ArticlePLoS computational biology2019
Size and structure of the sequence space of repeat proteins.
Article in PLoS computational biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed, 22 citations in OpenAlex.
- Descent from a common ancestor restricts exploration of protein sequence space.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Probing the dark energy in the functional protein universe.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Inferring protein-folding mechanisms from natural sequence diversity.Biophysical journal · 2025Article
- A metric and its derived protein network for evaluation of ortholog database inconsistency.BMC bioinformatics · 2025Article
- A transfer-learning approach to predict antigen immunogenicity and T-cell receptor specificity.eLife · 2023Article
- The Effect of Mutations in the TPR and Ankyrin Families of Alpha Solenoid Repeat Proteins.Frontiers in bioinformatics · 2021Review
- Navigating the amino acid sequence space between functional proteins using a deep learning framework.PeerJ. Computer science · 2021Article
- Exploring the sequence fitness landscape of a bridge between protein folds.PLoS computational biology · 2020Article
- Evolution Rapidly Optimizes Stability and Aggregation in Lattice Proteins Despite Pervasive Landscape Valleys and Mazes.Genetics · 2020Article
- Large Ankyrin repeat proteins are formed with similar and energetically favorable units.PloS one · 2020Article
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Authors and funding
6 authors at 2 institutions in 2 countries.
Funding
Abstract
The coding space of protein sequences is shaped by evolutionary constraints set by requirements of function and stability. We show that the coding space of a given protein family-the total number of sequences in that family-can be estimated using models of maximum entropy trained on multiple sequence alignments of naturally occuring amino acid sequences. We analyzed and calculated the size of three abundant repeat proteins families, whose members are large proteins made of many repetitions of conserved portions of ∼30 amino acids. While amino acid conservation at each position of the alignment explains most of the reduction of diversity relative to completely random sequences, we found that correlations between amino acid usage at different positions significantly impact that diversity. We quantified the impact of different types of correlations, functional and evolutionary, on sequence diversity. Analysis of the detailed structure of the coding space of the families revealed a rugged landscape, with many local energy minima of varying sizes with a hierarchical structure, reminiscent of fustrated energy landscapes of spin glass in physics. This clustered structure indicates a multiplicity of subtypes within each family, and suggests new strategies for protein design.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.