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Related Concept Videos

Evolutionary Relationships through Genome Comparisons02:54

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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 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.
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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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A Protocol for Computer-Based Protein Structure and Function Prediction
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Inference of Cytochrome P450 Evolutionary History Using Structural and Physicochemical Metrics.

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
Summary
This summary is machine-generated.

Cytochrome P450 (CYP) protein family relationships are difficult to resolve using traditional sequence-based phylogenetics. Physicochemical Dynamic Time Warping (PCDTW) methods, using molecular weight and hydrophobicity, offer a robust alternative for accurate phylogenetic reconstruction.

Keywords:
FoldtreePCDTWTwilight Zonephysicochemicalremote homologystructural phylogenetics

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Area of Science:

  • Biochemistry and Molecular Biology
  • Structural Biology
  • Bioinformatics and Computational Biology

Background:

  • Cytochrome P450s (CYPs) are crucial heme-binding enzymes involved in detoxification, ubiquitous across biological domains.
  • Resolving phylogenetic relationships within the CYP superfamily is challenging due to low sequence identities (<30%), hindering traditional phylogenetic methods.
  • Despite sequence divergence, CYP structures are conserved, suggesting structural and physicochemical properties may hold keys to evolutionary relationships.

Purpose of the Study:

  • To investigate the utility of Molecular Weight and Hydrophobicity Physicochemical Dynamic Time Warping (MWHP PCDTW) for resolving Cytochrome P450 (CYP) phylogenetic relationships.
  • To compare MWHP PCDTW with traditional sequence and structure-based phylogenetic methods.
  • To assess the ability of different phylogenetic approaches to distinguish true homology from random or convergent structural similarity.

Main Methods:

  • Applied MWHP PCDTW to analyze all CYPs from the Structural Classification of Proteins (SCOP) database.
  • Incorporated CYPs with experimentally resolved and predicted structures from the Protein Data Bank and AlphaFold (AF) Protein Structure Database.
  • Compared phylogenetic topologies generated by MWHP PCDTW with those from sequence alignment and structure-based methods.

Main Results:

  • MWHP PCDTW successfully resolved phylogenetic relationships within the CYP superfamily, overcoming limitations of low sequence identity.
  • Comparison revealed that structure-based methods may sometimes struggle to differentiate random/convergent similarity compared to physicochemical and sequence-based approaches.
  • Physicochemical properties, when used in phylogenetic analysis, proved effective in resolving both random structural similarity and potentially convergent evolutionary relationships.

Conclusions:

  • Physicochemical Dynamic Time Warping (PCDTW) is a valuable tool for inferring evolutionary relationships in protein families with divergent sequences, such as Cytochrome P450s.
  • The study validates the use of physicochemical properties for phylogenetic inference, complementing traditional sequence and structure-based analyses.
  • This approach enhances our understanding of CYP evolution and provides a method for resolving difficult phylogenetic questions in other protein superfamilies.