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RSC Advances Aug 2022DNA denaturation is related to many important biological phenomena, such as its replication, transcription and the interaction with some specific proteins for...
DNA denaturation is related to many important biological phenomena, such as its replication, transcription and the interaction with some specific proteins for single-stranded DNA. Dimethyl sulfoxide (DMSO) is a common chemical agent for DNA denaturation. In the present study, we investigate quantitatively the effects of different concentrations of DMSO on plasmid and linear DNA denaturation by atomic force microscopy (AFM) and UV spectrophotometry. We found that persistent length of DNA decreases significantly by adding a small amount of DMSO before ensemble DNA denaturation occurs; the persistence length of DNA in 3% DMSO solution decreases to 12 nm from about 50 nm without DMSO in solution. And local DNA denaturation occurs even at very low DMSO concentration (such as 0.1%), which can be directly observed in AFM imaging. Meanwhile, we observed the forming process of DNA contacts between different parts for plasmid DNA with increasing DMSO concentration. We suggest the initial mechanism of DNA denaturation as follows: DNA becomes more flexible due to the partial hydrogen bond braking in the presence of DMSO before local separation of the two complementary nucleotide chains.
PubMed: 36090395
DOI: 10.1039/d2ra02480b -
International Journal of Molecular... Feb 2023Amyloid fibril causes serious amyloidosis such as neurodegenerative diseases. The structure is composed of rigid β-sheet stacking conformation which makes it hard to... (Review)
Review
Amyloid fibril causes serious amyloidosis such as neurodegenerative diseases. The structure is composed of rigid β-sheet stacking conformation which makes it hard to disassemble the fibril state without denaturants. Infrared free electron laser (IR-FEL) is an intense picosecond pulsed laser that is oscillated through a linear accelerator, and the oscillation wavelengths are tunable from 3 μm to 100 μm. Many biological and organic compounds can be structurally altered by the mode-selective vibrational excitations due to the wavelength variability and the high-power oscillation energy (10-50 mJ/cm). We have found that several different kinds of amyloid fibrils in amino acid sequences were commonly disassembled by the irradiation tuned to amide I (6.1-6.2 μm) where the abundance of β-sheet decreased while that of α-helix increased by the vibrational excitation of amide bonds. In this review, we would like to introduce the IR-FEL oscillation system briefly and describe combination studies of experiments and molecular dynamics simulations on disassembling amyloid fibrils of a short peptide (GNNQQNY) from yeast prion and 11-residue peptide (NFLNCYVSGFH) from β2-microglobulin as representative models. Finally, possible applications of IR-FEL for amyloid research can be proposed as a future outlook.
Topics: Amyloid; Electrons; Peptides; Amides; Lasers
PubMed: 36835098
DOI: 10.3390/ijms24043686 -
European Journal of Medicinal Chemistry Dec 2021The heat shock response (HSR) is a highly conserved cellular pathway that is responsible for stress relief and the refolding of denatured proteins [1]. When a host cell... (Review)
Review
The heat shock response (HSR) is a highly conserved cellular pathway that is responsible for stress relief and the refolding of denatured proteins [1]. When a host cell is exposed to conditions such as heat shock, ischemia, or toxic substances, heat shock factor-1 (HSF-1), a transcription factor, activates the genes that encode for the heat shock proteins (Hsps), which are a family of proteins that work alongside other chaperones to relieve stress and refold proteins that have been denatured (Burdon, 1986) [2]. Along with the refolding of denatured proteins, Hsps facilitate the removal of misfolded proteins by escorting them to degradation pathways, thereby preventing the accumulation of misfolded proteins [3]. Research has indicated that many pathological conditions, such as diabetes, cancer, neuropathy, cardiovascular disease, and aging have a negative impact on HSR function and are commonly associated with misfolded protein aggregation [4,5]. Studies indicate an interplay between mitochondrial homeostasis and HSF-1 levels can impact stress resistance, proteostasis, and malignant cell growth, which further support the role of Hsps in pathological and metabolic functions [6]. On the other hand, Hsp activation by specific small molecules can induce the heat shock response, which can afford neuroprotection and other benefits [7]. This review will focus on the modulation of Hsps and the HSR as therapeutic options to treat these conditions.
