BACKGROUND T7 lysozyme (T7L), also known as N-acetylmuramoyl-L-alanine amidase, is a T7 bacteriophage gene product. It involves two functions: It can cut amide bonds in the bacterial cell wall and interacts with T7 RNA polymerase (T7RNAP) as a part of transcription inhibition. In this study, with the help of molecular dynamics (MD) calculations and computational interaction studies, we investigated the effect of varying pH conditions on conformational flexibilities of T7L and their influence on T7RNAP -T7L interactions. RESULTS From the MD studies of the T7L at three different pH strengths viz. 5, neutral and 7.9 it was observed that T7L structure at pH 5 exhibited less stable nature with more residue level fluctuations, decrease of secondary structural elements and less compactness as compared to its counterparts: neutral pH and pH 7.9. The T-pad analysis of the MD trajectories identified local fluctuations in few residues that influenced the conformational differences in three pH strengths. From the docking of the minimum energy representative structures of T7L at different pH strengths (obtained from the free energy landscape analysis) with T7RNAP structures at same pH strengths, we saw strong interaction patterns at pH 7.9 and pH 5. The MD analysis of these complexes also confirmed the observations of docking study. From the combined in silico studies, it was observed that there are conformational changes in N-terminal and near helix 1 of T7L at different pH strengths, which are involved in the T7RNAP interaction, thereby varying the interaction pattern. CONCLUSION Since T7L has been used for developing novel therapeutics and T7RNAP one of the most biologically useful protein in both in-vitro and in vivo experiments, this in silico study of pH dependent conformational differences in T7L and the differential interaction with T7RNAP at different pH can provide a significant insight into the structural investigations on T7L and T7RNAP in varying pH environments.

中文翻译：

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T7溶菌酶与T7 RNA聚合酶的pH依赖性差异相互作用的计算评估。

背景技术T7溶菌酶（T7L），也称为N-乙酰基村酰-L-丙氨酸酰胺酶，是T7噬菌体基因产物。它涉及两个功能：它可以切割细菌细胞壁中的酰胺键，并与T7 RNA聚合酶（T7RNAP）相互作用，作为转录抑制的一部分。在这项研究中，借助分子动力学（MD）计算和计算相互作用研究，我们研究了不同pH条件对T7L构象柔韧性的影响及其对T7RNAP -T7L相互作用的影响。结果从T7L在三种不同pH强度下的MD研究得出。如图5所示，与中性pH和pH 7.9的对应物相比，观察到在pH 5的T7L结构表现出较不稳定的性质，具有更大的残基水平波动，二级结构元素的减少和紧凑性。MD轨迹的T-pad分析确定了少数残基的局部波动，这些残基影响了三个pH强度的构象差异。从不同pH强度下T7L的最小能量代表结构（从自由能态分析获得）与相同pH强度下的T7RNAP结构对接，我们看到在pH 7.9和pH 5下有很强的相互作用模式。也证实了对接研究的观察结果。从组合的计算机模拟研究中，可以观察到在不同的pH强度下，T7L的N末端和1螺旋附近存在构象变化，这涉及T7RNAP相互作用，从而改变了相互作用模式。