The critical behavior of ribonucleic acid (RNA) secondary structures with quenched sequence randomness is studied by means of the constrained annealing method. A thermodynamic phase transition is induced by including the conformational weight of loop structures. In addition to the expected melting at high temperature, a cold-melting transition appears when the disorder strength induces competition between favorable and unfavorable base pairs. Our results suggest that the cold denaturation of RNA found experimentally might be triggered by quenched sequence disorder. We calculate hot- and cold-melting critical temperatures for competing favorable and unfavorable base-pair energies and present a folding phase diagram as a function of the loop exponent and temperature.
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http://dx.doi.org/10.1103/PhysRevE.101.012502 | DOI Listing |
Q Rev Biophys
January 2025
Elettra Sincrotrone Trieste, Italy.
Yeast frataxin (Yfh1) is a small natural protein from yeast that has the unusual property of undergoing cold denaturation at temperatures above the freezing point of water when under conditions of low ionic strength. This peculiarity, together with remarkable resilience, allows the determination, for the whole protein as well as for individual residues, of the stability curve, that is the temperature dependence of the free energy difference between the unfolded and folded forms. The ease of measuring stability curves without the need to add denaturants or introduce destabilizing mutations makes this protein an ideal 'tool' for investigating the influence of many environmental factors on protein stability.
View Article and Find Full Text PDFBiochem Mol Biol Educ
January 2025
Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, USA.
We created a novel laboratory experience where undergraduate students explore the techniques used to study protein misfolding, unfolding, and aggregation. Despite the importance of protein misfolding and aggregation diseases, protein unfolding is not typically explored in undergraduate biochemistry laboratory classes. Yeast alcohol dehydrogenase (YADH) is used in the undergraduate biochemistry laboratory course at Miami University as the model system to explore protein overexpression and purification, bioinformatics, and enzyme characterization.
View Article and Find Full Text PDFInt J Mol Sci
December 2024
Metabolic Engineering Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju 55365, Republic of Korea.
The black soldier fly, , is a voracious scavenger of various organic materials; therefore, it could be exploited as a biological system for processing daily food waste. In order to survey novel hydrolytic enzymes, we constructed a fosmid metagenome library using unculturable intestinal microorganisms from . Through functional screening of the library on carboxymethyl cellulose plates, we identified a fosmid clone, the product of which displayed hydrolytic activity.
View Article and Find Full Text PDFProtein Sci
January 2025
Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Kyoto, Japan.
Antibodies and antibody mimics are extensively used in the pharmaceutical industry, where stringent safety standards are required. Implementing heat sterilization during or after the manufacturing process could help prevent contamination by viruses and bacteria. However, conventional antibodies and antibody mimics are not suitable for heat sterilization because they irreversibly denature at high temperatures.
View Article and Find Full Text PDFDNA Repair (Amst)
December 2024
Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario 2000, Argentina. Electronic address:
The MSH7 protein is a binding partner of MSH2 forming the MutSγ complex. This complex contributes to the plant mismatch repair (MMR) system by recognizing DNA base-base mismatches. Here, we evaluated the impact of MSH7 on genetic diversity of the tenth generation (G) of wild type and MSH7 deficient Arabidopsis thaliana plants before and after two days exposure to 100 mM NaCl.
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