Is Asp-His-Ser/Thr-Trp tetrad hydrogen-bond network important to WD40-repeat proteins: a statistical and theoretical study.
WD40-repeat proteins are abundant and play important roles in forming protein complexes. The domain usually has seven WD40 repeats, which folds into a seven beta-sheet propeller with each beta-sheet in a four-strand structure. An analysis of 20 available WD40-repeat proteins in Protein Data Bank reveals that each protein has at least one Asp-His-Ser/Thr-Trp (D-H-S/T-W) hydrogen-bonded tetrad, and some proteins have up to six or seven such tetrads. The relative positions of the four residues in the tetrads are also found to be conserved. A sequence alignment analysis of 560 WD40-repeat protein sequences in human reveals very similar features, indicating that such tetrad may be a general feature of WD40-repeat proteins. We carried out density functional theory and found that these tetrads can lead to significant stabilization including hydrogen-bonding cooperativity. The hydrogen bond involving Trp is significant. These results lead us to propose that the tetrads may be critical to the stability and the mechanism of folding of these proteins.
Wu
Xian-Hui
XH
Laboratory of Chemical Genomics, Shenzhen Graduate School of Peking University, Shenzhen, China.
Zhang
Hui
H
Wu
Yun-Dong
YD
D000595:Amino Acid Sequence; D001224:Aspartic Acid / Q000737:chemistry*; D018360:Crystallography, X-Ray; D030562:Databases, Protein; D006639:Histidine / Q000737:chemistry*; D006801:Humans; D006860:Hydrogen Bonding; D008969:Molecular Sequence Data; D015394:Molecular Structure; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D012694:Serine / Q000737:chemistry*; D013912:Threonine / Q000737:chemistry*; D014364:Tryptophan / Q000737:chemistry*
D011506:Proteins; D013912:Threonine; D001224:Aspartic Acid; D012694:Serine; D006639:Histidine; D014364:Tryptophan