Navegar

Colección

Datos Estadísticas

Artículo

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:

With the advent of Synthetic Biology, a field between basic science and applied engineering, new computational tools are needed to help scientists reach their goal, their design, optimizing resources. In this chapter, we present a simple and powerful method to either know the DNA specificity of a wild-type protein or design new specificities by using the protein design algorithm FoldX. The only basic requirement is having a good resolution structure of the complex. Protein-DNA interaction design may aid the development of new parts designed to be orthogonal, decoupled, and precise in its target. Further, it could help to fine-tune the systems in terms of specificity, discrimination, and binding constants. In the age of newly developed devices and invented systems, computer-aided engineering promises to be an invaluable tool. © 2011 Elsevier Inc. All rights reserved.

Registro:

Documento: Artículo
Título:DNA-binding specificity prediction with FoldX
Autor:Nadra, A.D.; Serrano, L.; Alibés, A.
Filiación:Departamentos de Quimica Biologica y Fisiologia, Biologia Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Argentina
EMBL/CRG Systems Biology Research Unit, Center for Genomic Regulation (CRG), UPF, Barcelona, Spain
Palabras clave:adenine; algorithm; article; base pairing; computer prediction; DNA binding; DNA determination; DNA strand; DNA structure; nuclear magnetic resonance; nucleotide sequence; priority journal; protein DNA interaction; Algorithms; Base Sequence; Binding Sites; DNA; Molecular Sequence Data; Molecular Structure; Mutation; Protein Binding; Protein Conformation; Protein Folding; Proteins; Sensitivity and Specificity
Año:2011
Volumen:498
Página de inicio:3
Página de fin:18
DOI: http://dx.doi.org/10.1016/B978-0-12-385120-8.00001-2
Título revista:Methods in Enzymology
Título revista abreviado:Methods Enzymol.
ISSN:00766879
CODEN:MENZA
CAS:adenine, 22177-51-1, 2922-28-3, 73-24-5; DNA, 9007-49-2; Proteins
Registro:https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_00766879_v498_n_p3_Nadra

Referencias:

