Crystal packing modifies ligand binding affinity: The case of aldose reductase

Autores
Cousido-Siah, Alexandra; Petrova, Tatiana; Hazemann, Isabelle; Mitschler, André; Ruiz, Francesc X.; Howard, Eduardo Ignacio; Ginell, Stepahn; Atmanene, Cédric; Van Dorsselaer, Alain; Sanglier-Cienférani, Sarah; Joachimiak, Andrzej; Podjarny, Alberto
Año de publicación
2012
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
The relationship between the structures of protein-ligand complexes existing in the crystal and in solution, essential in the case of fragment-based screening by X-ray crystallography (FBS-X), has been often an object of controversy. To address this question, simultaneous co-crystallization and soaking of two inhibitors with different ratios, Fidarestat (FID; Kd = 6.5 nM) and IDD594 (594; Kd = 61 nM), which bind to h-aldose reductase (AR), have been performed. The subatomic resolution of the crystal structures allows the differentiation of both inhibitors, even when the structures are almost superposed. We have determined the occupation ratio in solution by mass spectrometry (MS) Occ(FID)/Occ(594) = 2.7 and by X-ray crystallography Occ(FID)/Occ(594) = 0.6. The occupancies in the crystal and in solution differ 4.6 times, implying that ligand binding potency is influenced by crystal contacts. A structural analysis shows that the Loop A (residues 122-130), which is exposed to the solvent, is flexible in solution, and is involved in packing contacts within the crystal. Furthermore, inhibitor 594 contacts the base of Loop A, stabilizing it, while inhibitor FID does not. This is shown by the difference in B-factors of the Loop A between the AR-594 and AR-FID complexes. A stable loop diminishes the entropic energy barrier to binding, favoring 594 versus FID. Therefore, the effect of the crystal environment should be taken into consideration in the X-ray diffraction analysis of ligand binding to proteins. This conclusion highlights the need for additional methodologies in the case of FBS-X to validate this powerful screening technique, which is widely used.
Fil: Cousido-Siah, Alexandra. Université de Strasbourg; Francia
Fil: Petrova, Tatiana. Russian Academy of Sciences. Institute of Mathematical Problems of Biology; Rusia
Fil: Hazemann, Isabelle. Université de Strasbourg; Francia
Fil: Mitschler, André. Université de Strasbourg; Francia
Fil: Ruiz, Francesc X.. Université de Strasbourg; Francia
Fil: Howard, Eduardo Ignacio. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Física de Líquidos y Sistemas Biológicos. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Física de Líquidos y Sistemas Biológicos; Argentina
Fil: Ginell, Stepahn. Argonne National Laboratory; Estados Unidos
Fil: Atmanene, Cédric. Centre National de la Recherche Scientifique; Francia. Université de Strasbourg. Laboratoire de Spectrométrie de Masse BioOrganique ; Francia
Fil: Van Dorsselaer, Alain. Centre National de la Recherche Scientifique; Francia. Université de Strasbourg. Laboratoire de Spectrométrie de Masse BioOrganique ; Francia
Fil: Sanglier-Cienférani, Sarah. Centre National de la Recherche Scientifique; Francia. Université de Strasbourg. Laboratoire de Spectrométrie de Masse BioOrganique ; Francia
Fil: Joachimiak, Andrzej. Argonne National Laboratory; Estados Unidos
Fil: Podjarny, Alberto. Université de Strasbourg; Francia
Materia
COMPETITIVE BINDING
HIGH RESOLUTION CRYSTALLOGRAPHY
LIGAND SOAKING
MASS SPECTROMETRY
PROTEIN CRYSTALLOGRAPHY
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by-nc-nd/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/83350
Acceder
id CONICETDig_fe69d6ab65165727b790ef680ff2303d
oai_identifier_str oai:ri.conicet.gov.ar:11336/83350
network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling Crystal packing modifies ligand binding affinity: The case of aldose reductaseCousido-Siah, AlexandraPetrova, TatianaHazemann, IsabelleMitschler, AndréRuiz, Francesc X.Howard, Eduardo IgnacioGinell, StepahnAtmanene, CédricVan Dorsselaer, AlainSanglier-Cienférani, SarahJoachimiak, AndrzejPodjarny, AlbertoCOMPETITIVE BINDINGHIGH RESOLUTION CRYSTALLOGRAPHYLIGAND SOAKINGMASS SPECTROMETRYPROTEIN CRYSTALLOGRAPHYhttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1The relationship between the structures of protein-ligand complexes existing in the crystal and in solution, essential in the case of fragment-based screening by X-ray crystallography (FBS-X), has been often an object of controversy. To address this question, simultaneous co-crystallization and soaking of two inhibitors with different ratios, Fidarestat (FID; Kd = 6.5 nM) and IDD594 (594; Kd = 61 nM), which bind