Analysis of evolutionary conservation patterns and their influence on identifying protein functional sites

Fang Chun; Noguchi Tamotsu; Yamana Hayato

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Analysis of evolutionary conservation patterns and their influence on identifying protein functional sites

机译：进化保守模式及其对识别蛋白质功能位点的影响分析

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Evolutionary conservation information included in position-specific scoring matrix (PSSM) has been widely adopted by sequence-based methods for identifying protein functional sites, because all functional sites, whether in ordered or disordered proteins, are found to be conserved at some extent. However, different functional sites have different conservation patterns, some of them are linear contextual, some of them are mingled with highly variable residues, and some others seem to be conserved independently. Every value in PSSMs is calculated independently of each other, without carrying the contextual information of residues in the sequence. Therefore, adopting the direct output of PSSM for prediction fails to consider the relationship between conservation patterns of residues and the distribution of conservation scores in PSSMs. In order to demonstrate the importance of combining PSSMs with the specific conservation patterns of functional sites for prediction, three different PSSM-based methods for identifying three kinds of functional sites have been analyzed. Results suggest that, different PSSM-based methods differ in their capability to identify different patterns of functional sites, and better combining PSSMs with the specific conservation patterns of residues would largely facilitate the prediction.

机译：位置特异性评分矩阵（PSSM）中包含的进化保守性信息已被基于序列的方法广泛用于识别蛋白质功能位点，因为发现所有功能位点（无论是有序的还是无序的蛋白质）在一定程度上都是保守的。但是，不同的功能位点具有不同的保守性模式，其中一些是线性关联的，其中一些与高度可变的残基混合在一起，而另一些似乎是独立保守的。 PSSM中的每个值都是彼此独立计算的，而不携带序列中残基的上下文信息。因此，采用PSSM的直接输出进行预测无法考虑PSSM中残基的保守模式与保守得分分布之间的关系。为了证明将PSSM与功能位点的特定保护模式结合起来进行预测的重要性，分析了三种基于PSSM的识别三种功能位点的方法。结果表明，不同的基于PSSM的方法识别不同功能位点模式的能力各不相同，更好地将PSSM与残基的特定保守模式结合将大大有助于预测。

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《Journal of Bioinformatics and Computational Biology》 |2014年第5期|共18页
作者
Fang Chun; Noguchi Tamotsu; Yamana Hayato;
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正文语种 eng
中图分类细胞生物学;
关键词
Conservation patterns; position-specific scoring matrix; functional sites;

机译：保护模式;位置特定的评分矩阵;功能部位;

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专利

1. Analysis of evolutionary conservation patterns and their influence on identifying protein functional sites [J] . Fang Chun, Noguchi Tamotsu, Yamana Hayato Journal of Bioinformatics and Computational Biology . 2014,第5期

机译：进化保守模式及其对识别蛋白质功能位点的影响分析
2. Comparative analysis of the small heat shock proteins in three angiosperm genomes identifies new subfamilies and reveals diverse evolutionary patterns [J] . Elizabeth R. Waters, Brian D. Aevermann, Zipporah Sanders-Reed Cell stress & chaperones . 2008,第2期

机译：对三个被子植物基因组中的小热激蛋白的比较分析确定了新的亚科，并揭示了不同的进化模式
3. Comparative analysis of the small heat shock proteins in three angiosperm genomes identifies new subfamilies and reveals diverse evolutionary patterns [J] . Elizabeth R. Waters, Brian D. Aevermann, Zipporah Sanders-Reed Cell Stress and Chaperones . 2008,第2期

机译：对三个被子植物基因组中的小热激蛋白的比较分析确定了新的亚科，并揭示了不同的进化模式
4. Analyzing Conservation Patterns and Its Influence on Identifying Protein Functional [C] . Chun FANG, Tamotsu Noguchi, Hayato Yamana International Conference on Bioinformatics and Computational Biology . 2014

机译：分析保护模式及其对鉴定蛋白功能的影响
5. Evolutionary Analysis of the CAP Superfamily of Proteins using Amino Acid Sequences and Splice Sites [D] . Abraham, Anup 2016

机译：使用氨基酸序列和剪接位点的蛋白质CAP超家族的进化分析。
6. Integration of evolutionary and desolvation energy analysis identifies functional sites in a plant immunity protein [O] . Manuela Casasoli, Luca Federici, Francesco Spinelli, 2009

