Molecular dynamics simulations of proteins and peptides: From folding to drug design

Current Protein and Peptide Science

Volumn 9, Issue 2, 2008, Pages 181-196

  Morra, Giulia ^a   Meli, Massimiliano ^a   Colombo, Giorgio ^a  

^a CNR   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

5 AMINO 4 IMIDAZOLECARBOXAMIDE RIBOSIDE; ANSAMYCIN DERIVATIVE; ANTINEOPLASTIC AGENT; LIGAND; LIPID; MONOMER; NUCLEIC ACID; OLIGOMER; PEPTIDE; PEPTIDE DERIVATIVE; PROTEIN; SHEPHERDIN; TANESPIMYCIN; UNCLASSIFIED DRUG;

AB INITIO CALCULATION; ANTINEOPLASTIC ACTIVITY; BIOINFORMATICS; CLINICAL TRIAL; COMPUTER SIMULATION; DRUG DESIGN; HUMAN; HYDROPHOBICITY; METHODOLOGY; MOLECULAR DYNAMICS; MOLECULAR EVOLUTION; NEOPLASM; NONHUMAN; POINT MUTATION; PROTEIN AGGREGATION; PROTEIN ASSEMBLY; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN INTERACTION; PROTEIN STABILITY; PROTEIN STRUCTURE; REVIEW; SUPRAMOLECULAR CHEMISTRY;

COMPUTER SIMULATION; DRUG DESIGN; MODELS, MOLECULAR; PEPTIDES; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEINS; THERMODYNAMICS;

EID: 42049106418     PISSN: 13892037     EISSN: None     Source Type: Journal    
DOI: 10.2174/138920308783955234     Document Type: Review

References (155)

1. Whitesides, G.M., Mathias, J.P. and Seto, C.T. (1991) Science, 254, 1312-1319.
2. Voet, D. and Voet, J.G. (2004) Biochemistry, Wiley: Hoboken, NJ.
3. Anfinsen, C.B. (1973) Science, 181, 223-230.
4. Levinthal, C. (1969) Univcrsity of Illinois, Press: Urbana.
5. Dill, K.A. and Chan, H.S. (1997) Nature Struct. Biol., 4, 10-19.
6. van Gunsteren, W.F., Burgi, R., Peter, C. and Daura, X. (2001) Angew. Chem. Int. Ed., 40, 352-355.
7. Rose, G.D., Fleming, P.J., Banavar, J.R. and Maritan, A. (2006) Proc. Natl. Acad. Sci. USA, 103, 16623-16633.
8. Fitzkee, N.C., Fleming, P.J., Gong, H.P., Panasik, N., Street, T.O. and Rose, G.D. (2005) Trends Bioch. Sci., 30, 73-80.
9. Watters, A.L., Deka, P., Corrent, C., Callender, D., Varani, G., Sosnick, T. and Baker, D. (2007) Cell, 128, 613-624.
10. Bradley, P., Misura, K.M.S. and Baker, D. (2005) Science, 309, 1868-1871.
11. Hao, M.-H. and Scheraga, H.A. (1998) J. Mol. Biol., 277, 973-983.
12. Srinivasan, R., Fleming, P.J. and Rose, G.D. (2004) Methods Eznymol., 383, 48.
13. Chiti, F. and Dobson, C.M. (2006) Annu. Rev. Biochem., 75, 333-366.
14. Berriman, J., Serpell, L.C., Oberg, K.A., Fink, A.L., Goedert, M. and Crowther, R.A. (2003) PNAS, 100, 9034-9038.
15. Serpell, L.C. (2000) Biochim. Biophys. Acta. 1502, 16-30.
16. Makin, O.S. and Serpell, L.C. (2005) FEBS J., 272, 5950-5961.
17. Lansbury, P.T. and Lashuel, H.A. (2006) Nature, 443, 774-779.
18. Cohen, E., Bieschke, J., Perciavalle, R.M., Kelly, J.W. and Dillin, A. (2006) Science, 313, 1604-1610.
19. Chapman, M.R., Robinson, L.S., Pinkner, J.S., Roth, R., Heuser, J., Hammar, M., Normark, S. and Hultgren, S.J. (2002) Science, 295, 851-855.
