Inductive effects in amino acids and peptides: Ionization constants and tryptophan fluorescence

Autores
Lara Popoca, Jesús; Thoke, Henrik S.; Stock, Roberto P.; Rudino Pinera, Enrique; Bagatolli, Luis Alberto
Año de publicación
2020
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Although inductive effects in organic compounds are known to influence chemical properties such as ionization constants, their specific contribution to the properties/behavior of amino acids and functional groups in peptides remains largely unexplored. In this study we developed a computationally economical algorithm for ab initio calculation of the magnitude of inductive effects for non-aromatic molecules. The value obtained by the algorithm is called the Inductive Index and we observed a high correlation (R2 = 0.9427) between our calculations and the pKa values of the alpha-amino groups of amino acids with non-aromatic side-chains. Using a series of modified amino acids, we also found similarly high correlations (R2 > 0.9600) between Inductive Indexes and two wholly independent chemical properties: i) the pKa values of ionizable side-chains and, ii) the fluorescence response of the indole group of tryptophan. After assessing the applicability of the method of calculation at the amino acid level, we extended our study to tryptophan-containing peptides and established that inductive contributions of neighboring side-chains are transmitted through peptide bonds. We discuss possible contributions to the study of proteins.
Fil: Lara Popoca, Jesús. Universidad Nacional Autónoma de México; México
Fil: Thoke, Henrik S.. International and Interdisciplinary Research Network; Dinamarca
Fil: Stock, Roberto P.. Universidad Nacional Autónoma de México; México
Fil: Rudino Pinera, Enrique. Universidad Nacional Autónoma de México; México
Fil: Bagatolli, Luis Alberto. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Investigación Médica Mercedes y Martín Ferreyra. Universidad Nacional de Córdoba. Instituto de Investigación Médica Mercedes y Martín Ferreyra; Argentina
Materia
AMINO ACIDS
COMPUTATIONAL MODEL
INDUCTIVE EFFECTS
IONIZATION CONSTANTS
PEPTIDES
TRYPTOPHAN FLUORESCENCE
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/140204
Acceder
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network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling Inductive effects in amino acids and peptides: Ionization constants and tryptophan fluorescenceLara Popoca, JesúsThoke, Henrik S.Stock, Roberto P.Rudino Pinera, EnriqueBagatolli, Luis AlbertoAMINO ACIDSCOMPUTATIONAL MODELINDUCTIVE EFFECTSIONIZATION CONSTANTSPEPTIDESTRYPTOPHAN FLUORESCENCEhttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1Although inductive effects in organic compounds are known to influence chemical properties such as ionization constants, their specific contribution to the properties/behavior of amino acids and functional groups in peptides remains largely unexplored. In this study we developed a computationally economical algorithm for ab initio calculation of the magnitude of inductive effects for non-aromatic molecules. The value obtained by the algorithm is called the Inductive Index and we observed a high correlation (R2 = 0.9427) between our calculations and the pKa values of the alpha-amino groups of amino acids with non-aromatic side-chains. Using a series of modified amino acids, we also found similarly high correlations (R2 > 0.9600) between Inductive Indexes and two wholly independent chemical properties: i) the pKa values of ionizable side-chains and, ii) the fluorescence response of the indole group of tryptophan. After assessing the applicability of the method of calculation at the amino acid level, we extended our study to tryptophan-containing peptides and established that inductive contributions of neighboring side-chains are transmitted through peptide bonds. We discuss possible contributions to the study of proteins.Fil: Lara Popoca, Jesús. Universidad Nacional Autónoma de México; MéxicoFil: Thoke, Henrik S.. International and Interdisciplinary Research Network; DinamarcaFil: Stock, Roberto P.. Universidad Nacional Autónoma de México; MéxicoFil: Rudino Pinera, Enrique. Universidad Nacional Autónoma de México; MéxicoFil: Bagatolli, Luis Alberto. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Investigación Médica Mercedes y Martín Ferreyra. Universidad Nacional de Córdoba. Instituto de Investigación Médica Mercedes y Martín Ferreyra; ArgentinaElsevier2020-12info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/140204Lara Popoca, Jesús; Thoke, Henrik S.; Stock, Roberto P.; Rudino Pinera, Enrique; Bagatolli, Luis Alberto; Inductive effects in amino acids and peptides: Ionization constants and tryptophan fluorescence; Elsevier; Biochemistry and Biophysics Reports; 24; 12-2020; 1-92405-5808CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/doi/10.1016/j.bbrep.2020.100802info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-29T10:01:17Zoai:ri.conicet.gov.ar:11336/140204instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982025-09-29 10:01:17.339CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Inductive effects in amino acids and peptides: Ionization constants and tryptophan fluorescence
title Inductive effects in amino acids and peptides: Ionization constants and tryptophan fluorescence
spellingShingle Inductive effects in amino acids and peptides: Ionization constants and tryptophan fluorescence
Lara Popoca, Jesús
AMINO ACIDS
COMPUTATIONAL MODEL
INDUCTIVE EFFECTS
IONIZATION CONSTANTS
PEPTIDES
TRYPTOPHAN FLUORESCENCE
title_short Inductive effects in amino acids and peptides: Ionization constants and tryptophan fluorescence
title_full Inductive effects in amino acids and peptides: Ionization constants and tryptophan fluorescence
title_fullStr Inductive effects in amino acids and peptides: Ionization constants and tryptophan fluorescence
title_full_unstemmed Inductive effects in amino acids and peptides: Ionization constants and tryptophan fluorescence
title_sort Inductive effects in amino acids and peptides: Ionization constants and tryptophan fluorescence
dc.creator.none.fl_str_mv Lara Popoca, Jesús
Thoke, Henrik S.
