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Molten globule-like intermediates have been shown to occur during protein folding and are thought to be involved in protein translocation and membrane insertion. However, the determinants of molten globule stability and the extent of specific packing in molten globules is currently unclear. Using far- and near-UV CD and intrinsic and ANS fluorescence, we show that four periplasmic binding proteins (LBP, LIVBP, MBP, and RBP) form molten globules at acidic pH values ranging from 3.0 to 3.4. Only two of these (LBP and LIVBP) have similar sequences, but all four proteins adopt similar three-dimensional structures. We found that each of the four molten globules binds to its corresponding ligand without conversion to the native state. Ligand binding affinity measured by isothermal titration calorimetry for the molten globule state of LIVBP was found to be comparable to that of the corresponding native state, whereas for LBP, MBP, and RBP, the molten globules bound ligand with approximately 5-30-fold lower affinity than the corresponding native states. All four molten globule states exhibited cooperative thermal unfolding assayed by DSC. Estimated values of DeltaCp of unfolding show that these molten globule states contain 28-67% of buried surface area relative to the native states. The data suggest that molten globules of these periplasmic binding proteins retain a considerable degree of long range order. The ability of these sequentially unrelated proteins to form highly ordered molten globules may be related to their large size as well as an intrinsic property of periplasmic binding protein folds.
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http://dx.doi.org/10.1021/bi700577m | DOI Listing |
J Phys Chem Lett
September 2025
School of Pharmaceutical Sciences, University of Geneva, Rue Michel-Servet 1, CH-1206 Geneva, CH, Switzerland.
Protein folding remains a formidable challenge despite significant advances, particularly in sequence-to-structure prediction. Accurately capturing thermodynamics and intermediates via simulations demands overcoming time scale limitations, making effective collective variable (CV) design for enhanced sampling crucial. Here, we introduce a strategy to automatically construct complementary, bioinspired CVs.
View Article and Find Full Text PDFBiophys J
August 2025
Institute of Chemistry, St. Petersburg State University, Universitetsky pr. 26, 198504 St. Petersburg, Russia.
The influence of dithiothreitol (DTT) and β-mercaptoethanol (β-MEt) or their mixtures with a chaotropic denaturant, namely guanidine hydrochloride (GuHCl) or urea, on the surface properties of lysozyme aqueous solutions was studied by the methods of dilatational surface rheology and ellipsometry. Adding 0.32 mM DTT to lysozyme solutions led to a considerable increase of the dynamic surface elasticity and a decrease of the dynamic surface tension as compared with the results for native protein solutions.
View Article and Find Full Text PDFBiomolecules
July 2025
Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA.
The gene is the site of congenital mutations linked to neurodevelopmental and musculoskeletal pathologies collectively termed ZARD (ZC4H2-Associated Rare Disorders). ZC4H2 consists of a coiled coil and a single novel zinc finger with four cysteines and two histidines, from which the protein obtains its name. Alpha Fold 3 confidently predicts a structure for the zinc finger but also for similarly sized random sequences, providing equivocal information on its folding status.
View Article and Find Full Text PDFJ Mol Biol
August 2025
Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA. Electronic address:
The coronavirus genome is transcribed by a replication-transcription complex (RTC) containing the RNA polymerase plus additional cofactors. The cofactor nsp8 is an important component of the RTC in both alpha and betacoronaviruses required for nsp12 polymerase activity, complex stability, and recruitment of other RTC cofactors. Here we use NMR and other biophysical methods to characterize the structural features and oligomeric state of full-length nsp8 in solution.
View Article and Find Full Text PDFJ Mol Biol
October 2025
Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, United States. Electronic address:
Unlike AI-based protein structure prediction, the sequence determinants of protein dynamics, and thus function, remain elusive. The nucleotide switch in Arf GTPases involves a massive structural change, which we showed recently in Arf1 is facilitated by a dynamic molten globule ensemble. Here we investigate the unresolved sequence-dynamics paradigm by comparing Arf1 and Arf6 using a combination of high-pressure NMR and other biophysical methods.
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