Skip to main content
SpringerLink
Log in

Computational approaches to shed light on molecular mechanisms in biological processes

  • Regular Article
  • Published:
Theoretical Chemistry Accounts Aims and scope Submit manuscript

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.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Similar content being viewed by others

References

  1. Special issue on Molecular Dynamics Simulations of Biomolecules (2002). Acc Chem Res 35(6)

  2. Rousseau F, Schymkowitz J (2005). Curr Opin Struct Biol 15:23

    CAS  Google Scholar 

  3. Tama F (2003). Protein Peptide Lett 10:119

    CAS  Google Scholar 

  4. Bhattacharyya K (2003). Acc Chem Res 36:95

    CAS  Google Scholar 

  5. Noodleman L, Lovell T, Han WG, Li J, Himo F (2004). Chem Rev 104:459

    CAS  Google Scholar 

  6. Himo F, Siegbahn PEM (2003). Chem Rev 103:2421

    CAS  Google Scholar 

  7. Siegbahn PEM, Blomberg MRA (200). Chem Rev 100:421

    Google Scholar 

  8. Dreuw A, Head-Gordon M (2005). Chem Rev 105:4009

    CAS  Google Scholar 

  9. Carter EA, Rossky PJ (2006). Acc Chem Res 39:71

    CAS  Google Scholar 

  10. Hasegawa K, Arakawa M, Funatsu K (2005). Curr Comput-Aided Drug Des 1:129

    CAS  Google Scholar 

  11. Walters WP, Goldman BB (2005). Curr Opin Drug Dis Dev 8:329

    CAS  Google Scholar 

  12. Murray JS, Politzer P (2003). Methods Princ Med Chem 17:233

    CAS  Google Scholar 

  13. Akamatsu M (2002). Curr Top Med Chem 2:1381

    CAS  Google Scholar 

  14. Hansch C, Hoekman D, Leo A, Weininger D, Selassie CD (2002). Chem Rev 102:783

    CAS  Google Scholar 

  15. Patrick GL (2005) An introduction to medicinal chemistry, 3rd edn. Oxford University Press, Oxford

    Google Scholar 

  16. Oprea TI, Waller CL (1997). In: Lipkowitz KB, Boyd DB (eds) Rev Comput Chem vol 11. VHC Publishers, New York, p 127, and references therein

  17. Coats EA, (1998). Perspect. Drug Discovery Des. vol 12. Kluwer Academic Publishers, UK, p 199

  18. Amadei A, Linssen AB, Berendsen HJC (1993). Proteins 17:412

    CAS  Google Scholar 

  19. Lin H, Truhlar DG (2006). Theoretical Chemistry Accounts, online first: 1, and references therein

  20. Friesner RA, Baik M-H, Gherman BF, Guallar V, Wirstam M, Murphy RB, Lippard SJ (2003). Coordination Chem Rev 238-239:267