Stock, Roberto P.
Rudino Pinera, Enrique
Bagatolli, Luis Alberto
author Lara Popoca, Jesús
author_facet Lara Popoca, Jesús
Thoke, Henrik S.
Stock, Roberto P.
Rudino Pinera, Enrique
Bagatolli, Luis Alberto
author_role author
author2 Thoke, Henrik S.
Stock, Roberto P.
Rudino Pinera, Enrique
Bagatolli, Luis Alberto
author2_role author
author
author
author
dc.subject.none.fl_str_mv AMINO ACIDS
COMPUTATIONAL MODEL
INDUCTIVE EFFECTS
IONIZATION CONSTANTS
PEPTIDES
TRYPTOPHAN FLUORESCENCE
topic AMINO ACIDS
COMPUTATIONAL MODEL
INDUCTIVE EFFECTS
IONIZATION CONSTANTS
PEPTIDES
TRYPTOPHAN FLUORESCENCE
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.6
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv Although inductive effects in organic compounds are known to influence chemical properties such as ionization constants, their specific contribution to the properties/behavior of amino acids and functional groups in peptides remains largely unexplored. In this study we developed a computationally economical algorithm for ab initio calculation of the magnitude of inductive effects for non-aromatic molecules. The value obtained by the algorithm is called the Inductive Index and we observed a high correlation (R2 = 0.9427) between our calculations and the pKa values of the alpha-amino groups of amino acids with non-aromatic side-chains. Using a series of modified amino acids, we also found similarly high correlations (R2 > 0.9600) between Inductive Indexes and two wholly independent chemical properties: i) the pKa values of ionizable side-chains and, ii) the fluorescence response of the indole group of tryptophan. After assessing the applicability of the method of calculation at the amino acid level, we extended our study to tryptophan-containing peptides and established that inductive contributions of neighboring side-chains are transmitted through peptide bonds. We discuss possible contributions to the study of proteins.
Fil: Lara Popoca, Jesús. Universidad Nacional Autónoma de México; México
Fil: Thoke, Henrik S.. International and Interdisciplinary Research Network; Dinamarca
Fil: Stock, Roberto P.. Universidad Nacional Autónoma de México; México
Fil: Rudino Pinera, Enrique. Universidad Nacional Autónoma de México; México
Fil: Bagatolli, Luis Alberto. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Investigación Médica Mercedes y Martín Ferreyra. Universidad Nacional de Córdoba. Instituto de Investigación Médica Mercedes y Martín Ferreyra; Argentina
description Although inductive effects in organic compounds are known to influence chemical properties such as ionization constants, their specific contribution to the properties/behavior of amino acids and functional groups in peptides remains largely unexplored. In this study we developed a computationally economical algorithm for ab initio calculation of the magnitude of inductive effects for non-aromatic molecules. The value obtained by the algorithm is called the Inductive Index and we observed a high correlation (R2 = 0.9427) between our calculations and the pKa values of the alpha-amino groups of amino acids with non-aromatic side-chains. Using a series of modified amino acids, we also found similarly high correlations (R2 > 0.9600) between Inductive Indexes and two wholly independent chemical properties: i) the pKa values of ionizable side-chains and, ii) the fluorescence response of the indole group of tryptophan. After assessing the applicability of the method of calculation at the amino acid level, we extended our study to tryptophan-containing peptides and established that inductive contributions of neighboring side-chains are transmitted through peptide bonds. We discuss possible contributions to the study of proteins.
publishDate 2020
dc.date.none.fl_str_mv 2020-12
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/11336/140204
Lara Popoca, Jesús; Thoke, Henrik S.; Stock, Roberto P.; Rudino Pinera, Enrique; Bagatolli, Luis Alberto; Inductive effects in amino acids and peptides: Ionization constants and tryptophan fluorescence; Elsevier; Biochemistry and Biophysics Reports; 24; 12-2020; 1-9
2405-5808
CONICET Digital
CONICET
url http://hdl.handle.net/11336/140204
identifier_str_mv Lara Popoca, Jesús; Thoke, Henrik S.; Stock, Roberto P.; Rudino Pinera, Enrique; Bagatolli, Luis Alberto; Inductive effects in amino acids and peptides: Ionization constants and tryptophan fluorescence; Elsevier; Biochemistry and Biophysics Reports; 24; 12-2020; 1-9
2405-5808
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/doi/10.1016/j.bbrep.2020.100802
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv Elsevier
publisher.none.fl_str_mv Elsevier
dc.source.none.fl_str_mv reponame:CONICET Digital (CONICET)
instname:Consejo Nacional de Investigaciones Científicas y Técnicas
reponame_str CONICET Digital (CONICET)
collection CONICET Digital (CONICET)
instname_str Consejo Nacional de Investigaciones Científicas y Técnicas
repository.name.fl_str_mv CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas
repository.mail.fl_str_mv dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar
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score 13.070432

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