Navegar

Colección

Datos Estadísticas

Artículo

Arroyo-Mañez, P.; Bikiel, D.E.; Boechi, L.; Capece, L.; Di Lella, S.; Estrin, D.A.; Martí, M.A.; Moreno, D.M.; Nadra, A.D.; Petruk, A.A. "Protein dynamics and ligand migration interplay as studied by computer simulation" (2011) Biochimica et Biophysica Acta - Proteins and Proteomics. 1814(8):1054-1064
Estamos trabajando para incorporar este artículo al repositorio
Consulte el artículo en la página del editor
Consulte la política de Acceso Abierto del editor

Abstract:

Since proteins are dynamic systems in living organisms, the employment of methodologies contemplating this crucial characteristic results fundamental to allow revealing several aspects of their function. In this work, we present results obtained using classical mechanical atomistic simulation tools applied to understand the connection between protein dynamics and ligand migration. Firstly, we will present a review of the different sampling schemes used in the last years to obtain both ligand migration pathways and the thermodynamic information associated with the process. Secondly, we will focus on representative examples in which the schemes previously presented are employed, concerning the following: i) ligand migration, tunnels, and cavities in myoglobin and neuroglobin; ii) ligand migration in truncated hemoglobin members; iii) NO escape and conformational changes in nitrophorins; iv) ligand selectivity in catalase and hydrogenase; and v) larger ligand migration: the P450 and haloalkane dehalogenase cases. This article is part of a Special Issue entitled: Protein Dynamics: Experimental and Computational Approaches. © 2010 Elsevier B.V. All rights reserved.

Registro:

Documento: Artículo
Título:Protein dynamics and ligand migration interplay as studied by computer simulation
Autor:Arroyo-Mañez, P.; Bikiel, D.E.; Boechi, L.; Capece, L.; Di Lella, S.; Estrin, D.A.; Martí, M.A.; Moreno, D.M.; Nadra, A.D.; Petruk, A.A.
Filiación:Departamento de Quimica Inorganica, Analitica Y Quimica-Fisica (INQUIMAE-CONICET), Facultad de Ciencias Exactas Y Naturales, Universidad de Buenos Aires, Ciudad de Buenos Aires, Argentina
Departamento de Química Orgánica, Facultad de Ciencias Exactas Y Naturales, Universidad de Buenos Aires, Ciudad de Buenos Aires, Argentina
Departamento de Química Biológica, Facultad de Ciencias Exactas Y Naturales, Universidad de Buenos Aires, Ciudad de Buenos Aires, Argentina
Departamento de Fisiología, Biología Molecular Y Celular, Facultad de Ciencias Exactas Y Naturales, Universidad de Buenos Aires, Ciudad de Buenos Aires, Argentina
Instituto Superior de Investigaciones Biológicas (INSIBIO-CONICET), Facultad de Bioquímica, Química Y Farmacia, Universidad Nacional de Tucumán, San Miguel de Tucumán, Argentina
Palabras clave:Ligand migration; Molecular dynamics; Protein dynamics; amine oxidase (copper containing); catalase; cytochrome P450; dehalogenase; hemoglobin; hemoprotein; hydrogenase; hydrolase; ligand; myoglobin; neuroglobin; nitric oxide; nitrophorin; unclassified drug; accelerated molecular dynamics; activated molecular dynamics; computer simulation; conformational transition; human; implicit ligand sampling; ligand binding; ligand migration; locally enhanced sampling; mathematical analysis; metadynamics; methodology; molecular dynamics; multiple steered molecular dynamic; nonhuman; Pichia angusta; priority journal; protein dynamics; protein energy landscape exploration; protein function; random activated molecular dynamics; review; thermodynamics; Binding Sites; Computer Simulation; Ligands; Models, Molecular; Molecular Dynamics Simulation; Proteins
Año:2011
Volumen:1814
Número:8
Página de inicio:1054
Página de fin:1064
DOI: http://dx.doi.org/10.1016/j.bbapap.2010.08.005
Título revista:Biochimica et Biophysica Acta - Proteins and Proteomics
Título revista abreviado:Biochim. Biophys. Acta Proteins Proteomics
ISSN:15709639
CODEN:BBAPB
CAS:amine oxidase (copper containing), 9001-53-0, 9014-75-9; catalase, 9001-05-2; cytochrome P450, 9035-51-2; dehalogenase, 9015-72-9; hemoglobin, 9008-02-0; hydrogenase, 9027-05-8; hydrolase, 9027-41-2; nitric oxide, 10102-43-9; Ligands; Proteins
Registro:https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_15709639_v1814_n8_p1054_ArroyoManez

