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相关概念视频

Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

6.9K
Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
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Gene Families01:57

Gene Families

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Gene families consist of groups of genes proposed to have originated from a common ancestor. Typically these arise through events in which a gene or genes are mistakenly duplicated during cell division. Unlike their parent genes (which are subject to selection pressure to maintain function), these gene copies do not need to preserve their sequences and may evolve at a relatively faster rate.
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...
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Protein Families02:47

Protein Families

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Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism.   Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members.   If these new proteins contain similar amino acids in key...
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Comparing Mitochondrial, Chloroplast, and Prokaryotic Genomes02:16

Comparing Mitochondrial, Chloroplast, and Prokaryotic Genomes

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The present-day mitochondrial and chloroplast genomes have retained some of the characteristics of their ancestral prokaryotes and also have acquired new attributes during their evolution within eukaryotic cells. Like prokaryotic genomes, mitochondrial and chloroplast genomes neither bind with histone-like proteins nor show complex packaging into chromosome-like structures, as observed in eukaryotes. Unlike mitotic cell divisions observed in eukaryotic cells, mitochondria and chloroplasts...
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Synteny and Evolution02:31

Synteny and Evolution

3.8K
John H. Renwick first coined the term “synteny” in 1971, which refers to the genes present on the same chromosomes, even if they are not genetically linked. The species with common ancestry tend to show conserved syntenic regions. Therefore, the concept of synteny is nowadays used to describe the evolutionary relationship between species.
Around 80 million years ago, the human and mice lineages diverged from the common ancestor. During the course of evolution, the ancestral...
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Protein Organization01:24

Protein Organization

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Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence....
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相关实验视频

Updated: Jan 17, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction
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A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

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使用结构和物理化学指标推断细胞染色体P450的进化史.

Jamie D Dixson1,2, Abhijay Azad3, Pamela A Padilla1

  • 1Department of Biological Sciences, University of North Texas, Denton, TX 76203, USA.

Genome biology and evolution
|September 19, 2025
PubMed
概括
此摘要是机器生成的。

通过使用传统的基于序列的遗传学,很难解决P450 (CYP) 蛋白质家族关系. 物理化学动态时间扭曲 (PCDTW) 方法,使用分子量和疏水性,为准确的遗传学重建提供了强大的替代方案.

关键词:
折叠树是一种折叠树.这是PCDTW.黄昏地区的黄昏区物理化学 物理化学远程同类学远程同类学结构性遗传学 结构性遗传学

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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
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Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group
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Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group

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相关实验视频

Last Updated: Jan 17, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
09:51

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

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Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group
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Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group

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科学领域:

  • 生物化学和分子生物学
  • 结构生物学 结构生物学
  • 生物信息学和计算生物学

背景情况:

  • 细胞染色体P450s (CYPs) 是关键的血结合酶,参与排毒,在生物领域无处不在.
  • 解决CYP超级家族内的遗传学关系是具有挑战性的,因为其低序列身份 (<30%),阻碍了传统的遗传学方法.
  • 尽管有序列分歧,但CYP结构仍然存在,这表明结构性和物理化学性质可能是进化关系的关键.

研究的目的:

  • 调查分子重量和水性物理化学动态时间变形 (MWHP PCDTW) 的实用性,以解决细胞染色体P450 (CYP) 的遗传关系.
  • 为了将MWHP PCDTW与传统的序列和基于结构的遗传学方法进行比较.
  • 评估不同种系学方法区分真实同质性与随机或融合结构相似性的能力.

主要方法:

  • 应用 MWHP PCDTW 来分析来自蛋白质结构分类 (SCOP) 数据库的所有 CYP.
  • 从蛋白质数据库和AlphaFold (AF) 蛋白质结构数据库中进行实验解决和预测结构的嵌入式CYP.
  • 通过MWHP PCDTW产生的族系学拓与序列对齐和基于结构的方法产生的族系学拓进行了比较.

主要成果:

  • MWHP PCDTW成功地解决了CYP超级家族内的系遗传关系,克服了低序列身份的局限性.
  • 对比显示,基于结构的方法有时可能在与物理化学和基于序列的方法相比,难以区分随机/融合相似性.
  • 物理化学性质,当用于遗传学分析时,证明在解决随机结构相似性和潜在的融合进化关系方面是有效的.

结论:

  • 物理化学动态时间变形 (PCDTW) 是一种有价值的工具,用于推断不同序列的蛋白质家族的进化关系,例如细胞染色体P450s.
  • 这项研究验证了物理化学性质用于基因推断的使用,补充了传统的序列和基于结构的分析.
  • 这种方法增强了我们对CYP演变的理解,并为解决其他蛋白质超级家族中困难的遗传学问题提供了一种方法.