20. Gebbink, M.F., Claessen, D., Bouma, B., Dijkhuizen, L. and Wosten, H.A. (2005) Nat. Rev. Microbiol., 3, 333-341.
21. Matsui, H., Gologan, B., Pan, S. and Douberly, G.E. (2001) Eur. Phys. J. D., 16, 403-406.
22. Aggeli, A., Bell, M., Boden, N., Keen, J.N., Knowles, P.F., McLeish, T.C.B., Pitkeathly, M. and Radford, S.E. (1997) Nature, 386, 259-262.
23. Matsui, H., Pan, S., Gologan, B. and Jonas, S.H. (2000) J. Phys. Chem. B., 104, 9576-9679.
24. Hartgerink, J.D., Beniash, E. and Stupp, S.I. (2001) Science, 294, 1648-1688.
25. Vauthey, S., Santoso, S., Gong, H.Y., Watson, N. and Zhang, S.G. (2002) Proc. Natl. Acad Sci. USA, 99, 5355-5360.
26. Tsai, C.J., Zheng, J., Aleman, C. and Nussinov, R. (2006) Trends. Biotechnol., 24, 449-454.
27. Mahler, A., Reches, M., Rechter, M., Cohen, S. and Gazit, E. (2006) Adv. Mater., 18, 1365-1370.
28. Reches, M. and Gazit, E. (2003) Science, 300, 625-627.
29. Hun Mok, K., Kuhn, L.T., Martin, G., Day, I.J., Lin, J.C., Andersen, N.H. and Hore, P.J. (2007) Nature, 447, 106-109.
30. Xu, Y., Purkayastha, P. and Gai, F. (2006) J. Am. Chem. Soc., 128, 15836-15842.
31. Jeganathan, S.v.B., M., Brutlach, H., Steinhoff, H.-J. and Mandelkow, E. (2006) Biochemistry, 45, 2283-2293.
32. Venanzi, M., Gatto, E., Bocchinfuso, G., Palleschi, A., Stella, L., Baldini, C., Formagglo, F. and Toniolo, C. (2006) J. Phys. Chem. B., 110, 22834-22841.
33. Thirumalai, D. and Hyeon, C. (2005) Biochemistry, 44, 4957-4970.
34. Klimov, D.K. and Thirumalai, D. (2004) J. Chem. Phys., 307, 251-258.
35. Brooks, C.L.I. and Boczko, E.M. (1995) Science, 269, 393-396.
36. Wu, X., Wang, S. and Brooks, B.R. (2002) J. Am. Chem. Soc., 124, 5282-5283.
37. Brooks, C.L.I. (1993) Curr. Op. Struct. Biol., 3, 92-98.
38. Brooks, C.L.I., Karplus, M. and Pettitt, B.M. (1988) John Wiley and Sons, New York.
39. van Gunsteren, W.F., Bakowies, D., Baron, R., Chandrasekhar, I., Christen, M., Daura, X., Gee, P., Geerke, D.P., Glättli, A., Hünenberger, P.H., Kastenholz, M.A., Oostenbrink, C., Schenk, M., Trzesniak, D., van der Vegt, N.F.A. and Yu, H.B. (2006) Angew. Chem. Int. Ed., 45, 4064-4092.
