Z,15E-bilirubin-IXalpha, J Mol Biol 381:394-406, 2008.
15. Verboven C, Rabijns, A, De Maeyer M, Van Baelen H, Bouillon R, De Ranter C, A structural basis for the unique binding features of the human Vitamin D-binding protein, Nat Struct Biol 9:131-136, 2002. (Pubitemid 34132416)
16. Otterbein LR, Cosio C, Graceffa P, Dominguez R, Crystal structures of the vitamin D-binding protein and its complex with actin: Structural basis of the actin-scavenger system, Proc Natl Acad Sci USA 99:8003-8008, 2002. (Pubitemid 34650995)
17. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE, The protein data bank, Nucleic Acids Res 28:235-242, 2000. (Pubitemid 30047768)
18. Chothia C, Lesk AM, The relation between the divergence of sequence and structure in proteins, EMBO J 5:823-826, 1986.
19. Kaczanowski S, Zielenkiewicz P, Why similar protein sequences encode similar threedimensional structures? Theor Chem Accoun 125:543-550, 2010.
20. Hsia JC, Er JS, Tan CT, Ester T, Ruoslahti E, α-Fetoprotein binding specificity for arachidonate, bilirubin, docosahexaenoate and palmitate, J Biol Chem 255:4224-4227, 1980.
21. Uriel J, de Nechaut B, Dupiers M, Estrogen-binding properties of rat, mouse and man fetospecific serum protein. Demonstration by immuno- autoradiographic methods, Biochem Biophys Res Commun 46:1175-1180, 1972.
22. Tatarinov YuS, Terentiev AA, Moldogazieva NT, Tagirova AK, Human alpha-fetoprotein and its purification by chromatography on immobilized estrogens, Tumor Biol 12:125-130, 1991.
23. Shahbazzadeh D, Estrogen binding activities of recombinant alpha-fetoproteins expressed in yeast, Hokkaido Igaku Zasshi 70:473-483, 1995.
24. Nishi S, Matsue H, Yoshida H, Yamamoto R, Sakai M, Localization of estrogen-binding site of alpha-fetoprotein in chimeric human-rat proteins, Proc Natl Acad Sci USA 88:3102-3105, 1991. (Pubitemid 21916567)
25. Mizejewski GJ, Biological roles of alpha-fetoprotein during pregnancy and prenatal development, Exp Biol Med 229:439-463, 2004. (Pubitemid 38736314)
26. Vakharia D, Mizejewski GJ, Human alpha-fetoprotein peptides bind estrogen receptor and estradiol and suppress breast cancer, Breast Cancer Res Treat 63:41-52, 2000.
27. Venclovas C, Margelevicius M, Comparative modeling in CASP6 using consensus approach to template selection, sequence-structure alignment, and structure assessment, Proteins 61(S7):99-205, 2005.
28. Boeckmann B, Blatter M-C, Famiglietti L, Hinz U, Lane L, Roechert B, Bairoch A, Protein variety and functional diversity: Swiss-Prot annotation in its biological context, Comptes Rendus Biologies 328:882-899, 2005. (Pubitemid 41683481)
29. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG, Clustal W and Clustal X version 2.0, Bioinformatics 23:2947-2948, 2007.
30. Eswar N, Marti-Renom MA, Webb B, Madhusudhan MS, Eramian D, Shen M, Pieper U, Sali A, Comparative Protein Structure Modeling With MODELLER, Curr Protocol Bioinform Suppl 15 5.6.1-5.6.30, 2006.
31. Zhang Y, Progress and challenges in protein structure prediction, Curr Opin Struct Biol 18:342-348, 2008.
32. Ginalski K, Comparative modeling for protein structure prediction, Curr Opin Struct Biol 16:172-177, 2006.
33. Zhang Y, Skolnick J, The protein structure prediction problem could be solved using the current PDB library, Proc Natl Acad Sci USA 102:1029-2034, 2005.
34. Maiorov VN, Crippen GM, Significance of root-mean-square deviation in comparing three-dimensional structures of globular proteins, J Mol Biol 235:625-634, 1994. (Pubitemid 24063583)
35. Morris AL, MacArthur MW, Hutchinson EG, Thornton JM, Stereochemical quality of proteins structure coordinates, Proteins 12:345-364, 1992.
36. Laskowski RA, MacArthur MW, Moss DS Thornton JM, PROCHECK: A program to check the stereochemical quality of protein structures, J Appl Cryst 26:283-291, 1993.
37. Froimowitz M, HyperChem: A software package for computational chemistry and molecular modeling, Biotechniques 14:1010-1013, 1993. (Pubitemid 23166821)
38. Pearlman DA, Case DA, Caldwell JW, Seibel GL, Singh UC, Weiner P, Kollman PA Amber 4.0, University of California, San Francisco, 1991.
39. Yang L, Tan CH, Hsieh MJ, Wang J, Duan Y, Cieplak P, Caldwell J, Kollman PA, Luo R, New-generation Amber united-atom force field, J Phys Chem B 110:13166-13176, 2006. (Pubitemid 44115654)
40. Schmidt MW, Baldridge KK, Boatz JA, Elbert ST, Gordon MS, Jensen JH, Koseki S, Matsunaga N, Nguyen KA, Su S, Windus TL, Dupuis M, Montgomery JA, General atomic and molecular electronic structure system, J Comput Chem 14:1347-1363, 1993.
41. Mulliken RS, Electronic population analysis on LCAO-MO molecular wave functions, I J Chem Phys 23:1833-1831, 1995.
42. Hinchliffe A, Modelling Molecular Structures, 2nd ed., England: John Wiley and Sons Ltd. p. 186, 2000.
43. Baker D, Sali A, Protein structure prediction and structural genomics, Science 294:93-96, 2001. (Pubitemid 32952955)
44. Morris GM, Goodsell DS, Halliday RS, Huey R, Hart WE, Belew RK, Olson AJ, Automated docking using a Lamarckian genetic algorithm and empirical binding free energy function, J Comput Chem 19:1639-2662, 1998.
45. Berendsen HJC, van der Spoel D, van Drunen R, Gromacs - A message-passing parallel molecular-dynamics implementation, Comp Phys Comm 91:43-56, 1995.
46. Gibbs PEM, Witke WF, Dugaiczyk AJ, The molecular clock runs at different rates among a closely related members of a gene family, Mol Evol 46:552-561, 1998. (Pubitemid 28194461)
47. Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE, UCSF Chimera - A visualization system for exploratory research and analysis, J Comput Chem 25:1605-1612, 2005.
48. Barker ME, Evolution of alpha-fetoprotein: Sequence comparisons among AFP species and with albumin species, Tumor Biol 9:123-136, 1988.