  • Alibs, A., Nadra, A.D., De Masi, F., Bulyk, M.L., Serrano, L., Stricher, F., Using protein design algorithms to understand the molecular basis of disease caused by protein-DNA interactions: The Pax6 example (2010) Nucleic Acids Res., 38, pp. 7422-7431
  • Alibs, A., Serrano, L., Nadra, A.D., Structure-based DNA-binding prediction and design (2010) Methods Mol. Biol., 649, pp. 77-88
  • Angarica, V.E., Perez, A.G., Vasconcelos, A.T., Collado-Vides, J., Contreras-Moreira, B., Prediction of TF target sites based on atomistic models of protein-DNA complexes (2008) BMC Bioinform., 9, p. 436
  • Arnould, S., Chames, P., Perez, C., Lacroix, E., Duclert, A., Epinat, J.-C., Stricher, F., Paques, F., Engineering of large numbers of highly specific homing endonucleases that induce recombination on novel DNA targets (2006) Journal of Molecular Biology, 355 (3), pp. 443-458. , DOI 10.1016/j.jmb.2005.10.065, PII S0022283605013252
  • Ashworth, J., Havranek, J.J., Duarte, C.M., Sussman, D., Monnat Jr., R.J., Stoddard, B.L., Baker, D., Computational redesign of endonuclease DNA binding and cleavage specificity (2006) Nature, 441 (7093), pp. 656-659. , DOI 10.1038/nature04818, PII N04818
  • Baeten, L., Reumers, J., Tur, V., Stricher, F., Lenaerts, T., Serrano, L., Rousseau, F., Schymkowitz, J., Reconstruction of protein backbones from the BriX collection of canonical protein fragments (2008) PLoS Comput. Biol., 4, p. 1000083
  • Bembom, O., (2007) SeqLogo: An R Package for Plotting DNA Sequence Logos, , http://bioconductor.org/packages/2.6/bioc/html/seqLogo.html
  • Benos, P.V., Lapedes, A.S., Stormo, G.D., Probabilistic code for DNA recognition by proteins of the EGR family (2002) Journal of Molecular Biology, 323 (4), pp. 701-727. , DOI 10.1016/S0022-2836(02)00917-8
  • Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N., Bourne, P.E., The Protein Data Bank (2000) Nucleic Acids Research, 28 (1), pp. 235-242
  • Endres, R.G., Wingreen, N.S., Weight matrices for protein-DNA binding sites from a single co-crystal structure (2006) Phys. Rev. e Stat. Nonlin. Soft Matter Phys., 73, p. 061921
  • Guerois, R., Nielsen, J.E., Serrano, L., Predicting changes in the stability of proteins and protein complexes: A study of more than 1000 mutations (2002) Journal of Molecular Biology, 320 (2), pp. 369-387. , DOI 10.1016/S0022-2836(02)00442-4
  • Havranek, J.J., Duarte, C.M., Baker, D., A simple physical model for the prediction and design of protein-DNA interactions (2004) Journal of Molecular Biology, 344 (1), pp. 59-70. , DOI 10.1016/j.jmb.2004.09.029, PII S0022283604011696
  • Jamal Rahi, S., Virnau, P., Mirny, L.A., Kardar, M., Predicting transcription factor specificity with all-atom models (2008) Nucleic Acids Res., 36, pp. 6209-6217
  • Liu, Z., Guo, J.T., Li, T., Xu, Y., Structure-based prediction of transcription factor binding sites using a protein-DNA docking approach (2008) Proteins, 72, pp. 1114-1124
  • Marcaida, M.J., Prieto, J., Redondo, P., Nadra, A.D., Alibs, A., Serrano, L., Grizot, S., Montoya, G., Crystal structure of I-DmoI in complex with its target DNA provides new insights into meganuclease engineering (2008) Proc. Natl. Acad. Sci. USA, 105, pp. 16888-16893
  • Morozov, A.V., Havranek, J.J., Baker, D., Siggia, E.D., Protein-DNA binding specificity predictions with structural models (2005) Nucleic Acids Research, 33 (18), pp. 5781-5798. , DOI 10.1093/nar/gki875
  • Newburger, D.E., Bulyk, M.L., UniPROBE: An online database of protein binding microarray data on protein-DNA interactions (2009) Nucleic Acids Res., 37, pp. 77-D82
  • Paillard, G., Deremble, C., Lavery, R., Looking into DNA recognition: Zinc finger binding specificity (2004) Nucleic Acids Research, 32 (22), pp. 6673-6682. , DOI 10.1093/nar/gkh1003
  • Redondo, P., Prieto, J., Munoz, I.G., Alibs, A., Stricher, F., Serrano, L., Cabaniols, J.P., Paques, F., Molecular basis of xeroderma pigmentosum group C DNA recognition by engineered meganucleases (2008) Nature, 456, pp. 107-111
  • Rohs, R., Jin, X., West, S.M., Joshi, R., Honig, B., Mann, R.S., Origins of specificity in protein-DNA recognition (2010) Annu. Rev. Biochem., 79, pp. 233-269
  • Sandelin, A., Alkema, W., Engstrom, P., Wasserman, W.W., Lenhard, B., JASPAR: An open-access database for eukaryotic transcription factor binding profiles (2004) Nucleic Acids Res., 32, pp. 91-D94
  • Schymkowitz, J., Borg, J., Stricher, F., Nys, R., Rousseau, F., Serrano, L., The FoldX web server: An online force field (2005) Nucleic Acids Res., 33, pp. 382-W388
  • Siggers, T.W., Honig, B., Structure-based prediction of C2H2 zinc-finger binding specificity: Sensitivity to docking geometry (2007) Nucleic Acids Research, 35 (4), pp. 1085-1097. , DOI 10.1093/nar/gkl1155

Citas:

---------- APA ----------
Nadra, A.D., Serrano, L. & Alibés, A. (2011) . DNA-binding specificity prediction with FoldX. Methods in Enzymology, 498, 3-18.
http://dx.doi.org/10.1016/B978-0-12-385120-8.00001-2
---------- CHICAGO ----------
Nadra, A.D., Serrano, L., Alibés, A. "DNA-binding specificity prediction with FoldX" . Methods in Enzymology 498 (2011) : 3-18.
http://dx.doi.org/10.1016/B978-0-12-385120-8.00001-2
---------- MLA ----------
Nadra, A.D., Serrano, L., Alibés, A. "DNA-binding specificity prediction with FoldX" . Methods in Enzymology, vol. 498, 2011, pp. 3-18.
http://dx.doi.org/10.1016/B978-0-12-385120-8.00001-2
---------- VANCOUVER ----------
Nadra, A.D., Serrano, L., Alibés, A. DNA-binding specificity prediction with FoldX. Methods Enzymol. 2011;498:3-18.
http://dx.doi.org/10.1016/B978-0-12-385120-8.00001-2