ArticleJournal of molecular biology2007
Structural analysis of kinetic folding intermediates for a TIM barrel protein, indole-3-glycerol phosphate synthase, by hydrogen exchange mass spectrometry and Gō model simulation.
Article in Journal of molecular biology, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed, 41 citations in OpenAlex.
- Accurate prediction of protein folding mechanisms by simple structure-based statistical mechanical models.Nature communications · 2023Article
- A conserved folding nucleus sculpts the free energy landscape of bacterial and archaeal orthologs from a divergent TIM barrel family.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Validation of DBFOLD: An efficient algorithm for computing folding pathways of complex proteins.PLoS computational biology · 2020Article
- Frustration and folding of a TIM barrel protein.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Clusters of isoleucine, leucine, and valine side chains define cores of stability in high-energy states of globular proteins: Sequence determinants of structure and stability.Protein science : a publication of the Protein Society · 2016Article
- Synthetic biology for the directed evolution of protein biocatalysts: navigating sequence space intelligently.Chemical Society reviews · 2015Review
- Autonomously folding protein fragments reveal differences in the energy landscapes of homologous RNases H.PloS one · 2015Article
- Folding of the RNA recognition motif (RRM) domains of the amyotrophic lateral sclerosis (ALS)-linked protein TDP-43 reveals an intermediate state.The Journal of biological chemistry · 2014Article
- Clusters of branched aliphatic side chains serve as cores of stability in the native state of the HisF TIM barrel protein.Journal of molecular biology · 2013Article
- Interplay between drying and stability of a TIM barrel protein: a combined simulation-experimental study.Journal of the American Chemical Society · 2013Article
- Indole-3-glycerol-phosphate synthase is recognized by a cold-inducible group II chaperonin in Thermococcus kodakarensis.Applied and environmental microbiology · 2012Article
- CLIPS-1D: analysis of multiple sequence alignments to deduce for residue-positions a role in catalysis, ligand-binding, or protein structure.BMC bioinformatics · 2012Article
- Article
- Topological frustration in beta alpha-repeat proteins: sequence diversity modulates the conserved folding mechanisms of alpha/beta/alpha sandwich proteins.Journal of molecular biology · 2010Article
- Insights from coarse-grained Gō models for protein folding and dynamics.International journal of molecular sciences · 2009Review
- Characterization of the unfolded state of repeat proteins.HFSP journal · 2008Article
- Microsecond acquisition of heterogeneous structure in the folding of a TIM barrel protein.Proceedings of the National Academy of Sciences of the United States of America · 2008Article
- The dual-basin landscape in GFP folding.Proceedings of the National Academy of Sciences of the United States of America · 2008Article
- NMR analysis of partially folded states and persistent structure in the alpha subunit of tryptophan synthase: implications for the equilibrium folding mechanism of a 29-kDa TIM barrel protein.Journal of molecular biology · 2008Article
- The foldon substructure of staphylococcal nuclease.Journal of molecular biology · 2008Article
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
Abstract
The structures of partially folded states appearing during the folding of a (betaalpha)(8) TIM barrel protein, the indole-3-glycerol phosphate synthase from Sulfolobus solfataricus (sIGPS), was assessed by hydrogen exchange mass spectrometry (HX-MS) and Gō model simulations. HX-MS analysis of the peptic peptides derived from the pulse-labeled product of the sub-millisecond folding reaction from the urea-denatured state revealed strong protection in the (betaalpha)(4) region, modest protection in the neighboring (betaalpha)(1-3) and (betaalpha)(5)beta(6) segments and no significant protection in the remaining N and C-terminal segments. These results demonstrate that this species is not a collapsed form of the unfolded state under native-favoring conditions nor is it the native state formed via fast-track folding. However, the striking contrast of these results with the strong protection observed in the (betaalpha)(2-5)beta(6) region after 5 s of folding demonstrates that these species represent kinetically distinct folding intermediates that are not identical as previously thought. A re-examination of the kinetic folding mechanism by chevron analysis of fluorescence data confirmed distinct roles for these two species: the burst-phase intermediate is predicted to be a misfolded, off-pathway intermediate, while the subsequent 5 s intermediate corresponds to an on-pathway equilibrium intermediate. Comparison with the predictions using a C(alpha) Gō model simulation of the kinetic folding reaction for sIGPS shows good agreement with the core of the structure offering protection against exchange in the on-pathway intermediate(s). Because the native-centric Gō model simulations do not explicitly include sequence-specific information, the simulation results support the hypothesis that the topology of TIM barrel proteins is a primary determinant of the folding free energy surface for the productive folding reaction. The early misfolding reaction must involve aspects of non-native structure not detected by the Gō model simulation.
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