Artículo

La versión final de este artículo es de uso interno. El editor solo permite incluir en el repositorio el artículo en su versión post-print. Por favor, si usted la posee enviela a
Consulte el artículo en la página del editor
Consulte la política de Acceso Abierto del editor

Abstract:

Allostery can be defined in a broad sense as a structural change in a protein. The theoretical framework for allostery includes several formulations. In the stereochemical view, the activation event causes a local conformational change that is propagated through residue-to-residue contacts to the rest of the protein through well-defined structural pathways. The thermodynamic, or population shift model, instead implies that the activated conformation is already present with non-negligible population in the nonactivated conformational ensemble, and therefore the activation merely shifts the equilibrium. Nitrophorins (NPs) are heme proteins that store and transport NO in a pH dependent manner, due to a conformational change. Using MD simulations, we show that the NP structural transition occurs in two different conformational free energy landscapes, each one corresponding to a pH condition and characterized by specific residue-residue interactions that characterize them. We also show that when the protonation state of the equilibrium state is modified the conformation becomes unstable and proceeds very fast to an intermediate stable state that is different for each pH condition. Finally, we will discuss that allosteric transition in NP4 does not occur due to a change in the relative population of both end states, but due to a drastic change in the free energy landscape of its conformational ensemble. © 2009 American Chemical Society.

Registro:

Documento: Artículo
Título:Molecular basis for the ph dependent structural transition of nitrophorin 4
Autor:Martí, M.A.; Estrin, D.A.; Roitberg, A.E.
Filiación:Departamento De Química Inorgánica, Analítica, Y Química Física, Facultad de Ciencias Exactas Y Naturales, Inquimae-Conicet, Buenos Aires, Argentina
Departamento De Química Biológica, Facultad de Ciencias Exactas Y Naturales, UniVersidad De Buenos Aires, Ciudad UniVersitaria, Pab.2, C1428EHA, Buenos Aires, Argentina
Quantum Theory and Project and Department of Chemistry, University of Florida, GainesVille, Florida 32611-8435, United States
Palabras clave:pH; Porphyrins; Activated conformations; Allosteric transitions; Allostery; Conformational changes; Conformational ensembles; Conformational free energies; Equilibrium state; Free energy landscapes; Heme proteins; Md simulations; Molecular basis; Nitrophorin-4; Ph conditions; pH dependents; Protonation state; Stable state; Structural changes; Structural transitions; Theoretical frameworks; Free energy; hemoprotein; nitrophorin; saliva protein; article; chemical model; chemistry; computer simulation; pH; protein conformation; Computer Simulation; Hemeproteins; Hydrogen-Ion Concentration; Models, Chemical; Protein Conformation; Salivary Proteins and Peptides
Año:2009
Volumen:113
Número:7
Página de inicio:2135
Página de fin:2142
DOI: http://dx.doi.org/10.1021/jp808055e
Título revista:Journal of Physical Chemistry B
Título revista abreviado:J Phys Chem B
ISSN:15206106
CODEN:JPCBF
CAS:Hemeproteins; Salivary Proteins and Peptides; nitrophorin
Registro:https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_15206106_v113_n7_p2135_Marti

Referencias:

