Whereas horse apomyoglobin is fully unfolded at pH 2 in the absence of salt, addition of a salt such as sodium chloride or sodium trichloroacetate stabilizes the molten globule state. Thermal unfolding of the salt-stabilized molten globule states of horse apomyoglobin at pH 2 measured by far-UV circular dichroism occurs not only on heating (i.e. heat-denaturation) but also on cooling (i.e. cold-denaturation). This demonstrates that a hydrophobic interaction contributes to the stability of the molten globule state and suggests that the unfolding transition can be represented by a cooperative two-state mechanism. To clarify the mechanism of conformational transition, we investigated the thermal unfolding of the chloride-stabilized molten globule state by differential scanning calorimetry. We observed a broad but distinct excess heat capacity peak, which is consistent with the unfolding transition measured by circular dichroism. To further characterize the molten globule states, we examined by far-UV circular dichroism the denaturant-induced unfolding transitions of the molten globule states stabilized by sodium chloride or sodium trichloroacetate. The urea-induced unfolding transitions of the molten globule states were explained by the two-state mechanism. The guanidine-hydrochloride-induced unfolding experiments clarified that the trichloroacetate-stabilized molten globule state is distinct from the chloride-stabilized one and that the former involves additional helical segment(s). These results support a view that the thermal unfolding of the molten globule states at pH 2 can be approximated by a two-state transition. However, several results suggested that a combined mechanism incorporating the two-state transition and a gradual structural change would be more general in describing the conformational transition of the molten globule states.
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http://dx.doi.org/10.1006/jmbi.1995.0373 | DOI Listing |
Nucleic Acids Res
January 2025
Department of Medicine, UofL Health Brown Cancer Center, University of Louisville, Louisville KY, 505 S Hancock St, Louisville, KY 40202, United States.
Time-resolved small-angle X-ray experiments are reported here that capture and quantify a previously unknown rapid collapse of the unfolded oligonucleotide as an early step in the folding of hybrid 1 and hybrid 2 telomeric G-quadruplex structures. The rapid collapse, initiated by a pH jump, is characterized by an exponential decrease in the radius of gyration from 24.3 to 12.
View Article and Find Full Text PDFJ Phys Chem B
January 2025
Department of Chemistry, Indian Institute of Technology Madras, Chennai 600036, India.
Knotted proteins have a unique topological feature with an open knot, and the physiological significance of these knots remains elusive. In addition, these proteins challenge our understanding of the protein folding process, and whether they retain their native state during unfolding/refolding cycles like other proteins is debated. Most folding studies on knotted proteins have been performed on 3 and 5 knots, monitoring the tryptophan fluorescence.
View Article and Find Full Text PDFJ Am Chem Soc
January 2025
Department of Polymer Science and Engineering, University of Massachusetts, Amherst, Massachusetts 01003, United States.
Direct translocation of RNA with secondary structures using single-molecule electrophoresis through protein nanopores shows significant fluctuations in the measured ionic current, in contrast to unstructured single-stranded RNA or DNA. We developed a multiscale model combining the oxRNA model for RNA with the 3-dimensional Poisson-Nernst-Planck formalism for electric fields within protein pores, aiming to map RNA conformations to ionic currents as RNA translocates through three protein nanopores: α-hemolysin, CsgG, and MspA. Our findings reveal three distinct stages of translocation (pseudoknot, melting, and molten globule) based on contact maps and current values.
View Article and Find Full Text PDFInt J Biol Macromol
January 2025
Bach Institute of Biochemistry, Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Leninsky pr. 33, Moscow 119071, Russia. Electronic address:
UV-irradiation is a stress factor for proteins, leading to disruption of their native structure. Test systems based on UV-irradiated proteins are relevant for researchers, as they allow working directly with damaged protein molecules, which can be important when studying the properties and mechanisms of action of various antiaggregation agents. The study of UV-irradiated proteins can also have applied significance, including medical.
View Article and Find Full Text PDFJ Biomol Struct Dyn
December 2024
Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India.
Nucleocapsid protein (N) of SARS-CoV-2 is a multivalent protein, which is responsible for viral replication, assembly, packaging and modulates host immune response. In this study, we report conformational measurements of N protein at different pH by observing transition in secondary and tertiary structural contents by biophysical and computational approaches. Spectroscopic measurements revealed that N protein loses its secondary and tertiary structure at extreme acidic pH while maintaining its native conformation at mild acidic and alkaline pH.
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