The Experts below are selected from a list of 882 Experts worldwide ranked by ideXlab platform
Wu Yun-dong - One of the best experts on this subject based on the ideXlab platform.
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Identifying the Hotspots on the Top Faces of WD40-Repeat Proteins from Their Primary Sequences by Beta-Bulges and DHSW Tetrads
plos one, 2012Co-Authors: Wu Xian-hui, Wang Yang, Zhuo Zhu, Jiang Fan, Wu Yun-dongAbstract: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 WDb-a Bulge: among a total of 259 WD40 blades, there are 243 such Beta-Bulges. The R-1 positions in these WDb-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 WDb-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.Multidisciplinary SciencesSCI(E)PubMed9ARTICLE8e43005
Wu Xian-hui - One of the best experts on this subject based on the ideXlab platform.
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Identifying the Hotspots on the Top Faces of WD40-Repeat Proteins from Their Primary Sequences by Beta-Bulges and DHSW Tetrads
plos one, 2012Co-Authors: Wu Xian-hui, Wang Yang, Zhuo Zhu, Jiang Fan, Wu Yun-dongAbstract: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 WDb-a Bulge: among a total of 259 WD40 blades, there are 243 such Beta-Bulges. The R-1 positions in these WDb-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 WDb-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.Multidisciplinary SciencesSCI(E)PubMed9ARTICLE8e43005
Alan R Davidson - One of the best experts on this subject based on the ideXlab platform.
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the identification of conserved interactions within the sh3 domain by alignment of sequences and structures
Protein Science, 2000Co-Authors: Stefan M Larson, Alan R DavidsonAbstract:The SH3 domain, comprised of approximately 60 residues, is found within a wide variety of proteins, and is a mediator of protein-protein interactions. Due to the large number of SH3 domain sequences and structures in the databases, this domain provides one of the best available systems for the examination of sequence and structural conservation within a protein family. In this study, a large and diverse alignment of SH3 domain sequences was constructed, and the pattern of conservation within this alignment was compared to conserved structural features, as deduced from analysis of eighteen different SH3 domain structures. Seventeen SH3 domain structures solved in the presence of bound peptide were also examined to identify positions that are consistently most important in mediating the peptide-binding function of this domain. Although residues at the two most conserved positions in the alignment are directly involved in peptide binding, residues at most other conserved positions play structural roles, such as stabilizing turns or comprising the hydrophobic core. Surprisingly, several highly conserved side-chain to main-chain hydrogen bonds were observed in the functionally crucial RT-Src loop between residues with little direct involvement in peptide binding. These hydrogen bonds may be important for maintaining this region in the precise conformation necessary for specific peptide recognition. In addition, a previously unrecognized yet highly conserved Beta-Bulge was identified in the second Beta-strand of the domain, which appears to provide a necessary kink in this strand, allowing it to hydrogen bond to both sheets comprising the fold.
Wang Yang - One of the best experts on this subject based on the ideXlab platform.
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Identifying the Hotspots on the Top Faces of WD40-Repeat Proteins from Their Primary Sequences by Beta-Bulges and DHSW Tetrads
plos one, 2012Co-Authors: Wu Xian-hui, Wang Yang, Zhuo Zhu, Jiang Fan, Wu Yun-dongAbstract: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 WDb-a Bulge: among a total of 259 WD40 blades, there are 243 such Beta-Bulges. The R-1 positions in these WDb-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 WDb-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.Multidisciplinary SciencesSCI(E)PubMed9ARTICLE8e43005
Jiang Fan - One of the best experts on this subject based on the ideXlab platform.
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Identifying the Hotspots on the Top Faces of WD40-Repeat Proteins from Their Primary Sequences by Beta-Bulges and DHSW Tetrads
plos one, 2012Co-Authors: Wu Xian-hui, Wang Yang, Zhuo Zhu, Jiang Fan, Wu Yun-dongAbstract: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 WDb-a Bulge: among a total of 259 WD40 blades, there are 243 such Beta-Bulges. The R-1 positions in these WDb-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 WDb-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.Multidisciplinary SciencesSCI(E)PubMed9ARTICLE8e43005