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首页> 外文期刊>The European physical journal, E. Soft matter >The diffusion constant of a labeled protein sliding along DNA
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The diffusion constant of a labeled protein sliding along DNA

机译：标记蛋白质沿DN​​A滑动的扩散常数

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摘要

Long ago inferred by biochemists, the linear diffusion of proteins along DNA has recently been observed at a single-molecule level using fluorescence microscopy. This imaging technique requires labeling the protein of interest with a fluorophore, usually an organic nanosized dye that is not supposed to impact the dynamics of the protein. Yet individual proteins can also be tracked using much larger labels, like quantum dots or beads. We investigate here the impact of such a large label on the protein diffusion along DNA. Solving a Fokker-Planck equation, we estimate the diffusion constant of a protein-label complex diffusing in a periodic potential that mimics the DNA-protein interaction, the link between the protein and the label being modeled as a Hookean spring. Our results indicate that the diffusion constant can generally be calculated by considering that the motion of the protein in the DNA potential is decoupled from the Brownian motion of the label. Our conclusions are in good agreement with the experimental results we obtained with the restriction enzyme EcoRV, assuming a rotation-coupled diffusion of the enzyme along DNA.
机译：由生物化学家推测很久以前，最近已经使用荧光显微镜在单分子水平上观察到蛋白质沿DN​​A的线性扩散。这种成像技术需要用荧光团标记目标蛋白，荧光团通常是有机纳米级染料，不应影响蛋白质的动力学。但是，也可以使用更大的标记（例如量子点或珠子）来跟踪单个蛋白质。我们在这里研究如此大的标签对蛋白质沿DN​​A扩散的影响。通过求解Fokker-Planck方程，我们估算了蛋白质-标签复合物的扩散常数，该蛋白质在模拟DNA-蛋白质相互作用的周期性电势中扩散，该蛋白质与标签之间的联系被建模为Hookean弹簧。我们的结果表明，通常可以通过考虑DNA电位中蛋白质的运动与标记物的布朗运动解耦来计算扩散常数。我们的结论与限制性酶EcoRV所获得的实验结果非常吻合，假定酶沿DNA旋转耦合扩散。

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