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
- Institución
- Consejo Nacional de Investigaciones Científicas y Técnicas
- OAI Identificador
- oai:ri.conicet.gov.ar:11336/83350
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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 Técnicas2025-09-29T09:42:50Zoai: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:34982025-09-29 09:42:50.359CONICET 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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1844613348455350272 |
score |
13.070432 |