Fernández Daniel, Vendrell Josep, Avilés Francesc X, Fernández-Recio Juan
Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain.
Proteins. 2007 Jul 1;68(1):131-44. doi: 10.1002/prot.21390.
The metallocarboxypeptidases (MCPs) belonging to the clan MC were studied by the Optimal Docking Area (ODA) method to evaluate protein-protein binding sites and to provide a basis for the identification of binding partners for this class of enzymes. The ODA method identifies surface patches with optimal desolvation energy based on the selection of low-energy docking regions, generated from a set of surface points around the protein. With few exceptions, the ODA method identified surface patches with a significant low-energy docking surface for all the MCPs with known three-dimensional structure. Overall, in 14 out of 24 cases, the detected ODA patches were correctly located (i.e. more than 50% of the predicted residues were in known protein-protein binding sites), yielding a global success rate of 58%. More specifically, the success rate increased up to 80% on the ODA patches detected for the catalytic domains of the M14A subfamily, independently on the partner. Interestingly, the ODA residues on the catalytic domain were correctly located in the interface with the N-terminal pro domain in all MCPs. The spatial distribution of the ODA patches for the different members of the family is in relation to the origin and function of the particular MCP, which allowed distinguishing between them. In good agreement with the experimentally characterized protein interfaces, the total average surface area of the theoretically derived ODA patches for the catalytic domain of MCPs is around 1700 A2 and their content in hydrophobic residues is about 40%. As a particular case, the average surface area of the ODA patches in MCPs of crop insect pests is about twice that of the MCPs of vertebrates, which might be related to their particular function. We recognized two binding regions for the catalytic domain of the MCPs, one of them accounting for nearly all the known intermolecular interactions made up by the enzymes. Protein inhibitors seem to have evolved to dock on this subset of ODA patches, evoking the binding mode of the N-terminal pro domains. The second binding region detected, for which no ligands have been identified so far, seems to be related to the acquisition/maintenance of the native structure of the peptidase. Overall, the ODA method has been successful in identifying low-energy docking areas in a set of structurally and functionally related proteins, suggesting that it can be easily extended to other families in the search for protein-protein binding sites and for their functional significance.
采用最优对接区域（ODA）方法对属于MC家族的金属羧肽酶（MCP）进行了研究，以评估蛋白质-蛋白质结合位点，并为鉴定这类酶的结合伴侣提供依据。ODA方法基于从蛋白质周围的一组表面点生成的低能量对接区域的选择，识别具有最优去溶剂化能的表面斑块。除少数例外，ODA方法为所有具有已知三维结构的MCP识别出具有显著低能量对接表面的表面斑块。总体而言，在24个案例中的14个案例中，检测到的ODA斑块定位正确（即预测残基的50%以上位于已知的蛋白质-蛋白质结合位点），全局成功率为58%。更具体地说，对于M14A亚家族催化结构域检测到的ODA斑块，成功率提高到了80%，与结合伴侣无关。有趣的是，所有MCP中催化结构域上的ODA残基都正确定位在与N端前结构域的界面处。该家族不同成员的ODA斑块的空间分布与特定MCP的起源和功能有关，这使得能够区分它们。与实验表征的蛋白质界面高度一致，MCP催化结构域理论推导的ODA斑块的总平均表面积约为1700 Å2，其疏水残基含量约为40%。作为一个特殊情况，农作物害虫MCP中ODA斑块的平均表面积约为脊椎动物MCP的两倍，这可能与其特定功能有关。我们识别出了MCP催化结构域的两个结合区域，其中一个几乎占了该酶所有已知的分子间相互作用。蛋白质抑制剂似乎已经进化到停靠在这一ODA斑块子集上，引发了N端前结构域的结合模式。检测到的第二个结合区域，目前尚未鉴定出配体，似乎与肽酶天然结构的获得/维持有关。总体而言，ODA方法成功地在一组结构和功能相关的蛋白质中识别出了低能量对接区域，表明它可以很容易地扩展到其他家族，以寻找蛋白质-蛋白质结合位点及其功能意义。