to h-aldose reductase (AR), have been performed. The subatomic resolution of the crystal structures allows the differentiation of both inhibitors, even when the structures are almost superposed. We have determined the occupation ratio in solution by mass spectrometry (MS) Occ(FID)/Occ(594) = 2.7 and by X-ray crystallography Occ(FID)/Occ(594) = 0.6. The occupancies in the crystal and in solution differ 4.6 times, implying that ligand binding potency is influenced by crystal contacts. A structural analysis shows that the Loop A (residues 122-130), which is exposed to the solvent, is flexible in solution, and is involved in packing contacts within the crystal. Furthermore, inhibitor 594 contacts the base of Loop A, stabilizing it, while inhibitor FID does not. This is shown by the difference in B-factors of the Loop A between the AR-594 and AR-FID complexes. A stable loop diminishes the entropic energy barrier to binding, favoring 594 versus FID. Therefore, the effect of the crystal environment should be taken into consideration in the X-ray diffraction analysis of ligand binding to proteins. This conclusion highlights the need for additional methodologies in the case of FBS-X to validate this powerful screening technique, which is widely used.Fil: Cousido-Siah, Alexandra. Université de Strasbourg; FranciaFil: Petrova, Tatiana. Russian Academy of Sciences. Institute of Mathematical Problems of Biology; RusiaFil: Hazemann, Isabelle. Université de Strasbourg; FranciaFil: Mitschler, André. Université de Strasbourg; FranciaFil: Ruiz, Francesc X.. Université de Strasbourg; FranciaFil: Howard, Eduardo Ignacio. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Física de Líquidos y Sistemas Biológicos. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Física de Líquidos y Sistemas Biológicos; ArgentinaFil: Ginell, Stepahn. Argonne National Laboratory; Estados UnidosFil: Atmanene, Cédric. Centre National de la Recherche Scientifique; Francia. Université de Strasbourg. Laboratoire de Spectrométrie de Masse BioOrganique ; FranciaFil: Van Dorsselaer, Alain. Centre National de la Recherche Scientifique; Francia. Université de Strasbourg. Laboratoire de Spectrométrie de Masse BioOrganique ; FranciaFil: Sanglier-Cienférani, Sarah. Centre National de la Recherche Scientifique; Francia. Université de Strasbourg. Laboratoire de Spectrométrie de Masse BioOrganique ; FranciaFil: Joachimiak, Andrzej. Argonne National Laboratory; Estados UnidosFil: Podjarny, Alberto. Université de Strasbourg; FranciaWiley-liss, Div John Wiley & Sons Inc2012-11info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/mswordapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/83350Cousido-Siah, Alexandra; Petrova, Tatiana; Hazemann, Isabelle; Mitschler, André; Ruiz, Francesc X.; et al.; Crystal packing modifies ligand binding affinity: The case of aldose reductase; Wiley-liss, Div John Wiley & Sons Inc; Proteins: Structure, Function And Genetics; 80; 11; 11-2012; 2552-25610887-3585CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/doi/10.1002/prot.24136info:eu-repo/semantics/altIdentifier/url/https://onlinelibrary.wiley.com/doi/full/10.1002/prot.24136info:eu-repo/semantics/altIdentifier/url/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC4671318&blobtype=pdfinfo:eu-repo/semantics/altIdentifier/url/https://www.ncbi.nlm.nih.gov/pubmed/22752989info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-nd/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-10-22T11:11:25Zoai:ri.conicet.gov.ar:11336/83350instacron: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:34982025-10-22 11:11:26.257CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Crystal packing modifies ligand binding affinity: The case of aldose reductase
title Crystal packing modifies ligand binding affinity: The case of aldose reductase
spellingShingle Crystal packing modifies ligand binding affinity: The case of aldose reductase
Cousido-Siah, Alexandra
COMPETITIVE BINDING
HIGH RESOLUTION CRYSTALLOGRAPHY
LIGAND SOAKING
MASS SPECTROMETRY
PROTEIN CRYSTALLOGRAPHY
title_short Crystal packing modifies ligand binding affinity: The case of aldose reductase
title_full Crystal packing modifies ligand binding affinity: The case of aldose reductase
title_fullStr Crystal packing modifies ligand binding affinity: The case of aldose reductase
title_full_unstemmed Crystal packing modifies ligand binding affinity: The case of aldose reductase
title_sort Crystal packing modifies ligand binding affinity: The case of aldose reductase
dc.creator.none.fl_str_mv Cousido-Siah, Alexandra
Petrova, Tatiana
Hazemann, Isabelle
Mitschler, André
Ruiz, Francesc X.