    Google Scholar 

  21. Ridder L, Mulholland AJ (2003). Curr Top Med Chem 3:1241

    CAS  Google Scholar 

  22. Mulholland AJ (2001). Theor Comput Chem 9:597

    Article  CAS  Google Scholar 

  23. Baroni M, Costantino G, Cruciani G, Riganelli D, Valigi R, Clementi S (1993). Quant Struct Act Relat 12:9

    CAS  Google Scholar 

  24. Lindgren F, Geladi P, Rännar S, Wold S (1994). J Chemom 8:349

    Google Scholar 

  25. Cosentino U, Moro G, Bonalumi D, Bonati L, Lasagni M, Todeschini R, Pitea D (2000). Chemom Intell Lab Syst 52:183

    CAS  Google Scholar 

  26. Holm L, Sander C (1993). J Mol Biol 233:123

    CAS  Google Scholar 

  27. Thompson JD, Higgins DG, Gibson TJ (1994). Nucleic Acids Res 22:4673

    CAS  Google Scholar 

  28. Sali A, Blundell TL (1993). J Mol Biol 234:779

    CAS  Google Scholar 

  29. Laskowski RA, MacArthur MW, Moss DS, Thornton JM (1993). J Appl Cryst 26:283

    CAS  Google Scholar 

  30. Sippl MJ (1993). Proteins 17:355

    CAS  Google Scholar 

  31. DeLano WL (2002) The PyMOL molecular graphics system. DeLano Scientific, San Carlos, CA, USA

    Google Scholar 

  32. Kelley LA, MacCallum RM, Sternberg MJE. (2000). J Mol Biol 299:499

    CAS  Google Scholar 

  33. Jones DT (1999). J Mol Biol 287:797

    CAS  Google Scholar 

  34. Alexandrov N, Nussinov R, Zimmer R. (1996). In: Hunter L, Klein TE (eds). Pac Symp Biocomput. World Scientific Publishing Co., Singapore, p 53

  35. Shi J, Blundell TL, Mizuguchi K. (2001). J Biol Mol 301:243

    Google Scholar 

  36. Rost B (1995). In: Rawlings C, Clark D, Altman R, Hunter L, Lengauer T, Wodak S (eds). The third international conference on intelligent system for molecular biology (ISMB). AAAI Press, Cambridge, UK, Menlo Park, CA, p 314

  37. Berendsen HJC, van der Spoel D, van Drunen R (1995). Comput Phys Comm 91:43

    CAS  Google Scholar 

  38. Lindahl E, Hess B, van der Spoel D (2001). J Mol Mod 7:306

    CAS  Google Scholar 

  39. Berendsen HJC, Postma JPM, van Gusteren WF, Hermans J (1981) Interaction models for water in relation to protein hydratation. Reidel, Dordrecht, p 331

    Google Scholar 

  40. Berendsen HJC, Postma JPM, van Gusteren WF, Di Nola A, Haak JR (1984). J Chem Phys 81:3684

    CAS  Google Scholar 

  41. Darden TA, York DM, Pedersen LG (1993). J Chem Phys 98:10089

    CAS  Google Scholar 

  42. Hess B, Bekker H, Berendsen HJC, Fraahje JGEM (1997). J Comp Chem 18:1463

    CAS  Google Scholar 

  43. Ahlrichs R, Bar M, Haser M, Horn H, Kolmel C (1989). Chem Phys Lett 162:165

    CAS  Google Scholar 

  44. Schafer A, Huber C, Ahlrichs R (1994). J Chem Phys 100:5829

    Google Scholar 

  45. Jensen F (2000) Introduction to computational chemistry. Wiley, Baffins Lane, Chichester, England

  46. Klamt A (1995). J Phys Chem 99:2224

    CAS  Google Scholar 

  47. Klamt A (1996). J Phys Chem 100:3349

    CAS  Google Scholar 

  48. Himo F, Noodleman L, Blomberg MRA, Siegbahn PEM (2002). J Phys Chem A 106:8757

    CAS  Google Scholar 

  49. Klamnt A (1995). J Phys Chem 99:2224

    Google Scholar 

  50. Klamnt A (1996). J Phys Chem 100:3349

    Google Scholar 

  51. Warshel A, Naray-Szabo G, Sussman F, Hwang J-K (1989). Biochemistry 28:3629

    CAS  Google Scholar 

  52. Bottoni A, Lanza CZ, Miscione GP, Spinelli D (2004). J Am Chem Soc 126:1542

    CAS  Google Scholar 

  53. Clark M, Cramer III RD, Van Opdenbosch N (1989). J Comp Chem 10:982

    CAS  Google Scholar 

  54. Goldberg DE (1989) Genetic algorithms in search, optimization and machine learning. Addison-Wesley, Massachusetts

    Google Scholar 

  55. Leardi R, Boggia R, Terrile M (1992). J Chemom 6:267

    CAS  Google Scholar 

  56. Safe S (1990). Crit Rev Toxicol 21:51

    CAS  Google Scholar 

  57. Schmidt JV, Bradfield CA (1996). Annu Rev Cell Dev Biol 12:55

    CAS  Google Scholar 

  58. Procopio M, Lahm A, Tramontano A, Bonati L, Pitea D (2002). Eur J Biochem 269:13

    CAS  Google Scholar 

  59. Denison MS, Pandini A, Nagy SR, Baldwin EP, Bonati L (2002). Chem Biol Interact 141:3

    CAS  Google Scholar 

  60. Gong W, Hao B, Mansy SS, Gonzalez G, Gilles-Gonzalez MA, Chan MK (1998). Proc Natl Acad Sci USA 95:15177

    CAS  Google Scholar 

  61. Murray IA, Reen RK, Leathery N, Ramadoss P, Bonati L, Gonzalez FJ, Peters JM, Perdew GH (2005). Archives Biochem Biophys 442:59

