Carboxyl-modified substrates are the most common chemical moieties that are frequently used as protein defibrillators. We studied the stability of protein–benzoic acid complexes with bovine serum albumin (BSA), zein and lysozyme proteins using various computational methods. Structural model for zein was built using homology modelling technique and molecular docking was used to prepare complex structures of all three proteins with benzoic acid. Molecular dynamics calculations performed on these complex structures provided a strong support for the stability of protein–benzoic acid complexes. The results from various analyses including root-mean-square deviation (RMSD) and radius of gyration showed the stability and compactness of all proteins–benzoic acid complexes. Moreover, exploration of structural fluctuations in proteins revealed the stability of active site residues. Two potential binding modes of benzoic acid with all three proteins were identified via cluster analysis. The binding mode which was retrieved from top cluster containing 86–91% of total conformations displayed very strong binding interactions for zein, BSA and lysozyme proteins. In addition, the results of binding mode showed that various interactions, including hydrogen binding, hydrophobic and electrostatic interactions were important for the optimal binding of benzoic acid with the active sites of proteins. Exploration of solvent accessible surface area showed that lysozyme-binding cavity was more exposed to the surface as compared to the other two proteins. Free energy analysis of all protein systems showed the stability of protein–benzoic acid complexes with lysozyme and BSA relatively more stable than zein system. The results of our study provided important insights to the dynamic and structural information about protein–benzoic acid interactions with BSA, zein and lysozyme proteins. This work is important in enhancing the stability of therapeutic protein drugs loaded on carboxyl substrates.

羧基修饰的底物是最常见的化学部分，经常用作蛋白质除纤颤剂。我们使用各种计算方法研究了蛋白质-苯甲酸与牛血清白蛋白（BSA），玉米蛋白和溶菌酶蛋白的稳定性。使用同源性建模技术建立玉米蛋白的结构模型，并使用分子对接来制备所有三种蛋白质与苯甲酸的复杂结构。对这些复杂结构进行的分子动力学计算为蛋白质-苯甲酸复合物的稳定性提供了有力的支持。各种分析（包括均方根偏差（RMSD）和回转半径）的结果表明，所有蛋白质-苯甲酸复合物的稳定性和紧密度。此外，蛋白质结构波动的探索揭示了活性位点残基的稳定性。通过聚类分析确定了苯甲酸与所有三种蛋白质的两种潜在结合方式。从包含总构象的86–91％的顶部簇中检索到的结合模式显示了玉米蛋白，BSA和溶菌酶蛋白的非常强的结合相互作用。此外，结合模式的结果表明，各种相互作用，包括氢键结合，疏水和静电相互作用，对于苯甲酸与蛋白质活性位点的最佳结合至关重要。对溶剂可及表面积的探索表明，与其他两种蛋白质相比，溶菌酶结合腔更暴露于表面。所有蛋白质系统的自由能分析显示，蛋白质-苯甲酸与溶菌酶和BSA的复合物的稳定性比玉米醇溶蛋白系统稳定。我们的研究结果为有关蛋白质-苯甲酸与BSA，玉米蛋白和溶菌酶蛋白质相互作用的动力学和结构信息提供了重要的见解。这项工作对增强载于羧基底物上的治疗性蛋白质药物的稳定性很重要。