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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Autores principales:	Ferreiro, Diego U., Dellarole, Mariano, Nadra, Alejandro Daniel, de Prat Gay, Gonzalo
Publicado:	2005
Materias:	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, 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
Acceso en línea:	https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_00219258_v280_n37_p32480_Ferreiro http://hdl.handle.net/20.500.12110/paper_00219258_v280_n37_p32480_Ferreiro
Aporte de:	Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA) de Universidad de Buenos Aires

id	paper:paper_00219258_v280_n37_p32480_Ferreiro
record_format	dspace
spelling	paper:paper_00219258_v280_n37_p32480_Ferreiro2023-06-08T14:43:26Z Free energy contributions to direct readout of a DNA sequence Ferreiro, Diego U. Dellarole, Mariano Nadra, Alejandro Daniel de Prat Gay, Gonzalo 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 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. 2005 https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_00219258_v280_n37_p32480_Ferreiro http://hdl.handle.net/20.500.12110/paper_00219258_v280_n37_p32480_Ferreiro
institution	Universidad de Buenos Aires
institution_str	I-28
repository_str	R-134
collection	Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (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, Diego U. Dellarole, Mariano Nadra, Alejandro Daniel de Prat Gay, Gonzalo 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.
author	Ferreiro, Diego U. Dellarole, Mariano Nadra, Alejandro Daniel de Prat Gay, Gonzalo
author_facet	Ferreiro, Diego U. Dellarole, Mariano Nadra, Alejandro Daniel de Prat Gay, Gonzalo
author_sort	Ferreiro, Diego 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	https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_00219258_v280_n37_p32480_Ferreiro http://hdl.handle.net/20.500.12110/paper_00219258_v280_n37_p32480_Ferreiro
work_keys_str_mv	AT ferreirodiegou freeenergycontributionstodirectreadoutofadnasequence AT dellarolemariano freeenergycontributionstodirectreadoutofadnasequence AT nadraalejandrodaniel freeenergycontributionstodirectreadoutofadnasequence AT depratgaygonzalo freeenergycontributionstodirectreadoutofadnasequence
_version_	1768543497295495168

Free energy contributions to direct readout of a DNA sequence

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