Howard, Eduardo Ignacio
Ginell, Stepahn
Atmanene, Cédric
Van Dorsselaer, Alain
Sanglier-Cienférani, Sarah
Joachimiak, Andrzej
Podjarny, Alberto
author Cousido-Siah, Alexandra
author_facet Cousido-Siah, Alexandra
Petrova, Tatiana
Hazemann, Isabelle
Mitschler, André
Ruiz, Francesc X.
Howard, Eduardo Ignacio
Ginell, Stepahn
Atmanene, Cédric
Van Dorsselaer, Alain
Sanglier-Cienférani, Sarah
Joachimiak, Andrzej
Podjarny, Alberto
author_role author
author2 Petrova, Tatiana
Hazemann, Isabelle
Mitschler, André
Ruiz, Francesc X.
Howard, Eduardo Ignacio
Ginell, Stepahn
Atmanene, Cédric
Van Dorsselaer, Alain
Sanglier-Cienférani, Sarah
Joachimiak, Andrzej
Podjarny, Alberto
author2_role author
author
author
author
author
author
author
author
author
author
author
dc.subject.none.fl_str_mv COMPETITIVE BINDING
HIGH RESOLUTION CRYSTALLOGRAPHY
LIGAND SOAKING
MASS SPECTROMETRY
PROTEIN CRYSTALLOGRAPHY
topic COMPETITIVE BINDING
HIGH RESOLUTION CRYSTALLOGRAPHY
LIGAND SOAKING
MASS SPECTROMETRY
PROTEIN CRYSTALLOGRAPHY
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.6
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv The relationship between the structures of protein-ligand complexes existing in the crystal and in solution, essential in the case of fragment-based screening by X-ray crystallography (FBS-X), has been often an object of controversy. To address this question, simultaneous co-crystallization and soaking of two inhibitors with different ratios, Fidarestat (FID; Kd = 6.5 nM) and IDD594 (594; Kd = 61 nM), which bind to h-aldose reductase (AR), have been performed. The subatomic resolution of the crystal structures allows the differentiation of both inhibitors, even when the structures are almost superposed. We have determined the occupation ratio in solution by mass spectrometry (MS) Occ(FID)/Occ(594) = 2.7 and by X-ray crystallography Occ(FID)/Occ(594) = 0.6. The occupancies in the crystal and in solution differ 4.6 times, implying that ligand binding potency is influenced by crystal contacts. A structural analysis shows that the Loop A (residues 122-130), which is exposed to the solvent, is flexible in solution, and is involved in packing contacts within the crystal. Furthermore, inhibitor 594 contacts the base of Loop A, stabilizing it, while inhibitor FID does not. This is shown by the difference in B-factors of the Loop A between the AR-594 and AR-FID complexes. A stable loop diminishes the entropic energy barrier to binding, favoring 594 versus FID. Therefore, the effect of the crystal environment should be taken into consideration in the X-ray diffraction analysis of ligand binding to proteins. This conclusion highlights the need for additional methodologies in the case of FBS-X to validate this powerful screening technique, which is widely used.
