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首頁> 美國衛(wèi)生研究院文獻>Biophysical Journal >Absolute Protein-Protein Association Rate Constants from Flexible Coarse-Grained Brownian Dynamics Simulations: The Role of Intermolecular Hydrodynamic Interactions in Barnase-Barstar Association
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Absolute Protein-Protein Association Rate Constants from Flexible Coarse-Grained Brownian Dynamics Simulations: The Role of Intermolecular Hydrodynamic Interactions in Barnase-Barstar Association

機譯：來自靈活的粗粒布朗動力學(xué)模擬的絕對蛋白質(zhì)-蛋白質(zhì)締合速率常數(shù)：分子間流體動力學(xué)相互作用在Barnase-Barstar締合中的作用

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Theory and computation have long been used to rationalize the experimental association rate constants of protein-protein complexes, and Brownian dynamics (BD) simulations, in particular, have been successful in reproducing the relative rate constants of wild-type and mutant protein pairs. Missing from previous BD studies of association kinetics, however, has been the description of hydrodynamic interactions (HIs) between, and within, the diffusing proteins. Here we address this issue by rigorously including HIs in BD simulations of the barnase-barstar association reaction. We first show that even very simplified representations of the proteins—involving approximately one pseudoatom for every three residues in the protein—can provide excellent reproduction of the absolute association rate constants of wild-type and mutant protein pairs. We then show that simulations that include intermolecular HIs also produce excellent estimates of association rate constants, but, for a given reaction criterion, yield values that are decreased by ∼35–80% relative to those obtained in the absence of intermolecular HIs. The neglect of intermolecular HIs in previous BD simulation studies, therefore, is likely to have contributed to the somewhat overestimated absolute rate constants previously obtained. Consequently, intermolecular HIs could be an important component to include in accurate modeling of the kinetics of macromolecular association events.
機譯：長期以來，一直使用理論和計算來合理化蛋白質(zhì)-蛋白質(zhì)復(fù)合物的實驗締合速率常數(shù)，特別是布朗動力學(xué)（BD）模擬已成功地再現(xiàn)了野生型和突變蛋白對的相對速率常數(shù)。然而，先前的BD關(guān)聯(lián)動力學(xué)研究缺少有關(guān)擴散蛋白之間和內(nèi)部的流體動力學(xué)相互作用（HIs）的描述。在這里，我們通過在barnase-barstar締合反應(yīng)的BD模擬中嚴格包含HI來解決此問題。我們首先表明，即使是非常簡化的蛋白質(zhì)表示（蛋白質(zhì)中每三個殘基都包含一個假原子），也可以很好地復(fù)制野生型和突變型蛋白質(zhì)對的絕對締合速率常數(shù)。然后，我們表明，包括分子間HI的模擬也可以很好地估計締合速率常數(shù)，但是，對于給定的反應(yīng)標(biāo)準(zhǔn)，與沒有分子間HI的情況相比，產(chǎn)率降低了約35-80％。因此，在先前的BD模擬研究中忽略分子間HI可能是導(dǎo)致先前獲得的某種程度上被高估的絕對速率常數(shù)的原因。因此，分子間HIs可能是重要的組成部分，可以包括在大分子締合事件動力學(xué)的精確建模中。

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