Revisiting the NMR structure of the ultrafast downhill folding protein gpW from bacteriophage λ.

GpW is a 68-residue protein from bacteriophage λ that participates in virus head morphogenesis. Previous NMR studies revealed a novel α+β fold for this protein. Recent experiments have shown that gpW folds in microseconds by crossing a marginal free energy barrier (i.e., downhill folding). These fea...

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Autores principales:	Lorenzo Sborgi, Abhinav Verma, Victor Muñoz, Eva de Alba
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2011
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/4847f6e232bd490f892207f1699b2fa7
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spelling	oai:doaj.org-article:4847f6e232bd490f892207f1699b2fa72021-11-18T07:34:53ZRevisiting the NMR structure of the ultrafast downhill folding protein gpW from bacteriophage λ.1932-620310.1371/journal.pone.0026409https://doaj.org/article/4847f6e232bd490f892207f1699b2fa72011-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22087227/?tool=EBIhttps://doaj.org/toc/1932-6203GpW is a 68-residue protein from bacteriophage λ that participates in virus head morphogenesis. Previous NMR studies revealed a novel α+β fold for this protein. Recent experiments have shown that gpW folds in microseconds by crossing a marginal free energy barrier (i.e., downhill folding). These features make gpW a highly desirable target for further experimental and computational folding studies. As a step in that direction, we have re-determined the high-resolution structure of gpW by multidimensional NMR on a construct that eliminates the purification tags and unstructured C-terminal tail present in the prior study. In contrast to the previous work, we have obtained a full manual assignment and calculated the structure using only unambiguous distance restraints. This new structure confirms the α+β topology, but reveals important differences in tertiary packing. Namely, the two α-helices are rotated along their main axis to form a leucine zipper. The β-hairpin is orthogonal to the helical interface rather than parallel, displaying most tertiary contacts through strand 1. There also are differences in secondary structure: longer and less curved helices and a hairpin that now shows the typical right-hand twist. Molecular dynamics simulations starting from both gpW structures, and calculations with CS-Rosetta, all converge to our gpW structure. This confirms that the original structure has strange tertiary packing and strained secondary structure. A comparison of NMR datasets suggests that the problems were mainly caused by incomplete chemical shift assignments, mistakes in NOE assignment and the inclusion of ambiguous distance restraints during the automated procedure used in the original study. The new gpW corrects these problems, providing the appropriate structural reference for future work. Furthermore, our results are a cautionary tale against the inclusion of ambiguous experimental information in the determination of protein structures.Lorenzo SborgiAbhinav VermaVictor MuñozEva de AlbaPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 6, Iss 11, p e26409 (2011)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Lorenzo Sborgi Abhinav Verma Victor Muñoz Eva de Alba Revisiting the NMR structure of the ultrafast downhill folding protein gpW from bacteriophage λ.
description	GpW is a 68-residue protein from bacteriophage λ that participates in virus head morphogenesis. Previous NMR studies revealed a novel α+β fold for this protein. Recent experiments have shown that gpW folds in microseconds by crossing a marginal free energy barrier (i.e., downhill folding). These features make gpW a highly desirable target for further experimental and computational folding studies. As a step in that direction, we have re-determined the high-resolution structure of gpW by multidimensional NMR on a construct that eliminates the purification tags and unstructured C-terminal tail present in the prior study. In contrast to the previous work, we have obtained a full manual assignment and calculated the structure using only unambiguous distance restraints. This new structure confirms the α+β topology, but reveals important differences in tertiary packing. Namely, the two α-helices are rotated along their main axis to form a leucine zipper. The β-hairpin is orthogonal to the helical interface rather than parallel, displaying most tertiary contacts through strand 1. There also are differences in secondary structure: longer and less curved helices and a hairpin that now shows the typical right-hand twist. Molecular dynamics simulations starting from both gpW structures, and calculations with CS-Rosetta, all converge to our gpW structure. This confirms that the original structure has strange tertiary packing and strained secondary structure. A comparison of NMR datasets suggests that the problems were mainly caused by incomplete chemical shift assignments, mistakes in NOE assignment and the inclusion of ambiguous distance restraints during the automated procedure used in the original study. The new gpW corrects these problems, providing the appropriate structural reference for future work. Furthermore, our results are a cautionary tale against the inclusion of ambiguous experimental information in the determination of protein structures.
format	article
author	Lorenzo Sborgi Abhinav Verma Victor Muñoz Eva de Alba
author_facet	Lorenzo Sborgi Abhinav Verma Victor Muñoz Eva de Alba
author_sort	Lorenzo Sborgi
title	Revisiting the NMR structure of the ultrafast downhill folding protein gpW from bacteriophage λ.
title_short	Revisiting the NMR structure of the ultrafast downhill folding protein gpW from bacteriophage λ.
title_full	Revisiting the NMR structure of the ultrafast downhill folding protein gpW from bacteriophage λ.
title_fullStr	Revisiting the NMR structure of the ultrafast downhill folding protein gpW from bacteriophage λ.
title_full_unstemmed	Revisiting the NMR structure of the ultrafast downhill folding protein gpW from bacteriophage λ.
title_sort	revisiting the nmr structure of the ultrafast downhill folding protein gpw from bacteriophage λ.
publisher	Public Library of Science (PLoS)
publishDate	2011
url	https://doaj.org/article/4847f6e232bd490f892207f1699b2fa7
work_keys_str_mv	AT lorenzosborgi revisitingthenmrstructureoftheultrafastdownhillfoldingproteingpwfrombacteriophagel AT abhinavverma revisitingthenmrstructureoftheultrafastdownhillfoldingproteingpwfrombacteriophagel AT victormunoz revisitingthenmrstructureoftheultrafastdownhillfoldingproteingpwfrombacteriophagel AT evadealba revisitingthenmrstructureoftheultrafastdownhillfoldingproteingpwfrombacteriophagel
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Revisiting the NMR structure of the ultrafast downhill folding protein gpW from bacteriophage λ.

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