Referencias:

  • Frauenfelder, H., Chen, G., Berendzen, J., Fenimore, P.W., Jansson, H., McMahon, B.H., Stroe, I.R., Young, R.D., (2009) Proc. Natl Acad. Sci. USA, 106, pp. 5129-5134
  • Frauenfelder, H., Fenimore, P.W., Young, R.D., (2007) IUBMB Life, 59, pp. 506-512
  • Frauenfelder, H., McMahon, B.H., Austin, R.H., Chu, K., Groves, J.T., (2001) Proc. Natl Acad. Sci. USA, 98, pp. 2370-2374
  • Frauenfelder, H., Parak, F., Young, R.D., (1988) Annu. Rev. Biophys. Biophys. Chem., 17, pp. 451-479
  • Jardetzky, O., (1996) Prog. Biophys. Mol. Biol., 65, pp. 171-219
  • Bakan, A., Bahar, I., (2009) Proc. Natl Acad. Sci. USA, 106, pp. 14349-14354
  • Kern, D., Zuiderweg, E.R.P., (2003) Curr. Opin. Struct. Biol., 13, pp. 748-757
  • Ostermann, A., Waschipky, R., Parak, F.G., Nienhaus, G.U., (2000) Nature, 404, pp. 205-208
  • Bidon-Chanal, A., Marti, M.A., Crespo, A., Milani, M., Orozco, M., Bolognesi, M., Luque, F.J., Estrin, D.A., (2006) Proteins: Struct., Funct., Bioinf., 64, pp. 457-464
  • Bidon-Chanal, A., Marti, M.A., Estrin, D.A., Luque, F.J., (2007) J. Am. Chem. Soc., 129, pp. 6782-6788
  • Marti, M.A., Bidon-Chanal, A., Crespo, A., Yeh, S.R., Guallar, V., Luque, F.J., Estrin, D.A., (2008) J. Am. Chem. Soc., 130, pp. 1688-1693
  • Marti, M.A., Lebrero, M.C.G., Roitberg, A.E., Estrin, D.A., (2008) J. Am. Chem. Soc., 130, pp. 1611-1618
  • Eaton, W.A., Henry, E.R., Hofrichter, J., Mozzarelli, A., (1999) Nat. Struct. Biol., 6, pp. 351-358
  • Pietrucci, F., Marinelli, F., Carloni, P., Laio, A., (2009) J. Am. Chem. Soc., 131, pp. 11811-11818
  • Ghosh, A., (2007) The Smallest Biomolecules: Diatomics and Their Interactions with Heme Proteins, 1. , Elsevier
  • Scott, E.E., Gibson, Q.H., Olson, J.S., (2001) J. Biol. Chem., 276, pp. 5177-5188
  • Wittenberg, J.B., Bolognesi, M., Wittenberg, B.A., Guertin, M., (2002) J. Biol. Chem., 277, pp. 871-874
  • Pesce, A., Milani, M., Nardini, M., Bolognesi, M., (2008) Meth. Enzymol., 436, pp. 303-315
  • De Sanctis, D., Dewilde, S., Pesce, A., Moens, L., Ascenzi, P., Hankeln, T., Burmester, T., Bolognesi, M., (2004) Biochem. Biophys. Res. Commun., 316, pp. 1217-1221
  • Milani, M., Pesce, A., Ouellet, Y., Dewilde, S., Friedman, J., Ascenzi, P., Guertin, M., Bolognesi, M., (2004) J. Biol. Chem., 279, pp. 21520-21525
  • Laverman, L.E., Ford, P.C., (2001) J. Am. Chem. Soc., 123, pp. 11614-11622
  • Swails, J.M., Meng, Y., Walker, F.A., Marti, M.A., Estrin, D.A., Roitberg, A.E., (2009) J. Phys. Chem. B, 113, pp. 1192-1201
  • Marti, M.A., Bikiel, D.E., Crespo, A., Nardini, M., Bolognesi, M., Estrin, D.A., (2006) Proteins: Struct., Funct., Genet., 62, pp. 641-648
  • Marti, M.A., Capece, L., Bikiel, D.E., Falcone, B., Estrin, D.A., (2007) Proteins: Struct., Funct., Bioinf., 68, pp. 480-487
  • Tilton, R.F., Kuntz, I.D., Petsko, G.A., (1984) Biochemistry, 23, pp. 2849-2857
