ArticleProceedings of the National Academy of Sciences of the United States of America2012
Denaturant-dependent folding of GFP.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed.
- Rapid evolutionary change in trait correlations of single proteins.Nature communications · 2024Article
- Brewing COFFEE: A sequence-specific coarse-grained energy function for simulations of DNA-protein complexes.bioRxiv : the preprint server for biology · 2023Article
- Organellar Glue: A Molecular Tool to Artificially Control Chloroplast-Chloroplast Interactions.ACS synthetic biology · 2022Article
- Cooperativity and Folding Kinetics in a Multidomain Protein with Interwoven Chain Topology.ACS central science · 2022Article
- Side-Chain Polarity Modulates the Intrinsic Conformational Landscape of Model Dipeptides.The journal of physical chemistry. B · 2021Article
- Machine-learned potentials for next-generation matter simulations.Nature materials · 2021Review
- Asymmetry in histone rotation in forced unwrapping and force quench rewrapping in a nucleosome.Nucleic acids research · 2021Article
- Article
- Shape changes and cooperativity in the folding of the central domain of the 16S ribosomal RNA.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Bead based facile assay for sensitive quantification of native state green fluorescent protein.RSC advances · 2020Article
- Successes and challenges in simulating the folding of large proteins.The Journal of biological chemistry · 2020Review
- Shaping the Cortical Landscape: Functions and Mechanisms of Top-Down Cortical Feedback Pathways.Frontiers in systems neuroscience · 2020Article
- Dynamics of a family of cyan fluorescent proteins probed by incoherent neutron scattering.Journal of the Royal Society, Interface · 2019Article
- Stabilizing Effect of Inherent Knots on Proteins Revealed by Molecular Dynamics Simulations.Biophysical journal · 2018Article
- Denaturants Alter the Flux through Multiple Pathways in the Folding of PDZ Domain.The journal of physical chemistry. B · 2018Article
- Mechanically switching single-molecule fluorescence of GFP by unfolding and refolding.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- The fluorescent monomeric protein Kusabira Orange. Pressure effect on its structure and stability.Biochemistry and biophysics reports · 2016Article
- Knotting and unknotting of a protein in single molecule experiments.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Nucleotides regulate the mechanical hierarchy between subdomains of the nucleotide binding domain of the Hsp70 chaperone DnaK.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- Molecular investigations into the mechanics of a muscle anchoring complex.Biophysical journal · 2015Article
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3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We use molecular simulations using a coarse-grained model to map the folding landscape of Green Fluorescent Protein (GFP), which is extensively used as a marker in cell biology and biotechnology. Thermal and Guanidinium chloride (GdmCl) induced unfolding of a variant of GFP, without the chromophore, occurs in an apparent two-state manner. The calculated midpoint of the equilibrium folding in GdmCl, taken into account using the Molecular Transfer Model (MTM), is in excellent agreement with the experiments. The melting temperatures decrease linearly as the concentrations of GdmCl and urea are increased. The structural features of rarely populated equilibrium intermediates, visible only in free energy profiles projected along a few order parameters, are remarkably similar to those identified in a number of ensemble experiments in GFP with the chromophore. The excellent agreement between simulations and experiments show that the equilibrium intermediates are stabilized by the chromophore. Folding kinetics, upon temperature quench, show that GFP first collapses and populates an ensemble of compact structures. Despite the seeming simplicity of the equilibrium folding, flux to the native state flows through multiple channels and can be described by the kinetic partitioning mechanism. Detailed analysis of the folding trajectories show that both equilibrium and several kinetic intermediates, including misfolded structures, are sampled during folding. Interestingly, the intermediates characterized in the simulations coincide with those identified in single molecule pulling experiments. Our predictions, amenable to experimental tests, show that MTM is a practical way to simulate the effect of denaturants on the folding of large proteins.
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