    CAS  Google Scholar 

  62. Erbel PJ, Card PB, Karakuzu O, Bruick RK, Gardner KH (2003). Proc Natl Acad Sci USA 100:15504

    CAS  Google Scholar 

  63. Card PB, Erbel PJ, Gardner KH (2005). J Mol Biol 353:664

    CAS  Google Scholar 

  64. Denison MS, Soshilov A, Song Y, Pandini A, Bonati L (2005) Organohalogen Compounds 114

  65. Pandini A, Denison MS, Song Y, Soshilov AA, Bonati L, Biochemistry (in press)

  66. Pandini A, Bonati L (2005). Protein Eng Des Sel 18:127

    CAS  Google Scholar 

  67. Hess B (2000). Phys Rev E 62:8438

    CAS  Google Scholar 

  68. Hess B (2002). Phys Rev E 65:031910–1

    Google Scholar 

  69. Hellingwerf KJ, Hendriks J, Gensch T (2003). J Phys Chem 107:1082

    CAS  Google Scholar 

  70. Amezcua C, Harper S, Rutter J, Gardner K (2002). Structure (Camb). 10:1349

    CAS  Google Scholar 

  71. Crosson S, Moffat K (2002). Plant Cell 14:1067

    CAS  Google Scholar 

  72. Pandini A, Mauri G, Bonati L (Submitted)

  73. Hedstrom L (2002). Chem Rev 102:4501

    CAS  Google Scholar 

  74. Papaleo E, Fantucci P, De Gioia L (2005). J Chem Theory Comput 1:1286

    CAS  Google Scholar 

  75. Sondermann H, Soisson SM, Boykevisch S, Yang S-S, Bar-Sagi D, Kuriyan J (2004). Cell 119:393

    CAS  Google Scholar 

  76. Greco C, Fantucci P, De Gioia L (2005). BMC Bioinformatics 6:S15

    Google Scholar 

  77. Sacco E, Fantinato S, Manzoni R, Metalli D, De Gioia L, Fantucci P, Alberghina L, Vanoni M (2005). FEBS Lett 579:6851

    CAS  Google Scholar 

  78. Mereghetti P, Papaleo E, Fantucci P, De Gioia L (Submitted)

  79. Prusiner SB (1991). Science 252:1515

    CAS  Google Scholar 

  80. Prusiner SB, Scott MR, De Armond SJ, Cohen FE (1998). Cell 93:337

    CAS  Google Scholar 

  81. De Armond SJ, Yang SL, Lee A, Bowler R,Tarabolous A, Groth D, Prusiner SB (1993). Proc Natl Acad Sci USA 90:6449

    CAS  Google Scholar 

  82. Williams A, Lucassen PJ, Ritchie D, Bruce M (1997). Expt Neurol 14:433

    Google Scholar 

  83. Stefani M, Dobson CM (2003). J Mol Med 81:678

    CAS  Google Scholar 

  84. Caughey BW, Dong A, Bhat KS, Ernst D, Hayes SF, Caughey WS (1991). Biochemistry 30:7672

    CAS  Google Scholar 

  85. Pan KM, Baldwin M, Nguyen J, Gasset M, Serban A, Groth D, Mehlhorn I, Huang Z, Fletterick RJ, Cohen FE, Prusiner SB (1993). Proc Natl Acad Sci USA 90:10962

    CAS  Google Scholar 

  86. James TL, Liu H, Ulyanov NB, Farr-Jones S, Zhang H, Donne DG, Kaneko K, Groth D, Mehlhorn I, Prusiner SB, Cohen FE (1997). Proc Natl Acad Sci USA 94:10086