  • Schmidt, M., Nienhaus, K., Pahl, R., Krasselt, A., Anderson, S., Parak, F., Nienhaus, G.U., Årajer, V., (2005) Proc. Natl Acad. Sci. USA, 102, pp. 11704-11709
  • Schotte, F., Lim, M., Jackson, T.A., Smirnov, A.V., Soman, J., Olson, J.S., Phillips Jr., G.N., Anfinrud, P.A., (2003) Science, 300, pp. 1944-1947
  • Bossa, C., Amadei, A., Daidone, I., Anselmi, M., Vallone, B., Brunori, M., Di Nola, A., (2005) Biophys. J., 89, pp. 465-474
  • Bossa, C., Anselmi, M., Roccatano, D., Amadei, A., Vallone, B., Brunori, M., Di Nola, A., (2004) Biophys. J., 86, pp. 3855-3862
  • Nutt, D.R., Meuwly, M., (2004) Proc. Natl Acad. Sci. USA, 101, pp. 5998-6002
  • Baron, R., Riley, C., Chenprakhon, P., Thotsaporn, K., Winter, R.T., Alfieri, A., Forneris, F., McCammon, J.A., (2009) Proc. Natl. Acad. Sci., 106, pp. 10603-10608
  • Boechi, L., Marti, M.A., Milani, M., Bolognesi, M., Luque, F.J., Estrin, D.A., (2008) Proteins, 73, pp. 372-379
  • Boechi, L., Arroyo Mañez, P., Luque, F.J., Marti, M.A., Estrin, D.A., (2009) Proteins, 78, pp. 962-970
  • Carrillo, O., Orozco, M., (2008) Proteins: Struct., Funct., Genet., 70, pp. 892-899
  • Nishihara, Y., Hayashi, S., Kato, S., (2008) Chem. Phys. Lett., 464, pp. 220-225
  • Ruscio, J.Z., Kumar, D., Shukla, M., Prisant, M.G., Murali, T.M., Onufriev, A.V., (2008) Proc. Natl Acad. Sci. USA, 105, pp. 9204-9209
  • Cohen, J., Arkhipov, A., Braun, R., Schulten, K., (2006) Biophys. J., 91, pp. 1844-1857
  • Cohen, J., Olsen, K.W., Schulten, K., (2008) Methods in Enzymology, 437, pp. 439-457. , R.K. Poole (Ed.)
  • Laio, A., Gervasio, F.L., (2008) Rep. Prog. Phys., 71
  • Leach, A.R., (2001) Pearson Education EMA, , Second Edition
  • Jarzynski, C., (1997) Phys. Rev. E, 56, p. 5018
  • Gervasio, F.L., Laio, A., Parrinello, M., (2004) J. Am. Chem. Soc., 127, pp. 2600-2607
  • Borrelli, K.W., Vitalis, A., Alcantara, R., Guallar, V., (2005) J. Chem. Theory Comput., 1, pp. 1304-1311
  • Jacobson, M.P., Pincus, D.L., Rapp, C.S., Day, T.J.F., Honig, B., Shaw, D.E., Friesner, R.A., (2004) Proteins: Struct., Funct., Genet., 55, pp. 351-367
  • Voter, A.F., (1997) Phys. Rev. Lett., 78, p. 3908
  • Voter, A.F., (1997) J. Chem. Phys., 106, pp. 4665-4677
  • Rahman, J.A., Tully, J.C., (2002) J. Chem. Phys., 116, pp. 8750-8760
  • Hamelberg, D., Mongan, J., McCammon, J.A., (1929) J. Chem. Phys., 120, pp. 11919-11929
  • Kalko, S.G., Lluis Test, J., (2001) J. Am. Chem. Soc., 123, pp. 9665-9672
  • Ludemann, S.K., Lounnas, V., Wade, R.C., (2000) J. Mol. Biol., 303, pp. 797-811
  • Xu, L., Liu, X., Zhao, W., Wang, X., (2009) J. Phys. Chem. B, 113, pp. 13596-13603
  • Golden, S.D., Olsen, K.W., (2008) Methods Enzymol., 437, pp. 459-475
  • Cohen, J., Kim, K., King, P., Seibert, M., Schulten, K., (2005) Structure, 13, pp. 1321-1329
  • Cohen, J., Kim, K., Posewitz, M., Ghirardi, M.L., (2005) Biochem. Soc. Trans., 33, pp. 80-82
  • Brunori, M., Gibson, Q.H., (2001) EMBO Rep., 2, pp. 674-679
  • Frauenfelder, H., McMahon, B.H., Fenimore, P.W., (2003) Proc. Natl. Acad. Sci., 100, pp. 8615-8617
