Xia Qian, Ding Yanrui
Laboratory of Media Design and Software Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China.
Key Laboratory of Industrial Biotechnology, Jiangnan University, Wuxi, Jiangsu, 214122, China.
Protein Pept Lett. 2019;26(9):702-716. doi: 10.2174/0929866526666190617091812.
Dynamic communication caused by mutation affects protein stability. The main objective of this study is to explore how mutations affect communication and to provide further insight into the relationship between heat resistance and signal propagation of Bacillus subtilis lipase (Lip A).
The relationship between dynamic communication and Lip A thermostability is studied by long-time MD simulation and residue interaction network. The Dijkstra algorithm is used to get the shortest path of each residue pair. Subsequently, time-series frequent paths and spatio-temporal frequent paths are mined through an Apriori-like algorithm.
Time-series frequent paths show that the communication between residue pairs, both in wild-type lipase (WTL) and mutant 6B, becomes chaotic with an increase in temperature; however, more residues in 6B can maintain stable communication at high temperature, which may be associated with the structural rigidity. Furthermore, spatio-temporal frequent paths reflect the interactions among secondary structures. For WTL at 300K, β7, αC, αB, the longest loop, αA and αF contact frequently. The 310-helix between β3 and αA is penetrated by spatio-temporal frequent paths. At 400K, only αC can be frequently transmitted. For 6B, when at 300K, αA and αF are in more tight contact by spatio-temporal frequent paths though I157M and N166Y. Moreover, the rigidity of the active site His156 and the C-terminal of Lip A are increased, as reflected by the spatio-temporal frequent paths. At 400K, αA and αF, 310-helix between β3 and αA, the longest loop, and the loop where the active site Asp133 is located can still maintain stable communication.
From the perspective of residue dynamic communication, it is obviously found that mutations cause changes in interactions between secondary structures and enhance the rigidity of the structure, contributing to the thermal stability and functional activity of 6B.
由突变引起的动态通讯会影响蛋白质稳定性。本研究的主要目的是探究突变如何影响通讯，并进一步深入了解枯草芽孢杆菌脂肪酶（Lip A）的耐热性与信号传播之间的关系。
通过长时间分子动力学模拟和残基相互作用网络研究动态通讯与Lip A热稳定性之间的关系。使用迪杰斯特拉算法获取每个残基对的最短路径。随后，通过类似Apriori的算法挖掘时间序列频繁路径和时空频繁路径。
时间序列频繁路径表明，野生型脂肪酶（WTL）和突变体6B中残基对之间的通讯都会随着温度升高而变得混乱；然而，6B中有更多残基能够在高温下保持稳定通讯，这可能与结构刚性有关。此外，时空频繁路径反映了二级结构之间的相互作用。对于300K下的WTL，β7、αC、αB、最长环、αA和αF频繁接触。β3和αA之间的310螺旋被时空频繁路径贯穿。在400K时，只有αC能够频繁传递。对于6B，在300K时，通过时空频繁路径，αA和αF通过I157M和N166Y接触更为紧密。此外，时空频繁路径反映出活性位点His156和Lip A C端的刚性增加。在400K时，αA和αF、β3和αA之间的310螺旋、最长环以及活性位点Asp133所在的环仍能保持稳定通讯。
从残基动态通讯的角度明显发现，突变导致二级结构之间相互作用发生变化并增强了结构刚性，有助于6B的热稳定性和功能活性。
