ArticleProceedings of the National Academy of Sciences of the United States of America2015
Control over overall shape and size in de novo designed proteins.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 79 papers.
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Who cites it
79 citing papers in PubMed.
- 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
- The Borderlands of Foldability: Lessons from Simplified Proteins.Trends in chemistry · 2026Article
- Evaluating zero-shot prediction of monomeric protein design success by AlphaFold, ESMFold, and ProteinMPNN.Protein science : a publication of the Protein Society · 2026Article
- Navigating protein-nucleic acid sequence-structure landscapes with deep learning.Current opinion in structural biology · 2025Review
- Buttressing ligand-binding pockets in de novo designed NTF2-like domains.Protein science : a publication of the Protein Society · 2025Article
- De novo design of ATPase based on a blueprint optimized for harboring the P-loop motif.Protein science : a publication of the Protein Society · 2025Article
- Structural and energetic analysis of stabilizing indel mutations.bioRxiv : the preprint server for biology · 2024Article
- Folds from fold: Exploring topological isoforms of a single-domain protein.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- AI in cellular engineering and reprogramming.Biophysical journal · 2024Review
- Design of amyloidogenic peptide traps.Nature chemical biology · 2024Article
- An ancestral fold reveals the evolutionary link between RNA polymerase and ribosomal proteins.Nature communications · 2024Article
- Validation of de novo designed water-soluble and transmembrane β-barrels by in silico folding and melting.Protein science : a publication of the Protein Society · 2024Article
- Density Function Theory Study on the Energy and Circular Dichroism Spectrum for Methylene-Linked Triazole Diads Depending on the Substitution Position and Conformation.Molecules (Basel, Switzerland) · 2024Article
- The structural landscape of the immunoglobulin fold by large-scale de novo design.Protein science : a publication of the Protein Society · 2024Article
- Design of complicated all-α protein structures.Nature structural & molecular biology · 2024Article
- Rationale in Custom Design of Transmembrane β-Barrel Pores.Methods in molecular biology (Clifton, N.J.) · 2024Article
- ProRefiner: an entropy-based refining strategy for inverse protein folding with global graph attention.Nature communications · 2023Article
- Single-chain dimers from de novo immunoglobulins as robust scaffolds for multiple binding loops.Nature communications · 2023Article
- Design of stimulus-responsive two-state hinge proteins.Science (New York, N.Y.) · 2023Article
- Large language models generate functional protein sequences across diverse families.Nature biotechnology · 2023Article
19 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
We recently described general principles for designing ideal protein structures stabilized by completely consistent local and nonlocal interactions. The principles relate secondary structure patterns to tertiary packing motifs and enable design of different protein topologies. To achieve fine control over protein shape and size within a particular topology, we have extended the design rules by systematically analyzing the codependencies between the lengths and packing geometry of successive secondary structure elements and the backbone torsion angles of the loop linking them. We demonstrate the control afforded by the resulting extended rule set by designing a series of proteins with the same fold but considerable variation in secondary structure length, loop geometry, β-strand registry, and overall shape. Solution NMR structures of four designed proteins for two different folds show that protein shape and size can be precisely controlled within a given protein fold. These extended design principles provide the foundation for custom design of protein structures performing desired functions.
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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.