  • Vallone, B., Brunori, M., (2004) Ital. J. Biochem., 53, pp. 46-52
  • Schlichting, I., Berendzen, J., Phillips, G.N., Sweet, R.M., (1994) Nature, 371, pp. 808-812
  • Hartmann, H., Zinser, S., Komninos, P., Schneider, R.T., Nienhaus, G.U., Parak, F., (1996) Proc. Natl Acad. Sci. USA, 93, pp. 7013-7016
  • Wittenberg, J.B., Wittenberg, B.A., (2003) J. Exp. Biol., 206, pp. 2011-2020
  • Brunori, M., Vallone, B., (2007) Cell. Mol. Life Sci., 64, pp. 1259-1268
  • Pesce, A., Bolognesi, M., Bocedi, A., Ascenzi, P., Dewilde, S., Moens, L., Hankeln, T., Burmester, T., (2002) EMBO Rep., 3, pp. 1146-1151
  • Pesce, A., Dewilde, S., Nardini, M., Moens, L., Ascenzi, P., Hankeln, T., Burmester, T., Bolognesi, M., (2004) Structure, 35, pp. 63-65
  • Trent, J.T., Watts, R.A., Hargrove, M.S., (2001) J. Biol. Chem., 276, pp. 30106-30110
  • Vallone, B., Nienhaus, K., Brunori, M., Nienhaus, G.U., (2004) Proteins: Struct., Funct., Bioinf., 56, pp. 85-92
  • Capece, L., Marti, M.A., Bidon-Chanal, A., Nadra, A., Luque, F.J., Estrin, D.A., (2008) Proteins: Struct., Funct., Bioinf., 75, pp. 885-894
  • Hamdane, D., Kiger, L., Dewilde, S., Green, B.N., Pesce, A., Uzan, J., Burmester, T., Marden, M.C., (2003) J. Biol. Chem., 278, pp. 51713-51721
  • Nadra, A.D., Martí, M.A., Pesce, A., Bolognesi, M., Estrin, D.A., (2007) Proteins: Struct., Funct., Bioinf., 71, pp. 695-705
  • Vallone, B., Nienhaus, K., Matthes, A., Brunori, M., Nienhaus, G.U., (2004) Proc. Natl Acad. Sci. USA, 101, pp. 17351-17356
  • Abbruzzetti, S., Faggiano, S., Bruno, S., Spyrakis, F., Mozzarelli, A., Dewilde, S., Moens, L., Viappiani, C., (2009) Proc. Natl. Acad. Sci., 106, pp. 18984-18989
  • Bocahut, A., Bernad, S., Sebban, P., Sacquin-Mora, S., (2009) J. Phys. Chem. B, 113, pp. 16257-16267
  • Lutz, S., Nienhaus, K., Nienhaus, G.U., Meuwly, M., (2009) J. Phys. Chem. B, 113, pp. 15334-15343
  • Orlowski, S., Nowak, W., (2008) Biosystems, 94, pp. 263-266
  • Banushkina, P., Meuwly, M., (2005) J. Phys. Chem. B, 109, pp. 16911-16917
  • Crespo, A., MartÃ-, M.A., Kalko, S.G., Morreale, A., Orozco, M., Gelpi, J.L., Luque, F.J., Estrin, D.A., (2005) J. Am. Chem. Soc., 127, pp. 4433-4444
  • Lama, A., Pawaria, S., Bidon-Chanal, A., Anand, A., Gelpi, J.L., Arya, S., Marti, M., Dikshit, K.L., (2009) J. Biol. Chem., 284, pp. 14457-14468
  • Guallar, V., Lu, C., Borrelli, K., Egawa, T., Yeh, S.-R., (2009) J. Biol. Chem., 284, pp. 3106-3116
  • Johnson, B.J., Cohen, J., Welford, R.W., Pearson, A.R., Schulten, K., Klinman, J.P., Wilmot, C.M., (2007) J. Biol. Chem., 282, pp. 17767-17776
  • Goto, Y., Klinman, J.P., (2002) Biochemistry, 41, pp. 13637-13643
  • Mills, S.A., Goto, Y., Su, Q., Plastino, J., Klinman, J.P., (2002) Biochemistry, 41, pp. 10577-10584
  • Cai, D., Klinman, J.P., (1994) Biochemistry, 33, pp. 7647-7653
