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Publicly Available Published by De Gruyter April 7, 2012

Exploring metal-driven stereoselectivity of glycopeptides by free-energy calculations

  • Adriana Pietropaolo

A formalism to quantify the chemical stereoselectivity, based on free energy of binding calculations, is here discussed. It is used to explain the stereoselectivity of two diastereoisomeric frameworks, comprising the dimer of a copper(II)-peptide core of L- and D-carnosine, respectively, each bound to two chains of D-trehalose, in which copper(II) adopts a type-II coordination geometry. The stereocenter of carnosine is varied both L and D, giving rise to two diastereoisomers. A thermodynamic cycle crossing the formation of the two enantiomeric copper(II) peptide cores was devised. A harmonic restraining potential that depends only on the bond distance was added to ensure reversibility in bond formation and dissociation, for an accurate estimate of the free energy. The calculation of the free energy of binding between D-trehalose and the two enantiomeric copper(II) peptide cores reproduces the free-energy quantities observed from stability constants and isothermal titration calorimetry (ITC) measurements. This is an example of chirality selection based on free-energy difference.


Conference

IUPAC Congress, IUPAC Congress, CONGRESS, IUPAC Congress, 43rd, San Juan, Puerto Rico, 2011-07-30–2011-08-07


References

1 10.1146/annurev.biochem.68.1.487, H. D. Ly, S. G. Withers. Annu. Rev. Biochem.68, 487 (1999).Search in Google Scholar PubMed

2 L. G. Barrientos, A. M. Gronenborn. Mini. Rev. Med. Chem.5, 21 (2005).10.2174/1389557053402783Search in Google Scholar

3 10.1126/science.164.3876.142, J. Corrigan. Science164, 142 (1969).Search in Google Scholar PubMed

4 N. Fujii. Orig. Life Evol. Biosphere32, 103 (2002).10.1023/A:1016031014871Search in Google Scholar

5 10.1042/BST0381307, P. G. Hitchen, K. Twigger, E. Valiente, R. H. Langdon, B. W. Wren, A. Dell. Biochem. Soc. Trans.38, 1307 (2010).Search in Google Scholar PubMed

6 10.1038/nchembio.437, K. Mariño, J. Bones, J. J. Kattla, P. M. Rudd. Nat. Chem. Biol.6, 713 (2010).Search in Google Scholar PubMed

7 10.1126/science.291.5512.2370, P. M. Rudd, T. Elliott, P. Cresswell, I. A. Wilson, R. A. Dwek. Science291, 2370 (2001).Search in Google Scholar PubMed

8 10.1093/glycob/12.4.43R, R. G. Spiro. Glycobiology12, 43R (2002).Search in Google Scholar

9 Y. C. Lee. FASEB J.6, 3193 (1992).10.1096/fasebj.6.13.1397841Search in Google Scholar PubMed

10 10.1021/ja067466n, N. E. Fahmi, L. Dedkova, B. Wang, S. Golovine, S. M. Hecht. J. Am. Chem. Soc.129, 3586 (2007).Search in Google Scholar PubMed

11 10.1021/ja0722729, Q. Ma, Z. Xu, B. R. Schroeder, W. Sun, F. Wei, S. Hashimoto, K. Konishi, C. J. Leitheiser, S. M. Hecht. J. Am. Chem. Soc.129, 12439 (2007).Search in Google Scholar PubMed

12 10.1038/nmat879, R. M. Hazen, D. S. Sholl. Nat. Mater.2, 367 (2003).Search in Google Scholar

13 10.1002/(SICI)1520-636X(2000)12:4<237::AID-CHIR10>3.0.CO;2-6, X. Huang, K. Nakanishi, N. Berova. Chirality12, 237 (2000).Search in Google Scholar

14 10.1021/ja017159b, R. Lauceri, A. Raudino, L. M. Scolaro, N. Micali, R. Purrello. J. Am. Chem. Soc.124, 894 (2002).Search in Google Scholar

