Cost-effective Potential for Accurate Polarizable Embedding Calculations in Protein Environments.
Cost-effective Potential for Accurate Polarizable Embedding Calculations in Protein Environments.
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在蛋白质环境中进行精确的极化嵌入计算具有成本效益的潜力。
DOI：
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发表时间：
2019
影响因子：
5.5
通讯作者：
Jógvan Magnus Haugaard Olsen
中科院分区：
文献类型：
--
作者：
P. Reinholdt;E. Kjellgren;Casper Steinmann;Jógvan Magnus Haugaard Olsen
基于片段的极化嵌入（PE）模型与适当的电子结构方法相结合，构成了一种高效、准确的多尺度方法，用于计算中心片段的光谱性质，包括通过嵌入势从其分子环境中产生的影响。然而，与嵌入势的计算相关的计算开销相对较高，这是从对环境的单个片段的第一性原理计算中得出的。为了降低与计算嵌入电位参数相关的计算成本，我们开发了一套针对包括蛋白质在内的大规模PE计算的氨基酸特异性可转移参数。基于氨基酸的参数是通过同时拟合一组参考电位来获得的，这些电位是基于从依赖于主干的旋转体库中导出的结构。开发的具有成本效益的极化蛋白电位（CP3）由原子中心电荷和标准氨基酸的各向同性偶极子-偶极子极化率组成。在电位的再现方面，CP3在小的三肽测试系统和大的蛋白质中表现出一致和可接受的准确性。我们通过实际蛋白质系统的应用表明，通过使用蛋白质环境的纯CP3表示可以获得可接受的精度，从而完全省略了与计算嵌入电位参数相关的成本。通过混合描述，CP3仅用于描述距离中心量子部分超过阈值距离的氨基酸，可以实现与基于全片段的方法相当的高精度。
The fragment-based polarizable embedding (PE) model combined with an appropriate electronic-structure method constitutes a highly efficient and accurate multiscale approach for computing spectroscopic properties of a central moiety including effects from its molecular environment through an embedding potential. There is, however, a comparatively high computational overhead associated with the computation of the embedding potential which is derived from first principles calculations on individual fragments of the environment. To reduce the computational cost associated with the calculation of embedding-potential parameters, we developed a set of amino-acid-specific transferable parameters tailored for large-scale PE calculations that include proteins. The amino-acid-based parameters are obtained by simultaneously fitting to a set of reference electric potentials based on structures derived from a backbone-dependent rotamer library. The developed cost-effective polarizable protein potential (CP3) consists of atom-centered charges and isotropic dipole--dipole polarizabilities of the standard amino acids. In terms of reproduction of electric potentials, the CP3 is shown to perform consistently and with acceptable accuracy across both small tripeptide test systems and larger proteins. We show, through applications on realistic protein systems, that acceptable accuracy can be obtained by using a pure CP3 representation of the protein environment, thus altogether omitting the cost associated with the calculation of embedding-potential parameters. High accuracy comparable to the full fragment-based approach can be achieved through a mixed description where the CP3 is used only to describe amino acids beyond a threshold distance from the central quantum part.
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影响因子：
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作者：
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DOI：
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发表时间：
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期刊：
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影响因子：
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作者：
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DOI：
10.1021/jp910674d
发表时间：
2010-03-04
期刊：
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影响因子：
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作者：
Ponder JW;Wu C;Ren P;Pande VS;Chodera JD;Schnieders MJ;Haque I;Mobley DL;Lambrecht DS;DiStasio RA Jr;Head-Gordon M;Clark GN;Johnson ME;Head-Gordon T
通讯作者：
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