40. Scheraga, H.A., Khalili, M. and Liwo, A. (2007) Annu. Rev. Phys. Chem., 58, 57-83.
41. Kwak, W. and Hansmann, U.H.E. (2005) Phys. Rev. Lett., 95, 138102.
42. Shea, J.E. and Brooks, C.L. (2001) Annu. Rev. Phys. Chem., 52, 499-535.
43. Shea, J.E., Onuchic, J.N. and Brooks, C.L. (2000) J. Chem. Phys., 113, 7663-7671.
44. Shea, J.E., Onuchic, J.N. and Brooks, C.L. (2002) Proc. Natl. Acad. Sci. USA, 99, 16064-16068.
45. Warshel, A. and Levitt, M. (1976) J. Mol. Bio., 106, 421-437.
46. Levitt, M. and Warshel, A. (1975) Nature, 253, 694-698.
47. Levy, Y. and Onuchic, J.N. (2006) Acc. Chem. Res., 39, 135-142.
48. Suzuki, Y. and Onuchic, J.N. (2005) J. Phys. Chem. B., 109, 16503-16510.
49. Chan, H.S. and Dill, K. (1996) Proteins: Struct. Funct. Genet., 24, 335-344.
50. Chan, H.S. and Dill, K. (1997) Proteins: Struct. Funct. Genet., 8, 2-33.
51. Dobson, C.M., Sali, A. and Karplus, M. (1998) Angew. Chem. Int. Ed., 37, 869-893.
52. Mirny, L. and Shakhnovich, E.I. (2001) Ann. Rev. Biophys. Biomol. Struct., 30, 361-389.
53. Mirny, L.A., Abkevich, V.I. and Shakhnovich, E.I. (1998) Proc. Natl. Acad. Sci. USA, 95, 4976-4981.
54. Abkevich, V.I., Gutin, A.M. and Shakhnovich, E.I. (1994) Biochemistry, 22, 10026.
55. Kolinsky, A. and Skolnick, J. (1994) Proteins, 18, 338-352.
56. Cieplak, M., Henkel, M., Karbowski, J. and Banavar, J.R. (1998) Phys. Rev. Lett., 80, 3654-3657.
57. Arnold, F.H. (1998) Acc. Chem. Res., 31, 125-131.
58. Bloom, J.D., Silberg, J.J., Wilke, C.O., Drummond, D.A., Adami, C. and Arnold, F.H. (2005) Proc. Natl. Acad Sci. USA, 102, 606-611.
