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arXiv 2012.11111cond-mat.soft
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拥挤诱导蛋白质稳定性变化的理论和模拟及其在$λ$阻遏物中的应用

Theory and simulations for crowding-induced changes in stability of proteins with applications to $λ$ repressor

Natalia D. Denesyuk, D. Thirumalai

摘要:

实验和理论已经表明,当拥挤粒子和蛋白质之间的空间相互作用占主导地位时,这会引起Asakura-Oosawa耗尽力,那么与无限稀释的情况相比,蛋白质的稳定性会增加。我们使用的理论参数,拥挤的体积分数($Φ_C$)依赖于增加的熔化温度的球状蛋白质,$ΔT_m(Φ_C) \approx Φ_C^α$,其中$α= \frac{1}{(3 ν_{eff} - 1)}$。有效Flory指数$ν_{eff}$将未折叠状态下的回转半径与蛋白质中氨基酸残基的数量相关联。我们推导出绑定1.25 $\le α\le$ 2.0。在球形拥挤粒子的存在下,使用$λ$阻遏物的分子模拟证实了理论预测。以前的模拟和实验的分析证实了预测的理论界为$α$。我们发现,拥挤颗粒和氨基酸残基之间的非特异性吸引力必须是实质性的,以完全否定增强的蛋白质稳定性,由于蛋白质内吸引力Asakura-Oosawa(AO)耗尽潜力。使用这些发现,我们提供了一个非常温和的(通常小于0.5千卡/摩尔)在细胞环境中的某些蛋白质的不稳定的替代解释。细胞环境是多分散的,含有大小拥挤剂。AO参数表明,蛋白质将被定位在大的(尺寸超过蛋白质)拥挤,预计对稳定性的影响可以忽略不计。包含拥挤颗粒混合物的{ \it In vitro}实验可以验证或使预测无效。

英文摘要:

Experiments and theories have shown that when steric interactions between crowding particles and proteins are dominant, which give rise to Asakura-Oosawa depletion forces, then the stabilities of the proteins increase compared to the infinite dilution case. We show using theoretical arguments that the crowder volume fraction ($Φ_C$) dependent increase in the melting temperature of globular proteins, $ΔT_m(Φ_C) \approx Φ_C^α$ where $α= \frac{1}{(3 ν_{eff} - 1)}$. The effective Flory exponent, $ν_{eff}$, relates the radius of gyration in the unfolded state to the number of amino acid residues in the protein. We derive the bound 1.25 $\le α\le$ 2.0. The theoretical predictions are confirmed using molecular simulations of $λ$ repressor in the presence of spherical crowding particles. Analyses of previous simulations and experiments confirm the predicted theoretical bound for $α$. We show that the non-specific attractions between crowding particles and amino acid residues have to be substantial to fully negate the enhanced protein stabilities due to intra protein attractive Asakura-Oosawa (AO) depletion potential. Using the findings, we provide an alternate explanation for the very modest (often less than 0.5 Kcal/mol) destabilization in certain proteins in the cellular milieu. Cellular environment is polydisperse containing large and small crowding agents. AO arguments suggest that proteins would be localized between large (sizes exceeding that of the proteins) crowders, which are predicted to have negligible effect on stability. {\it In vitro} experiments containing mixtures of crowding particles could validate or invalidate the predictions.

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