ArticleProtein engineering, design & selection : PEDS2019
Molecular dynamics simulations suggest stabilizing mutations in a de novo designed α/β protein.
Article in Protein engineering, design & selection : PEDS, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
What it found
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Who cites it
8 citing papers in PubMed, 14 citations in OpenAlex.
- RINAMI: Residue-attributed interpretable neural network for predicting absolute folding free energy by merging structure and sequence information.Protein science : a publication of the Protein Society · 2026Article
- Temperature-Dependent Thumb Domain Dynamics of Xylanase TsaGH11: Insights from Molecular Dynamics Simulations.International journal of molecular sciences · 2026Article
- Multidomain DNA-Protein Mining Reveals Polymorphic Variations in RhlB Enhancing Monorhamnolipid Biosynthesis.ACS synthetic biology · 2026Article
- dUTP pyrophosphatases from hyperthermophilic eubacterium and archaeon: Structural and functional examinations on the suitability for PCR application.Protein science : a publication of the Protein Society · 2024Article
- De novo design of drug-binding proteins with predictable binding energy and specificity.Science (New York, N.Y.) · 2024Article
- Article
- The stability and dynamics of computationally designed proteins.Protein engineering, design & selection : PEDS · 2022Review
- KEAP1 Cancer Mutants: A Large-Scale Molecular Dynamics Study of Protein Stability.International journal of molecular sciences · 2021Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Designing functional proteins that can withstand extreme heat is beneficial for industrial and protein therapeutic applications. Thus, elucidating the atomic-level determinants of thermostability is a major interest for rational protein design. To that end, we compared the structure and dynamics of a set of previously designed, thermostable proteins based on the activation domain of human procarboxypeptidase A2 (AYEwt). The mutations in these designed proteins were intended to increase hydrophobic core packing and inter-secondary-structure interactions. To evaluate whether these design strategies were successfully deployed, we performed all-atom, explicit-solvent molecular dynamics (MD) simulations of AYEwt and three designed variants at both 25 and 100°C. Our MD simulations agreed with the relative experimental stabilities of the designs based on their secondary structure content, Cα root-mean-square deviation/fluctuation, and buried-residue solvent accessible surface area. Using a contact analysis, we found that the designs stabilize inter-secondary structure interactions and buried hydrophobic surface area, as intended. Based on our analysis, we designed three additional variants to test the role of helix stabilization, core packing, and a Phe → Met mutation on thermostability. We performed the additional MD simulations and analysis on these variants, and these data supported our predictions.
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Registered trials
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