Artículo
Jenik, M.; Parra, R.G.; Radusky, L.G.; Turjanski, A.; Wolynes, P.G.; Ferreiro, D.U. "Protein frustratometer: A tool to localize energetic frustration in protein molecules" (2012) Nucleic Acids Research. 40(W1):W348-W351
Estamos trabajando para incorporar este artículo al repositorio
Consulte la política de Acceso Abierto del editor
Abstract:
The frustratometer is an energy landscape theory-inspired algorithm that aims at quantifying the location of frustration manifested in protein molecules. Frustration is a useful concept for gaining insight to the proteins biological behavior by analyzing how the energy is distributed in protein structures and how mutations or conformational changes shift the energetics. Sites of high local frustration often indicate biologically important regions involved in binding or allostery. In contrast, minimally frustrated linkages comprise a stable folding core of the molecule that is conserved in conformational changes. Here, we describe the implementation of these ideas in a webserver freely available at the National EMBNet node-Argentina, at URL: http://lfp.qb.fcen.uba. ar/embnet/. © 2012 The Author(s).
Registro:
| Documento: | Artículo |
| Título: | Protein frustratometer: A tool to localize energetic frustration in protein molecules |
| Autor: | Jenik, M.; Parra, R.G.; Radusky, L.G.; Turjanski, A.; Wolynes, P.G.; Ferreiro, D.U. |
| Filiación: | Protein Physiology Laboratory, Departamento de Química Biológica-CONICET, Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina Structural Bioinformatics Laboratory, Departamento de Química Biológica, Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE, Universidad de Buenos Aires, Buenos Aires C1428EHA, Argentina Department of Chemistry, Rice University, Houston, TX 77251, United States |
| Palabras clave: | protein; algorithm; article; energy transfer; frustration; frustratometer; information processing; priority journal; protein analysis; protein conformation; protein domain; protein structure; structure analysis; web browser; Algorithms; Internet; Mutation; Protein Conformation; Protein Folding; Protein Structure, Tertiary; Proteins; Software; User-Computer Interface |
| Año: | 2012 |
| Volumen: | 40 |
| Número: | W1 |
| Página de inicio: | W348 |
| Página de fin: | W351 |
| DOI: | http://dx.doi.org/10.1093/nar/gks447 |
| Título revista: | Nucleic Acids Research |
| Título revista abreviado: | Nucleic Acids Res. |
| ISSN: | 03051048 |
| CODEN: | NARHA |
| CAS: | protein, 67254-75-5; Proteins |
| Registro: | https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_03051048_v40_nW1_pW348_Jenik |
Referencias:
- Onuchic, J.N., Luthey-Schulten, Z., Wolynes, P.G., Theory of protein folding: The energy landscape perspective (1997) Ann. Rev. Phys. Chem., 48, pp. 545-600
- Bryngelson, J.D., Wolynes, P.G., Spin glasses and the statistical mechanics of protein folding (1987) Proc. Natl Acad. Sci. USA, 84, pp. 7524-7528
- Clementi, C., Nymeyer, H., Onuchic, J.N., Topological and energetic factors: What determines the structural details of the transition state ensemble and "en-route" intermediates for protein folding? An investigation for small globular proteins (2000) J. Mol. Biol., 298, pp. 937-953
- Koga, N., Takada, S., Roles of native topology and chain-length scaling in protein folding: A simulation study with a go-like model (2001) J. Mol. Biol., 313, pp. 171-180
