ArticleJournal of molecular biology2019
Fitness Effects of Single Amino Acid Insertions and Deletions in TEM-1 β-Lactamase.
Article in Journal of molecular biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
24 citing papers in PubMed, 51 citations in OpenAlex.
- Using Domain Insertion to Create Sulfite Reductases That Present Chemical-Dependent Activities.ACS synthetic biology · 2026Article
- How far can you go? Extrapolating values of catalytic activity from known protein landscapes in natural and directed evolution.Chemical Society reviews · 2026Review
- Controllable protein design via autoregressive direct coupling analysis conditioned on principal components.PLoS computational biology · 2026Article
- Uncovering differential tolerance to deletions versus substitutions with a protein language model.Cell systems · 2025Article
- Deep indel mutagenesis reveals the impact of amino acid insertions and deletions on protein stability and function.Nature communications · 2025Article
- Inferring the Selective History of CNVs Using a Maximum Likelihood Model.Genome biology and evolution · 2025Article
- Article
- Structural and energetic analysis of stabilizing indel mutations.bioRxiv : the preprint server for biology · 2024Article
- Instability throughout the Saccharomyces cerevisiae genome resulting from Pms1 endonuclease deficiency.Nucleic acids research · 2024Article
- Dissecting Allosteric Mutations for Antibiotic Resistance by Time-Dependent Linear Response Theory.Journal of chemical theory and computation · 2024Article
- Insertion-Deletion Events Are Depleted in Protein Regions with Predicted Secondary Structure.Genome biology and evolution · 2024Article
- Evolution of Transcript Abundance is Influenced by Indels in Protein Low Complexity Regions.Journal of molecular evolution · 2024Article
- ProteinGym: Large-Scale Benchmarks for Protein Design and Fitness Prediction.bioRxiv : the preprint server for biology · 2023Article
- Machine Learning-Guided Protein Engineering.ACS catalysis · 2023Review
- A cellular selection identifies elongated flavodoxins that support electron transfer to sulfite reductase.Protein science : a publication of the Protein Society · 2023Article
- DIMPLE: deep insertion, deletion, and missense mutation libraries for exploring protein variation in evolution, disease, and biology.Genome biology · 2023Article
- An atlas of amyloid aggregation: the impact of substitutions, insertions, deletions and truncations on amyloid beta fibril nucleation.Nature communications · 2022Article
- Slow Protein Dynamics Elicits New Enzymatic Functions by Means of Epistatic Interactions.Molecular biology and evolution · 2022Article
- Elucidating the Structural Impacts of Protein InDels.Biomolecules · 2022Article
- A two-step PCR assembly for construction of gene variants across large mutational distances.Biology methods & protocols · 2021Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
Short insertions and deletions (InDels) are a common type of mutation found in nature and a useful source of variation in protein engineering. InDel events have important consequences in protein evolution, often opening new pathways for adaptation. However, much less is known about the effects of InDels compared to point mutations and amino acid substitutions. In particular, deep mutagenesis studies on the distribution of fitness effects of mutations have focused almost exclusively on amino acid substitutions. Here, we present a near-comprehensive analysis of the fitness effects of single amino acid InDels in TEM-1 β-lactamase. While we found InDels to be largely deleterious, partially overlapping deletion-tolerant and insertion-tolerant regions were observed throughout the protein, especially in unstructured regions and at the end of helices. The signal sequence of TEM-1 tolerated InDels more than the mature protein. Most regions of the protein tolerated insertions more than deletions, but a few regions tolerated deletions more than insertions. We examined the relationship between InDel tolerance and a variety of measures to help understand its origin. These measures included evolutionary variation in β-lactamases, secondary structure identity, tolerance to amino acid substitutions, solvent accessibility, and side-chain weighted contact number. We found secondary structure, weighted contact number, and evolutionary variation in class A beta-lactamases to be the somewhat predictive of InDel fitness effects.
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Registered trials
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.