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Chembiochem : a European Journal of... Aug 2023This review aims to analyse the role of solution nuclear magnetic resonance spectroscopy in pressure-induced in vitro studies of protein unfolding. Although this... (Review)
Review
This review aims to analyse the role of solution nuclear magnetic resonance spectroscopy in pressure-induced in vitro studies of protein unfolding. Although this transition has been neglected for many years because of technical difficulties, it provides important information about the forces that keep protein structure together. We first analyse what pressure unfolding is, then provide a critical overview of how NMR spectroscopy has contributed to the field and evaluate the observables used in these studies. Finally, we discuss the commonalities and differences between pressure-, cold- and heat-induced unfolding. We conclude that, despite specific peculiarities, in both cold and pressure denaturation the important contribution of the state of hydration of nonpolar side chains is a major factor that determines the pressure dependence of the conformational stability of proteins.
Topics: Protein Denaturation; Proteins; Magnetic Resonance Spectroscopy; Protein Unfolding; Protein Conformation; Thermodynamics; Protein Folding; Cold Temperature
PubMed: 37154795
DOI: 10.1002/cbic.202300164 -
International Journal of Molecular... Feb 2024Proteins are large biomolecules with a specific structure that is composed of one or more long amino acid chains. Correct protein structures are directly linked to their... (Review)
Review
Proteins are large biomolecules with a specific structure that is composed of one or more long amino acid chains. Correct protein structures are directly linked to their correct function, and many environmental factors can have either positive or negative effects on this structure. Thus, there is a clear need for methods enabling the study of proteins, their correct folding, and components affecting protein stability. There is a significant number of label-free methods to study protein stability. In this review, we provide a general overview of these methods, but the main focus is on fluorescence-based low-instrument and -expertise-demand techniques. Different aspects related to thermal shift assays (TSAs), also called differential scanning fluorimetry (DSF) or ThermoFluor, are introduced and compared to isothermal chemical denaturation (ICD). Finally, we discuss the challenges and comparative aspects related to these methods, as well as future opportunities and assay development directions.
Topics: Protein Stability; Proteins; Amino Acids; Fluorometry; Biological Assay; Protein Denaturation
PubMed: 38339045
DOI: 10.3390/ijms25031764 -
Expert Reviews in Molecular Medicine Apr 2024Target deconvolution can help understand how compounds exert therapeutic effects and can accelerate drug discovery by helping optimise safety and efficacy, revealing... (Review)
Review
Target deconvolution can help understand how compounds exert therapeutic effects and can accelerate drug discovery by helping optimise safety and efficacy, revealing mechanisms of action, anticipate off-target effects and identifying opportunities for therapeutic expansion. Chemoproteomics, a combination of chemical biology with mass spectrometry has transformed target deconvolution. This review discusses modification-free chemoproteomic approaches that leverage the change in protein thermodynamics induced by small molecule ligand binding. Unlike modification-based methods relying on enriching specific protein targets, these approaches offer proteome-wide evaluations, driven by advancements in mass spectrometry sensitivity, increasing proteome coverage and quantitation methods. Advances in methods based on denaturation/precipitation by thermal or chemical denaturation, or by protease degradation are evaluated, emphasising the evolving landscape of chemoproteomics and its potential impact on future drug-development strategies.
Topics: Humans; Proteome; Drug Discovery; Mass Spectrometry; Drug Development
PubMed: 38604802
DOI: 10.1017/erm.2024.6 -
RSC Advances Oct 2023The entry of micro- and nanoplastics (MNPs) into the human body is inevitable. They enter blood circulation through ingestion, inhalation, and dermal contact by crossing... (Review)
Review
The entry of micro- and nanoplastics (MNPs) into the human body is inevitable. They enter blood circulation through ingestion, inhalation, and dermal contact by crossing the gut-lung-skin barrier (the epithelium of the digestive tract, the respiratory tract, and the cutaneous layer). There are many reports on their toxicities to organs and tissues. This paper presents the first thorough assessment of MNP-driven bloodstream toxicity and the mechanism of toxicity from the viewpoint of both MNP and environmental co-pollutant complexes. Toxic impacts include plasma protein denaturation, hemolysis, reduced immunity, thrombosis, blood coagulation, and vascular endothelial damage, among others, which can lead to life-threatening diseases. Protein corona formation, oxidative stress, cytokine alterations, inflammation, and cyto- and genotoxicity are the key mechanisms involved in toxicity. MNPs change the secondary structure of plasma proteins, thereby preventing their transport functions (for nutrients, drugs, oxygen, ). MNPs inhibit erythropoiesis by influencing hematopoietic stem cell proliferation and differentiation. They cause red blood cell and platelet aggregation, as well as increased adherence to endothelial cells, which can lead to thrombosis and cardiovascular disease. White blood cells and immune cells phagocytose MNPs, provoking inflammation. However, research gaps still exist, including gaps regarding the combined toxicity of MNPs and co-pollutants, toxicological studies in human models, advanced methodologies for toxicity analysis, bioaccumulation studies, inflammation and immunological responses, dose-response relationships of MNPs, and the effect of different physiochemical characteristics of MNPs. Furthermore, most studies have analyzed toxicity using prepared MNPs; hence, studies must be undertaken using true-to-life MNPs to determine the real-world scenario. Additionally, nanoplastics may further degrade into monomers, whose toxic effects have not yet been explored. The research gaps highlighted in this review will inspire future studies on the toxicity of MNPs in the vascular/circulatory systems utilizing models to enable more reliable health risk assessment.
