ArticleJournal of molecular biology2011
Alternate states of proteins revealed by detailed energy landscape mapping.
Article in Journal of molecular biology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 273 papers.
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Who cites it
273 citing papers in PubMed.
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- Directed evolution of APOX for proximity labeling using phenols with high redox potentials.Cell chemical biology · 2026Article
- Conformational equilibria in the activation of cystine-knot hormone receptors.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- High-throughput biochemical phenotyping of SHP2 variants reveals the molecular basis of diseases and allosteric drug inhibition.bioRxiv : the preprint server for biology · 2026Article
- Strigolactones and sesquiterpene lactones induce Orobanche cumana germination via KAI2d receptors through distinct processes.The Plant journal : for cell and molecular biology · 2026Article
- Structural and evolutionary dissection of NADPH-binding motifs in NADPH-preferring ene-reductases.Protein science : a publication of the Protein Society · 2026Article
- Small-molecule binding and sensing with a designed protein family.Nature communications · 2026Article
213 more citing papers are in PubMed but not listed here.
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Authors and funding
8 authors.
Funding
Abstract
What conformations do protein molecules populate in solution? Crystallography provides a high-resolution description of protein structure in the crystal environment, while NMR describes structure in solution but using less data. NMR structures display more variability, but is this because crystal contacts are absent or because of fewer data constraints? Here we report unexpected insight into this issue obtained through analysis of detailed protein energy landscapes generated by large-scale, native-enhanced sampling of conformational space with Rosetta@home for 111 protein domains. In the absence of tightly associating binding partners or ligands, the lowest-energy Rosetta models were nearly all <2.5 Å C(α)RMSD from the experimental structure; this result demonstrates that structure prediction accuracy for globular proteins is limited mainly by the ability to sample close to the native structure. While the lowest-energy models are similar to deposited structures, they are not identical; the largest deviations are most often in regions involved in ligand, quaternary, or crystal contacts. For ligand binding proteins, the low energy models may resemble the apo structures, and for oligomeric proteins, the monomeric assembly intermediates. The deviations between the low energy models and crystal structures largely disappear when landscapes are computed in the context of the crystal lattice or multimer. The computed low-energy ensembles, with tight crystal-structure-like packing in the core, but more NMR-structure-like variability in loops, may in some cases resemble the native state ensembles of proteins better than individual crystal or NMR structures, and can suggest experimentally testable hypotheses relating alternative states and structural heterogeneity to function.
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Registered trials
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