ArticleCurrent genomics2010
The nature of protein domain evolution: shaping the interaction network.
Article in Current genomics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed.
- Phylogeny constrains and environment modulates glycoside hydrolase architecture.Current research in microbial sciences · 2026Article
- Convergent Evolution in Tumor Genomes Targets Functional Domains.bioRxiv : the preprint server for biology · 2026Article
- Rewiring Oncogenic Transcriptional Complexes with Domain-ALTeration Chimeras (DALTACs) in Prostate Cancer.bioRxiv : the preprint server for biology · 2026Article
- Machine learning-trained protein domain insertion for the design of switchable proteins.Nature methods · 2025Article
- Phylogenetic and Evolutionary Analysis of Plant Small RNA 2'-O-Methyltransferase (HEN1) Protein Family.Journal of molecular evolution · 2023Article
- High-throughput discovery and characterization of viral transcriptional effectors in human cells.Cell systems · 2023Article
- Consequences of Genetic Recombination on Protein Folding Stability.Journal of molecular evolution · 2023Article
- Protein domains provide a new layer of information for classifying human variations in rare diseases.Frontiers in bioinformatics · 2023Article
- Phylogenetic reconciliation.PLoS computational biology · 2022Article
- Identification and relative expression analysis of3 Biotech · 2022Article
- A novel region within a conserved domain in ATG7 emerged in vertebrates.Autophagy reports · 2022Article
- Conserved Structure and Evolution of DPF Domain of PHF10-The Specific Subunit of PBAF Chromatin Remodeling Complex.International journal of molecular sciences · 2021Review
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- Mix and match: Patchwork domain evolution of the land plant-specific Ca2+-permeable mechanosensitive channel MCA.PloS one · 2021Article
- Understanding the Targeting Mechanisms of Multi-Specific Biologics in Immunotherapy with Multiscale Modeling.iScience · 2020Article
- Deciphering the functional role of hypothetical proteins fromMolecular biology research communications · 2020Article
- One gene, multiple ecological strategies: A biofilm regulator is a capacitor for sustainable diversity.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Pseudo-RNA-Binding Domains Mediate RNA Structure Specificity in Upstream of N-Ras.Cell reports · 2020Article
- A critical review of five machine learning-based algorithms for predicting protein stability changes upon mutation.Briefings in bioinformatics · 2020Review
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The proteomes that make up the collection of proteins in contemporary organisms evolved through recombination and duplication of a limited set of domains. These protein domains are essentially the main components of globular proteins and are the most principal level at which protein function and protein interactions can be understood. An important aspect of domain evolution is their atomic structure and biochemical function, which are both specified by the information in the amino acid sequence. Changes in this information may bring about new folds, functions and protein architectures. With the present and still increasing wealth of sequences and annotation data brought about by genomics, new evolutionary relationships are constantly being revealed, unknown structures modeled and phylogenies inferred. Such investigations not only help predict the function of newly discovered proteins, but also assist in mapping unforeseen pathways of evolution and reveal crucial, co-evolving inter- and intra-molecular interactions. In turn this will help us describe how protein domains shaped cellular interaction networks and the dynamics with which they are regulated in the cell. Additionally, these studies can be used for the design of new and optimized protein domains for therapy. In this review, we aim to describe the basic concepts of protein domain evolution and illustrate recent developments in molecular evolution that have provided valuable new insights in the field of comparative genomics and protein interaction networks.
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