    CAS  Google Scholar 

  87. Donne DG, Viles JH, Groth D, Mehlhorn I, James TL, Cohen FE, Prusiner SB, Wright PE, Dyson HJ (1997). Proc Natl Acad Sci USA 94:13452

    CAS  Google Scholar 

  88. Zhan R, Liu H, Lührs T, Riek R, von Schroetter C, Garcia L, Billiter M, Calzolai L, Wider G, Wüthrich K (2000). Proc Natl Acad Sci USA 97:145

    Google Scholar 

  89. Wille H, Zhang GF, Baldwin MA, Cohen FE, Prusiner SB (1996). J Mol Biol 259:608

    CAS  Google Scholar 

  90. Wille H, Michelitsch MD, Guenebaut V, Supattopone S, Serban A, Cohen FE, Agard DA, Prusiner SB (2001). Proc Natl Acad Sci USA 98:11686

    Google Scholar 

  91. Wille H, Michelitsch MD, Guènebaut V, Supattopone S, Serban A, Cohen FE, Agard DA, Prusiner SB (2002). Proc Natl Acad Sci USA 99:3563

    CAS  Google Scholar 

  92. Peretz D, Williamson RA, Matsunaga Y, Serban H, Pinilla C, Bastidas RB, Rozenhsteyn R, James TL, Houghten RA, Cohen FE et al (1997). J Mol Biol 273:614

    CAS  Google Scholar 

  93. Williamson RA, Peretz D, Pinilla C, Ball H, Bastidas RB, Rozenshteyn R, Houghten RA, Prusiner SB, Burton DR (1998). J Virol 72:9413

    CAS  Google Scholar 

  94. Forloni G, Angeretti N, Chiesa R, Monzani E, Salmona M, Bugiani O, Tagliavini F, (1993). Nature 362:543

    CAS  Google Scholar 

  95. Brown DR, Schmidt B, Kretzschmer HA (1996). Nature 380:345

    CAS  Google Scholar 

  96. Forloni G, Del Bo R, Angeretti N, Chiesa R, Smiroldo S, Doni R, Ghibaudi E, Salmona M, Porro M, Verga L, Giaccone G, Bugiani O, Tagliavini F (1994). Eur J Neurosci 6:1415

    CAS  Google Scholar 

  97. Tagliavini F, Prelli F, Verga L, Giaccone G, Sarma R, Gorevic P, Ghetti B, Passerini F, Ghibaudi E, Forloni G, Salmona M, Bugiani O, Frangioni B (1993). Proc Natl Acad Sci USA 90:9678

    CAS  Google Scholar 

  98. Tagliavini F, Prelli F, Porro M, Rossi G, Giaccone G, Farlow MR, Dlouhy SR, Ghetti B, Bugiani O, Frangione B (1994). Cell 79:695

    CAS  Google Scholar 

  99. Selvaggini C, De Gioa L, Cantù L, Ghibaudi E, Diomede L, Passerini F, Forloni G, Bugiani O, Tagliavini F, Salmona M (1993). Biochem Biophys Res Commun 194:1380

    CAS  Google Scholar 

  100. De Gioia L, Selvaggini C, Ghibaudi E, Diomede L, Bugiani O, Forloni G, Tagliavini F, Salmona M (1994). J Biol Chem 269:7859

    CAS  Google Scholar 

  101. Salmona M, Malesani P, De Gioia L, Gorla S, Bruschi, M, Molinari A DellaVedova R, Pedrotti B, Marrari MA, Awan T, Bugiani O, Forloni G, Tagliavini F (1999). Biochem J 342:207

