ArticleNucleic acids research2018
Circular permutation profiling by deep sequencing libraries created using transposon mutagenesis.
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed, 24 citations in OpenAlex.
- Rational Design of a Circularly Permuted Flavin-Based Fluorescent Protein.Chembiochem : a European journal of chemical biology · 2024Article
- Multiparametric domain insertional profiling of adeno-associated virus VP1.Molecular therapy. Methods & clinical development · 2023Article
- A cellular selection identifies elongated flavodoxins that support electron transfer to sulfite reductase.Protein science : a publication of the Protein Society · 2023Article
- Article
- Probing ion channel functional architecture and domain recombination compatibility by massively parallel domain insertion profiling.Nature communications · 2021Article
- Comprehensive deletion landscape of CRISPR-Cas9 identifies minimal RNA-guided DNA-binding modules.Nature communications · 2021Article
- A systematic approach to inserting split inteins for Boolean logic gate engineering and basal activity reduction.Nature communications · 2021Article
- Targeted insertional mutagenesis libraries for deep domain insertion profiling.Nucleic acids research · 2020Article
- Protein tolerance to random circular permutation correlates with thermostability and local energetics of residue-residue contacts.Protein engineering, design & selection : PEDS · 2019Article
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Deep mutational scanning has been used to create high-resolution DNA sequence maps that illustrate the functional consequences of large numbers of point mutations. However, this approach has not yet been applied to libraries of genes created by random circular permutation, an engineering strategy that is used to create open reading frames that express proteins with altered contact order. We describe a new method, termed circular permutation profiling with DNA sequencing (CPP-seq), which combines a one-step transposon mutagenesis protocol for creating libraries with a functional selection, deep sequencing and computational analysis to obtain unbiased insight into a protein's tolerance to circular permutation. Application of this method to an adenylate kinase revealed that CPP-seq creates two types of vectors encoding each circularly permuted gene, which differ in their ability to express proteins. Functional selection of this library revealed that >65% of the sampled vectors that express proteins are enriched relative to those that cannot translate proteins. Mapping enriched sequences onto structure revealed that the mobile AMP binding and rigid core domains display greater tolerance to backbone fragmentation than the mobile lid domain, illustrating how CPP-seq can be used to relate a protein's biophysical characteristics to the retention of activity upon permutation.
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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.