Biologistics--diffusion coefficients for complete proteome of Escherichia coli.
Biologistics--diffusion coefficients for complete proteome of Escherichia coli.
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DOI：
10.1093/bioinformatics/bts537
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发表时间：
2012-11-15
期刊：
影响因子：
--
通讯作者：
Holyst R
中科院分区：
文献类型：
--
作者：
Kalwarczyk T;Tabaka M;Holyst R
动机：生物学为定量分析细胞内的运输(扩散)过程及其时空相关性提供了数据。蛋白质的迁移率是描述基因调控反应速率所必需的少数参数之一。虽然了解体内扩散受限的生化反应需要尽可能多的天然蛋白质的迁移率数据，但目前还没有包含特定细胞类型蛋白质扩散系数(DC)的完整信息的数据库。结果：我们证明了一种在任何类型的细胞中测定任何分子的体内DC的方法，而不考虑其分子的分子、大小和结构。我们用K12菌株蛋白质组的所有蛋白质(4302条记录)的体内DC数据库以及氨基酸、糖、RNA和DNA的DC的例子来举例说明该方法。该数据库来源于标度相关粘度参考曲线(SdVRC)。构建原核或真核细胞的sdVRC需要使用荧光相关光谱(FCS)、光漂白后荧光恢复(FRAP)、核磁共振(NMR)或粒子示踪等技术进行~20次活体测量。SdVRC的形状对于每个生物体来说是不同的，但曲线的数学形式保持不变。该方法具有很高的预测能力，因为在单个细胞类型中对几个惰性、适当选择的探针的DC的测量允许确定数千种蛋白质的DC。此外，获得的迁移率数据还可以定量研究体内的生化相互作用。联系方式：rholyst@ichf.edu.pl补充信息：补充数据可在BioInformation Online上获得。
Motivation: Biologistics provides data for quantitative analysis of transport (diffusion) processes and their spatio-temporal correlations in cells. Mobility of proteins is one of the few parameters necessary to describe reaction rates for gene regulation. Although understanding of diffusion-limited biochemical reactions in vivo requires mobility data for the largest possible number of proteins in their native forms, currently, there is no database that would contain the complete information about the diffusion coefficients (DCs) of proteins in a given cell type. Results: We demonstrate a method for the determination of in vivo DCs for any molecule—regardless of its molecular weight, size and structure—in any type of cell. We exemplify the method with the database of in vivo DC for all proteins (4302 records) from the proteome of K12 strain of Escherichia coli, together with examples of DC of amino acids, sugars, RNA and DNA. The database follows from the scale-dependent viscosity reference curve (sdVRC). Construction of sdVRC for prokaryotic or eukaryotic cell requires ~20 in vivo measurements using techniques such as fluorescence correlation spectroscopy (FCS), fluorescence recovery after photobleaching (FRAP), nuclear magnetic resonance (NMR) or particle tracking. The shape of the sdVRC would be different for each organism, but the mathematical form of the curve remains the same. The presented method has a high predictive power, as the measurements of DCs of several inert, properly chosen probes in a single cell type allows to determine the DCs of thousands of proteins. Additionally, obtained mobility data allow quantitative study of biochemical interactions in vivo. Contact: rholyst@ichf.edu.pl Supplementary information: Supplementary data are available at Bioinformatics Online.
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影响因子：
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DOI：
10.1073/pnas.1114477108
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