59. England, J.L., Shakhnovich, B.E. and Shakhnovich, E.I. (2003) Proc. Natl. Acad. Sci. USA, 100, 8727-8731.
60. Bloom, J.D., Labthavikul, S.T., Otey, C.R. and Arnold, F.H. (2006) Proc. Natl. Acad. Sci. USA, 103, 5869-74.
61. Levitt, M., Gerstein, M., Huang, E., Subbiah, S. and Tsai, J. (1997) Ann. Rev. Biochem., 66, 549-579.
62. Park, B. and Levitt, M. (1996) J. Mol. Biol., 258, 367-392.
63. Shakbnovicb, E. (2006) Chemical Reviews, 106 1559-1588.
64. Kolinski, A.G. and Skolnick, J. (1998) Chem. Phys., 108, 2608-2617.
65. Kolinski, A.G. and Skolnick, J. (1993) J. Chem. Phys., 98, 7420-7433.
66. Liwo, A., Mey, K. and Scheraga, H.A. (2005) Proc. Natl. Acad. Sci. USA, 102, 2362-2367
67. Wei, G.H., Mousseau, N. and Derreumaux, P. (2004) Biophys. J., 87, 3648-3656.
68. Santini, S., Mousseau, N. and Derreumaux, P. (2004) J. Am. Chem. Soc., 126, 11509-11516.
69. Mousseau, N. and Derreumaux, P. (2005) Acc. Chem. Res., 38, 885-891.
70. Derreumaux, P. (2000) Phys. Rev. Lett., 85, 206-209.
71. Ding, F. and Dokholyan, N.V. (2005) Trends Biotech., 23 450-455.
72. Khare, S.D., Ding, F., Gwanmesia, K.N. and Dokbolyan, N.V. (2005) PLoS Computational Biology, 1, 230-235.
73. Duan, Y. and Kollman, P.A. (1998) Science, 282, 740-749.
74. Kubelka, J., Eaton, W.A. and Hofrichter, J. (2003) J. Mol. Biol., 329, 625-630.
75. Daura, X., vanGunsteren, W.F., Rigo, D., Jaun, B. and Seebach, D. (1997) Chem. Eur. J., 3, 1410-1417.
76. Daura, X., Jaun, B., Seebach, D., van Gunsteren, W.F. and Mark, A.E. (1998) J. Mol. Biol., 280, 925-932.
77. Lei, HX, Dastidar, S.G. and Duan, Y. (2006) J. Phys. Chem. B., 110, 22001-22008.
78. Khandogin, J., Chen, J.H. and Brooks, C.L. (2006) Proc. Natl. Acad. Sci. USA, 103, 18546-18550.
79. Simmerling, C., Stockbine, B. and Roitberg, A.E. (2002) J. Am. Chem. Soc., 124, 11258-12259.
80. Roe, D.R., Hornak, V. and Simmerling, C. (2005) J. Mol. Biol., 352, 370-381.
81. Jang, S., Shin, S. and Pak, Y. (2002) J. Am. Chem. Soc., 124, 4976-4977.
82. Gsponer, J. and Callisch, A. (2002) Proc. Natl. Acad. Sci. USA, 99, 6719-6724.
83. Sugita, Y. and Okamoto, Y. (1999) Chem. Phys. Lett, 314, 141-151.
84. Sugita, Y. and Okamoto, Y. (2000) Chem. Phys. Lett., 329, 261-270.
85. Baumketner, A. and Shea, J.E. (2006) Theoret. Chem. Acc., 116, 262-273
86. Garcia, A.E. and Onuchic, J.N. (2003) Proc. Natl. Acad. Sci. USA, 100, 13898-13903.
87. Hofinger, S., Almeida, B. and Hansmann, U.H.E. (2007) Proteins: Struct. Funct. Bioinf, 68, 662-669.
88. Pascbek, D., Nymeyer, H. and Garcia, A.E. (2007) J. Struct. Biol., 157, 524-533.
89. Jang, S., K.E., Pak, Y. (2007) Proteins: Struct. Funct. Bioinf., 66, 53-60.
90. Kannan, S. and Zacharias, M. (2007) Protein,: Struct. Funct. Bioinf, 66, 697-706.
91. Liu, P., Huang, X.H., Zhou, R.H. and Berne, B.J. (2006) J. Phys. Chem. B., 110, 19018-19022.
92. Smith, C.K. and Regan, L. (1995) Science, 270, 990-982.
93. Colombo, G., DeMori, G.M.S. and Roccatano, D. (2003) Prot. Sci., 12, 538-550.
94. Booth, D.R. (1997) Nature, 385, 787.
95. Kelly, J.W. (1997) Structure, 5, 595.
96. Colombo, G., Roccatano, D. and Mark, A.E. (2002) Proteins: Struct. Funct. Genet., 46, 380-392.
97. Soto, P. and Colombo, G. (2004) Proteins: Struct. Funct. Bioinf., 57, 734-746.