15 10.1021/ja9030903, A. H. Hoveyda, P. J. Lombardi, R. V. O’Brien, A. R. Zhugralin. J. Am. Chem. Soc.131, 8378 (2009).Search in Google Scholar

16 10.1002/chem.201100313, G. I. Grasso, G. Arena, F. Bellia, G. Maccarrone, M. Parrinello, A. Pietropaolo, G. Vecchio, E. Rizzarelli. Chem.—Eur. J.17, 9448 (2011).Search in Google Scholar

17 10.1039/b718436k, F. Bellia, D. La Mendola, C. Pedone, E. Rizzarelli, M. Saviano, G. Vecchio. Chem. Soc. Rev.38, 2756 (2009).Search in Google Scholar

18 10.1073/pnas.202427399, A. Laio, M. Parrinello Proc. Natl. Acad. Sci. USA99, 12562 (2002).Search in Google Scholar

19 C. Chipot, A. Pohorille. Free Energy Calculations: Theory and Applications in Chemistry and Biology, Springer, Berlin (2007).10.1007/978-3-540-38448-9Search in Google Scholar

20 10.1002/jcc.21842, A. Pietropaolo, D. Branduardi, M. Bonomi, M. Parrinello. J. Comput. Chem.32, 2627 (2011).Search in Google Scholar

21 10.1073/pnas.0902092106, J. Pfaendtner, D. Branduardi, M. Parrinello, T. D. Pollard, G. A. Voth. Proc. Natl. Acad. Sci.USA106, 12723 (2009).Search in Google Scholar

22 10.1002/wcms.31, A. Barducci, M. Bonomi, M. Parrinello. Wiley Interdisc. Rev.: Comput. Mol. Sci.1, 826 (2011).Search in Google Scholar

23 10.1021/ja0512780, D. Branduardi, F. L. Gervasio, A. Cavalli, M. Recanatini, M. Parrinello. J. Am. Chem. Soc.127, 9147 (2005).Search in Google Scholar PubMed

24 10.1103/PhysRevLett.104.190601, M. Bonomi, M. Parrinello. Phys. Rev. Lett.104, 190601 (2010).Search in Google Scholar PubMed

25 X. Daura, W. F. Van Gunsteren, A. E. Mark. Angew. Chem., Int. Ed.34, 269 (1999).10.1002/(SICI)1097-0134(19990215)34:3<269::AID-PROT1>3.0.CO;2-3Search in Google Scholar

26 10.1002/anie.200502655, W. F. van Gunsteren, D. Bakowies, R. Baron, I. Chandrasekhar, M. Christen, X. Daura, P. Gee, D. P. Geerke, A. Glättli, P. H. Hünenberger, M. A. Kastenholz, C. Oostenbrink, M. Schenk, D. Trzesniak, N. F. van der Vegt, H. B. Yu. Angew. Chem., Int. Ed.45, 4064 (2006).Search in Google Scholar PubMed

27 10.1103/PhysRevE.52.2893, H. Grubmüller. Phys. Rev. E52, 2893 (1995).Search in Google Scholar

28 10.1126/science.271.5251.997, H. Grubmüller, B. Heymann, P. Tavan. Science271, 997 (1996).Search in Google Scholar PubMed

29 10.1073/pnas.1011511107, G. A. Tribello, M. Ceriotti, M. Parrinello. Proc. Natl. Acad. Sci. USA107, 17509 (2010).Search in Google Scholar PubMed PubMed Central

30 10.1073/pnas.1108486108, M. Ceriotti, G. A. Tribello, M. Parrinello. Proc. Natl. Acad. Sci. USA108, 13023 (2011).Search in Google Scholar PubMed PubMed Central

31 10.1103/PhysRevLett.100.020603, A. Barducci, G. Bussi, M. Parrinello. Phys. Rev. Lett.100, 020603 (2008).Search in Google Scholar PubMed

32 10.1063/1.1749657, J. G. Kirkwood. J. Chem. Phys.3, 300 (1935).Search in Google Scholar

