ArticleBiochemistry2017
A Gradient of Sitewise Diversity Promotes Evolutionary Fitness for Binder Discovery in a Three-Helix Bundle Protein Scaffold.
Article in Biochemistry, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed.
- Phased affinity-controlled delivery of vascular endothelial growth factor, fibroblast growth factor-2, and platelet derived growth factor enhances in vitro angiogenesis.Journal of controlled release : official journal of the Controlled Release Society · 2026Article
- Engineering Murine Cross-Reactivity Into an Affibody to Human Death Receptor 5.Biotechnology and bioengineering · 2026Article
- Engineered B7-H3 Binding in Modular Gp2 Miniproteins.Biotechnology and bioengineering · 2026Article
- Rhodopsin molecular evolution from mouse to human phenylalanine 88 to leucine substitution enhances thermal stability and post-activation decay.Scientific reports · 2026Article
- Insights into rhodopsin molecular evolution from mice with "humanized" Phe-88 to Leu substitution.Research square · 2025Article
- PANCS-Binders: a rapid, high-throughput binder discovery platform.Nature methods · 2025Article
- Applying Computational Protein Design to Engineer Affibodies for Affinity-controlled Delivery of Vascular Endothelial Growth Factor and Platelet-Derived Growth Factor.Biomacromolecules · 2025Article
- High-throughput protein binder discovery by rapid in vivo selection.bioRxiv : the preprint server for biology · 2025Article
- Enzyme-substrate co-display on yeast empowers engineering of tobacco etch virus protease activity.Protein engineering, design & selection : PEDS · 2025Article
- Sequence-developability mapping of affibody and fibronectin paratopes via library-scale variant characterization.Protein engineering, design & selection : PEDS · 2024Article
- Hyperstable Synthetic Mini-Proteins as Effective Ligand Scaffolds.ACS synthetic biology · 2023Article
- Determinants of Developability and Evolvability of Synthetic Miniproteins as Ligand Scaffolds.Journal of molecular biology · 2023Article
- Moderate-Affinity Affibodies Modulate the Delivery and Bioactivity of Bone Morphogenetic Protein-2.Advanced healthcare materials · 2023Article
- Protein engineering via sequence-performance mapping.Cell systems · 2023Review
- Protein Fitness Prediction Is Impacted by the Interplay of Language Models, Ensemble Learning, and Sampling Methods.Pharmaceutics · 2023Article
- Discovery of a Non-competitive TNFR1 Antagonist Affibody with Picomolar Monovalent Potency That Does Not Affect TNFR2 Function.Molecular pharmaceutics · 2023Article
- Design of an artificial phage-display library based on a new scaffold improved for average stability of the randomized proteins.Scientific reports · 2023Article
- Machine Learning-driven Protein Library Design: A Path Toward Smarter Libraries.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Site-wise Diversification of Combinatorial Libraries Using Insights from Structure-guided Stability Calculations.Methods in molecular biology (Clifton, N.J.) · 2022Article
- High-throughput developability assays enable library-scale identification of producible protein scaffold variants.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
Engineered proteins provide clinically and industrially impactful molecules and utility within fundamental research, yet inefficiencies in discovering lead variants with new desired functionality, while maintaining stability, hinder progress. Improved function, which can result from a few strategic mutations, is fundamentally separate from discovering novel function, which often requires large leaps in sequence space. While a highly diverse combinatorial library covering immense sequence space would empower protein discovery, the ability to sample only a minor subset of sequence space and the typical destabilization of random mutations preclude this strategy. A balance must be reached. At library scale, compounding several destabilizing mutations renders many variants unable to properly fold and devoid of function. Broadly searching sequence space while reducing the level of destabilization may enhance evolution. We exemplify this balance with affibody, a three-helix bundle protein scaffold. Using natural ligand data sets, stability and structural computations, and deep sequencing of thousands of binding variants, a protein library was designed on a sitewise basis with a gradient of mutational levels across 29% of the protein. In direct competition of biased and uniform libraries, both with 1 × 10
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