Kamguia Steve D, Njabon Eric N, Patouossa Issofa, Emadak Alphonse, Forlemu Neville
Laboratory of Applied Physical and Analytical Chemistry, Department of Inorganic Chemistry, Faculty of Sciences, University of Yaoundé 1, P.O. Box 812, Yaoundé 00237, Cameroon.
Department of Chemistry, Georgia Gwinnett College, 1000 University Center Lane, Lawrenceville, Georgia 30043, United States.
ACS Omega. 2025 Feb 19;10(8):7907-7919. doi: 10.1021/acsomega.4c08755. eCollection 2025 Mar 4.
Homology modeling can help bridge the gap between missing 3D structures and available primary sequences of protein. More environmentally friendlier insecticides against domestic nuisance can target the octopamine receptor proteins, only expressed in invertebrates. Herein, octopamine receptor homologues from and , which do not have tertiary structures in the Protein Data Bank (PDB), were built using homology modeling and evaluated with various molecular modeling tools. AlphaFold models (AFM), which use artificial intelligence from DeepMind, showed structural validity when superimposed on Swiss-Model models (SMM) for both insect octopamine receptor species. The UCSF Chimera and Modeler models (CMM) did not match those by AlphaFold and Swiss-Model irrespective of the insect species receptor model compared. The greatest discrepancy between any two structures resulted between AFM and CMM with only 21.46% similarity and 14.92% similarity between backbone αCs of their superimposed 3D structures, respectively, for cockroach and mosquito, yet their primary sequences are highly identical. The highest sequence identity for superimposed 3D structures occurred between AFM and SMM of cockroach at 75%, and their corresponding mosquito sequence at 35.12% just surpassed the threshold of pairwise structural validity set above 30%. The local model quality obtained from ProSA web server ranks AFM above SMM and CMM in that order, even though all models had good -scores. Ramachandran plot paints a different picture where the CMM have a higher percentage of residues in the accepted zone and AFM have a few residues in the wrong places. However, the data from VADAR statistics show that AFM models are more thermodynamically stable with lower fraction of buried amino acids or charges. Docking studies conducted on UCSF Chimera software showed similarity in active site residues for AFM and SMM involved in a number of electrostatic and hydrophobic interactions. These include residues GLU202, LEU102, ASP95, and ASP105 for cockroach models and residues VAL24 and LEU174 for mosquito models. The active site of all protein models contains some identical residues found in bound complexes including GLU, LEU, APS, and SER, which happen to be in different positions. ANOVA analysis revealed no significant difference in docking energies, an indication that even when active site residues are different, they still conserve the essential qualities needed for binding. Thus, despite the differences in structures, based on validation evaluation, such differences are unlikely to affect binding with octopamine. However, for studies where the quaternary structure of a protein is crucial, the AFM that preserves the full quaternary structure is recommendable.
同源建模有助于弥合蛋白质缺失的三维结构与可用一级序列之间的差距。更环保的家用驱虫杀虫剂可以靶向仅在无脊椎动物中表达的章鱼胺受体蛋白。在此，利用同源建模构建了来自[未提及具体物种]且在蛋白质数据库（PDB）中没有三级结构的章鱼胺受体同源物，并使用各种分子建模工具进行了评估。使用来自DeepMind的人工智能的AlphaFold模型（AFM），在与两种昆虫章鱼胺受体物种的瑞士模型模型（SMM）叠加时显示出结构有效性。无论比较哪种昆虫物种受体模型，加州大学旧金山分校（UCSF）的Chimera和Modeler模型（CMM）都与AlphaFold和瑞士模型的模型不匹配。在任何两个结构之间，最大的差异出现在AFM和CMM之间，对于蟑螂和蚊子，它们叠加的三维结构的主链αC之间的相似性分别仅为21.46%和14.92%，然而它们的一级序列高度相同。叠加的三维结构的最高序列同一性出现在蟑螂的AFM和SMM之间，为75%，其相应的蚊子序列为35.12%，刚刚超过设定的30%以上的成对结构有效性阈值。从ProSA网络服务器获得的局部模型质量按顺序将AFM排在SMM和CMM之上，尽管所有模型都有良好的分数。拉氏图描绘了一幅不同的图景，其中CMM在接受区域的残基百分比更高，而AFM有一些残基处于错误的位置。然而，来自VADAR统计的数据表明，AFM模型在热力学上更稳定，埋藏氨基酸或电荷的比例更低。在UCSF Chimera软件上进行的对接研究表明，参与许多静电和疏水相互作用的AFM和SMM的活性位点残基具有相似性。这些包括蟑螂模型的GLU202、LEU102、ASP95和ASP105残基以及蚊子模型的VAL24和LEU174残基。所有蛋白质模型的活性位点都包含一些在结合复合物中发现的相同残基，包括GLU、LEU、APS和SER，它们恰好处于不同的位置。方差分析显示对接能量没有显著差异，这表明即使活性位点残基不同，它们仍然保留了结合所需的基本特性。因此，尽管结构存在差异，但基于验证评估，这种差异不太可能影响与章鱼胺的结合。然而，对于蛋白质四级结构至关重要的研究，推荐保留完整四级结构的AFM。
