Identifying the hotspots on the top faces of WD40-repeat proteins from their primary sequences by β-bulges and DHSW tetrads.

The analysis of 36 available crystal structures of WD40 repeat proteins reveals widespread existence of a beta-bulge formed at the beginning of strand a and the end of strand b, termed as WD(b-a) bulge: among a total of 259 WD40 blades, there are 243 such β-bulges. The R(1) positions in these WD(b-a...

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Autores principales:	Xian-Hui Wu, Yang Wang, Zhu Zhuo, Fan Jiang, Yun-Dong Wu
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2012
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/f572f291cc244ae3b695064cdca8d267
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spelling	oai:doaj.org-article:f572f291cc244ae3b695064cdca8d2672021-11-18T07:08:37ZIdentifying the hotspots on the top faces of WD40-repeat proteins from their primary sequences by β-bulges and DHSW tetrads.1932-620310.1371/journal.pone.0043005https://doaj.org/article/f572f291cc244ae3b695064cdca8d2672012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22916195/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203The analysis of 36 available crystal structures of WD40 repeat proteins reveals widespread existence of a beta-bulge formed at the beginning of strand a and the end of strand b, termed as WD(b-a) bulge: among a total of 259 WD40 blades, there are 243 such β-bulges. The R(1) positions in these WD(b-a) bulges have fair distributions of Arg, His, Ile, Leu, Lys, Met, Phe, Trp, Tyr and Val residues. These residues protrude on the top face of the WD40 proteins and can serve as hotspots for protein-protein interactions. An analysis of 29 protein complexes formed by 17 WD proteins reveals that these R(1) residues, along with two other residues (R(1)-2 and D-1), are indeed widely involved in protein-protein interactions. Interestingly, these WD(b-a) bulges can be easily identified by the 4-amino acid sequences of (V, L, I), R(1), R(2), (V, L, I), along with some other significant amino acids. Thus, the hotspots of WD40 proteins on the top face can be readily predicted based on the primary sequences of the proteins. The literature-reported mutagenesis studies for Met30, MDV1, Tup11, COP1 and SPA1, which crystal structures are not available, can be readily understood based on the feature-based method. Applying the method, the twelve potential hotspots on the top face of Tup11 from S. japonicas have been identified. Our ITC measurements confirm seven of them, Tyr382, Arg284, Tyr426, Tyr508, Leu559, Lys575 and Ile601, are essential for recognizing Fep1. The ITC measurements further convinced that the feature-based method provides accurate prediction of hotspots on the top face.Xian-Hui WuYang WangZhu ZhuoFan JiangYun-Dong WuPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 8, p e43005 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Xian-Hui Wu Yang Wang Zhu Zhuo Fan Jiang Yun-Dong Wu Identifying the hotspots on the top faces of WD40-repeat proteins from their primary sequences by β-bulges and DHSW tetrads.
description	The analysis of 36 available crystal structures of WD40 repeat proteins reveals widespread existence of a beta-bulge formed at the beginning of strand a and the end of strand b, termed as WD(b-a) bulge: among a total of 259 WD40 blades, there are 243 such β-bulges. The R(1) positions in these WD(b-a) bulges have fair distributions of Arg, His, Ile, Leu, Lys, Met, Phe, Trp, Tyr and Val residues. These residues protrude on the top face of the WD40 proteins and can serve as hotspots for protein-protein interactions. An analysis of 29 protein complexes formed by 17 WD proteins reveals that these R(1) residues, along with two other residues (R(1)-2 and D-1), are indeed widely involved in protein-protein interactions. Interestingly, these WD(b-a) bulges can be easily identified by the 4-amino acid sequences of (V, L, I), R(1), R(2), (V, L, I), along with some other significant amino acids. Thus, the hotspots of WD40 proteins on the top face can be readily predicted based on the primary sequences of the proteins. The literature-reported mutagenesis studies for Met30, MDV1, Tup11, COP1 and SPA1, which crystal structures are not available, can be readily understood based on the feature-based method. Applying the method, the twelve potential hotspots on the top face of Tup11 from S. japonicas have been identified. Our ITC measurements confirm seven of them, Tyr382, Arg284, Tyr426, Tyr508, Leu559, Lys575 and Ile601, are essential for recognizing Fep1. The ITC measurements further convinced that the feature-based method provides accurate prediction of hotspots on the top face.
format	article
author	Xian-Hui Wu Yang Wang Zhu Zhuo Fan Jiang Yun-Dong Wu
author_facet	Xian-Hui Wu Yang Wang Zhu Zhuo Fan Jiang Yun-Dong Wu
author_sort	Xian-Hui Wu
title	Identifying the hotspots on the top faces of WD40-repeat proteins from their primary sequences by β-bulges and DHSW tetrads.
title_short	Identifying the hotspots on the top faces of WD40-repeat proteins from their primary sequences by β-bulges and DHSW tetrads.
title_full	Identifying the hotspots on the top faces of WD40-repeat proteins from their primary sequences by β-bulges and DHSW tetrads.
title_fullStr	Identifying the hotspots on the top faces of WD40-repeat proteins from their primary sequences by β-bulges and DHSW tetrads.
title_full_unstemmed	Identifying the hotspots on the top faces of WD40-repeat proteins from their primary sequences by β-bulges and DHSW tetrads.
title_sort	identifying the hotspots on the top faces of wd40-repeat proteins from their primary sequences by β-bulges and dhsw tetrads.
publisher	Public Library of Science (PLoS)
publishDate	2012
url	https://doaj.org/article/f572f291cc244ae3b695064cdca8d267
work_keys_str_mv	AT xianhuiwu identifyingthehotspotsonthetopfacesofwd40repeatproteinsfromtheirprimarysequencesbybbulgesanddhswtetrads AT yangwang identifyingthehotspotsonthetopfacesofwd40repeatproteinsfromtheirprimarysequencesbybbulgesanddhswtetrads AT zhuzhuo identifyingthehotspotsonthetopfacesofwd40repeatproteinsfromtheirprimarysequencesbybbulgesanddhswtetrads AT fanjiang identifyingthehotspotsonthetopfacesofwd40repeatproteinsfromtheirprimarysequencesbybbulgesanddhswtetrads AT yundongwu identifyingthehotspotsonthetopfacesofwd40repeatproteinsfromtheirprimarysequencesbybbulgesanddhswtetrads
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Identifying the hotspots on the top faces of WD40-repeat proteins from their primary sequences by β-bulges and DHSW tetrads.

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