Free energy contributions to direct readout of a DNA sequence
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...
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| Acceso en línea: | http://hdl.handle.net/20.500.12110/paper_00219258_v280_n37_p32480_Ferreiro http://repositoriouba.sisbi.uba.ar/gsdl/cgi-bin/library.cgi?a=d&c=artiaex&d=paper_00219258_v280_n37_p32480_Ferreiro_oai |
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I28-R145-paper_00219258_v280_n37_p32480_Ferreiro_oai2020-10-19 Ferreiro, D.U. Dellarole, M. Nadra, A.D. De Prat-Gay, G. 2005 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. Fil:Ferreiro, D.U. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:Dellarole, M. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:Nadra, A.D. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:De Prat-Gay, G. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. application/pdf http://hdl.handle.net/20.500.12110/paper_00219258_v280_n37_p32480_Ferreiro info:eu-repo/semantics/openAccess http://creativecommons.org/licenses/by/2.5/ar J. Biol. Chem. 2005;280(37):32480-32484 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 Free energy contributions to direct readout of a DNA sequence info:eu-repo/semantics/article info:ar-repo/semantics/artículo info:eu-repo/semantics/publishedVersion http://repositoriouba.sisbi.uba.ar/gsdl/cgi-bin/library.cgi?a=d&c=artiaex&d=paper_00219258_v280_n37_p32480_Ferreiro_oai |
| institution |
Universidad de Buenos Aires |
| institution_str |
I-28 |
| repository_str |
R-145 |
| collection |
Repositorio Digital de la Universidad de Buenos Aires (UBA) |
| topic |
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 |
| spellingShingle |
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 Ferreiro, D.U. Dellarole, M. Nadra, A.D. De Prat-Gay, G. Free energy contributions to direct readout of a DNA sequence |
| topic_facet |
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 |
| description |
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. |
| format |
Artículo Artículo publishedVersion |
| author |
Ferreiro, D.U. Dellarole, M. Nadra, A.D. De Prat-Gay, G. |
| author_facet |
Ferreiro, D.U. Dellarole, M. Nadra, A.D. De Prat-Gay, G. |
| author_sort |
Ferreiro, D.U. |
| title |
Free energy contributions to direct readout of a DNA sequence |
| title_short |
Free energy contributions to direct readout of a DNA sequence |
| title_full |
Free energy contributions to direct readout of a DNA sequence |
| title_fullStr |
Free energy contributions to direct readout of a DNA sequence |
| title_full_unstemmed |
Free energy contributions to direct readout of a DNA sequence |
| title_sort |
free energy contributions to direct readout of a dna sequence |
| publishDate |
2005 |
| url |
http://hdl.handle.net/20.500.12110/paper_00219258_v280_n37_p32480_Ferreiro http://repositoriouba.sisbi.uba.ar/gsdl/cgi-bin/library.cgi?a=d&c=artiaex&d=paper_00219258_v280_n37_p32480_Ferreiro_oai |
| work_keys_str_mv |
AT ferreirodu freeenergycontributionstodirectreadoutofadnasequence AT dellarolem freeenergycontributionstodirectreadoutofadnasequence AT nadraad freeenergycontributionstodirectreadoutofadnasequence AT depratgayg freeenergycontributionstodirectreadoutofadnasequence |
| _version_ |
1766026557904650240 |