    CAS  Google Scholar 

  102. Ragg E, Tagliavini F, Malesani P, Monticelli L, Bugiani O, Forloni G, Salmona M (1999). Eur J Biochem 266:1192

    CAS  Google Scholar 

  103. Kuwata K, Matumoto T, Cheng H, Nagayama K, James TL, Roder H (2003). Proc Natl Acad Sci USA 100:14790

    CAS  Google Scholar 

  104. Levy Y, Hanan E, Solomon B, Becker OM (2001). Proteins 45:382

    CAS  Google Scholar 

  105. Kazmirski SL, Alonso DOV, Cohen FE, Prusiner SB, Daggett V (1995). Chem Biol 2:305

    CAS  Google Scholar 

  106. Daidone I, Simona F, Roccatano D, Broglia RA, Tiana G, Colombo G, Di Nola A (2004). Proteins 57:198

    CAS  Google Scholar 

  107. Inouye H, Kirschner DA (1998). J Struct Biol 122:247

    CAS  Google Scholar 

  108. Calzolai L, Zahn R (2003). J Biol Chem 278:35592–35596

    CAS  Google Scholar 

  109. Langella E, Improta R, Crescenzi O, Barone V (2006). Proteins 64:167

    CAS  Google Scholar 

  110. Villa A, Mark AE, Saracino GAA, Cosentino U, Pitea D, Moro G, Salmona M (2006). J Phys Chem B 110:1423

    CAS  Google Scholar 

  111. Dobson CM (2003). Nature 426:884

    CAS  Google Scholar 

  112. Govaerts C, Wille H, Prusiner SB, Cohen FE (2004). Proc Natl Acad Sci USA 101:8342

    CAS  Google Scholar 

  113. DeMarco ML, Daggett V (2004). Proc Natl Acad Sci USA 101:2293

    CAS  Google Scholar 

  114. Gobbi M, Colombo L, Morbin M, Mazzoleni G, Accardo E, Vanoni M, Del Bavero E, Cantù L, Kirschner DA, Manzoni C, Beeg M, Ceci P, Ubezio P, Forloni G, Tagliavini F, Salmona M (2006). J Biol Chem 281:843

    CAS  Google Scholar 

  115. Laws DD, Bitter HML, Liu K, Ball HL, Kaneko K, Wille H, Cohen FE, Prusiner SB, Pines A, Wemmer DE (2001). Proc Natl Acad Sci USA 98:11686

    CAS  Google Scholar 

  116. Supattopone S, Bosque P, Muramoto T, Wille H, Aagaard C, Peretz D, Nguyen HOB, Heinrich C, Torchia M, Safar J, Cohen FE, DeArmond SJ, Prusiner SB, Scott M (1999). Cell 96:869

    Google Scholar 

  117. Florio T, Paludi D, Villa V, Rossi Principe D, Corsaro A, Millo E, Damonte G, D’Arrigo C, Russo C, Schettini G, Aceto A (2003). J Neurochem 85:62

    Article  CAS  Google Scholar 

  118. Jobling MF, Stewart AR, White AR, McLean C, Friedhuber A, Maher F, Beyereuther K, Masters CL, Barrow CL, Collins SJ, Cappai R (1999). J Neurochem 73:1557

