ArticleStructure (London, England : 1993)2012
Increasing sequence diversity with flexible backbone protein design: the complete redesign of a protein hydrophobic core.
Article in Structure (London, England : 1993), 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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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.
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Who cites it
25 citing papers in PubMed, 65 citations in OpenAlex.
- Elucidating the catalytic mechanism of a previously undescribed carbohydrate esterase family 7 acetyl xylan esterase (LaCE7A).The FEBS journal · 2026Article
- DivPro: diverse protein sequence design with direct structure recovery guidance.Bioinformatics (Oxford, England) · 2025Article
- An expandable, modular de novo protein platform for precision redox engineering.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Engineering the kinetic stability of a β-trefoil protein by tuning its topological complexity.Frontiers in molecular biosciences · 2023Article
- Active site center redesign increases protein stability preserving catalysis in thioredoxin.Protein science : a publication of the Protein Society · 2022Article
- Computational design of a sensitive, selective phase-changing sensor protein for the VX nerve agent.Science advances · 2022Article
- From Protein Design to the Energy Landscape of a Cold Unfolding Protein.The journal of physical chemistry. B · 2022Article
- Perturbing the energy landscape for improved packing during computational protein design.Proteins · 2021Article
- Dynamics, a Powerful Component of Current and Future in Silico Approaches for Protein Design and Engineering.International journal of molecular sciences · 2020Review
- Article
- Designing protein structures and complexes with the molecular modeling program Rosetta.The Journal of biological chemistry · 2019Review
- Advances in protein structure prediction and design.Nature reviews. Molecular cell biology · 2019Review
- Rosetta FunFolDes - A general framework for the computational design of functional proteins.PLoS computational biology · 2018Article
- Structural insights into the catalytic mechanism of a novel glycoside hydrolase family 113 β-1,4-mannanase fromThe Journal of biological chemistry · 2018Article
- An iterative computational design approach to increase the thermal endurance of a mesophilic enzyme.Biotechnology for biofuels · 2018Article
- The coming of age of de novo protein design.Nature · 2016Review
- Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics.PLoS computational biology · 2016Review
- The role of negative selection in protein evolution revealed through the energetics of the native state ensemble.Proteins · 2016Article
- Protein stability: computation, sequence statistics, and new experimental methods.Current opinion in structural biology · 2015Review
- Optimization of rotamers prior to template minimization improves stability predictions made by computational protein design.Protein science : a publication of the Protein Society · 2015Article
Corrections and comments
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
Abstract
Protein design tests our understanding of protein stability and structure. Successful design methods should allow the exploration of sequence space not found in nature. However, when redesigning naturally occurring protein structures, most fixed backbone design algorithms return amino acid sequences that share strong sequence identity with wild-type sequences, especially in the protein core. This behavior places a restriction on functional space that can be explored and is not consistent with observations from nature, where sequences of low identity have similar structures. Here, we allow backbone flexibility during design to mutate every position in the core (38 residues) of a four-helix bundle protein. Only small perturbations to the backbone, 1-2 Å, were needed to entirely mutate the core. The redesigned protein, DRNN, is exceptionally stable (melting point >140°C). An NMR and X-ray crystal structure show that the side chains and backbone were accurately modeled (all-atom RMSD = 1.3 Å).
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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.