Journal of the American Chemical Society carbonylable.7,56 Superoxide dismutase 1 in familial amyotrophic lateral sclerosis,7,52 human β2-microglobulin in end-stage renal failure,52,57 and β-actin and R/β-tubulin in multiple sclerosis58 are further examples of such proteins. Importantly, our results provide a novel explanation that links aggregation and carbonyla- tion in these systems, even at relatively low levels of carbonyla- tion typically seen in vivo. One way to test this connection experimentally would be to use Lys to Leu, Arg to Val, and Pro to Val point mutations for high-resolution, site-speciﬁc studies of the structural and functional consequences of carbonylation, as these mutations, according to our results, quantitatively match the eﬀects of hydrophobicity increase and charge removal in the course of carbonylation. Such studies, hand in hand with further computational analyses, may provide an atomistic picture behind protein carbonylation and its cellular consequences, protein aggre- gation, and cell senescence. ’ ASSOCIATED CONTENT bS Supporting Information. Figures showing TI, MHP vs rmsd free energy surfaces, and Zagg results; table of physico- chemical properties of Asa, Gsa, Leu, and Val; parametrization of Asa and Gsa residues; and details of TI calculation. This material is available free of charge via the Internet at http://pubs.acs.org. ’ AUTHOR INFORMATION Corresponding Author bojan.zagrovic@univie.ac.at ’ ACKNOWLEDGMENT This work was supported in part by the National Foundation of Science, Higher Education and Technological Development of Croatia (EMBO Installation grant to B.Z.), the Unity through Knowledge Fund (UKF 1A grant to B.Z.), and the Austrian Science Fund FWF (START grant Y 514-B11 to B.Z.). We thank A. Polyansky for help with MHP calculations, R. Zubac for help with entropy calculations, R. Santos for help with graphical representation of villin headpiece, and the members of the Laboratory of Computational Biophysics at MFPL for useful advice and assistance. ’ REFERENCES (1) Stadtman, E. R. Science 1992, 257, 1220. (2) Berlett, B. S.; Stadtman, E. R. J. Biol. Chem. 1997, 272, 20313. (3) Levine, R. L.; Stadtman, E. R. Exp. Gerontol. 2001, 36, 1495. (4) Nystrom, T. EMBO J. 2005, 24, 1311. (5) Requena, J. R.; Levine, R. L.; Stadtman, E. R. Amino Acids 2003, 25, 221. (6) Maisonneuve, E.; Ducret, A.; Khoueiry, P.; Lignon, S.; Longhi, S.; Talla, E.; Dukan, S. PLoS One 2009, 4, e7269. (7) Dalle-Donne, I.; Giustarini, D.; Colombo, R.; Rossi, R.; Milzani, A. Trends Mol. Med. 2003, 9, 169. (8) Dalle-Donne, I.; Rossi, R.; Colombo, R.; Giustarini, D.; Milzani, A. Clin. Chem. 2006, 52, 601. (9) Dalle-Donne, I.; Aldini, G.; Carini, M.; Colombo, R.; Rossi, R.; Milzani, A. J. Cell. Mol. Med. 2006, 10, 389. (10) Levine, R. L. Free Radical Biol. Med. 2002, 32, 790. (11) Grune, T.; Jung, T.; Merker, K.; Davies, K. J. Int. J. Biochem. Cell Biol. 2004, 36, 2519. (12) Davies, K. J. Biochimie 2001, 83, 301. ARTICLE (13) Krisko, A.; Radman, M. Proc. Natl. Acad. Sci. U.S.A. 2010, 107, 14373. (14) Davies, K. J. A.; Delsignore, M. E. J. Biol. Chem. 1987, 262, 9908. (15) Gardner, P. R.; Nguyen, D. D. H.; White, C. W. Proc. Natl. Acad. Sci. U.S.A. 1994, 91, 12248. (16) Lasch, P.; Petras, T.; Ullrich, O.; Backmann, J.; Naumann, D.; Grune, T. J. Biol. Chem. 2001, 276, 9492. (17) Bota, D. A.; Davies, K. J. A. Nat. Cell Biol. 2002, 4, 674. (18) Le, H. T.; Chaﬀotte, A. F.; Demey-Thomas, E.; Vinh, J.; Friguet, B.; Mary, J. J. Mol. Biol. 2009, 393, 58. (19) Perez, V. I.; Buﬀenstein, R.; Masamsetti, V.; Leonard, S.; Salmon, A. B.; Mele, J.; Andziak, B.; Yang, T.; Edrey, Y.; Friguet, B.; Ward, W.; Richardson, A.; Chaudhuri, A. Proc. Natl. Acad. Sci. U.S.A. 2009, 106, 3059. (20) Wu, W.; Wu, X. J.; Hu, Y. F. LWT-Food Sci. Technol. 