机译：整合进化和去溶剂化能量分析可确定植物免疫蛋白中的功能位点
7. : "This paper deals with the functionality of the flaked stone assemblages from several Neolithic sites of the NE of the Iberian Peninsula. The chronological framework ranges from the mid-6th to the mid-4th millennium cal. BCE, which corresponds to the Early and Middle Neolithic. This long period ranges from the arrival of the first farming communities in the Iberian Peninsula, around 5600-5500 cal. BCE, to 3600-3500 cal. BCE, two millennia later, when Neolithic communities had stably occupied most of the available territory, from the mountainous areas of the Pyrenees to the coastal areas of the Mediterranean.In this context, the NE of the Iberian Peninsula is one of the areas where a major number of use-wear analyses have been carried out, especially for what concerns the Neolithic period. This is mainly due to the interest shown by the directors of the excavations and by the Spanish use-wear specialists as well; both participated and cooperated in order to enlarge the number of contexts studied, making the NE of the Iberian Peninsula one of the areas of Europe with the largest number of ‘functional studies’. As a result, today we have a reliable picture of the type of lithic tools used by the first farming groups, how they were used, and which needs they were satisfying.The methodology employed for this type of analysis is today broadly shared by most use-wear specialists. A stereoscopic microscope is used together with a reflected-light microscope for the analysis of the archaeological specimens. Afterwards, the observed use-wear traces are compared with the traces from experimental tools. This study primarily made use of the tools preserved at the ‘Traceoteque’ of the Institución Milà y Fontanals of the CSIC of Barcelona.This paper presents the results obtained for the different types of analysed sites and the relative lithic assemblages. In this way, tools from different contexts are compared: open-air sites, caves and rock-shelters, pit-sites, burials, and mining sites. Such a diversity of contexts allowed for the exploration of the existence of recurrences and differences in the functionality of the lithic tools from one site to another. The results obtained have also provided information on some aspects related to the economic processes carried out at the different sites, caves, rock-shelters and open-air contexts. It has been possible to gain fresh data on the types of tasks carried out and their relative importance for each site, their relation with the geographical and environmental context and the natural resources available there. In addition, analysing tools recovered from burials – mainly individual inhumations – provided information on the relationships between the buried individuals and the working tools, in particular exploring the relationships between sex and age patterns and the types of tools deposited as goods.In conclusion, use-wear analysis allowed for the exploration of a variety of issues; from technical aspects related to the production and management of the lithic resources to social aspects related to the subsistence activities and the individuals that carried them out." [O] . Gibaja Bao, Juan Francisco, Mazzucco, Niccolo 2015

机译：：“本文研究了伊比利亚半岛东北部几个新石器时代遗址的片状石材组合的功能。时间框架从公元前6世纪中叶到4世纪中叶，分别对应于早期和早期。新石器时代中期，这段时间的长短是从伊比利亚半岛的第一个农业社区到来，大约在公元前5600-5500 cal，到了两千年后的3600-3500 BCE，当时新石器时代的社区稳定地占据了大部分可用土地。从比利牛斯山脉山区到地中海沿岸地区。在这种情况下，伊比利亚半岛东北部是进行过大量使用磨损分析的地区之一，尤其是在关注方面新石器时代，这主要是由于发掘负责人和西班牙使用服装专家表现出的浓厚兴趣；他们参与和合作以扩大孔蒂的数量xts进行了研究，使伊比利亚半岛的NE成为“功能研究”数量最多的欧洲地区之一。结果，今天我们可以可靠地了解第一批耕作小组使用的石器工具的类型，使用方法以及它们满足的需求。今天，大多数使用方法广泛共享用于这种类型的分析的方法穿专家。立体显微镜与反射光显微镜一起用于分析考古样本。然后，将观察到的使用磨损痕迹与实验工具的痕迹进行比较。这项研究主要利用了巴塞罗那CSIC的米拉·丰塔纳尔研究所的“ Traceoteque”中保存的工具。本文介绍了针对不同类型的分析地点和相对石器组合所获得的结果。通过这种方式，可以比较来自不同环境的工具：露天场所，洞穴和岩石避难所，露天场所，埋葬场所和采矿场所。如此多样的上下文允许探索重复性的存在以及从一个站点到另一个站点的石器工具的功能差异。所获得的结果还提供了与在不同地点，洞穴，避难所和露天环境中进行的经济过程有关的某些方面的信息。可以获得有关所执行任务的类型及其对每个站点的相对重要性，它们与地理和环境环境以及那里可用自然资源的关系的新数据。此外，对从墓葬中回收的工具（主要是个人遗体）进行分析，可提供有关被掩埋的个体与工作工具之间关系的信息，尤其是探索性别与年龄模式之间的关系以及作为商品存放的工具的类型。磨损分析允许探索各种问题；从与石器资源的生产和管理有关的技术方面到与自给活动及其实施者有关的社会方面。”

Analysis of evolutionary conservation patterns and their influence on identifying protein functional sites

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