Topics: Animals; Heat-Shock Proteins; Heat-Shock Response; Humans; Molecular Structure; Neuroprotective Agents; Small Molecule Libraries
PubMed: 34563965
DOI: 10.1016/j.ejmech.2021.113846 -
Cancers Dec 2021Recent advancements have tangibly changed the cancer treatment landscape. However, curative therapy for this dreadful disease remains an unmet need. Sonodynamic therapy... (Review)
Review
Recent advancements have tangibly changed the cancer treatment landscape. However, curative therapy for this dreadful disease remains an unmet need. Sonodynamic therapy (SDT) is a minimally invasive anti-cancer therapy involving a chemical sonosensitizer and focused ultrasound. A high-intensity focused ultrasound (HIFU) beam is used to destroy or denature targeted cancer tissues. Some SDTs are based on unfocused ultrasound (US). In some SDTs, HIFU is combined with a drug, known as a chemical sonosensitizer, to amplify the drug's ability to damage cancer cells preferentially. The mechanism by which US interferes with cancer cell function is further amplified by applying acoustic sensitizers. Combining multiple chemical sonosensitizers with US creates a substantial synergistic effect that could effectively disrupt tumorigenic growth, induce cell death, and elicit an immune response. Therefore, the minimally invasive SDT treatment is currently attracting attention. It can be combined with targeted therapy (double-targeting cancer therapy) and immunotherapy in the future and is expected to be a boon for treating previously incurable cancers. In this paper, we will consider the current state of this therapy and discuss parts of our research.
PubMed: 34944804
DOI: 10.3390/cancers13246184 -
Molecules (Basel, Switzerland) Jun 2022Although oligomeric proteins are predominant in cells, their folding is poorly studied at present. This work is focused on the denaturant- and mutation-induced...
Although oligomeric proteins are predominant in cells, their folding is poorly studied at present. This work is focused on the denaturant- and mutation-induced disassembly of the hexameric mutant Y55W of the Qβ host factor (Hfq) from mesophilic (). Using intrinsic tryptophan fluorescence, dynamic light scattering (DLS), and high-performance liquid chromatography (HPLC), we show that the dissociation of Hfq Y55W occurs either under the effect of GuHCl or during the pre-denaturing transition, when the protein concentration is decreased, with both events proceeding through the accumulation of stable intermediate states. With an extremely low pH of 1.4, a low ionic strength, and decreasing protein concentration, the accumulated trimers and dimers turn into monomers. Also, we report on the structural features of monomeric Hfq resulting from a triple mutation (D9A/V43R/Y55W) within the inter-subunit surface of the protein. This globular and rigidly packed monomer displays a high thermostability and an oligomer-like content of the secondary structure, although its urea resistance is much lower.
Topics: Circular Dichroism; Mutation; Protein Denaturation; Protein Folding; Protein Structure, Secondary; Pseudomonas aeruginosa; Thermodynamics; Tryptophan; Urea
PubMed: 35744948
DOI: 10.3390/molecules27123821 -
Neuroscience Letters Jan 2020Heat shock proteins (HSPs) are chaperones that catalyze the refolding of denatured proteins. In addition to their ability to prevent protein denaturation and... (Review)
Review
Heat shock proteins (HSPs) are chaperones that catalyze the refolding of denatured proteins. In addition to their ability to prevent protein denaturation and aggregation, the HSPs have also been shown to modulate many signaling pathways. Among HSPs, the inducible 70 kDa HSP (HSP70) has especially been shown to improve neurological outcome in experimental models of brain ischemia and injury. HSP70 can modulate various aspects of the programmed cell death pathways and inflammation. This review will focus on potential mechanisms of the neuroprotective effects of HSP70 in stroke and brain trauma models. We also comment on potential ways in which HSP70 could be translated into clinical therapies.
Topics: Animals; Apoptosis; Brain Injuries; Brain Ischemia; HSP70 Heat-Shock Proteins; Humans; Neuroprotection
PubMed: 31759081
DOI: 10.1016/j.neulet.2019.134642 -
Role of freezing-induced myofibrillar protein denaturation in the generation of thaw loss: A review.Meat Science Aug 2022Formation of thaw loss cannot generally be avoided when meat is frozen and then thawed. Explanations have mainly focused on the damage to muscle fibers resulting from... (Review)
Review
Formation of thaw loss cannot generally be avoided when meat is frozen and then thawed. Explanations have mainly focused on the damage to muscle fibers resulting from ice crystallization and the freezing-induced denaturation of myofibrillar proteins, the latter of which has, however, not received much research focus. This review discusses the relationship between myofibrillar protein denaturation and water-holding capacity of meat in freezing-thawing with the aim to improve the understanding the relative importance of protein denaturation in the formation of thaw loss. The contribution of decreased pH and high ionic strength in the unfrozen water in freezing is emphasized and we hypothesize that these two factors are causing protein denaturation and conformational changes within muscle fibers, and consequently loss of water-holding capacity. Slow freezing produces more thaw loss than fast freezing, and this is discussed here in relation to the impacts on myofibrillar protein denaturation induced by the freezing rate.
