%MinMax: A versatile tool for calculating and comparing synonymous codon usage and its impact on protein folding.
%MinMax: A versatile tool for calculating and comparing synonymous codon usage and its impact on protein folding.
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%MinMax:%20A%20versatile%20tool%20用于%20计算%20和%20比较%20同义%20密码子%20用法%20和%20其%20影响%20on%20蛋白质%20折叠。
DOI：
10.1002/pro.3336
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发表时间：
2018
期刊：
影响因子：
--
通讯作者：
Clark,PatriciaL
中科院分区：
文献类型：
--
作者：
Rodriguez,Anabel;Wright,Gabriel;Emrich,Scott;Clark,PatriciaL
大多数氨基酸可以由多个同义密码子编码，但这些密码子很少以相同的频率使用。在许多编码序列中，罕见同义密码子和常见同义密码子的使用模式是非随机的，是经过选择的。此外，改变这些模式的同义取代可以对编码蛋白质的折叠效率产生实质性的影响。这激发了人们对探索同义密码子使用模式的广泛兴趣。对于许多蛋白质化学家、生物物理学家和结构生物学家来说，密码子分析的主要动机是识别和保存最有可能影响功能蛋白高产产量的使用模式。在这里，我们描述了%MinMax的核心功能和新特性，这是一个密码子使用计算器，免费提供基于web的门户和可下载的脚本（http://www.codons.org）。%MinMax评估用于编码感兴趣的蛋白质序列的同义密码子的相对使用频率，并将这些结果与严格的零模型进行比较。至关重要的是，对于分析普通宿主生物中密码子的使用，%MinMax只需要编码序列作为输入；使用用户输入密码子频率表，%MinMax可用于评估来自任何全测序基因组的任何编码序列的同义密码子使用模式。%MinMax没有假设转移核糖核酸浓度或其他分子水平的相互作用对翻译速率的影响，但其输出足以预测同义密码子替换对共翻译折叠机制的影响。一个包含在%MinMax中的简单计算可以用来协调异源基因表达的密码子使用频率。
Most amino acids can be encoded by more than one synonymous codon, but these are rarely used with equal frequency. In many coding sequences the usage patterns of rare versus common synonymous codons is nonrandom and under selection. Moreover, synonymous substitutions that alter these patterns can have a substantial impact on the folding efficiency of the encoded protein. This has ignited broad interest in exploring synonymous codon usage patterns. For many protein chemists, biophysicists and structural biologists, the primary motivation for codon analysis is identifying and preserving usage patterns most likely to impact high‐yield production of functional proteins. Here we describe the core functions and new features of %MinMax, a codon usage calculator freely available as a web‐based portal and downloadable script (http://www.codons.org). %MinMax evaluates the relative usage frequencies of the synonymous codons used to encode a protein sequence of interest and compares these results to a rigorous null model. Crucially, for analyzing codon usage in common host organisms %MinMax requires only the coding sequence as input; with a user‐input codon frequency table, %MinMax can be used to evaluate synonymous codon usage patterns for any coding sequence from any fully sequenced genome. %MinMax makes no assumptions regarding the impact of transfer ribonucleic acid concentrations or other molecular‐level interactions on translation rates, yet its output is sufficient to predict the effects of synonymous codon substitutions on cotranslational folding mechanisms. A simple calculation included within %MinMax can be used to harmonize codon usage frequencies for heterologous gene expression.