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Abstract:

The energetic contributions of individual DNA-contacting side chains to specific DNA recognition in the human papillomavirus 16 E2C-DNA complex is small (less than 1.0 kcal mol-1), independent of the physical and chemical nature of the interaction, and is strictly additive. The sum of the individual contributions differs 1.0 kcal mol-1 from the binding energy of the wild-type protein. This difference corresponds to the contribution from the deformability of the DNA, known as "indirect readout." Thus, we can dissect the energetic contribution to DNA binding into 90% direct and 10% indirect readout components. The lack of high energy interactions indicates the absence of "hot spots," such as those found in protein-protein interfaces. These results are compatible with a highly dynamic and "wet" protein-DNA interface, yet highly specific and tight, where individual interactions are constantly being formed and broken. © 2005 by The American Society for Biochemistry and Molecular Biology, Inc.

Registro:

Documento: Artículo
Título:Free energy contributions to direct readout of a DNA sequence
Autor:Ferreiro, D.U.; Dellarole, M.; Nadra, A.D.; De Prat-Gay, G.
Filiación:Instituto Leloir, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Patricias Argentinas 435, 1405 Buenos Aires, Argentina
Palabras clave:Additives; Binding energy; Complexation; Formability; Free energy; Proteins; Viruses; DNA recognition; Energy interaction; Papillomavirus; Protein-DNA interface; DNA sequences; DNA; protein E2C; unclassified drug; virus DNA; virus protein; article; binding affinity; DNA binding; DNA protein complex; DNA sequence; DNA structure; energy transfer; Human papillomavirus type 16; nonhuman; priority journal; protein DNA interaction; protein protein interaction; sequence analysis; wild type; Amino Acid Sequence; Circular Dichroism; Crystallography, X-Ray; Databases, Protein; DNA; DNA, Viral; DNA-Binding Proteins; Hydrogen Bonding; Kinetics; Models, Molecular; Molecular Sequence Data; Mutation; Nucleic Acid Conformation; Oncogene Proteins, Viral; Protein Binding; Protein Structure, Tertiary; Sequence Homology, Amino Acid; Temperature; Thermodynamics; Viral Proteins; Human papillomavirus type 16
Año:2005
Volumen:280
Número:37
Página de inicio:32480
Página de fin:32484
DOI: http://dx.doi.org/10.1074/jbc.M505706200
Título revista:Journal of Biological Chemistry
Título revista abreviado:J. Biol. Chem.
ISSN:00219258
CODEN:JBCHA
CAS:DNA, 9007-49-2; DNA, 9007-49-2; DNA, Viral; DNA-Binding Proteins; E2 protein, Human papillomavirus type 16; Oncogene Proteins, Viral; Viral Proteins
PDF:https://bibliotecadigital.exactas.uba.ar/download/paper/paper_00219258_v280_n37_p32480_Ferreiro.pdf
Registro:https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_00219258_v280_n37_p32480_Ferreiro

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Citas:

---------- APA ----------
Ferreiro, D.U., Dellarole, M., Nadra, A.D. & De Prat-Gay, G. (2005) . Free energy contributions to direct readout of a DNA sequence. Journal of Biological Chemistry, 280(37), 32480-32484.
http://dx.doi.org/10.1074/jbc.M505706200
---------- CHICAGO ----------
Ferreiro, D.U., Dellarole, M., Nadra, A.D., De Prat-Gay, G. "Free energy contributions to direct readout of a DNA sequence" . Journal of Biological Chemistry 280, no. 37 (2005) : 32480-32484.
http://dx.doi.org/10.1074/jbc.M505706200
---------- MLA ----------
Ferreiro, D.U., Dellarole, M., Nadra, A.D., De Prat-Gay, G. "Free energy contributions to direct readout of a DNA sequence" . Journal of Biological Chemistry, vol. 280, no. 37, 2005, pp. 32480-32484.
http://dx.doi.org/10.1074/jbc.M505706200
---------- VANCOUVER ----------
Ferreiro, D.U., Dellarole, M., Nadra, A.D., De Prat-Gay, G. Free energy contributions to direct readout of a DNA sequence. J. Biol. Chem. 2005;280(37):32480-32484.
http://dx.doi.org/10.1074/jbc.M505706200