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
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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
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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
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Volumen: | 280
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Número: | 37
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Página de inicio: | 32480
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Página de fin: | 32484
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DOI: |
http://dx.doi.org/10.1074/jbc.M505706200 |
Título revista: | Journal of Biological Chemistry
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Título revista abreviado: | J. Biol. Chem.
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ISSN: | 00219258
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CODEN: | JBCHA
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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
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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