2010, 43, 133. (21) van Gunsteren, W. F.; Bakowies, D.; Baron, R.; Chandrasekhar, I.; Christen, M.; Daura, X.; Gee, P.; Geerke, D. P.; Glattli, A.; Hunenber- ger, P. H.; Kastenholz, M. A.; Oostenbrink, C.; Schenk, M.; Trzesniak, D.; van der Vegt, N. F.; Yu, H. B. Angew. Chem. Int. Ed. 2006, 45, 4064. (22) Khurana, S.; George, S. P. FEBS Lett. 2008, 582, 2128. (23) Friederich, E.; Vancompernolle, K.; Louvard, D.; Vandekerckhove, J. J. Biol. Chem. 1999, 274, 26751. (24) Dalle-Donne, I.; Rossi, R.; Giustarini, D.; Gagliano, N.; Lusini, L.; Milzani, A.; Di Simplicio, P.; Colombo, R. Free Radical Biol. Med. 2001, 31, 1075. (25) Dalle-Donne, I.; Rossi, R.; Milzani, A.; Di Simplicio, P.; Colombo, R. Free Radical Biol. Med. 2001, 31, 1624. (26) McKnight, C. J.; Matsudaira, P. T.; Kim, P. S. Nat. Struct. Biol. 1997, 4, 180. (27) Duan, Y.; Kollman, P. A. Science 1998, 282, 740. (28) Zagrovic, B.; Snow, C. D.; Shirts, M. R.; Pande, V. S. J. Mol. Biol. 2002, 323, 927. (29) Zagrovic, B.; Snow, C. D.; Khaliq, S.; Shirts, M. R.; Pande, V. S. J. Mol. Biol. 2002, 323, 153. (30) Meng, J.; Vardar, D.; Wang, Y.; Guo, H. C.; Head, J. F.; McKnight, C. J. Biochemistry 2005, 44, 11963. (31) Lei, H.; Wu, C.; Liu, H.; Duan, Y. Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 4925. (32) Cornilescu, G.; Hadley, E. B.; Woll, M. G.; Markley, J. L.; Gellman, S. H.; Cornilescu, C. C. Protein Sci. 2007, 16, 14. (33) Gronwald, W.; Hohm, T.; Hoﬀmann, D. BMC Bioinformatics 2008, 9, 109. (34) Schuler, L. D.; Walde, P.; Luisi, P. L.; van Gunsteren, W. F. Eur. Biophys. J. 2001, 30, 330. (35) Schuler, L. D.; Daura, X.; van Gunsteren, W. F. J. Comput. Chem. 2001, 22, 1205. (36) Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.; Hermans, J. Interaction models for water in relation to protein hydration; Reidel: Dordrecht, 1981. (37) Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.; Dinola, A.; Haak, J. R. J. Chem. Phys. 1984, 81, 3684. (38) Lindahl, E.; Hess, B.; van der Spoel, D. J. Mol. Modell. 2001, 7, 306. (39) Kabsch, W.; Sander, C. Biopolymers 1983, 22, 2577. (40) Andricioaei, I.; Karplus, M. J. Chem. Phys. 2001, 115, 6289. (41) Levy, R. M.; Srinivasan, A. R.; Olson, W. K.; McCammon, J. A. Biopolymers 1984, 23, 1099. (42) Efremov, R. G.; Chugunov, A. O.; Pyrkov, T. V.; Priestle, J. P.; Arseniev, A. S.; Jacoby, E. Curr. Med. Chem. 2007, 14, 393. (43) Chiti, F.; Stefani, M.; Taddei, N.; Ramponi, G.; Dobson, C. M. Nature 2003, 424, 805. (44) Tartaglia, G. G.; Pawar, A. P.; Campioni, S.; Dobson, C. M.; Chiti, F.; Vendruscolo, M. J. Mol. Biol. 2008, 380, 425. (45) Dobson, C. M. Nature 2003, 426, 884. (46) Godoy-Ruiz, R.; Henry, E. R.; Kubelka, J.; Hofrichter, J.; Munoz, V.; Sanchez-Ruiz, J. M.; Eaton, W. A. J. Phys. Chem. B 2008, 112, 5938. 7023 dx.doi.org/10.1021/ja110577e |J. Am. Chem. Soc. 2011, 133, 7016–7024