ArticleMethods in enzymology2020
The use of consensus sequence information to engineer stability and activity in proteins.
Article in Methods in enzymology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- Protein stability is determined by single-site bias rather than pairwise covariance.Nature chemical biology · 2026Article
- Comparison of multiple antigens for use in indirect ELISAs for detection of anti-capripoxvirus antibodies in sheep, goats, and cattle.Journal of clinical microbiology · 2026Article
- An Engineered β-glucosidase from Bacteroides Thetaiotaomicron for Production of Rubusoside from Stevioside.Applied biochemistry and biotechnology · 2026Article
- Protein engineering: status report.Protein engineering, design & selection : PEDS · 2026Review
- Characterization of a consensus-designedmBio · 2025Article
- Statistical Thermodynamics of the Protein Ensemble: Mediating Function and Evolution.Annual review of biophysics · 2025Review
- Insight into Protein Engineering: FromCurrent pharmaceutical design · 2025Review
- Design of ancestral mammalian alkaline phosphatase bearing high stability and productivity.Applied and environmental microbiology · 2024Article
- Computation-guided engineering of distal mutations in an artificial enzyme.Faraday discussions · 2024Article
- Ancestral Reconstruction and the Evolution of Protein Energy Landscapes.Annual review of biophysics · 2024Review
- Molecular recognition and activation mechanism of short-chain fatty acid receptors FFAR2/3.Cell research · 2024Article
- Engineering styrene biosynthesis: designing a functional trans-cinnamic acid decarboxylase in Pseudomonas.Microbial cell factories · 2024Article
- Comparative analysis of reconstructed ancestral proteins with their extant counterparts suggests primitive life had an alkaline habitat.Scientific reports · 2024Article
- Reverse transcription loop-mediated isothermal amplification (RT-LAMP) primer design based on Indonesia SARS-CoV-2 RNA sequence.Journal, genetic engineering & biotechnology · 2023Article
- Thermal Stability Enhancement of L-Asparaginase fromFoods (Basel, Switzerland) · 2023Article
- High-Accuracy Prediction of Stabilizing Surface Mutations to the Three-Helix Bundle, UBA(1), with EmCAST.Journal of the American Chemical Society · 2023Article
- Enzymatic Conjugation of Modified RNA Fragments by Ancestral RNA Ligase AncT4_2.Applied and environmental microbiology · 2022Article
- Singular value decomposition of protein sequences as a method to visualize sequence and residue space.Protein science : a publication of the Protein Society · 2022Article
- The stability and dynamics of computationally designed proteins.Protein engineering, design & selection : PEDS · 2022Review
- Structural plasticity in the loop region of engineered lipocalins with novel ligand specificities, so-called Anticalins.Journal of structural biology: X · 2022Review
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3 authors.
Funding
Abstract
The goal of protein design is to create proteins that are stable, soluble, and active. Here we focus on one approach to protein design in which sequence information is used to create a "consensus" sequence. Such consensus sequences comprise the most common residue at each position in a multiple sequence alignment (MSA). After describing some general ideas that relate MSA and consensus sequences and presenting a statistical thermodynamic framework that relates consensus and non-consensus sequences to stability, we detail the process of designing a consensus sequence and survey reports of consensus design and characterization from the literature. Many of these consensus proteins retain native biological activities including ligand binding and enzyme activity. Remarkably, in most cases the consensus protein shows significantly higher stability than extant versions of the protein, as measured by thermal or chemical denaturation, consistent with the statistical thermodynamic model. To understand this stability increase, we compare various features of consensus sequences with the extant MSA sequences from which they were derived. Consensus sequences show enrichment in charged residues (most notably glutamate and lysine) and depletion of uncharged polar residues (glutamine, serine, and asparagine). Surprisingly, a survey of stability changes resulting from point substitutions show little correlation with residue frequencies at the corresponding positions within the MSA, suggesting that the high stability of consensus proteins may result from interactions among residue pairs or higher-order clusters. Whatever the source, the large number of reported successes demonstrates that consensus design is a viable route to generating active and in many cases highly stabilized proteins.
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