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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

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: Wu, Xian-Hui, Wang, Yang, Zhuo, Zhu, Jiang, Fan, Wu, Yun-Dong
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3419727/
https://www.ncbi.nlm.nih.gov/pubmed/22916195
http://dx.doi.org/10.1371/journal.pone.0043005
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author Wu, Xian-Hui
Wang, Yang
Zhuo, Zhu
Jiang, Fan
Wu, Yun-Dong
author_facet Wu, Xian-Hui
Wang, Yang
Zhuo, Zhu
Jiang, Fan
Wu, Yun-Dong
author_sort Wu, Xian-Hui
collection PubMed
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.
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spelling pubmed-34197272012-08-22 Identifying the Hotspots on the Top Faces of WD40-Repeat Proteins from Their Primary Sequences by β-Bulges and DHSW Tetrads Wu, Xian-Hui Wang, Yang Zhuo, Zhu Jiang, Fan Wu, Yun-Dong PLoS One Research Article 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. Public Library of Science 2012-08-15 /pmc/articles/PMC3419727/ /pubmed/22916195 http://dx.doi.org/10.1371/journal.pone.0043005 Text en © 2012 Wu et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Wu, Xian-Hui
Wang, Yang
Zhuo, Zhu
Jiang, Fan
Wu, Yun-Dong
Identifying the Hotspots on the Top Faces of WD40-Repeat Proteins from Their Primary Sequences by β-Bulges and DHSW Tetrads
title 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_short 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
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3419727/
https://www.ncbi.nlm.nih.gov/pubmed/22916195
http://dx.doi.org/10.1371/journal.pone.0043005
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