ArticleProceedings of the National Academy of Sciences of the United States of America2011
Experimental free energy surfaces reveal the mechanisms of maintenance of protein solubility.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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Who cites it
39 citing papers in PubMed.
- Structure and Dynamics of the Misfolding Intermediate in the Pathogenic T183A Prion Protein Mutant.Journal of chemical theory and computation · 2025Article
- A review on computational models for predicting protein solubility.Journal of microbiology (Seoul, Korea) · 2025Review
- Biophysical characterization of the phase separation of TDP-43 devoid of the C-terminal domain.Cellular & molecular biology letters · 2024Article
- Metal interactions of α-synuclein probed by NMR amide-proton exchange.Frontiers in chemistry · 2023Article
- The role of structural dynamics in the thermal adaptation of hyperthermophilic enzymes.Frontiers in molecular biosciences · 2022Article
- Quantitative Measurement of the Affinity of Toxic and Nontoxic Misfolded Protein Oligomers for Lipid Bilayers and of its Modulation by Lipid Composition and Trodusquemine.ACS chemical neuroscience · 2021Article
- Understanding the Role of Protein Glycation in the Amyloid Aggregation Process.International journal of molecular sciences · 2021Review
- Divergence Entropy-Based Evaluation of Hydrophobic Core in Aggressive and Resistant Forms of Transthyretin.Entropy (Basel, Switzerland) · 2021Article
- Structure-aware protein solubility prediction from sequence through graph convolutional network and predicted contact map.Journal of cheminformatics · 2021Article
- Soluble Prion Peptide 107-120 Protects Neuroblastoma SH-SY5Y Cells against Oligomers Associated with Alzheimer's Disease.International journal of molecular sciences · 2020Article
- The Structure of Amyloid Versus the Structure of Globular Proteins.International journal of molecular sciences · 2020Article
- Microsecond sub-domain motions and the folding and misfolding of the mouse prion protein.eLife · 2019Article
- Backbone NMR assignments of HypF-N under conditions generating toxic and non-toxic oligomers.Biomolecular NMR assignments · 2018Article
- Signature of Pareto optimization in the Escherichia coli proteome.Scientific reports · 2018Article
- The structural basis of nanobody unfolding reversibility and thermoresistance.Scientific reports · 2018Article
- Water is an active matrix of life for cell and molecular biology.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Concurrent structural and biophysical traits link with immunoglobulin light chains amyloid propensity.Scientific reports · 2017Article
- Direct Conversion of an Enzyme from Native-like to Amyloid-like Aggregates within Inclusion Bodies.Biophysical journal · 2017Article
- Antibody Aggregation: Insights from Sequence and Structure.Antibodies (Basel, Switzerland) · 2016Review
- Rational design of mutations that change the aggregation rate of a protein while maintaining its native structure and stability.Scientific reports · 2016Article
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Authors and funding
7 authors.
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Abstract
The identification of the factors that enable normally folded proteins to remain in their soluble and functional states is crucial for a comprehensive understanding of any biological system. We have determined a series of energy landscapes of the acylphosphatase from Drosophila melanogaster under a variety of conditions by combining NMR measurements with restrained molecular dynamics simulations. We thus analyzed the differences in the structures, dynamics, and energy surfaces of the protein in its soluble state or in situations where it aggregates through conformational states that have native-like structure, folding stability, and enzymatic activity. The study identifies the nature of the energy barriers that under normal physiological conditions prevent the protein ensemble from populating dangerous aggregation-prone states. We found that such states, although similar to the native conformation, have altered surface charge distribution, alternative topologies of the β-sheet region, and modified solvent exposure of hydrophobic surfaces and aggregation-prone regions of the sequence. The identified barriers allow the protein to undergo functional dynamics while remaining soluble and without a significant risk of misfolding and aggregation into nonfunctional and potentially toxic species.
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