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Protein Unfolding Induced by Chemical Agents
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Protein Unfolding Induced by Chemical Agents

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Biochemistry".

Deadline for manuscript submissions: 20 March 2025 | Viewed by 2351

Special Issue Editors

Prof. Dr. Gyula Batta

E-Mail Website
Guest Editor
Faculty of Science and Technology, Institute of Chemistry, Department of Organic Chemistry, University of Debrecen, H-4032 Debrecen, Hungary
Interests: antibacterial activity; protein structures; antimicrobial proteins; glycopeptides
Special Issues, Collections and Topics in MDPI journals
Dr. Orsolya Tőke

E-Mail Website
Guest Editor
Research Centre for Natural Sciences, Centre for Structural Science, H-1117 Budapest, Hungary
Interests: protein structure and dynamics; protein-lipid interactions; cellular signaling; membrane peptides; protein folding; NMR spectroscopy
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Protein folding and unfolding has been an important research area since the Anfinsen dogma was established. We know that biologically important proteins work best around room temperature, atmospheric pressure, neutral pH, and in the absence of chemicals (e.g. small, organic molecules). However, the equilibrium that favours folded protein conformation can be shifted by changing any of the conditions mentioned above. Here, we aim at chemical unfolding as it has pharmaceutical importance. Importantly, folding and unfolding time scales are generally too fast for straight experimental (e.g. NMR, AFM, FRET) observations. Therefore, often the equilibria are studied by physical methods as shifted to irreversible „denatured” states. Sometimes even the unfolded states are interesting because they provide insight into the nature of disordered proteins (IDPs). In addition to experimental techniques, in-silico, molecular dynamics simulations may be of help for understanding the mechanism of chemical denaturation.

Prof. Dr. Gyula Batta
Dr. Orsolya Tőke
Guest Editors

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Keywords

  • protein stability
  • chemical unfolding
  • denaturing conditions
  • protein folding
  • folding pathway
  • misfolding
  • conformational flexibility
  • disordered state
  • protein aggregation
  • protein drugs

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Published Papers (3 papers)