  • Duff, A.P., Trambaiolo, D.M., Cohen, A.E., Ellis, P.J., Juda, G.A., Shepard, E.M., Langley, D.B., Guss, J.M., (2004) J. Mol. Biol., 344, pp. 599-607
  • Andersen, J.F., Montfort, W.R., (2000) J. Biol. Chem., 275, pp. 30496-30503
  • Andersen, J.F., Ding, X.D., Balfour, C., Shokhireva, T.K., Champagne, D.E., Walker, F.A., Montfort, W.R., (2000) Biochemistry, 39, pp. 10118-10131
  • Andersen, J.F., Weichsel, A., Balfour, C.A., Champagne, D.E., Montfort, W.R., (1998) Structure, 6, pp. 1315-1327
  • Weichsel, A., Andersen, J.F., Champagne, D.E., Walker, F.A., Montfort, W.R., (1998) Nat. Struct. Biol., 5, pp. 304-309
  • Maes, E.M., Weichsel, A., Andersen, J.F., Shepley, D., Montfort, W.R., (2004) Biochemistry, 43, pp. 6679-6690
  • Kondrashov, D.A., Roberts, S.A., Weichsel, A., Montfort, W.R., (2004) Biochemistry, 43, pp. 13637-13647
  • Menyhárd, D.K., Keserü, G.M., (2005) FEBS Lett., 579, pp. 5392-5398
  • Amara, P., Andreoletti, P., Jouve Test, H.M., (2001) Protein Sci., 10, pp. 1927-1935
  • Volbeda, A., (1999) Ecoles Phys. Chim. Vivant, 1, pp. 47-52
  • Peters, J.W., (1999) Curr. Opin. Struct. Biol., 9, pp. 670-676
  • Nicolet, Y., Cavazza, C., Fontecilla-Camps, J.C., (2002) J. Inorg. Biochem., 91, pp. 1-8
  • Jensen, M.O., Yin, Y., Tajkhorshid, E., Schulten, K., (2007) Biophys. J., 93, pp. 92-102
  • Wang, T., Duan, Y., (2007) J. Am. Chem. Soc., 129, pp. 6970-6971
  • Wang, Y., Schulten, K., Tajkhorshid, E., (2005) Structure, 13, pp. 1107-1118
  • Tai, K., Fowler, P., Mokrab, Y., Stansfeld, P., Sansom, M.S., (2008) Meth. Cell Biol., 90, pp. 233-265
  • Jensen, M.Ø., Borhani, D.W., Lindorff-Larsen, K., Maragakis, P., Jogini, V., Eastwood, M.P., Dror, R.O., Shaw, D.E., (2010) Proc. Natl. Acad. Sci., 107, pp. 5833-5838
  • Carlsson, P., Burendahl, S., Nilsson, L., (2006) Biophys. J., 91
  • Perakyla, M., (2009) Eur. Biophys. J., 38, pp. 185-198
  • Martinez, L., Sonoda, M.T., Webb, P., Baxter, J.D., Skaf, M.S., Polikarpov, I., (2005) Biophys. J., 89, pp. 2011-2023
  • Martinez, L., Webb, P., Polikarpov, I., Skaf, M.S., (2006) J. Med. Chem., 49, pp. 23-26
  • Genest, D., N, G., Arrault, A., Marot, C., Morin-Allory, L., Genest, M., (2008) Eur. Biophys. J., 37, pp. 369-379
  • Aird, A., Wrachtrup, J., Schulten, K., Tietz, C., (2007) Biophys. J., 92, pp. 23-33
  • Sheu, S.-H., Kaya, T., Waxman, D.J., Vajda, S., (2005) Biochemistry, 44, pp. 1193-1209
  • Burendahl, S., Danciulescu, C., Nilsson, L., (2009) Proteins: Struct., Funct., Bioinf., 77, pp. 842-856
  • Winn, P.J., Ludemann, S.K., Gauges, R., Lounnas, V., Wade, R.C., (2002) Proc. Natl. Acad. Sci., 99, pp. 5361-5366
  • Pongprayoon, P., Beckstein, O., Wee, C.L., Sansom, M.S., (2009) Proc. Natl. Acad. Sci., 106, pp. 21614-21618
  • Masetti, M., Cavalli, A., Recanatini, M., Gervasio, F.L., (2009) J. Phys. Chem. B, 113, pp. 4807-4816
  • Klvana, M., Pavlova, M., Koudelakova, T., Chaloupkova, R., Dvorak, P., Prokop, Z., Stsiapanava, A., Damborsky, J., (2009) J. Mol. Biol., 392, pp. 1339-1356

