Department of Physics, Clarkson University, Potsdam, NY 13699, USA.
Nanotechnology. 2016 May 20;27(20):205201. doi: 10.1088/0957-4484/27/20/205201. Epub 2016 Apr 4.
Protein filtration is important in many fields of science and technology such as medicine, biology, chemistry, and engineering. Recently, protein separation and filtering with nanoporous membranes has attracted interest due to the possibility of fast separation and high throughput volume. This, however, requires understanding of the protein's dynamics inside and in the vicinity of the nanopore. In this work, we utilize a Brownian dynamics approach to study the motion of the model protein insulin in the membrane-electrolyte electrostatic potential. We compare the results of the atomic model of the protein with the results of a coarse-grained and a single-bead model, and find that the coarse-grained representation of protein strikes the best balance between the accuracy of the results and the computational effort required. Contrary to common belief, we find that to adequately describe the protein, a single-bead model cannot be utilized without a significant effort to tabulate the simulation parameters. Similar to results for nanoparticle dynamics, our findings also indicate that the electric field and the electro-osmotic flow due to the applied membrane and electrolyte biases affect the capture and translocation of the biomolecule by either attracting or repelling it to or from the nanopore. Our computational model can also be applied to other types of proteins and separation conditions.
蛋白质过滤在医学、生物学、化学和工程等许多科学技术领域都很重要。最近，由于具有快速分离和高通量体积的可能性，利用纳米多孔膜进行蛋白质分离和过滤引起了人们的兴趣。然而，这需要了解蛋白质在纳米孔内部和附近的动力学。在这项工作中，我们利用布朗动力学方法研究了模型蛋白胰岛素在膜-电解质静电势中的运动。我们将蛋白质的原子模型的结果与粗粒化和单珠模型的结果进行了比较，并发现蛋白质的粗粒化表示在结果的准确性和所需的计算工作量之间达到了最佳平衡。与普遍的看法相反，我们发现为了充分描述蛋白质，如果不花费大量精力来制表模拟参数，则不能使用单珠模型。与纳米颗粒动力学的结果类似，我们的研究结果还表明，由于施加的膜和电解质偏置引起的电场和电动流动会通过吸引或排斥它来或远离纳米孔来影响生物分子的捕获和易位。我们的计算模型也可以应用于其他类型的蛋白质和分离条件。