Fil: Cousido-Siah, Alexandra. Université de Strasbourg; Francia
Fil: Petrova, Tatiana. Russian Academy of Sciences. Institute of Mathematical Problems of Biology; Rusia
Fil: Hazemann, Isabelle. Université de Strasbourg; Francia
Fil: Mitschler, André. Université de Strasbourg; Francia
Fil: Ruiz, Francesc X.. Université de Strasbourg; Francia
Fil: Howard, Eduardo Ignacio. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Física de Líquidos y Sistemas Biológicos. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Física de Líquidos y Sistemas Biológicos; Argentina
Fil: Ginell, Stepahn. Argonne National Laboratory; Estados Unidos
Fil: Atmanene, Cédric. Centre National de la Recherche Scientifique; Francia. Université de Strasbourg. Laboratoire de Spectrométrie de Masse BioOrganique ; Francia
Fil: Van Dorsselaer, Alain. Centre National de la Recherche Scientifique; Francia. Université de Strasbourg. Laboratoire de Spectrométrie de Masse BioOrganique ; Francia
Fil: Sanglier-Cienférani, Sarah. Centre National de la Recherche Scientifique; Francia. Université de Strasbourg. Laboratoire de Spectrométrie de Masse BioOrganique ; Francia
Fil: Joachimiak, Andrzej. Argonne National Laboratory; Estados Unidos
Fil: Podjarny, Alberto. Université de Strasbourg; Francia
description The relationship between the structures of protein-ligand complexes existing in the crystal and in solution, essential in the case of fragment-based screening by X-ray crystallography (FBS-X), has been often an object of controversy. To address this question, simultaneous co-crystallization and soaking of two inhibitors with different ratios, Fidarestat (FID; Kd = 6.5 nM) and IDD594 (594; Kd = 61 nM), which bind to h-aldose reductase (AR), have been performed. The subatomic resolution of the crystal structures allows the differentiation of both inhibitors, even when the structures are almost superposed. We have determined the occupation ratio in solution by mass spectrometry (MS) Occ(FID)/Occ(594) = 2.7 and by X-ray crystallography Occ(FID)/Occ(594) = 0.6. The occupancies in the crystal and in solution differ 4.6 times, implying that ligand binding potency is influenced by crystal contacts. A structural analysis shows that the Loop A (residues 122-130), which is exposed to the solvent, is flexible in solution, and is involved in packing contacts within the crystal. Furthermore, inhibitor 594 contacts the base of Loop A, stabilizing it, while inhibitor FID does not. This is shown by the difference in B-factors of the Loop A between the AR-594 and AR-FID complexes. A stable loop diminishes the entropic energy barrier to binding, favoring 594 versus FID. Therefore, the effect of the crystal environment should be taken into consideration in the X-ray diffraction analysis of ligand binding to proteins. This conclusion highlights the need for additional methodologies in the case of FBS-X to validate this powerful screening technique, which is widely used.
publishDate 2012
dc.date.none.fl_str_mv 2012-11
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/11336/83350
Cousido-Siah, Alexandra; Petrova, Tatiana; Hazemann, Isabelle; Mitschler, André; Ruiz, Francesc X.; et al.; Crystal packing modifies ligand binding affinity: The case of aldose reductase; Wiley-liss, Div John Wiley & Sons Inc; Proteins: Structure, Function And Genetics; 80; 11; 11-2012; 2552-2561
0887-3585
CONICET Digital
CONICET
url http://hdl.handle.net/11336/83350
identifier_str_mv Cousido-Siah, Alexandra; Petrova, Tatiana; Hazemann, Isabelle; Mitschler, André; Ruiz, Francesc X.; et al.; Crystal packing modifies ligand binding affinity: The case of aldose reductase; Wiley-liss, Div John Wiley & Sons Inc; Proteins: Structure, Function And Genetics; 80; 11; 11-2012; 2552-2561
0887-3585
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/doi/10.1002/prot.24136
info:eu-repo/semantics/altIdentifier/url/https://onlinelibrary.wiley.com/doi/full/10.1002/prot.24136
info:eu-repo/semantics/altIdentifier/url/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC4671318&blobtype=pdf
info:eu-repo/semantics/altIdentifier/url/https://www.ncbi.nlm.nih.gov/pubmed/22752989
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by-nc-nd/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by-nc-nd/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/msword
application/pdf
application/pdf
dc.publisher.none.fl_str_mv Wiley-liss, Div John Wiley & Sons Inc
publisher.none.fl_str_mv Wiley-liss, Div John Wiley & Sons Inc
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 12.982451

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