Topics: Freezing; Meat; Protein Denaturation; Proteins; Water
PubMed: 35533633
DOI: 10.1016/j.meatsci.2022.108841 -
Protein and Peptide Letters 2020Marine sessile organisms display a color palette that is the result of the expression of fluorescent and non-fluorescent proteins. Fluorescent proteins have uncovered...
BACKGROUND
Marine sessile organisms display a color palette that is the result of the expression of fluorescent and non-fluorescent proteins. Fluorescent proteins have uncovered transcriptional regulation, subcellular localization of proteins, and the fate of cells during development. Chromoproteins have received less attention until recent years as bioreporters. Here, we studied the properties of aeBlue, a a 25.91 kDa protein from the anemone Actinia equina.
OBJECTIVE
To assess the properties of aeBlue chromoprotein under different physicochemical conditions.
METHODS
In this article, during the purification of aeBlue we uncovered that it suffered a color shift when frozen. We studied the color shift by different temperature incubation and physicochemical conditions and light spectroscopy. To assess the possible structural changes in the protein, circular dichroism analysis, size exclusion chromatography and native PAGE was performed.
RESULTS
We uncover that aeBlue chromoprotein, when expressed from a synthetic construct in Escherichia coli, showed a temperature dependent color shift. Protein purified at 4 °C by metal affinity chromatography exhibited a pinkish color and shifts back at higher temperatures to its intense blue color. Circular dichroism analysis revealed that the structure in the pink form of the protein has reduced secondary structure at 4 °C, but at 35 °C and higher, the structure shifts to a native conformation and Far UV- vis CD spectra revealed the shift in an aromatic residue of the chromophore. Also, the chromophore retains its properties in a wide range of conditions (pH, denaturants, reducing and oxidants agents). Quaternary structure is also maintained as a tetrameric conformation as shown by native gel and size exclusion chromatography.
CONCLUSION
Our results suggest that the chromophore position in aeBlue is shifted from its native position rendering the pink color and the process to return it to its native blue conformation is temperature dependent.
Topics: Amino Acid Sequence; Animals; Cloning, Molecular; Color; Coloring Agents; Escherichia coli; Gene Expression; Hydrogen-Ion Concentration; Light; Luminescent Proteins; Models, Molecular; Oxidation-Reduction; Pigments, Biological; Protein Conformation; Protein Denaturation; Proteins; Sea Anemones; Spectrophotometry; Temperature
PubMed: 31385759
DOI: 10.2174/0929866526666190806145740 -
European Journal of Case Reports in... 2021Splenosis is a benign condition which results from the self-implantation of splenic tissue on intra or extraperitoneal surfaces, after splenic trauma or splenectomy....
UNLABELLED
Splenosis is a benign condition which results from the self-implantation of splenic tissue on intra or extraperitoneal surfaces, after splenic trauma or splenectomy. Patients are usually asymptomatic but may present with varied symptoms related to the implantation site. The diagnosis is a challenge because abdominal splenosis can mimic several diseases, including neoplasm. The gold standard examination for its diagnosis is scintigraphy with 99mTc-labelled heat-denatured erythrocyte. When splenosis is found in an asymptomatic patient, surgical removal is not indicated. A 57-year-old male patient presented with sporadic epigastric pain and a suspected mass in the recto-sigmoid transition. Abdominal ultrasound, CT and MRI identified this mass, its characteristics and location, but failed to distinguish its nature. However, given the patient's past history of splenectomy and because the mass showed a similar sign to that of the splenic parenchyma, a hypothesis of abdominal splenosis was raised, which was confirmed by scintigraphy with 99mTc-labelled heat-denatured erythrocyte. In this case, the diagnosis was obtained before the patient was subjected to more invasive procedures, which are associated with high morbidity, and, as in most cases, no targeted intervention was necessary.
LEARNING POINTS
Increasing numbers of cases of abdominal trauma will result in more frequent splenosis.Diagnosis is sometimes complex as splenosis mimics several diseases.The usual complementary imaging studies often fail to diagnose this entity so clinical suspicion is fundamental for correct diagnosis and treatment.
PubMed: 33585344
DOI: 10.12890/2021_002219