98. Espinosa, J.F., Munoz, V. and Gellman, S.H. (2001) J. Mol. Biol., 306, 397-402.
99. Soto, P. and Zangi, R. (2005) J. Phys. Chem. B, 109, 1281-1288.
100. Colombo, G. and Micheletti, C. (2006) Theoret. Chem. Acc., 116, 75-86
101. De Mori, G.M.S., Micheletti, C. and Colombo, G. (2004) J. Phys. Chem. B, 108, 12267-12270.
102. De Mori, G.M.S., Colombo, G. and Micheletti, C. (2005) Proteins: Struct. Funct. Bioinf., 58, 459-471
103. Fogolari, F., Tosatto, S.C.E. and Colombo, G. (2005) BMC Bioinformatics, 6, 301.
104. Liu, P. and Voth, G. (2007) J. Chem. Phys., 126, 045106.
105. Lyman, E., Ytreberg, F.M. and Zuckerman, D.M. (2006) Phys. Rev. Lett., 96, 028105.
106. Jaenicke, R. and Boehm, G. (1998) Curr. Op. Struct. Biol., 8, 738-48.
107. Dill, K.A. (1990) Biochemistry, 29, 7133-55.
108. Zeldovich, K.B., Berezovsky, I.N. and Shakhnovich, E.I. (2007) Plos Comput. Biol., 3, e5.
109. Robinson-Rechavi, M. and Godzik, A. (2005) Structure, 12, 857-860.
110. Robinson-Rechavi, M., Alibés, A. and Godzik, A. (2006) J. Mol. Biol., 356.
111. Plaxco, K.W., Simons, K.T. and Baker, D. (1998) J. Mol. Biol., 277, 985-994.
112. Colombo, G. and Merz, K.M.Jr. (1999) J. Am. Chem. Soc., 121, 6895-6903.
113. Gilis, D. and Rooman, M. (1997) J. Mol. Biol., 272, 276-290.
114. Larson, S.M. and Davidson, A.R. (2000) Protein Sci., 9, 2170-2180.
115. Guerois, R., Nielsen, J.E. and Serrano, L. (2002) J. Mol. Biol., 320, 320-387.
116. Pitera, J.W. and Kollman, P.A. (2000) Proteins, 41, 385-397.
117. Vendruscolo, M., Paci, E., Dobson, C.M. and Karplus, M. (2001) Nature, 409, 641-645.
118. Paci, E., Vendruscolo, M., Dobson, C.M. and Karplus, M. (2002) J. Mol. Biol., 324, 151-163.
119. Lindorff-Larsen, K., Paci, E., Serrano, L., Dobson, C.M. and Vendruscolo, M. (2003) Biophys. J., 85, 1207-14.
120. Takada, S. (1999) Proc. Natl. Acad. Sci. USA, 96, 11698-11700.
121. Bryngelson, J.D., Onuchic, J.N., Socci, N.D. and Wolynes, P.G. (1995) Proteins: Struct. Funct. Genet., 21, 167-195.
122. Kleiner, A. and Shakhnovich, E. (2007) Biophys. J., 92, 2054-61.
123. Hubner, I.A., Oliveberg, M. and Shakhnovich, E.I. (2004) Proc. Natl. Acad. Sci. USA, 101, 8354-9.
124. Berezovsky, I.N., Chen, W.W., Choi, P.J. and Shakhnovich, E.I. (2005) PLoS Comput. Biol., 1, 322-332.
125. Brown, S. and Head-Gordon, T. (2004) Protein Sci., 13, 958-70.
126. Das, P., Matysiak, S. and Clementi, C. (2005) Proc. Natl. Acad. Sci. USA, 102, 10141-10146.
127. Perl, D., Welker, C., Schindler, T., Schroder, K., Marahiel, M.A., Jaenicke, R. and Schmid, F.X. (1998) Nat. Struct. Biol., 5, 229-235.
128. Alm, E. and Baker, D. (1999) Proc. Natl. Acad. Sci. USA, 96, 11305-11310.
129. Xiao, L. and Honig, B. (1999) J. Mol. Biol., 289, 1435-44.
130. Elcock, A.H. (1998) J. Mol. Biol., 284, 489-502.
131. Tiana, G., Simona, F., Mori, G.M.S.D., Broglia, R.A. and Colombo, G. (2004) Protein Sci., 13, 113-124.
132. Colacino, S., Tiana, G., Broglia, R.A. and Colombo, G. (2006) Proteins: Struct. Funct. Bioinfor., 62, 698-707.
133. Colacino, S., Tiana, G. and Colombo, G. (2006) BMC Struct. Biol., 6.
134. Ragona, L., Colombo, G., Catalano, M. and Molinari, H. (2005) Proteins: Struct. Funct. Bioinfor., 61, 366-376.
135. Nelson, R., Sawaya, M.R., Balbirnie, M., Madsen, A.O., Rickel, C., Grothe, R. and Eisenberg, D. (2005) Nature, 435, 773-778.
