Interaction of glycine, lysine, proline and histidine with dipalmitoylphosphatidylcholine lipid bilayers: a theoretical and experimental study

Autores
Porasso, Rodolfo Daniel; Ale, Norma Mercedes; Ciocco Aloia, Facundo; Masone, Diego Fernando; del Popolo, Mario Gabriel; Ben Altabef, Aida; Gomez Zavaglia, Andrea; Díaz, Sonia Beatriz; Vila, Jorge Alberto
Año de publicación
2015
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
The interaction of unblocked glycine, lysine, proline, and histidine (in their three forms, namely two tautomers and the protonated form) with a dipalmitoylphosphatidylcholine (DPPC) bilayer was assessed using extensive atomistic molecular dynamics simulations. Free energy profiles for the insertion of each amino acid into the lipid bilayer were computed along an appropriated reaction coordinate. The simulation results for glycine in the presence of DPPC were compared with experimental data obtained by Fourier transform infrared spectroscopy. Experimental results predict, in good agreement with simulations, the existence of intermolecular interactions between the DPPC head groups and glycine. Atomistic simulations were further extended to investigate the free energy profiles for lysine, proline and histidine, leading to the following conclusions: (i) lysine free energy profiles computed using a united atom force-field and an analog molecule, where the side-chain is truncated at the β-carbon atom, differ significantly from each other; (ii) the free energy profiles for the three forms of histidine are all very similar, although the charged form interacts mostly with the carbonyl groups of DPPC, while the tautomers interact with the phosphate groups; and (iii) proline does not show a minimum in the free energy profile, pointing to the absence of binding to the membrane lipids. Overall, this work contributes to our general understanding of the various factors affecting the interactions between amino acids and a model cell membrane, and may spur progress in the effort to develop new molecular models to study larger biological systems.
Fil: Porasso, Rodolfo Daniel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico San Luis. Instituto de Matemática Aplicada de San Luis; Argentina
Fil: Ale, Norma Mercedes. Universidad Nacional de Tucuman. Facultad de Bioquimica, Quimica y Farmacia. Instituto de Quimica Fisica; Argentina
Fil: Ciocco Aloia, Facundo. Universidad Nacional de Cuyo; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Masone, Diego Fernando. Universidad Nacional de Cuyo; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: del Popolo, Mario Gabriel. Universidad Nacional de Cuyo; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Ben Altabef, Aida. Universidad Nacional de Tucuman. Facultad de Bioquimica, Quimica y Farmacia. Instituto de Quimica Fisica; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Tucumán. Instituto de Quimica del Noroeste; Argentina
Fil: Gomez Zavaglia, Andrea. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico La Plata. Centro de Investigaciones en Criotecnología de Alimentos (i); Argentina
Fil: Díaz, Sonia Beatriz. Universidad Nacional de Tucuman. Facultad de Bioquimica, Quimica y Farmacia. Instituto de Quimica Fisica; Argentina
Fil: Vila, Jorge Alberto. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico San Luis. Instituto de Matemática Aplicada de San Luis; Argentina. Cornell University; Estados Unidos
Materia
Dppc Lipid Bilayers
Glycine, Lysine, Proline, Hystidine
Interactios
Ftir
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by-nc/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/5807
Acceder
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oai_identifier_str oai:ri.conicet.gov.ar:11336/5807
network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling Interaction of glycine, lysine, proline and histidine with dipalmitoylphosphatidylcholine lipid bilayers: a theoretical and experimental studyPorasso, Rodolfo DanielAle, Norma MercedesCiocco Aloia, FacundoMasone, Diego Fernandodel Popolo, Mario GabrielBen Altabef, AidaGomez Zavaglia, AndreaDíaz, Sonia BeatrizVila, Jorge AlbertoDppc Lipid BilayersGlycine, Lysine, Proline, HystidineInteractiosFtirhttps://purl.org/becyt/ford/1.3https://purl.org/becyt/ford/1The interaction of unblocked glycine, lysine, proline, and histidine (in their three forms, namely two tautomers and the protonated form) with a dipalmitoylphosphatidylcholine (DPPC) bilayer was assessed using extensive atomistic molecular dynamics simulations. Free energy profiles for the insertion of each amino acid into the lipid bilayer were computed along an appropriated reaction coordinate. The simulation results for glycine in the presence of DPPC were compared with experimental data obtained by Fourier transform infrared spectroscopy. Experimental results predict, in good agreement with simulations, the existence of intermolecular interactions between the DPPC head groups and glycine. Atomistic simulations were further extended to investigate the free energy profiles for lysine, proline and histidine, leading to the following conclusions: (i) lysine free energy profiles computed using a united atom force-field and an analog molecule, where the side-chain is truncated at the β-carbon atom, differ significantly from each other; (ii) the free energy profiles for the three forms of histidine are all very similar, although the charged form interacts mostly with the carbonyl groups of DPPC, while the tautomers interact with the phosphate groups; and (iii) proline does not show a minimum in the free energy profile, pointing to the absence of binding to the membrane lipids. Overall, this work contributes to our general understanding of the various factors affecting the interactions between amino acids and a model cell membrane, and may spur progress in the effort to develop new molecular models to study larger biological systems.Fil: Porasso, Rodolfo Daniel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico San Luis. Instituto de Matemática Aplicada de San Luis; ArgentinaFil: Ale, Norma Mercedes. Universidad Nacional de Tucuman. Facultad de Bioquimica, Quimica y Farmacia. Instituto de Quimica Fisica; ArgentinaFil: Ciocco Aloia, Facundo. Universidad Nacional de Cuyo; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Masone, Diego Fernando. Universidad Nacional de Cuyo; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: del Popolo, Mario Gabriel. Universidad Nacional de Cuyo; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Ben Altabef, Aida. Universidad Nacional de Tucuman. Facultad de Bioquimica, Quimica y Farmacia. Instituto de Quimica Fisica; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Tucumán. Instituto de Quimica del Noroeste; ArgentinaFil: Gomez Zavaglia, Andrea. