Novel amino acid distance matrices based on conductance measure

IF 4.6 Q2 MATERIALS SCIENCE, BIOMATERIALS ACS Applied Bio Materials Pub Date : 2024-10-17 DOI:10.1016/j.biosystems.2024.105355
Nikola Štambuk , Elena Fimmel , Paško Konjevoda , Krunoslav Brčić-Kostić , Antonija Gračanin , Hadi Saleh
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Abstract

Ancestral relationships among biological species are often represented and analyzed by means of phylogenetic trees. Substitution and distance matrices are two main types of matrices that are used in phylogeny analyses. Substitution matrices describe a frequency change of amino acids in nucleotide or protein sequence over time, while distance matrices estimate phylogeny using a matrix of pairwise distances based on a particular code or analytical concept. Recent investigation by Elena Fimmel and coworkers (Life 11:1338, 2021) showed that: 1. the robustness of a genetic code against point mutations can be described using the conductance measure, and 2. all possible point mutations of the genetic code can be represented as a weighted graph with weights that correspond to the probabilities of these mutations. In this article, we constructed and tested three novel distance matrices based on conductance measure, that take into account the point mutation robustness of the Standard Genetic Code (SGC). These distance matrices are based on maximum (CMAX), average (CAVG), and minimum (CMIN) conductance-optimized distances between codons coding for individual amino acids. The performance of those distance matrices was tested on a dataset of RecA proteins in Bacteria, Archaea (RadA homolog) and Eukarya (Rad51 homolog). RecA protein and its functional homologs were selected for this investigation since they are essential for the repair and maintenance of DNA, and consequently well conserved and present in all domains of life. PAM250 and BLOSUM62 matrices were usually used as a standard for distance matrix testing. PAM250 and BLOSUM62 substitution matrices specified accurately three biological domains of life according to Carl Woese and George Fox (Proc Natl Acad Sci U S A 74:5088, 1977). An identical result was obtained using three novel distance matrices (CMIN, CMAX, CAVG). This result supports the applicability of novel distance matrices based on the conductance method and suggests that further investigations based on this approach are justified.
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基于电导测量的新型氨基酸距离矩阵
生物物种之间的始祖关系通常通过系统发生树来表示和分析。取代矩阵和距离矩阵是系统发生分析中使用的两种主要矩阵。替代矩阵描述的是核苷酸或蛋白质序列中氨基酸随着时间推移而发生的频率变化,而距离矩阵则根据特定的代码或分析概念,利用成对距离矩阵来估计系统发生。Elena Fimmel 及其同事的最新研究(Life 11:1338, 2021)表明:1:1.遗传密码对点突变的稳健性可以用电导测量来描述;2.遗传密码所有可能的点突变都可以用加权图来表示,加权图的权重与这些突变的概率相对应。在本文中,我们构建并测试了三个基于电导测量的新型距离矩阵,它们考虑到了标准遗传密码(SGC)的点突变鲁棒性。这些距离矩阵基于编码单个氨基酸的密码子之间的最大(CMAX)、平均(CAVG)和最小(CMIN)电导优化距离。这些距离矩阵的性能在细菌、古生菌(RadA 同源物)和真核生物(Rad51 同源物)的 RecA 蛋白数据集上进行了测试。本次研究选择了 RecA 蛋白及其功能同源物,因为它们对 DNA 的修复和维护至关重要,因此在所有生命领域中都得到了很好的保护。PAM250 和 BLOSUM62 矩阵通常用作距离矩阵测试的标准。根据 Carl Woese 和 George Fox 的研究(Proc Natl Acad Sci U S A 74:5088,1977 年),PAM250 和 BLOSUM62 取代矩阵准确地指定了生命的三个生物领域。使用三个新的距离矩阵(CMIN、CMAX、CAVG)也得到了相同的结果。这一结果证明了基于电导法的新型距离矩阵的适用性,并表明基于这种方法的进一步研究是合理的。
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来源期刊
ACS Applied Bio Materials
ACS Applied Bio Materials Chemistry-Chemistry (all)
CiteScore
9.40
自引率
2.10%
发文量
464
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