  • Formaneck, M.S., Ma, L., Cui, Q., (2006) Proteins, 63, p. 846
  • Ma, L., Cui, Q., (2007) J. Am. Chem. Soc, 129, p. 10261
  • Szabo, A., Karplus, M., (1972) J. Mol. Biol, 72, p. 163
  • Monod, J., Wyman, J., Changeux, J.P., (1965) J. Mol. Biol, 12, p. 88
  • Perutz, M.F., (1970) Nature, 228, p. 726
  • Yu, E.W., Koshland, D.E., (2001) Proc. Nat. Acad. Sci. U.S.A, 98, p. 9517
  • Kern, D., Zuiderweg, E.R., (2003) Curr. Opin. Struct. Biol, 13, p. 748
  • Swain, J.F., Gierasch, L.M., (2006) Curr. Opin. Struct. Biol, 16, p. 102
  • Xu, C., Tobi, D., Bahar, I., (2003) J. Mol. Biol, 333, p. 153
  • Tama, F., Sanejouand, Y.H., (2001) Protein Eng, 14, p. 1
  • Tousignant, A., Pelletier, J.N., (2004) Chem. Biol, 11, p. 1037
  • Yang, L.-W., Bahar, I., (2005) Structure (London), 13, p. 893
  • Frauenfelder, H., Fenimore, P.W., Young, R.D., (2007) IUBMB Life, 59, p. 506
  • Bahar, I., Atilgan, A.R., Erman, B., (1997) Folding Des, 2, p. 173
  • Yang, L.-W., Eyal, E., Chennubhotla, C., Jee, J., Gronenborn, A.M., Bahar, I., (2007) Structure, 15, p. 741
  • Go, N., Noguti, T., Nishikawa, T., (1983) Proc. Natl. Acad. Sci. U.S.A, 80, p. 3696
  • Levitt, M., Sander, C., Stern, P.S., (1985) J. Mol. Biol, 181, p. 423
  • Amadei, A., (1993) Proteins: Struct., Funct., Genet, 17, p. 412
  • Rueda, M.; Ferrer-Costa, C.; Meyer, T.; Pérez, A.; Camps, J.; Hospital, A.; GelpÍ, J. L.; Orozco, M. Proc. Nat. Acad. Sci. U.S.A. 2007, 104, 796; Montfort, W.R., Weichsel, A., Andersen, J.F., (2000) Biochim. Biophys. Acta, 1482, p. 110
  • Ribeiro, J.M.C., Hazzard, J.M.H., Nussenzveig, R.H., Champagne, D.E., Walker, F.A., (1993) Science, 260, p. 539
  • Champagne, D.E., Nussenzveig, R.H., Ribeiro, J.M.C., (1995) J. Biol. Chem, 270, p. 8691
  • Andersen, J.F., Ding, X.D., Balfour, C., Shokhireva, T.K., Champagne, D.E., Walker, F.A., Montfort, W.R., (2000) Biochemistry, 39, p. 10118
  • Andersen, J.F., Montfort, W.R., (2000) J. Biol. Chem, 275, p. 30496
  • Andersen, J.F., Weichsel, A., Balfour, C.A., Champagne, D.E., Montfort, W.R., (1998) Structure, 6, p. 1315
  • Weichsel, A., Andersen, J.F., Champagne, D.E., Walker, F.A., Montfort, W.R., (1998) Nat. Struct. Biol, 5, p. 304
  • Andersen, J.F., Champagne, D.E., Weichsel, A., Ribeiro, J.M.C., Balfour, C.A., Dress, V., Montfort, W.R., (1997) Biochemistry, 36, p. 4423
  • Ribeiro, J.M.C., Nussenzveig, R.H., (1993) FEBS Lett, 330, p. 165
  • Flower, D.R., North, A.C.T., Sansom, C.E., (2000) Biochim. Biophys. Acta, 1482, p. 9
  • Kondrashov, D.A., Roberts, S.A., Weichsel, A., Montfort, W.R., (2004) Biochemistry, 43, p. 13637
  • Maes, E.M., Weichsel, A., Andersen, J.F., Shepley, D., Montfort, W.R., (2004) Biochemistry, 43, p. 6679
  • Kondrashov, D.A., Montfort, W.R., (2007) J. Phys. Chem. B, 111, p. 9244
  • Marti, M.A., Lebrero, M.C.G., Roitberg, A.E., Estrin, D.A., (2008) J. Am. Chem. Soc, 130, p. 1611
  • Maes, E.M., Roberts, S.A., Weichsel, A., Montfort, W.R., (2005) Biochemistry, 44, p. 12690
  • Menyhárd, D.K., Keserü, G.M., (2005) FEBS Lett, 579, p. 5392
  • Berendsen, H.J.C., Postma, J.P.M., Van Gunsteren, W.F., DiNola, A., Haak, J.R., (1984) J. Chem. Phys, 81, p. 3684
  • Ryckaert, J.P., Ciccotti, G., Berendsen, H.J.C., (1977) J. Comput. Phys, 23, p. 327
  • Hornak, V., Abel, R., Okur, A., Strockbine, B., Roitberg, A., Simmerling, C., (2006) Proteins: Struct., Funct., Genet, 65, p. 712
  • Marti, M.A., Crespo, A., Capece, L., Boechi, L., Bikiel, D.E., Scherlis, D.A., Estrin, D.A., (2006) J. Inorg. Biochem, 100, p. 761
  • Bikiel, D.E., Boechi, L., Capece, L., Crespo, A., De Biase, P.M., Di Lella, S., Gonzalez Lebrero, M.C., Estrin, D.A., (2006) Phys. Chem. Chem. Phys, 8, p. 5611
  • Pearlman, D.A., Case, D.A., Caldwell, J.W., Ross, W.S., Cheatham Iii, T.E., DeBolt, S., Ferguson, D., Kollman, P., (1995) Comput. Phys. Commun, 91, p. 1

Citas:

---------- APA ----------
Martí, M.A., Estrin, D.A. & Roitberg, A.E. (2009) . Molecular basis for the ph dependent structural transition of nitrophorin 4. Journal of Physical Chemistry B, 113(7), 2135-2142.
http://dx.doi.org/10.1021/jp808055e
---------- CHICAGO ----------
Martí, M.A., Estrin, D.A., Roitberg, A.E. "Molecular basis for the ph dependent structural transition of nitrophorin 4" . Journal of Physical Chemistry B 113, no. 7 (2009) : 2135-2142.
http://dx.doi.org/10.1021/jp808055e
---------- MLA ----------
Martí, M.A., Estrin, D.A., Roitberg, A.E. "Molecular basis for the ph dependent structural transition of nitrophorin 4" . Journal of Physical Chemistry B, vol. 113, no. 7, 2009, pp. 2135-2142.
http://dx.doi.org/10.1021/jp808055e
---------- VANCOUVER ----------
Martí, M.A., Estrin, D.A., Roitberg, A.E. Molecular basis for the ph dependent structural transition of nitrophorin 4. J Phys Chem B. 2009;113(7):2135-2142.
http://dx.doi.org/10.1021/jp808055e