    CAS  Google Scholar 

  119. Macyk W, Franke A, Stochel G (2005). Coord Chem Rev 249:2437

    CAS  Google Scholar 

  120. Armstrong FA (2004). Curr Opin Chem Biol 8:133

    CAS  Google Scholar 

  121. Evans DJ, Pickett CJ (2003). Chem Soc Rev 32:268

    Google Scholar 

  122. Volbeda A, Fontecilla-Camps JC (2005). Coord Chem Rev 249:1609

    CAS  Google Scholar 

  123. Bruschi M, Zampella G, Fantucci P, De Gioia L (2005). Coord Chem Rev 249:1620

    CAS  Google Scholar 

  124. Butler A, Clague MJ, Meister GE (1994). Chem Rev 94:625

    CAS  Google Scholar 

  125. Plass W (2003). Coord Chem Rev 237:205

    CAS  Google Scholar 

  126. Messerschmidt A, Wever R (1996). Proc Natl Acad Sci USA 93:392

    CAS  Google Scholar 

  127. Messerschmidt A, Prade L, Wever R (1997). Biol Chem 378:309

    Article  CAS  Google Scholar 

  128. Ban F, Rankin KN, Gauld JW, Boyd RJ (2002). Theoretical Chemistry Accounts 108:1

    CAS  Google Scholar 

  129. Friesner RA (2005). Proc Natl Acad Sci USA 102:6648

    CAS  Google Scholar 

  130. Niu S, Hall MB (2000). Chem Rev 100:353

    CAS  Google Scholar 

  131. Siegbahn PEM, Blomberg MRA (2000). Chem Rev 100:421

    CAS  Google Scholar 

  132. Lovell T, Himo F, Han W-G, Noodleman L (2003). Coord Chem Rev 238–239:211

    Google Scholar 

  133. Friesner RA, Baik M-H, Gherman BF, Guallar V, Wirstam M, Murphy RB, Lippard SJ (2003). Coord Chem Rev 238–239:267

    Google Scholar 

  134. Improta R, Barone V (2004). J Comput Chem 25:1333

    CAS  Google Scholar 

  135. Becke AD (1988). Phys Rev A 38:3098

    CAS  Google Scholar 

  136. Perdew JP (1986). Phys Rev B 33:8822

    Google Scholar 

  137. De Gioia L, Fantucci P, Guigliarelli B, Bertrand P (1999). Inorg Chem 38:2658

    CAS  Google Scholar 

  138. De Gioia L, Fantucci P, Guigliarelli B, Bertrand P (1999). Int J Quantum Chem 73:187

    CAS  Google Scholar 

  139. Stein M, Lubitz W (2002). Curr Opin Chem Biol 6:243

    CAS  Google Scholar 

  140. Reiher M, Salomon O, Sellmann D, Hess BA (2001). Chem Eur J 7:5195

    CAS  Google Scholar 

  141. Cavallo L, Jacobsen H (2003). J Phys Chem A 107:5466

    CAS  Google Scholar 

  142. Paulsen H, Duelund L, Winkler H, Toftlund H, Trautwein AX (2001). Inorg Chem 40:2201

    CAS  Google Scholar 

  143. Poli R, Harvey JN (2003). Chem Soc Rev 32:1

    CAS  Google Scholar 

  144. Bruschi M, De Gioia L, Zampella G, Reiher M, Fantucci P, Stein M (2004). J Biol Inorg Chem 9:873

    CAS  Google Scholar 

  145. Bruschi M, Fantucci P, De Gioia L (2003). Inorg Chem 42:4773

    CAS  Google Scholar 

  146. Bruschi M, Fantucci P, De Gioia L (2002). Inorg Chem 41:1421

    CAS  Google Scholar 

  147. Fan H-J, Hall MB (2001). J Am Chem Soc 123:3828

    CAS  Google Scholar 

  148. Bruschi M, Fantucci P, De Gioia L (2004). Inorg Chem 43:3733

    CAS  Google Scholar 

  149. Tard C, Liu X, Ibrahim SK, Bruschi M, De Gioia L, Davies SC, Yang X, Wang LS, Sawers G, Pickett CJ (2005). Nature 433:610

    CAS  Google Scholar 

  150. Zampella G, Greco C, Fantucci P, De Gioia L (2006). Inorg Chem 45:4109

    CAS  Google Scholar 

  151. Boyke CA, van der Vlugt JI, Rauchfuss TB, Wilson SR, Zampella G, De Gioia L (2005). J Am Chem Soc 127:11010

    CAS  Google Scholar 

  152. Zampella G, Bruschi M, Fantucci P, De Gioia L. (2005). J Am Chem Soc 127:13180

    CAS  Google Scholar 

  153. George SJ, Cui Z, Razavet M, Pickett CJ, (2002). Chem Eur J 8:4037

    CAS  Google Scholar 

  154. Zampella G, Bruschi M, Fantucci P, Razavet M, Pickett CJ, De Gioia L (2005). Chem Eur J 11:509

    CAS  Google Scholar 

  155. Zampella G, Kravitz JY, Webster CE, Fantucci P, Hall MB, Carlson HA, Pecoraro VL, De Gioia L (2004). Inorg Chem 43:4127

    CAS  Google Scholar 

  156. Zampella G, Fantucci P, Pecoraro VL, De Gioia L (2005). J Am Chem Soc 127:953

    CAS  Google Scholar 

  157. Todeschini R, Moro G, Boggia R, Bonati L, Cosentino U, Lasagni M, Pitea D (1997). Chemom Intell Lab Syst 36:65

    CAS  Google Scholar 

  158. Cramer RD, Patterson DE, Bunce JD (1998). J Am Chem Soc 110:5959

    Google Scholar 

  159. Forloni G, Varì MR, Colombo L, Bugiani O, Tagliavini F, Salmona M (2003). Curr Med Chem – Imun Endoc and Metab Agents 3:185

