Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, USA.
Protein Sci. 2012 May;21(5):697-706. doi: 10.1002/pro.2055.
A software suite, SABER (Selection of Active/Binding sites for Enzyme Redesign), has been developed for the analysis of atomic geometries in protein structures, using a geometric hashing algorithm (Barker and Thornton, Bioinformatics 2003;19:1644-1649). SABER is used to explore the Protein Data Bank (PDB) to locate proteins with a specific 3D arrangement of catalytic groups to identify active sites that might be redesigned to catalyze new reactions. As a proof-of-principle test, SABER was used to identify enzymes that have the same catalytic group arrangement present in o-succinyl benzoate synthase (OSBS). Among the highest-scoring scaffolds identified by the SABER search for enzymes with the same catalytic group arrangement as OSBS were L-Ala D/L-Glu epimerase (AEE) and muconate lactonizing enzyme II (MLE), both of which have been redesigned to become effective OSBS catalysts, demonstrated by experiments. Next, we used SABER to search for naturally existing active sites in the PDB with catalytic groups similar to those present in the designed Kemp elimination enzyme KE07. From over 2000 geometric matches to the KE07 active site, SABER identified 23 matches that corresponded to residues from known active sites. The best of these matches, with a 0.28 Å catalytic atom RMSD to KE07, was then redesigned to be compatible with the Kemp elimination using RosettaDesign. We also used SABER to search for potential Kemp eliminases using a theozyme predicted to provide a greater rate acceleration than the active site of KE07, and used Rosetta to create a design based on the proteins identified.
一个名为 SABER（用于酶重新设计的活性/结合部位选择）的软件套件，已经开发出来用于分析蛋白质结构中的原子几何形状，使用几何哈希算法（Barker 和 Thornton，Bioinformatics 2003;19:1644-1649）。SABER 用于探索蛋白质数据库（PDB）以定位具有特定催化基团 3D 排列的蛋白质，以识别可能被重新设计以催化新反应的活性部位。作为原理验证测试，SABER 用于识别具有与 o-琥珀酰苯甲酸合酶（OSBS）相同催化基团排列的酶。通过 SABER 搜索具有与 OSBS 相同催化基团排列的酶的最高分支架中，L-Ala D/L-Glu 差向异构酶（AEE）和粘康酸内酯酶 II（MLE）的得分最高，这两种酶都已被重新设计为有效的 OSBS 催化剂，实验证明了这一点。接下来，我们使用 SABER 在 PDB 中搜索具有与设计的 Kemp 消除酶 KE07 中存在的催化基团相似的天然存在的活性部位。从超过 2000 个与 KE07 活性部位的几何匹配中，SABER 鉴定出 23 个与已知活性部位残基相对应的匹配。其中最好的匹配，其催化原子 RMSD 与 KE07 的为 0.28 Å，然后使用 RosettaDesign 进行重新设计以与 Kemp 消除兼容。我们还使用 SABER 使用理论预测比 KE07 活性部位提供更大的速率加速的拟酶搜索潜在的 Kemp 消除酶，并使用 Rosetta 基于鉴定的蛋白质创建设计。