PubMed: 37901269
DOI: 10.1039/d3ra05620a -
Current Opinion in Structural Biology Jun 2024Specimen preparation is a critical but challenging step in high-resolution cryogenic electron microscopy (cryo-EM) structural analysis of macromolecules. In the past... (Review)
Review
Specimen preparation is a critical but challenging step in high-resolution cryogenic electron microscopy (cryo-EM) structural analysis of macromolecules. In the past decade, graphene has gained much recognition as the supporting substrate to optimize cryo-EM specimen preparation. It improves macromolecule embedding in ice, reduces beam-induced motion, while imposing negligible background noise. Various types of graphene-coated cryo-EM grids were implemented to improve the robustness and efficiency of specimen preparation. Graphene functionalization by different means has been proved specifically useful in addressing challenges related to the air-water interface (AWI), such as preferential orientation and sample denaturation. Graphene sandwich specimen preparation sets a new direction to explore in cryo-EM analysis of biological specimens. In this review, we discuss the current challenges and future prospects of graphene application in cryo-EM analysis of macromolecules.
Topics: Cryoelectron Microscopy; Graphite; Macromolecular Substances; Specimen Handling
PubMed: 38688075
DOI: 10.1016/j.sbi.2024.102823 -
Journal of Artificial Organs : the... Jun 2024Excessive albumin losses during HC (haemocatharsis) are considered a potential cause of hypoalbuminemia-a key risk factor for mortality. This review on total albumin... (Review)
Review
Excessive albumin losses during HC (haemocatharsis) are considered a potential cause of hypoalbuminemia-a key risk factor for mortality. This review on total albumin losses considers albumin "leaking" into the dialysate and losses due to protein/membrane interactions (i.e. adsorption, "secondary membrane formation" and denaturation). The former are fairly easy to determine, usually varying at the level of ~ 2 g to ~ 7 g albumin loss per session. Such values, commonly accepted as representative of the total albumin losses, are often quoted as limits/standards of permissible albumin loss per session. On albumin mass lost due to adsorption/deposition, which is the result of complicated interactions and rather difficult to determine, scant in vivo data exist and there is great uncertainty and confusion regarding their magnitude; this is possibly responsible for neglecting their contribution to the total losses at present. Yet, many relevant in vitro studies suggest that losses of albumin due to protein/membrane interactions are likely comparable to (or even greater than) those due to leaking, particularly in the currently favoured high-convection HDF (haemodiafiltration) treatment. Therefore, it is emphasised that top research priority should be given to resolve these issues, primarily by developing appropriate/facile in vivo test-methods and related analytical techniques.
Topics: Humans; Dialysis Solutions; Hemodiafiltration; Hypoalbuminemia; Renal Dialysis; Serum Albumin
PubMed: 38238597
DOI: 10.1007/s10047-023-01430-y -
Acta Biochimica Polonica Nov 2023Diabetes mellitus is one of the important independent risk factors for the development of neurological disorders such as ischemic stroke, transient ischemic attacks,... (Review)
Review
Diabetes mellitus is one of the important independent risk factors for the development of neurological disorders such as ischemic stroke, transient ischemic attacks, vascular dementia and neurodegenerative processes. Hyperglycemia plays a crucial role as a trigger in the pathogenesis of these disorders. In this review, we summarize the existing data on the molecular mechanisms of diabetic encephalopathy development, consider the features of oxidative and nitrosative stresses, changes in the thiol-disulfide system, as well as mitochondrial and endothelial dysfunction in diabetes. We focus on the role of HSP 70 in cellular responses in diabetic encephalopathy. HSP70 protein is an important component of the endogenous system of neuroprotection. It acts as an intracellular chaperone, providing the folding, retention, and transport of synthesized proteins, as well as their degradation under both normoxic and stress-induced denaturation conditions. HSP70 can be considered a molecular marker and a promising therapeutic target in the treatment of diabetes mellitus.