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12 pages, 904 KiB  
Article
On the Stabilizing Effect of Aspartate and Glutamate and Its Counteraction by Common Denaturants
by Guido Izzi, Marco Campanile, Pompea Del Vecchio and Giuseppe Graziano
Int. J. Mol. Sci. 2024, 25(17), 9360; https://doi.org/10.3390/ijms25179360 - 29 Aug 2024
Viewed by 493
Abstract
By performing differential scanning calorimetry(DSC) measurements on RNase A, we studied the stabilization provided by the addition of potassium aspartate(KAsp) or potassium glutamate (KGlu) and found that it leads to a significant increase in the denaturation temperature of the protein. The stabilization proves [...] Read more.
By performing differential scanning calorimetry(DSC) measurements on RNase A, we studied the stabilization provided by the addition of potassium aspartate(KAsp) or potassium glutamate (KGlu) and found that it leads to a significant increase in the denaturation temperature of the protein. The stabilization proves to be mainly entropic in origin. A counteraction of the stabilization provided by KAsp or KGlu is obtained by adding common denaturants such as urea, guanidinium chloride, or guanidinium thiocyanate. A rationalization of the experimental data is devised on the basis of a theoretical approach developed by one of the authors. The main contribution to the conformational stability of globular proteins comes from the gain in translational entropy of water and co-solute ions and/or molecules for the decrease in solvent-excluded volume associated with polypeptide folding (i.e., there is a large decrease in solvent-accessible surface area). The magnitude of this entropic contribution increases with the number density and volume packing density of the solution. The two destabilizing contributions come from the conformational entropy of the chain, which should not depend significantly on the presence of co-solutes, and from the direct energetic interactions between co-solutes and the protein surface in both the native and denatured states. It is the magnitude of the latter that discriminates between stabilizing and destabilizing agents. Full article
(This article belongs to the Special Issue Protein Unfolding Induced by Chemical Agents)
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19 pages, 2557 KiB  
Article
The Thioredoxin Fold Protein (TFP2) from Extreme Acidophilic Leptospirillum sp. CF-1 Is a Chaperedoxin-like Protein That Prevents the Aggregation of Proteins under Oxidative Stress
by Claudia Muñoz-Villagrán, Javiera Acevedo-Arbunic, Elisabeth Härtig, Susanne Sievers, Daniela Zühlke, Francisco Issotta, Carolina Mascayano, Dieter Jahn, Martina Jahn and Gloria Levicán
Int. J. Mol. Sci. 2024, 25(13), 6905; https://doi.org/10.3390/ijms25136905 - 24 Jun 2024
Viewed by 800 | Correction
Abstract
Extreme acidophilic bacteria like Leptospirillum sp. require an efficient enzyme system to counteract strong oxygen stress conditions in their natural habitat. The genome of Leptospirillum sp. CF-1 encodes the thioredoxin-fold protein TFP2, which exhibits a high structural similarity to the thioredoxin domain of [...] Read more.
Extreme acidophilic bacteria like Leptospirillum sp. require an efficient enzyme system to counteract strong oxygen stress conditions in their natural habitat. The genome of Leptospirillum sp. CF-1 encodes the thioredoxin-fold protein TFP2, which exhibits a high structural similarity to the thioredoxin domain of E. coli CnoX. CnoX from Escherichia coli is a chaperedoxin that protects protein substrates from oxidative stress conditions using its holdase function and a subsequent transfer to foldase chaperones for refolding. Recombinantly produced and purified Leptospirillum sp. TFP2 possesses both thioredoxin and chaperone holdase activities in vitro. It can be reduced by thioredoxin reductase (TrxR). The tfp2 gene co-locates with genes for the chaperone foldase GroES/EL on the chromosome. The “tfp2 cluster” (ctpA-groES-groEL-hyp-tfp2-recN) was found between 1.9 and 8.8-fold transcriptionally up-regulated in response to 1 mM hydrogen peroxide (H2O2). Leptospirillum sp. tfp2 heterologously expressed in E. coli wild type and cnoX mutant strains lead to an increased tolerance of these E. coli strains to H2O2 and significantly reduced intracellular protein aggregates. Finally, a proteomic analysis of protein aggregates produced in E. coli upon exposition to oxidative stress with 4 mM H2O2, showed that Leptospirillum sp. tfp2 expression caused a significant decrease in the aggregation of 124 proteins belonging to fifteen different metabolic categories. These included several known substrates of DnaK and GroEL/ES. These findings demonstrate that Leptospirillum sp. TFP2 is a chaperedoxin-like protein, acting as a key player in the control of cellular proteostasis under highly oxidative conditions that prevail in extreme acidic environments. Full article
(This article belongs to the Special Issue Protein Unfolding Induced by Chemical Agents)
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2 pages, 175 KiB  
Correction
Correction: Muñoz-Villagrán et al. The Thioredoxin Fold Protein (TFP2) from Extreme Acidophilic Leptospirillum sp. CF-1 Is a Chaperedoxin-like Protein That Prevents the Aggregation of Proteins under Oxidative Stress. Int. J. Mol. Sci. 2024, 25, 6905
by Claudia Muñoz-Villagrán, Javiera Acevedo-Arbunic, Elisabeth Härtig, Susanne Sievers, Daniela Zühlke, Francisco Issotta, Carolina Mascayano, Dieter Jahn, Martina Jahn and Gloria Levicán
Int. J. Mol. Sci. 2024, 25(23), 12489; https://doi.org/10.3390/ijms252312489 - 21 Nov 2024
Viewed by 131
Abstract
Susanne Sievers and Daniela Zühlke were not included as authors in the original publication [...] Full article
(This article belongs to the Special Issue Protein Unfolding Induced by Chemical Agents)
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