ArticleCurrent research in structural biology2019
Thermodynamics and folding landscapes of large proteins from a statistical mechanical model.
Article in Current research in structural biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 33 citations in OpenAlex.
- Selective control of ligand binding through a distal mutation that alters the protein native ensemble.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Local and Global Breathing Motions Prime the Access to Buried Binding Site in an Antibiotic-Sequestering Protein.ACS bio & med chem Au · 2025Article
- A finely balanced order-disorder equilibrium sculpts the folding-binding landscape of an antibiotic sequestering protein.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Molecular and thermodynamic determinants of self-assembly and hetero-oligomerization in the enterobacterial thermo-osmo-regulatory protein H-NS.Nucleic acids research · 2024Article
- Conflicting Interfacial Electrostatic Interactions as a Design Principle to Modulate Long-Range Interdomain Communication.ACS bio & med chem Au · 2024Article
- Conformational Tuning Shapes the Balance between Functional Promiscuity and Specialization in ParalogousBiochemistry · 2023Article
- Thermodynamic architecture and conformational plasticity of GPCRs.Nature communications · 2023Article
- Ensemble origins and distance-dependence of long-range mutational effects in proteins.iScience · 2022Article
- Loss of stability and unfolding cooperativity in hPGK1 upon gradual structural perturbation of its N-terminal domain hydrophobic core.Scientific reports · 2022Article
- The Wako-Saitô-Muñoz-Eaton Model for Predicting Protein Folding and Dynamics.Molecules (Basel, Switzerland) · 2022Review
- Allosteric Communication in the Multifunctional and Redox NQO1 Protein Studied by Cavity-Making Mutations.Antioxidants (Basel, Switzerland) · 2022Article
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- Weakening of interaction networks with aging in tip-link protein induces hearing loss.The Biochemical journal · 2021Article
- A hierarchy of coupling free energies underlie the thermodynamic and functional architecture of protein structures.Current research in structural biology · 2021Review
Corrections and comments
- Erratum issued
Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
Statistical mechanical models that afford an intermediate resolution between macroscopic chemical models and all-atom simulations have been successful in capturing folding behaviors of many small single-domain proteins. However, the applicability of one such successful approach, the Wako-Saitô-Muñoz-Eaton (WSME) model, is limited by the size of the protein as the number of conformations grows exponentially with protein length. In this work, we surmount this size limitation by introducing a novel approximation that treats stretches of 3 or 4 residues as blocks, thus reducing the phase space by nearly three orders of magnitude. The performance of the 'bWSME' model is validated by comparing the predictions for a globular enzyme (RNase H) and a repeat protein (IκBα), against experimental observables and the model without block approximation. Finally, as a proof of concept, we predict the free-energy surface of the 370-residue, multi-domain maltose binding protein and identify an intermediate in good agreement with single-molecule force-spectroscopy measurements. The bWSME model can thus be employed as a quantitative predictive tool to explore the conformational landscapes of large proteins, extract the structural features of putative intermediates, identify parallel folding paths, and thus aid in the interpretation of both ensemble and single-molecule experiments.
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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.