136. Ellis-Behnke, R.G., Liang, Y.X., You, S.W., Tay, D.K., Zhang, S., So, K.F. and Schneider, G.E. (2006) Proc. Natl. Acad. Sci. USA, 5054-5059.
137. Kayed, R., Head, E., Thompson, J.L., McIntire, T.M., Milton, S.C., Cotman, C.W. and Glabe, C.G. (2003) Science, 300, 486-489
138. Bucciantini, M., Giannoni, E., Chiti, F., Baroni, F., Formigli, L., Zurdo, J.S., Taddei, N., Ramponi, G., Dobjon, C.M. and Stefani, M. (2002), Nature, 416 507-511.
139. Nilsson, M.R. (2004) Methods, 34 151-160
140. Bitan, G. and Teplow, D.B. (2000) Acc. Chem. Res., 37, 357-364.
141. Daidone, I., Simona, F., Roccatano, D., Broglia, R.A., Tiana, G., Colombo, G. and Nola, A.D. (2004) Proteins: Struct., Funct. Bioinfor., 57, 198-204.
142. Zanuy, D., Gunasekaran, K., Ma, B.Y., Tsai, H.H., Tsai, C.J. and Nussinov, R. (2004) Amyloid, 11, 143-161.
143. Ma, B. and Nussinov, R. (2002) Proc. Natl. Acad. Sci. USA, 99. 14126-14131.
144. Cruz, L., Urbane, B., Borreguero, J.M., Lazo, N.D., Teplow, D.B. and Stanley, H.E. (2005) Proc. Natl. Acad. Sci. USA, 102, 18258-18263.
145. Dokholyan, N.V. (2006) Curr. Op. Struct. Biol., 16 79-85.
146. Flock, D., Colacino, S., Colombo, G., Di Nola, A. (2006) Proteins. Struct. Funct. Bioinfor., 62, 183-192.
147. Cuniasse, P., Raynal, I., Yiotakis, A. and Dive, V. (1997) J. Am. Chem. Soc., 119, 5239-5248.
148. Favrin, G., Irback, A. and Mohanty, S. (2005) Biophys. J., 87, 3657-3664.
149. Burkoth, T.S., Benzinger, T.L.S., Urban, V., Lynn, D.G., Meredith, S.C. and Thiyagarajan, P. (1999) J. Am. Chem. Soc., 121, 7429-7430.
150. Zheng, J., Ma, B.Y., Tsai, C.J. and Nussinov, R. (2006) Biophys. J., 91, 824-833.
151. Plescia, J., Salz, W., Xia, F., Pennati, M., Zaffaroni, N., Daidone, M.G., Meli, M., Dohi, T., Fortugno, P., Nefedova, Y., Gabrilovich, D.I. Colombo, G. and Altieri, D.C. (2005) Cancer Cell, 7, 457-467.
152. Gyurkocza, B., Plescia, J., Raskett, G.M., Garlick, D.S., Lowry, P.A., Carter, B.Z., Andreeff, M., Meli, M., Colombo, G. and Altieri, D.C. (2006) J. Natl. Cancer Inst., 98, 1068-1077.
153. Meli, M., Pennati, M., Curto, M., Daidone, M.G., Plescia, J., Toba, S., Altieri, D.C., Zaffaroni, N. and Colombo, G. (2006) J. Med. Chem., 49, 7721-7730.
154. Altieri, D.C. (2003) Nat. Rev. Cancer, 3, 46-54.
155. Fortugno, P., Beltrami, E., Plescia, J., Fontana, J., Pradhan, D., Marchisio, P.C., Sessa, W.C. and Altieri, D.C. (2003) Proc. Natl. Acad. Sci. USA, 100, 13791-13796.