33 10.1002/jcc.21295, J. L. Knight, C. L. Brooks III. J. Comput. Chem.30, 1692 (2009).Search in Google Scholar PubMed PubMed Central

34 10.1021/ct800011m, W. L. Jorgensen, L. L. Thomas. J. Chem. Theory Comput.4, 869 (2008).Search in Google Scholar PubMed PubMed Central

35 10.1063/1.472109, X. Kong, C. L. Brooks III. J. Chem. Phys.105, 2414 (1996).Search in Google Scholar

36 10.1093/protein/7.3.385, J. Aqvist, C. Medina, J. E. Samuelsson. Protein Eng.7, 385 (1994).Search in Google Scholar PubMed

37 10.1063/1.477419, M. Sprik, G. Ciccotti. J. Chem. Phys.109, 7737 (1998).Search in Google Scholar

38 10.1063/1.431685, J. N. Patey, J. P. Valleau. J. Chem. Phys.63, 2334 (1975).Search in Google Scholar

39 M. Parrinello. In Physical Biology from Atoms to Medicine, A. H. Zewail (Ed.), pp. 247–265, Imperial College Press, London (2008).10.1142/9781848162013_0011Search in Google Scholar

40 10.1016/j.sbi.2010.01.011, V. Leone, F. Marinelli, P. Carloni, M. Parrinello. Curr. Opin. Struct. Biol.20, 148 (2010).Search in Google Scholar PubMed

41 10.1016/j.cpc.2004.12.014, J. VandeVondele, M. Krack, F. Mohamed, M. Parrinello, T. Chassaing, J. Hutter. Comput. Phys. Commun.167, 103 (2005).Search in Google Scholar

42 10.1107/S0365110X67000787, H. C. Freeman, J. T. Szymanski. Acta Crystallogr.22, 406 (1967).Search in Google Scholar PubMed

43 G. Lippert, J. Hutter, M. Parrinello. Mol. Phys.92, 477 (1997).10.1080/00268979709482119Search in Google Scholar

44 10.1103/PhysRevLett.77.3865, J. P. Perdew, K. Burke, M. Ernzerhof. Phys. Rev. Lett.77, 3865 (1996).Search in Google Scholar PubMed

45 10.1103/PhysRevB.54.1703, S. Goedecker, M. Teter, J. Hutter. Phys. Rev. B: Condens. Matter54, 1703 (1996).Search in Google Scholar

46 10.1103/PhysRevB.58.3641, C. Hartwigsen, S. Goedecker, J. Hutter. Phys. Rev. B: Condens. Matter58, 3641 (1998).Search in Google Scholar

47 10.1021/ja00392a016, W. L. Jorgensen. J. Am. Chem. Soc.103, 335 (1981).Search in Google Scholar

48 10.1103/PhysRevA.31.1695, W. G. Hoover. Phys. Rev. A31, 1695 (1985).Search in Google Scholar PubMed

49 10.1080/00268978400101201, S. Nosé. Mol. Phys.52, 255 (1984).Search in Google Scholar

50 10.1002/jcc.20289, J. C. Phillips, R. Braun, W. Wang, J. Gumbart, E. Tajkhorshid, E. Villa, C. Chipot, R. D. Skeel, L. Kalé, K. Schulten. J. Comput. Chem.26, 1781 (2005).Search in Google Scholar PubMed PubMed Central

51 10.1002/jcc.20065, A. D. MacKerell Jr., M. Feig, C. L. Brooks III. J. Comput. Chem.25, 1400 (2004).Search in Google Scholar PubMed

52 10.1016/j.cpc.2009.05.011, M. Bonomi, D. Branduardi, G. Bussi, C. Camilloni, D. Provasi, P. Raiteri, D. Donadio, F. Marinelli, F. Pietrucci, R. A. Broglia, M. Parrinello. Comput. Phys. Commun.180, 1961 (2009).Search in Google Scholar

Online erschienen: 2012-4-7
Erschienen im Druck: 2012-4-7

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