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico La Plata. Centro de Investigaciones en Criotecnología de Alimentos (i); ArgentinaFil: Díaz, Sonia Beatriz. Universidad Nacional de Tucuman. Facultad de Bioquimica, Quimica y Farmacia. Instituto de Quimica Fisica; ArgentinaFil: Vila, Jorge Alberto. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico San Luis. Instituto de Matemática Aplicada de San Luis; Argentina. Cornell University; Estados UnidosRoyal Society of Chemistry2015-05info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfapplication/pdfapplication/pdfapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/5807Porasso, Rodolfo Daniel; Ale, Norma Mercedes; Ciocco Aloia, Facundo; Masone, Diego Fernando; del Popolo, Mario Gabriel; et al.; Interaction of glycine, lysine, proline and histidine with dipalmitoylphosphatidylcholine lipid bilayers: a theoretical and experimental study; Royal Society of Chemistry; RSC Advances; 5; 54; 5-2015; 43537-435462046-2069enginfo:eu-repo/semantics/altIdentifier/url/http://pubs.rsc.org/en/content/articlelanding/2015/ra/c5ra03236ainfo:eu-repo/semantics/altIdentifier/doi/10.1039/C5RA03236Ainfo:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-29T10:18:39Zoai:ri.conicet.gov.ar:11336/5807instacron: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 10:18:39.33CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Interaction of glycine, lysine, proline and histidine with dipalmitoylphosphatidylcholine lipid bilayers: a theoretical and experimental study
title Interaction of glycine, lysine, proline and histidine with dipalmitoylphosphatidylcholine lipid bilayers: a theoretical and experimental study
spellingShingle Interaction of glycine, lysine, proline and histidine with dipalmitoylphosphatidylcholine lipid bilayers: a theoretical and experimental study
Porasso, Rodolfo Daniel
Dppc Lipid Bilayers
Glycine, Lysine, Proline, Hystidine
Interactios
Ftir
title_short Interaction of glycine, lysine, proline and histidine with dipalmitoylphosphatidylcholine lipid bilayers: a theoretical and experimental study
title_full Interaction of glycine, lysine, proline and histidine with dipalmitoylphosphatidylcholine lipid bilayers: a theoretical and experimental study
title_fullStr Interaction of glycine, lysine, proline and histidine with dipalmitoylphosphatidylcholine lipid bilayers: a theoretical and experimental study
title_full_unstemmed Interaction of glycine, lysine, proline and histidine with dipalmitoylphosphatidylcholine lipid bilayers: a theoretical and experimental study
title_sort Interaction of glycine, lysine, proline and histidine with dipalmitoylphosphatidylcholine lipid bilayers: a theoretical and experimental study
dc.creator.none.fl_str_mv Porasso, Rodolfo Daniel
Ale, Norma Mercedes
Ciocco Aloia, Facundo
Masone, Diego Fernando
del Popolo, Mario Gabriel
Ben Altabef, Aida
Gomez Zavaglia, Andrea
Díaz, Sonia Beatriz
Vila, Jorge Alberto
author Porasso, Rodolfo Daniel
author_facet Porasso, Rodolfo Daniel
Ale, Norma Mercedes
Ciocco Aloia, Facundo
Masone, Diego Fernando
del Popolo, Mario Gabriel
Ben Altabef, Aida
Gomez Zavaglia, Andrea
Díaz, Sonia Beatriz
Vila, Jorge Alberto
author_role author
author2 Ale, Norma Mercedes
Ciocco Aloia, Facundo
Masone, Diego Fernando
del Popolo, Mario Gabriel
Ben Altabef, Aida
Gomez Zavaglia, Andrea
Díaz, Sonia Beatriz
Vila, Jorge Alberto
author2_role author
author
author
author
author
author
author
author
dc.subject.none.fl_str_mv Dppc Lipid Bilayers
Glycine, Lysine, Proline, Hystidine
Interactios
Ftir
topic Dppc Lipid Bilayers
Glycine, Lysine, Proline, Hystidine
Interactios
Ftir
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.3
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv The interaction of unblocked glycine, lysine, proline, and histidine (in their three forms, namely two tautomers and the protonated form) with a dipalmitoylphosphatidylcholine (DPPC) bilayer was assessed using extensive atomistic molecular dynamics simulations. Free energy profiles for the insertion of each amino acid into the lipid bilayer were computed along an appropriated reaction coordinate. The simulation results for glycine in the presence of DPPC were compared with experimental data obtained by Fourier transform infrared spectroscopy. Experimental results predict, in good agreement with simulations, the existence of intermolecular interactions between the DPPC head groups and glycine. Atomistic simulations were further extended to investigate the free energy profiles for lysine, proline and histidine, leading to the following conclusions: (i) lysine free energy profiles computed using a united atom force-field and an analog molecule, where the side-chain is truncated at the β-carbon atom, differ significantly from each other; (ii) the free energy profiles for the three forms of histidine are all very similar, although the charged form interacts mostly with the carbonyl groups of DPPC, while the tautomers interact with the phosphate groups; and (iii) proline does not show a minimum in the free energy profile, pointing to the absence of binding to the membrane lipids. Overall, this work contributes to our general understanding of the various factors affecting the interactions between amino acids and a model cell membrane, and may spur progress in the effort to develop new molecular models to study larger biological systems.
