The role of side chain entropy and mutual information for improving the de novo design of Kemp eliminases KE07 and KE70
The role of side chain entropy and mutual information for improving the de novo design of Kemp eliminases KE07 and KE70
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DOI：
10.1039/c6cp03622h
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发表时间：
2016-07-28
影响因子：
3.3
通讯作者：
Head-Gordon, Teresa
中科院分区：
文献类型：
--
作者：
Bhowmick, Asmit;Sharma, Sudhir C.;Head-Gordon, Teresa
计算了两种从头设计的肯普消除酶KE 07和KE 70及其在实验室定向进化（LDE）结束时的最大改进版本的残基对之间的侧链熵和互熵信息。我们发现，熵，而不仅仅是焓，有助于不稳定的反应物状态复杂的设计酶的偏好，以及有利于稳定的过渡态复杂的最佳LDE酶。此外，最高侧链耦合的残基，通过测量的互信息，实验突变时，被发现减少或消灭催化活性，其中一些是远离活性位点。总之，我们的研究结果表明侧链波动及其耦合如何成为从头酶的重要设计特征，并且还可以在未来的酶设计项目中代替LDE步骤或除了LDE步骤之外用于计算步骤。
Side chain entropy and mutual entropy information between residue pairs have been calculated for two de novo designed Kemp eliminase enzymes, KE07 and KE70, and for their most improved versions at the end of laboratory directed evolution (LDE). We find that entropy, not just enthalpy, helped to destabilize the preference for the reactant state complex of the designed enzyme as well as favoring stabilization of the transition state complex for the best LDE enzymes. Furthermore, residues with the highest side chain couplings as measured by mutual information, when experimentally mutated, were found to diminish or annihilate catalytic activity, some of which were far from the active site. In summary, our findings demonstrate how side chain fluctuations and their coupling can be an important design feature for de novo enzymes, and furthermore could be utilized in the computational steps in lieu of or in addition to the LDE steps in future enzyme design projects.