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Theor Chem Acc. 2007 May 01;117(5):723-741. doi: 10.1007/s00214-006-0203-4.

Computational approaches to shed light on molecular mechanisms in biological processes.

Theoretical chemistry accounts

Giorgio Moro, Laura Bonati, Maurizio Bruschi, Ugo Cosentino, Luca De Gioia, Pier Carlo Fantucci, Alessandro Pandini, Elena Papaleo, Demetrio Pitea, Gloria A A Saracino, Giuseppe Zampella

Affiliations

  1. Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Piazza della Scienza, Milano 20126, Italy.

PMID: 21415934 PMCID: PMC3057205 DOI: 10.1007/s00214-006-0203-4

Abstract

Computational approaches based on Molecular Dynamics simulations, Quantum Mechanical methods and 3D Quantitative Structure-Activity Relationships were employed by computational chemistry groups at the University of Milano-Bicocca to study biological processes at the molecular level. The paper reports the methodologies adopted and the results obtained on Aryl hydrocarbon Receptor and homologous PAS proteins mechanisms, the properties of prion protein peptides, the reaction pathway of hydrogenase and peroxidase enzymes and the defibrillogenic activity of tetracyclines.

References

  1. J Am Chem Soc. 1988 Aug 1;110(18):5959-67 - PubMed
  2. J Neurochem. 1999 Oct;73(4):1557-65 - PubMed
  3. Inorg Chem. 2003 Jul 28;42(15):4773-81 - PubMed
  4. Proc Natl Acad Sci U S A. 2003 Dec 9;100(25):14790-5 - PubMed
  5. J Biol Inorg Chem. 2004 Oct;9(7):873-84 - PubMed
  6. J Am Chem Soc. 2005 Sep 28;127(38):13180-9 - PubMed
  7. Curr Opin Drug Discov Devel. 2005 May;8(3):329-33 - PubMed
  8. J Am Chem Soc. 2004 Feb 11;126(5):1542-50 - PubMed
  9. Eur J Neurosci. 1994 Sep 1;6(9):1415-22 - PubMed
  10. J Mol Model. 2005 Feb;11(1):17-25 - PubMed
  11. Crit Rev Toxicol. 1990;21(1):51-88 - PubMed
  12. Proc Natl Acad Sci U S A. 1993 Oct 15;90(20):9678-82 - PubMed
  13. J Mol Biol. 1999 Apr 9;287(4):797-815 - PubMed
  14. J Mol Biol. 2000 Jul 28;300(5):1309-22 - PubMed
  15. Chem Biol Interact. 2002 Sep 20;141(1-2):3-24 - PubMed
  16. Protein Eng Des Sel. 2005 Mar;18(3):127-37 - PubMed
  17. Nature. 1993 Apr 8;362(6420):543-6 - PubMed
  18. J Mol Biol. 2000 Jun 2;299(2):499-520 - PubMed
  19. Chem Rev. 2002 Dec;102(12):4501-24 - PubMed
  20. J Mol Biol. 1996 Jun 21;259(4):608-21 - PubMed
  21. Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics. 2000 Dec;62(6 Pt B):8438-48 - PubMed
  22. Inorg Chem. 2004 Jun 14;43(12):3733-41 - PubMed
  23. Cell. 1999 Mar 19;96(6):869-78 - PubMed
  24. J Mol Biol. 1993 Dec 5;234(3):779-815 - PubMed
  25. Chem Rev. 2004 Feb;104(2):459-508 - PubMed
  26. J Biol Chem. 1994 Mar 18;269(11):7859-62 - PubMed
  27. Eur J Biochem. 1999 Dec;266(3):1192-201 - PubMed
  28. Cell. 2004 Oct 29;119(3):393-405 - PubMed
  29. BMC Bioinformatics. 2005 Dec 01;6 Suppl 4:S15 - PubMed
  30. J Phys Chem B. 2006 Jan 26;110(3):1423-8 - PubMed
  31. J Neurochem. 2003 Apr;85(1):62-72 - PubMed
  32. Proc Natl Acad Sci U S A. 1998 Dec 22;95(26):15177-82 - PubMed
  33. Inorg Chem. 2004 Jul 12;43(14):4127-36 - PubMed
  34. Proc Natl Acad Sci U S A. 2004 Jun 1;101(22):8342-7 - PubMed
  35. Proc Natl Acad Sci U S A. 2005 May 10;102(19):6648-53 - PubMed
  36. Phys Rev B Condens Matter. 1986 Jun 15;33(12):8822-8824 - PubMed
  37. Structure. 2002 Oct;10(10):1349-61 - PubMed
  38. Phys Rev E Stat Nonlin Soft Matter Phys. 2002 Mar;65(3 Pt 1):031910 - PubMed
  39. Proteins. 1993 Dec;17(4):412-25 - PubMed
  40. Chemistry. 2005 Jan 7;11(2):509-20 - PubMed
  41. Curr Top Med Chem. 2002 Dec;2(12):1381-94 - PubMed
  42. Chem Biol. 1995 May;2(5):305-15 - PubMed
  43. Plant Cell. 2002 May;14(5):1067-75 - PubMed
  44. Proc Natl Acad Sci U S A. 2002 Aug 6;99(16):10849-54 - PubMed
