Wimley William C
Department of Biochemistry SL43, Tulane University Health Sciences Center, New Orleans, Louisiana 70112-2699, USA.
Protein Sci. 2002 Feb;11(2):301-12. doi: 10.1110/ps.29402.
The amino acid composition and architecture of all beta-barrel membrane proteins of known three-dimensional structure have been examined to generate information that will be useful in identifying beta-barrels in genome databases. The database consists of 15 nonredundant structures, including several novel, recent structures. Known structures include monomeric, dimeric, and trimeric beta-barrels with between 8 and 22 membrane-spanning beta-strands each. For this analysis the membrane-interacting surfaces of the beta-barrels were identified with an experimentally derived, whole-residue hydrophobicity scale, and then the barrels were aligned normal to the bilayer and the position of the bilayer midplane was determined for each protein from the hydrophobicity profile. The abundance of each amino acid, relative to the genomic abundance, was calculated for the barrel exterior and interior. The architecture and diversity of known beta-barrels was also examined. For example, the distribution of rise-per-residue values perpendicular to the bilayer plane was found to be 2.7 +/- 0.25 A per residue, or about 10 +/- 1 residues across the membrane. Also, as noted by other authors, nearly every known membrane-spanning beta-barrel strand was found to have a short loop of seven residues or less connecting it to at least one adjacent strand. Using this information we have begun to generate rapid screening algorithms for the identification of beta-barrel membrane proteins in genomic databases. Application of one algorithm to the genomes of Escherichia coli and Pseudomonas aeruginosa confirms its ability to identify beta-barrels, and reveals dozens of unidentified open reading frames that potentially code for beta-barrel outer membrane proteins.
已对所有已知三维结构的β-桶状膜蛋白的氨基酸组成和结构进行了研究，以生成有助于在基因组数据库中识别β-桶状蛋白的信息。该数据库包含15个非冗余结构，包括几个新的、最近解析的结构。已知结构包括单体、二聚体和三聚体β-桶状蛋白，每个β-桶状蛋白含有8至22个跨膜β-链。在该分析中，利用实验得出的全残基疏水性标度确定β-桶状蛋白的膜相互作用表面，然后将β-桶状蛋白垂直于双层排列，并根据疏水性图谱确定每种蛋白质双层中间平面的位置。计算了β-桶状蛋白外部和内部每种氨基酸相对于基因组丰度的丰度。还研究了已知β-桶状蛋白的结构和多样性。例如，发现垂直于双层平面的每残基上升值分布为每残基2.7±0.25 Å，或跨膜约10±1个残基。此外，正如其他作者所指出的，几乎每个已知的跨膜β-桶状链都有一个七个残基或更少的短环将其与至少一个相邻链相连。利用这些信息，我们已开始生成用于在基因组数据库中识别β-桶状膜蛋白的快速筛选算法。将一种算法应用于大肠杆菌和铜绿假单胞菌的基因组，证实了其识别β-桶状蛋白的能力，并揭示了数十个潜在编码β-桶状外膜蛋白的未鉴定开放阅读框。
