Free energy contributions to direct readout of a DNA sequence

Autores
Ferreiro, D.U.; Dellarole, M.; Nadra, A.D.; De Prat-Gay, G.
Año de publicación
2005
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
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.
Fuente
J. Biol. Chem. 2005;280(37):32480-32484
Materia
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
Nivel de accesibilidad
acceso abierto
Condiciones de uso
http://creativecommons.org/licenses/by/2.5/ar
Repositorio
Biblioteca Digital (UBA-FCEN)
Institución
Universidad Nacional de Buenos Aires. Facultad de Ciencias Exactas y Naturales
OAI Identificador
paperaa:paper_00219258_v280_n37_p32480_Ferreiro
Acceder
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oai_identifier_str paperaa:paper_00219258_v280_n37_p32480_Ferreiro
network_acronym_str BDUBAFCEN
repository_id_str 1896
network_name_str Biblioteca Digital (UBA-FCEN)
spelling Free energy contributions to direct readout of a DNA sequenceFerreiro, D.U.Dellarole, M.Nadra, A.D.De Prat-Gay, G.AdditivesBinding energyComplexationFormabilityFree energyProteinsVirusesDNA recognitionEnergy interactionPapillomavirusProtein-DNA interfaceDNA sequencesDNAprotein E2Cunclassified drugvirus DNAvirus proteinarticlebinding affinityDNA bindingDNA protein complexDNA sequenceDNA structureenergy transferHuman papillomavirus type 16nonhumanpriority journalprotein DNA interactionprotein protein interactionsequence analysiswild typeAmino Acid SequenceCircular DichroismCrystallography, X-RayDatabases, ProteinDNADNA, ViralDNA-Binding ProteinsHydrogen BondingKineticsModels, MolecularMolecular Sequence DataMutationNucleic Acid ConformationOncogene Proteins, ViralProtein BindingProtein Structure, TertiarySequence Homology, Amino AcidTemperatureThermodynamicsViral ProteinsHuman papillomavirus type 16The 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.2005info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfhttp://hdl.handle.net/20.500.12110/paper_00219258_v280_n37_p32480_FerreiroJ. Biol. Chem. 2005;280(37):32480-32484reponame:Biblioteca Digital (UBA-FCEN)instname:Universidad Nacional de Buenos Aires. Facultad de Ciencias Exactas y Naturalesinstacron:UBA-FCENenginfo:eu-repo/semantics/openAccesshttp://creativecommons.org/licenses/by/2.5/ar2025-09-18T10:09:19Zpaperaa:paper_00219258_v280_n37_p32480_FerreiroInstitucionalhttps://digital.bl.fcen.uba.ar/Universidad públicaNo correspondehttps://digital.bl.fcen.uba.ar/cgi-bin/oaiserver.cgiana@bl.fcen.uba.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:18962025-09-18 10:09:20.931Biblioteca Digital (UBA-FCEN) - Universidad Nacional de Buenos Aires. Facultad de Ciencias Exactas y Naturalesfalse
dc.title.none.fl_str_mv Free energy contributions to direct readout of a DNA sequence
title Free energy contributions to direct readout of a DNA sequence
spellingShingle Free energy contributions to direct readout of a DNA sequence
Ferreiro, D.U.
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
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
dc.creator.none.fl_str_mv Ferreiro, D.U.
Dellarole, M.
Nadra, A.D.
De Prat-Gay, G.
author Ferreiro, D.U.
author_facet Ferreiro, D.U.
Dellarole, M.
Nadra, A.D.
De Prat-Gay, G.
author_role author
author2 Dellarole, M.
Nadra, A.D.
De Prat-Gay, G.
author2_role author
author
author
dc.subject.none.fl_str_mv 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
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
dc.description.none.fl_txt_mv 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.
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.
publishDate 2005
dc.date.none.fl_str_mv 2005
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/20.500.12110/paper_00219258_v280_n37_p32480_Ferreiro
url http://hdl.handle.net/20.500.12110/paper_00219258_v280_n37_p32480_Ferreiro
dc.language.none.fl_str_mv eng
language eng
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
http://creativecommons.org/licenses/by/2.5/ar
eu_rights_str_mv openAccess
rights_invalid_str_mv http://creativecommons.org/licenses/by/2.5/ar
dc.format.none.fl_str_mv application/pdf
dc.source.none.fl_str_mv J. Biol. Chem. 2005;280(37):32480-32484
reponame:Biblioteca Digital (UBA-FCEN)
instname:Universidad Nacional de Buenos Aires. Facultad de Ciencias Exactas y Naturales
instacron:UBA-FCEN
reponame_str Biblioteca Digital (UBA-FCEN)
collection Biblioteca Digital (UBA-FCEN)
instname_str Universidad Nacional de Buenos Aires. Facultad de Ciencias Exactas y Naturales
instacron_str UBA-FCEN
institution UBA-FCEN
repository.name.fl_str_mv Biblioteca Digital (UBA-FCEN) - Universidad Nacional de Buenos Aires. Facultad de Ciencias Exactas y Naturales
repository.mail.fl_str_mv ana@bl.fcen.uba.ar
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score 13.001348

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