  45. Proc Natl Acad Sci U S A. 2001 Sep 25;98(20):11686-90 - PubMed
  46. Biochemistry. 1989 May 2;28(9):3629-37 - PubMed
  47. Proc Natl Acad Sci U S A. 2003 Dec 23;100(26):15504-9 - PubMed
  48. Eur J Biochem. 2002 Jan;269(1):13-8 - PubMed
  49. J Struct Biol. 1998;122(1-2):247-55 - PubMed
  50. Pac Symp Biocomput. 1996;:53-72 - PubMed
  51. J Am Chem Soc. 2005 Aug 10;127(31):11010-8 - PubMed
  52. Proc Natl Acad Sci U S A. 1996 Jan 9;93(1):392-6 - PubMed
  53. Proc Natl Acad Sci U S A. 2000 Jan 4;97(1):145-50 - PubMed
  54. J Virol. 1998 Nov;72(11):9413-8 - PubMed
  55. J Mol Biol. 1997 Oct 31;273(3):614-22 - PubMed
  56. Nature. 2005 Feb 10;433(7026):610-3 - PubMed
  57. J Am Chem Soc. 2001 Apr 25;123(16):3828-9 - PubMed
  58. Nature. 2003 Dec 18;426(6968):884-90 - PubMed
  59. Proc Natl Acad Sci U S A. 2004 Feb 24;101(8):2293-8 - PubMed
  60. Chem Rev. 2005 Nov;105(11):4009-37 - PubMed
  61. Curr Opin Chem Biol. 2004 Apr;8(2):133-40 - PubMed
  62. Proc Natl Acad Sci U S A. 1997 Sep 16;94(19):10086-91 - PubMed
  63. J Comput Chem. 2004 Aug;25(11):1333-41 - PubMed
  64. Biochem J. 1999 Aug 15;342 ( Pt 1):207-14 - PubMed
  65. Cell. 1998 May 1;93(3):337-48 - PubMed
  66. Acc Chem Res. 2003 Feb;36(2):95-101 - PubMed
  67. Phys Rev A Gen Phys. 1988 Sep 15;38(6):3098-3100 - PubMed
  68. Proc Natl Acad Sci U S A. 1997 Dec 9;94(25):13452-7 - PubMed
  69. Nature. 1996 Mar 28;380(6572):345-7 - PubMed
  70. Chemistry. 2001 Dec 3;7(23):5195-202 - PubMed
  71. Chem Rev. 2002 Mar;102(3):783-812 - PubMed
  72. Inorg Chem. 2002 Mar 25;41(6):1421-9 - PubMed
  73. Proteins. 1993 Dec;17(4):355-62 - PubMed
  74. J Pharm Sci. 1979 Aug;68(8):999-1002 - PubMed
  75. Inorg Chem. 2001 Apr 23;40(9):2201-3 - PubMed
  76. Proteins. 2001 Dec 1;45(4):382-96 - PubMed
  77. Protein Pept Lett. 2003 Apr;10(2):119-32 - PubMed
  78. Chemistry. 2002 Sep 2;8(17):4037-46 - PubMed
  79. Biochemistry. 1991 Aug 6;30(31):7672-80 - PubMed
  80. Proteins. 2004 Oct 1;57(1):198-204 - PubMed
  81. J Biol Chem. 2003 Sep 12;278(37):35592-6 - PubMed
  82. Inorg Chem. 2006 May 15;45(10):4109-18 - PubMed
  83. J Mol Med (Berl). 2003 Nov;81(11):678-99 - PubMed
  84. Proteins. 2006 Jul 1;64(1):167-77 - PubMed
  85. Chem Soc Rev. 2003 Sep;32(5):268-75 - PubMed
  86. Chem Rev. 2000 Feb 9;100(2):353-406 - PubMed
  87. J Biol Chem. 2006 Jan 13;281(2):843-9 - PubMed
  88. Curr Opin Struct Biol. 2005 Feb;15(1):23-30 - PubMed
  89. J Am Chem Soc. 2005 Jan 26;127(3):953-60 - PubMed
  90. J Chem Theory Comput. 2005 Nov;1(6):1286-97 - PubMed
  91. Chem Rev. 2000 Feb 9;100(2):421-38 - PubMed
  92. Chem Soc Rev. 2003 Jan;32(1):1-8 - PubMed
  93. Proc Natl Acad Sci U S A. 2002 Mar 19;99(6):3563-8 - PubMed
  94. Curr Opin Chem Biol. 2002 Apr;6(2):243-9 - PubMed
  95. Microbiol Mol Biol Rev. 2001 Jun;65(2):232-60 ; second page, table of contents - PubMed
  96. Arch Biochem Biophys. 2005 Oct 1;442(1):59-71 - PubMed
  97. FEBS Lett. 2001 Jan 5;487(3):404-7 - PubMed
  98. Proc Natl Acad Sci U S A. 1993 Jul 15;90(14):6449-53 - PubMed
  99. Science. 1991 Jun 14;252(5012):1515-22 - PubMed
  100. J Mol Biol. 1993 Sep 5;233(1):123-38 - PubMed
  101. Annu Rev Cell Dev Biol. 1996;12:55-89 - PubMed
  102. Proc Natl Acad Sci U S A. 1993 Dec 1;90(23):10962-6 - PubMed
  103. Nucleic Acids Res. 1994 Nov 11;22(22):4673-80 - PubMed
  104. FEBS Lett. 2005 Dec 19;579(30):6851-8 - PubMed
  105. Biol Chem. 1997 Mar-Apr;378(3-4):309-15 - PubMed
  106. Biochem Biophys Res Commun. 1993 Aug 16;194(3):1380-6 - PubMed
  107. Chem Rev. 2003 Jun;103(6):2421-56 - PubMed
  108. Curr Top Med Chem. 2003;3(11):1241-56 - PubMed
  109. J Mol Biol. 2005 Oct 28;353(3):664-77 - PubMed
  110. Cell. 1994 Nov 18;79(4):695-703 - PubMed

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