- Chavez, L.L., Onuchic, J.N., Clementi, C., Quantifying the roughness on the free energy landscape: Entropic bottlenecks and protein folding rates (2004) J. Am. Chem. Soc., 126, pp. 8426-8432
- Ferreiro, D.U., Cho, S.S., Komives, E.A., Wolynes, P.G., The energy landscape of modular repeat proteins: Topology determines folding mechanism in the ankyrin family (2005) J. Mol. Biol., 354, pp. 679-692
- Levy, Y., Wolynes, P.G., Onuchic, J.N., Protein topology determines binding mechanism (2004) Proc. Natl Acad. Sci. USA, 101, pp. 511-516
- Yang, S., Cho, S.S., Levy, Y., Cheung, M.S., Levine, H., Wolynes, P.G., Onuchic, J.N., Domain swapping is a consequence of minimal frustration (2004) Proc. Natl Acad. Sci. USA, 101, pp. 13786-13791
- Frauenfelder, H., Sligar, S.G., Wolynes, P.G., The energy landscapes and motions of proteins (1991) Science (New York, N.Y.), 254, pp. 1598-1603
- Hegler, J.A., Weinkam, P., Wolynes, P.G., The spectrum of biomolecular states and motions (2008) HFSP J., 2, pp. 307-313
- Ferreiro, D.U., Hegler, J.A., Komives, E.A., Wolynes, P.G., Localizing frustration in native proteins and protein assemblies (2007) Proc. Natl Acad. Sci. USA, 104, pp. 19819-19824
- Ferreiro, D.U., Hegler, J.A., Komives, E.A., Wolynes, P.G., On the role of frustration in the energy landscapes of allosteric proteins (2011) Proc. Natl Acad. Sci. USA, 108, pp. 3499-3503
- Papoian, G.A., Ulander, J., Eastwood, M.P., Luthey-Schulten, Z., Wolynes, P.G., Water in protein structure prediction (2004) Proc. Natl Acad. Sci. USA, 101, pp. 3352-3357
- Whitford, P.C., Onuchic, J.N., Wolynes, P.G., Energy landscape along an enzymatic reaction trajectory: Hinges or cracks? (2008) HFSP J, 2, pp. 61-64
- Ferreiro, D.U., Wolynes, P.G., The capillarity picture and the kinetics of one-dimensional protein folding (2008) Proc. Natl Acad. Sci. USA, 105, pp. 9853-9854
- Sutto, L., Latzer, J., Hegler, J.A., Ferreiro, D.U., Wolynes, P.G., Consequences of localized frustration for the folding mechanism of the IM7 protein (2007) Proc. Natl Acad. Sci. USA, 104, pp. 19825-19830
- Wiederstein, M., Sippl, M.J., Prosa-web: Interactive web service for the recognition of errors in three-dimensional structures of proteins (2007) Nucleic Acids Res., 35, pp. W407-W410
Citas:
---------- APA ----------
Jenik, M., Parra, R.G., Radusky, L.G., Turjanski, A., Wolynes, P.G. & Ferreiro, D.U. (2012) . Protein frustratometer: A tool to localize energetic frustration in protein molecules. Nucleic Acids Research, 40(W1), W348-W351.http://dx.doi.org/10.1093/nar/gks447
---------- CHICAGO ----------
Jenik, M., Parra, R.G., Radusky, L.G., Turjanski, A., Wolynes, P.G., Ferreiro, D.U. "Protein frustratometer: A tool to localize energetic frustration in protein molecules" . Nucleic Acids Research 40, no. W1 (2012) : W348-W351.http://dx.doi.org/10.1093/nar/gks447
---------- MLA ----------
Jenik, M., Parra, R.G., Radusky, L.G., Turjanski, A., Wolynes, P.G., Ferreiro, D.U. "Protein frustratometer: A tool to localize energetic frustration in protein molecules" . Nucleic Acids Research, vol. 40, no. W1, 2012, pp. W348-W351.http://dx.doi.org/10.1093/nar/gks447
---------- VANCOUVER ----------
Jenik, M., Parra, R.G., Radusky, L.G., Turjanski, A., Wolynes, P.G., Ferreiro, D.U. Protein frustratometer: A tool to localize energetic frustration in protein molecules. Nucleic Acids Res. 2012;40(W1):W348-W351.http://dx.doi.org/10.1093/nar/gks447
