纳米通道中具有横向离子传输的蛋白质的测序
Sequencing proteins with transverse ionic transport in nanochannels
摘要：
{ \it De novo}蛋白质测序对于了解控制活生物体功能的细胞过程以及所有翻译后事件和蛋白质由其相应DNA密码构建后发生的其他序列修饰至关重要。通过获得组成给定蛋白质的氨基酸的顺序，然后可以通过结构预测来确定其二级和三级结构，其用于创建蛋白质聚集疾病（例如阿尔茨海默病）的模型。质谱法是当前选择用于{ \it de novo}测序的技术。然而，由于一些氨基酸具有相同的质量，因此在许多情况下不能完全确定序列。在这里，我们提出了一种新的{ \it从头}蛋白质测序技术，包括通过合成纳米通道转位多肽，并通过交叉的{ \it垂直}纳米通道测量每个氨基酸的离子电流。为了计算由给定氨基酸阻断的横向离子电流，我们使用Monte Carlo方法以及Ramachandran图来确定可用的流动面积，由从分子动力学获得的离子的局部密度和从Stokes方程获得的局部流速比来修改。我们发现，由真核基因编码的20个蛋白质氨基酸的离子电流的分布是统计学上不同的，显示这种技术的{ \it从头}蛋白质测序的潜力。
英文摘要：
{\it De novo} protein sequencing is essential for understanding cellular processes that govern the function of living organisms and all post-translational events and other sequence modifications that occur after a protein has been constructed from its corresponding DNA code. By obtaining the order of the amino acids that composes a given protein one can then determine both its secondary and tertiary structures through structure prediction, which is used to create models for protein aggregation diseases such as Alzheimer's Disease. Mass spectrometry is the current technique of choice for {\it de novo} sequencing. However, because some amino acids have the same mass the sequence cannot be completely determined in many cases. Here, we propose a new technique for {\it de novo} protein sequencing that involves translocating a polypeptide through a synthetic nanochannel and measuring the ionic current of each amino acid through an intersecting {\it perpendicular} nanochannel. To calculate the transverse ionic current blockaded by a given amino acid we use a Monte Carlo method along with Ramachandran plots to determine the available flow area, modified by the local density of ions obtained from molecular dynamics and the local flow velocity ratio derived from the Stokes equation. We find that the distribution of ionic currents for each of the 20 proteinogenic amino acids encoded by eukaryotic genes is statistically distinct, showing this technique's potential for {\it de novo} protein sequencing.
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