ArticlePLoS computational biology2012
Defining the nature of thermal intermediate in 3 state folding proteins: apoflavodoxin, a study case.
Article in PLoS computational biology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- Prophage landscapes in clinical MRSA: safety profiling and discovery of Lys81, a broad-spectrum bacteriolytic enzyme.Frontiers in microbiology · 2026Article
- Calculation of Protein Folding Thermodynamics Using Molecular Dynamics Simulations.Journal of chemical information and modeling · 2023Article
- Pre-Molten, Wet, and Dry Molten Globules en Route to the Functional State of Proteins.International journal of molecular sciences · 2023Review
- Protein conformation stabilized by newly formed turns for thermal resilience.Biophysical journal · 2023Article
- A look at the face of the molten globule: Structural model of the Helicobacter pylori apoflavodoxin ensemble at acidic pH.Protein science : a publication of the Protein Society · 2022Article
- Insights into Fluctuations of Structure of Proteins: Significance of Intermediary States in Regulating Biological Functions.Polymers · 2022Review
- Exploring the complete mutational space of the LDL receptor LA5 domain using molecular dynamics: linking SNPs with disease phenotypes in familial hypercholesterolemia.Human molecular genetics · 2016Article
- Rational stabilization of complex proteins: a divide and combine approach.Scientific reports · 2015Article
- Decoding Structural Properties of a Partially Unfolded Protein Substrate: En Route to Chaperone Binding.PLoS computational biology · 2015Article
- Quantifying the Sources of Kinetic Frustration in Folding Simulations of Small Proteins.Journal of chemical theory and computation · 2014Article
- Understanding the relevance of local conformational stability and dynamics to the aggregation propensity of an IgG1 and IgG2 monoclonal antibodies.Protein science : a publication of the Protein Society · 2013Article
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5 authors.
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No grant is acknowledged in the PubMed record.
Abstract
The early stages of the thermal unfolding of apoflavodoxin have been determined by using atomistic multi microsecond-scale molecular dynamics (MD) simulations complemented with a variety of experimental techniques. Results strongly suggest that the intermediate is reached very early in the thermal unfolding process and that it has the properties of an "activated" form of the native state, where thermal fluctuations in the loops break loop-loop contacts. The unrestrained loops gain then kinetic energy corrupting short secondary structure elements without corrupting the core of the protein. The MD-derived ensembles agree with experimental observables and draw a picture of the intermediate state inconsistent with a well-defined structure and characteristic of a typical partially disordered protein. Our results allow us to speculate that proteins with a well packed core connected by long loops might behave as partially disordered proteins under native conditions, or alternatively behave as three state folders. Small details in the sequence, easily tunable by evolution, can yield to one or the other type of proteins.
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