Citas:

---------- APA ----------
Arroyo-Mañez, P., Bikiel, D.E., Boechi, L., Capece, L., Di Lella, S., Estrin, D.A., Martí, M.A.,..., Petruk, A.A. (2011) . Protein dynamics and ligand migration interplay as studied by computer simulation. Biochimica et Biophysica Acta - Proteins and Proteomics, 1814(8), 1054-1064.
http://dx.doi.org/10.1016/j.bbapap.2010.08.005
---------- CHICAGO ----------
Arroyo-Mañez, P., Bikiel, D.E., Boechi, L., Capece, L., Di Lella, S., Estrin, D.A., et al. "Protein dynamics and ligand migration interplay as studied by computer simulation" . Biochimica et Biophysica Acta - Proteins and Proteomics 1814, no. 8 (2011) : 1054-1064.
http://dx.doi.org/10.1016/j.bbapap.2010.08.005
---------- MLA ----------
Arroyo-Mañez, P., Bikiel, D.E., Boechi, L., Capece, L., Di Lella, S., Estrin, D.A., et al. "Protein dynamics and ligand migration interplay as studied by computer simulation" . Biochimica et Biophysica Acta - Proteins and Proteomics, vol. 1814, no. 8, 2011, pp. 1054-1064.
http://dx.doi.org/10.1016/j.bbapap.2010.08.005
---------- VANCOUVER ----------
Arroyo-Mañez, P., Bikiel, D.E., Boechi, L., Capece, L., Di Lella, S., Estrin, D.A., et al. Protein dynamics and ligand migration interplay as studied by computer simulation. Biochim. Biophys. Acta Proteins Proteomics. 2011;1814(8):1054-1064.
http://dx.doi.org/10.1016/j.bbapap.2010.08.005