The effect of protein relaxation on charge-charge interactions and dielectric constants of proteins.
The effect of protein relaxation on charge-charge interactions and dielectric constants of proteins.
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蛋白质弛豫对蛋白质电荷-电荷相互作用和介电常数的影响。
DOI：
10.1016/s0006-3495(98)77885-3
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发表时间：
1998
影响因子：
3.4
通讯作者：
Warshel,A
中科院分区：
文献类型：
--
作者：
Sham,YY;Muegge,I;Warshel,A
在线性响应近似的框架下，用半微观形式的蛋白质偶极朗之万偶极子方法(∈/S)研究了蛋白质极性基团的重组对电荷-电荷相互作用和相应的有效介电常数(PDLD/S)的影响。这是通过评估球形红杆菌反应中心的电离残基之间的相互作用来完成的，同时考虑了蛋白质重组能量。结果发现，对蛋白质弛豫的明确考虑会导致∈效应的显著增加，而不考虑这种弛豫的半显微镜模型迫使人们在泊松-玻尔兹曼模型的所谓的“蛋白质介电常数”∈_p或在∈/S模型中使用较大的值。由于电离残留物的重组和水渗透程度的变化，预计∈效应将进一步增加。这一发现进一步支持了这样的观点，即∈in(或∈p)代表未被明确考虑的贡献。本研究还系统地说明了∈Eff的性质，支持了我们之前报道的电荷相互作用对应于这种“介电常数”的很大值的观点，即使在蛋白质内部也是如此。本文还指出，蛋白质中可电离基团之间相互作用的∈效应与决定蛋白质中离子对自由能的有效介电常数∈‘Eff有很大的不同(∈’Effect反映了蛋白质偶极取向的影响)。最后讨论了与寻找一般∈有关的问题。阐明了再现蛋白质驰豫对电荷相互作用影响的∈不等于再现单个电荷形成时相应效应的∈。这反映了在宏观模型中塑造微观概念的尝试存在根本性的不一致。因此，人们应该要么使用大的∈In用于电荷-电荷相互作用，而使用小的∈In用于电荷-偶极相互作用，要么从微观上考虑蛋白质的驰豫。
The effect of the reorganization of the protein polar groups on charge-charge interaction and the corresponding effective dielectric constant (∈eff) is examined by the semimicroscopic version of the Protein Dipole Langevin Dipoles (PDLD/S) method within the framework of the Linear Response Approximation (LRA). This is done by evaluating the interactions between ionized residues in the reaction center ofRhodobacter sphaeroides, while taking into account the protein reorganization energy. It is found that an explicit consideration of the protein relaxation leads to a significant increase in ∈effand that semimicroscopic models that do not take this relaxation into account force one to use a large value for the so-called "protein dielectric constant," ∈p, of the Poisson-Boltzmann model or for the corresponding ∈inin the PDLD/S model. An additional increase in ∈effis expected from the reorganization of ionized residues and from changes in the degree of water penetration. This finding provides further support for the idea that ∈in(or ∈p) represents contributions that are not considered explicitly. The present study also provides a systematic illustration of the nature of ∈eff, supporting our previously reported view that charge-charge interactions correspond to a large value of this "dielectric constant," even in protein interiors. It is also pointed out that ∈efffor the interaction between ionizable groups in proteins is very different from the effective dielectric constant, ∈′eff, that determines the free energy of ion pairs in proteins (∈′effreflects the effect of preoriented protein dipoles). Finally, the problems associated with the search for a general ∈inare discussed. It is clarified that the ∈inthat reproduces the effect of protein relaxation on charge-charge interaction is not equal to the ∈inthat reproduces the corresponding effect upon formation of individual charges. This reflects fundamental inconsistencies in attempts to cast microscopic concepts in a macroscopic model. Thus one should either use a large ∈infor charge-charge interactions and a small ∈infor charge-dipole interactions or consider the protein relaxation microscopically.