Laskar Aparna, Rodger Euan J, Chatterjee Aniruddha, Mandal Chhabinath
Indian Institute of Chemical Biology (CSIR Unit, Government of India), Kolkata, West Bengal, India.
BMC Res Notes. 2012 May 24;5:256. doi: 10.1186/1756-0500-5-256.
Serine proteases account for over a third of all known proteolytic enzymes; they are involved in a variety of physiological processes and are classified into clans sharing structural homology. The PA clan of endopeptidases is the most abundant and over two thirds of this clan is comprised of the S1 family of serine proteases, which bear the archetypal trypsin fold and have a catalytic triad in the order Histidine, Aspartate, Serine. These proteases have been studied in depth and many three dimensional structures have been experimentally determined. However, these structures mostly consist of bacterial and animal proteases, with a small number of plant and fungal proteases and as yet no structures have been determined for protozoa or archaea. The core structure and active site geometry of these proteases is of interest for many applications. This study investigated the structural properties of different S1 family serine proteases from a diverse range of taxa using molecular modeling techniques.
Our predicted models from protozoa, archaea, fungi and plants were combined with the experimentally determined structures of 16 S1 family members and used for analysis of the catalytic core. Amino acid sequences were submitted to SWISS-MODEL for homology-based structure prediction or the LOOPP server for threading-based structure prediction. Predicted models were refined using INSIGHT II and SCRWL and validated against experimental structures. Investigation of secondary structures and electrostatic surface potential was performed using MOLMOL. The structural geometry of the catalytic core shows clear deviations between taxa, but the relative positions of the catalytic triad residues were conserved. Some highly conserved residues potentially contributing to the stability of the structural core were identified. Evolutionary divergence was also exhibited by large variation in secondary structure features outside the core, differences in overall amino acid distribution, and unique surface electrostatic potential patterns between species.
Encompassing a wide range of taxa, our structural analysis provides an evolutionary perspective on S1 family serine proteases. Focusing on the common core containing the catalytic site of the enzyme, this analysis is beneficial for future molecular modeling strategies and structural analysis of serine protease models.
丝氨酸蛋白酶占所有已知蛋白水解酶的三分之一以上；它们参与多种生理过程，并根据结构同源性分为不同的家族。内肽酶的PA家族最为丰富，该家族三分之二以上由丝氨酸蛋白酶的S1家族组成，这些丝氨酸蛋白酶具有典型的胰蛋白酶折叠结构，其催化三联体的顺序为组氨酸、天冬氨酸、丝氨酸。这些蛋白酶已得到深入研究，许多三维结构已通过实验确定。然而，这些结构大多是细菌和动物蛋白酶的结构，只有少数植物和真菌蛋白酶的结构，目前尚未确定原生动物或古细菌的蛋白酶结构。这些蛋白酶的核心结构和活性位点几何形状在许多应用中都备受关注。本研究使用分子建模技术研究了来自不同分类群的不同S1家族丝氨酸蛋白酶的结构特性。
我们从原生动物、古细菌、真菌和植物中预测的模型与16个S1家族成员的实验确定结构相结合，并用于催化核心的分析。氨基酸序列提交给SWISS-MODEL进行基于同源性的结构预测，或提交给LOOPP服务器进行基于穿线法的结构预测。预测模型使用INSIGHT II和SCRWL进行优化，并根据实验结构进行验证。使用MOLMOL对二级结构和静电表面电位进行研究。催化核心的结构几何形状在不同分类群之间存在明显差异，但催化三联体残基的相对位置是保守的。确定了一些可能有助于结构核心稳定性的高度保守残基。核心之外的二级结构特征的巨大差异、整体氨基酸分布的差异以及物种之间独特的表面静电势模式也表现出进化分歧。
我们的结构分析涵盖了广泛的分类群，为S1家族丝氨酸蛋白酶提供了一个进化视角。该分析聚焦于包含酶催化位点的共同核心，有利于未来的分子建模策略以及丝氨酸蛋白酶模型的结构分析。