Fil: Porasso, Rodolfo Daniel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico San Luis. Instituto de Matemática Aplicada de San Luis; Argentina
Fil: Ale, Norma Mercedes. Universidad Nacional de Tucuman. Facultad de Bioquimica, Quimica y Farmacia. Instituto de Quimica Fisica; Argentina
Fil: Ciocco Aloia, Facundo. Universidad Nacional de Cuyo; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Masone, Diego Fernando. Universidad Nacional de Cuyo; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: del Popolo, Mario Gabriel. Universidad Nacional de Cuyo; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Ben Altabef, Aida. Universidad Nacional de Tucuman. Facultad de Bioquimica, Quimica y Farmacia. Instituto de Quimica Fisica; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Tucumán. Instituto de Quimica del Noroeste; Argentina
Fil: Gomez Zavaglia, Andrea. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico La Plata. Centro de Investigaciones en Criotecnología de Alimentos (i); Argentina
Fil: Díaz, Sonia Beatriz. Universidad Nacional de Tucuman. Facultad de Bioquimica, Quimica y Farmacia. Instituto de Quimica Fisica; Argentina
Fil: Vila, Jorge Alberto. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico San Luis. Instituto de Matemática Aplicada de San Luis; Argentina. Cornell University; Estados Unidos
description The interaction of unblocked glycine, lysine, proline, and histidine (in their three forms, namely two tautomers and the protonated form) with a dipalmitoylphosphatidylcholine (DPPC) bilayer was assessed using extensive atomistic molecular dynamics simulations. Free energy profiles for the insertion of each amino acid into the lipid bilayer were computed along an appropriated reaction coordinate. The simulation results for glycine in the presence of DPPC were compared with experimental data obtained by Fourier transform infrared spectroscopy. Experimental results predict, in good agreement with simulations, the existence of intermolecular interactions between the DPPC head groups and glycine. Atomistic simulations were further extended to investigate the free energy profiles for lysine, proline and histidine, leading to the following conclusions: (i) lysine free energy profiles computed using a united atom force-field and an analog molecule, where the side-chain is truncated at the β-carbon atom, differ significantly from each other; (ii) the free energy profiles for the three forms of histidine are all very similar, although the charged form interacts mostly with the carbonyl groups of DPPC, while the tautomers interact with the phosphate groups; and (iii) proline does not show a minimum in the free energy profile, pointing to the absence of binding to the membrane lipids. Overall, this work contributes to our general understanding of the various factors affecting the interactions between amino acids and a model cell membrane, and may spur progress in the effort to develop new molecular models to study larger biological systems.
publishDate 2015
dc.date.none.fl_str_mv 2015-05
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/11336/5807
Porasso, Rodolfo Daniel; Ale, Norma Mercedes; Ciocco Aloia, Facundo; Masone, Diego Fernando; del Popolo, Mario Gabriel; et al.; Interaction of glycine, lysine, proline and histidine with dipalmitoylphosphatidylcholine lipid bilayers: a theoretical and experimental study; Royal Society of Chemistry; RSC Advances; 5; 54; 5-2015; 43537-43546
2046-2069
url http://hdl.handle.net/11336/5807
identifier_str_mv Porasso, Rodolfo Daniel; Ale, Norma Mercedes; Ciocco Aloia, Facundo; Masone, Diego Fernando; del Popolo, Mario Gabriel; et al.; Interaction of glycine, lysine, proline and histidine with dipalmitoylphosphatidylcholine lipid bilayers: a theoretical and experimental study; Royal Society of Chemistry; RSC Advances; 5; 54; 5-2015; 43537-43546
2046-2069
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/url/http://pubs.rsc.org/en/content/articlelanding/2015/ra/c5ra03236a
info:eu-repo/semantics/altIdentifier/doi/10.1039/C5RA03236A
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by-nc/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by-nc/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/pdf
application/pdf
application/pdf
application/pdf
application/pdf
dc.publisher.none.fl_str_mv Royal Society of Chemistry
publisher.none.fl_str_mv Royal Society of Chemistry
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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