ArticleProtein science : a publication of the Protein Society2022
A newly introduced salt bridge cluster improves structural and biophysical properties of de novo TIM barrels.
Article in Protein science : a publication of the Protein Society, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
12 citing papers in PubMed.
- Customizing the structure of minimal TIM barrels to craft efficient de novo enzymes.Nature chemical biology · 2026Article
- Stability and cooperativity in chimeric de novo TIM barrels via quarter swapping.Protein science : a publication of the Protein Society · 2026Article
- Designing de novo TIM barrels: insights into stabilization, diversification, and functionalization strategies.Biochemical Society transactions · 2026Review
- The Bacteriophage VMY 22 Has Enhanced the Stability of Its Functional Proteins via Adaptive Evolution in a Temperature-Varying Environment.Bioengineering (Basel, Switzerland) · 2026Article
- Enzyme-Embedded Biodegradable Plastic for Sustainable Applications: Advances, Challenges, and Perspectives.ACS applied bio materials · 2025Review
- Diversifying de novo TIM barrels by hallucination.Protein science : a publication of the Protein Society · 2024Article
- Solvent Tolerance Improvement of Lipases Enhanced Their Applications: State of the Art.Molecules (Basel, Switzerland) · 2024Review
- Stepwise introduction of stabilizing mutations reveals nonlinear additive effects in de novo TIM barrels.Protein science : a publication of the Protein Society · 2024Article
- ProtGPT2 is a deep unsupervised language model for protein design.Nature communications · 2022Article
- A newly introduced salt bridge cluster improves structural and biophysical properties of de novo TIM barrels.Protein science : a publication of the Protein Society · 2022Article
- What Have We Learned from Design of Function in Large Proteins?Biodesign research · 2022Review
- De Novo Design of a Highly Stable Ovoid TIM Barrel: Unlocking Pocket Shape towards Functional Design.Biodesign research · 2022Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Protein stability can be fine-tuned by modifying different structural features such as hydrogen-bond networks, salt bridges, hydrophobic cores, or disulfide bridges. Among these, stabilization by salt bridges is a major challenge in protein design and engineering since their stabilizing effects show a high dependence on the structural environment in the protein, and therefore are difficult to predict and model. In this work, we explore the effects on structure and stability of an introduced salt bridge cluster in the context of three different de novo TIM barrels. The salt bridge variants exhibit similar thermostability in comparison with their parental designs but important differences in the conformational stability at 25°C can be observed such as a highly stabilizing effect for two of the proteins but a destabilizing effect to the third. Analysis of the formed geometries of the salt bridge cluster in the crystal structures show either highly ordered salt bridge clusters or only single salt bridges. Rosetta modeling of the salt bridge clusters results in a good prediction of the tendency on stability changes but not the geometries observed in the three-dimensional structures. The results show that despite the similarities in protein fold, the salt bridge clusters differently influence the structural and stability properties of the de novo TIM barrel variants depending on the structural background where they are introduced.
Indexed as
Identifiers
What OpenQuestion holds
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.