Topics: Humans; Oxidative Stress; Diabetes Mellitus; Hyperglycemia; Oxidation-Reduction
PubMed: 37991083
DOI: 10.18388/abp.2020_6953 -
Scientific Reports Nov 2023Thermal shift assay (TSA) with altered temperature has been the most widely used method for monitoring protein stability for drug research. However, there is a pressing...
Thermal shift assay (TSA) with altered temperature has been the most widely used method for monitoring protein stability for drug research. However, there is a pressing need for isothermal techniques as alternatives. This urgent demand arises from the limitations of TSA, which can sometimes provide misleading ranking of protein stability and fail to accurately reflect protein stability under physiological conditions. Although differential scanning fluorimetry has significantly improved throughput in comparison to differential scanning calorimetry and differential static light scattering throughput, all these methods exhibit moderate sensitivity. In contrast, current isothermal chemical denaturation (ICD) techniques may not offer the same throughput capabilities as TSA, but it provides more precise information about protein stability and interactions. Unfortunately, ICD also suffers from limited sensitivity, typically in micromolar range. We have developed a novel method to overcome these challenges, namely throughput and sensitivity. The novel Förster Resonance Energy Transfer (FRET)-Probe as an external probe is highly applicable to isothermal protein stability monitoring but also to conventional TSA. We have investigated ICD for multiple proteins with focus on KRAS with covalent inhibitors and three chemical denaturants performed at nanomolar protein concentration. Data showed corresponding inhibitor-induced stabilization of KRAS to those reported by nucleotide exchange assay.
Topics: Proto-Oncogene Proteins p21(ras); Protein Stability; Fluorometry; Calorimetry, Differential Scanning; Proteins; Protein Denaturation
PubMed: 37973851
DOI: 10.1038/s41598-023-46720-w -
Methods in Molecular Biology (Clifton,... 2024Label-retention expansion microscopy (LR-ExM) is a sample preparation technique, which embeds the cells or tissues in a swellable hydrogel and expands the sample so that...
Label-retention expansion microscopy (LR-ExM) is a sample preparation technique, which embeds the cells or tissues in a swellable hydrogel and expands the sample so that one can achieve a high resolution with any conventional fluorescence microscopes. Fluorescence loss during polymerization and protein denaturation have been a major limitation of standard expansion microscopy. To minimize fluorescence loss, LR-ExM uses trifunctional anchors, which can survive from polymerization and denaturation, and then introduce fluorophores after expansion. By using LR-ExM, one can study the structure of primary cilia at molecular-scale resolution with a much higher signal-to-noise ratio, compared with previously introduced expansion microscopy methods. In this chapter, we describe a detailed procedure showing how LR-ExM is used to study ciliary proteins.
Topics: Microscopy, Fluorescence; Proteins; Hydrogels
PubMed: 37856018
DOI: 10.1007/978-1-0716-3507-0_4 -
Journal of Molecular Biology Oct 2023The study of protein folding plays a crucial role in improving our understanding of protein function and of the relationship between genetics and phenotypes. In...
The study of protein folding plays a crucial role in improving our understanding of protein function and of the relationship between genetics and phenotypes. In particular, understanding the thermodynamics and kinetics of the folding process is important for uncovering the mechanisms behind human disorders caused by protein misfolding. To address this issue, it is essential to collect and curate experimental kinetic and thermodynamic data on protein folding. K-Pro is a new database designed for collecting and storing experimental kinetic data on monomeric proteins, with a two-state folding mechanism. With 1,529 records from 62 proteins corresponding to 65 structures, K-Pro contains various kinetic parameters such as the logarithm of the folding and unfolding rates, Tanford's β and the ϕ values. When available, the database also includes thermodynamic parameters associated with the kinetic data. K-Pro features a user-friendly interface that allows browsing and downloading kinetic data of interest. The graphical interface provides a visual representation of the protein and mutants, and it is cross-linked to key databases such as PDB, UniProt, and PubMed. K-Pro is open and freely accessible through https://folding.biofold.org/k-pro and supports the latest versions of popular browsers.
Topics: Humans; Databases, Protein; Kinetics; Protein Denaturation; Protein Folding; Proteins; Thermodynamics; Mutant Proteins
PubMed: 37625584
DOI: 10.1016/j.jmb.2023.168245