    CAS  Google Scholar 

  160. Forloni, G, Iussich S, Awan T, Colombo L, Angeretti N, Girola L, Bertani I, Poli G, Caramelli M, Grazia Bruzzone M, Farina L, Limido L, Rossi G, Giaccone G, Ironside JW, Bugiani O, Salmona M, Tagliavini F (2002). Proc Natl Acad Sci USA 99:10849

    CAS  Google Scholar 

  161. Forloni G, Colombo L, Girola L, Tagliavini F, Salmona M (2001). FEBS Lett 487:404

    CAS  Google Scholar 

  162. Tagliavini F, Forloni G, Colombo L, Rossi G, Girola L, Canciani B, Angeretti N, Giampaolo L, Peressini E, Awan T, De Gioia L, Ragg E, Bugiani O, Salmona M (2000). J Mol Biol 300:1309

    CAS  Google Scholar 

  163. Chopra I, Roberts M (2001). Microbiol Mol Biol Rev 65:232

    CAS  Google Scholar 

  164. Mitscher LA (1978) The chemistry of tetracycline antibiotics. Marcel Dekker, New York

    Google Scholar 

  165. De Leenheer AP, Nelis HJ (1979). J Pharm Sci 68:999

    CAS  Google Scholar 

  166. Schneider S (2001). In: Greenwald RA, Hillen W, Nelson M (eds). Tetracyclines in biology, chemistry and medicine. Birkhaüser Verlag, Basel, p 65

  167. Cosentino U, Varì MR, Saracino AAG, Pitea D, Moro G, Salmona M (2005). J Mol Model 11:17

    CAS  Google Scholar 

  168. Chang G, Guida WC, Still WC (1989). J Am Chem Soc 111:4379

    CAS  Google Scholar 

  169. Saunders M, Houk KN, Dong Wu Y, Still CW, Lipton M, Chang G, Guida WC (1990). J Am Chem Soc 112:1419

    CAS  Google Scholar 

  170. Still WC, Tempczyk A, Hawley RC, Hendrickson T (1990). J Am Chem Soc 112:6127

    CAS  Google Scholar 

  171. Weiser J, Weiser AA, Shenkin PS, Still WC (1998). J Comput Chem 19:797

    CAS  Google Scholar 

  172. Mohamadi F, Richards NGJ, Guida WC, Liskamp R, Lipton M, Caufield C, Chang G, Hendrikson T, Still WC (1990). J Comput Chem 11:440

    CAS  Google Scholar 

  173. Maestro Molecular Modeling Interface V. 4.1.012, Schrödinger, Inc., Portland, Oregon 97201

Download references

Author information

Authors and Affiliations

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

    Giorgio Moro, Luca De Gioia, Pier Carlo Fantucci, Elena Papaleo, Gloria A. A. Saracino & Giuseppe Zampella

  2. Dipartimento di Scienze dell’Ambiente e del Territorio, Università di Milano-Bicocca, Piazza della Scienza, Milano, 20126, Italy

    Laura Bonati, Maurizio Bruschi, Ugo Cosentino, Alessandro Pandini & Demetrio Pitea

Authors
  1. Giorgio Moro
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Laura Bonati
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Maurizio Bruschi
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Ugo Cosentino
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Luca De Gioia
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Pier Carlo Fantucci
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Alessandro Pandini
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Elena Papaleo
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Demetrio Pitea
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Gloria A. A. Saracino
    View author publications

    You can also search for this author in PubMed Google Scholar

  11. Giuseppe Zampella
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Giorgio Moro.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Moro, G., Bonati, L., Bruschi, M. et al. Computational approaches to shed light on molecular mechanisms in biological processes. Theor Chem Account 117, 723–741 (2007). https://doi.org/10.1007/s00214-006-0203-4

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00214-006-0203-4

Keywords

Search

Navigation