Pawłowski K, Zhang B, Rychlewski L, Godzik A
Department of Molecular Biology, The Burnham Institute, La Jolla, California 92037, USA.
Proteins. 1999 Jul 1;36(1):20-30.
Fold assignments for proteins from the Helicobacter pylori genome are carried out using BASIC, a profile-profile alignment algorithm recently tested on the Mycoplasma genitalium and Escherichia coli genomes. The fold assignments are followed by automated function evaluation, based on the multilevel description of functional sites in proteins. Over 40% of the proteins encoded in the H. pylori genome can be recognized as belonging to a protein family with known structure. Previous estimates suggested that only 10-15% of genome proteins could be characterized this way. This dramatic increase in the number of recognized homologies between H. pylori proteins and structurally characterized protein families is partly due to the rapid increase of the database of known protein structures, but mostly it is due to the significant improvement in prediction algorithms. Knowledge of a protein fold adds a new dimension to our understanding of its function and, similarly, structure prediction can also add to understanding, verification, and/or prediction of function for uncharacterized proteins. Several examples analyzed in more detail in this article illustrate insights that can be achieved from structure and detailed function prediction.
利用BASIC对幽门螺杆菌基因组中的蛋白质进行折叠分类，BASIC是一种最近在生殖支原体和大肠杆菌基因组上进行测试的profile-profile比对算法。在折叠分类之后，基于蛋白质功能位点的多级描述进行自动功能评估。幽门螺杆菌基因组中超过40%的编码蛋白质可被识别为属于具有已知结构的蛋白质家族。先前的估计表明，只有10%-15%的基因组蛋白质能够以这种方式进行表征。幽门螺杆菌蛋白质与结构已表征的蛋白质家族之间已识别同源性数量的显著增加，部分原因是已知蛋白质结构数据库的快速增长，但主要是由于预测算法的显著改进。了解蛋白质折叠为我们对其功能的理解增添了新的维度，同样，结构预测也可以增进对未表征蛋白质功能的理解、验证和/或预测。本文更详细分析的几个例子说明了从结构和详细功能预测中可以获得的见解。
