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Advances in Colloid and Interface... Oct 2022Although the anionic surfactant sodium dodecyl sulfate, SDS, has been used for more than half a century as a versatile and efficient protein denaturant for protein... (Review)
Review
Although the anionic surfactant sodium dodecyl sulfate, SDS, has been used for more than half a century as a versatile and efficient protein denaturant for protein separation and size estimation, there is still controversy about its mode of interaction with proteins. The term "rod-like" structures for the complexes that form between SDS and protein, originally introduced by Tanford, is not sufficiently descriptive and does not distinguish between the two current vying models, namely protein-decorated micelles a.k.a. the core-shell model (in which denatured protein covers the surface of micelles) versus beads-on-a-string model (where unfolded proteins are surrounded by surfactant micelles). Thanks to a combination of structural, kinetic and computational work particularly within the last 5-10 years, it is now possible to rule decisively in favor of the core-shell model. This is supported unambiguously by a combination of calorimetric and small-angle X-ray scattering (SAXS) techniques and confirmed by increasingly sophisticated molecular dynamics simulations. Depending on the SDS:protein ratio and the protein molecular mass, the formed structures can range from multiple partly unfolded protein molecules surrounding a single shared micelle to a single polypeptide chain decorating multiple micelles. We also have much new insight into how this species forms. It is preceded by the binding of small numbers of SDS molecules which subsequently grow by accretion. Time-resolved SAXS analysis reveals an asymmetric attack by SDS micelles followed by distribution of the increasingly unfolded protein around the micelle. The compactness of the protein chain continues to evolve at higher SDS concentrations according to single-molecule studies, though the protein remains completely denatured on the tertiary structural level. SDS denaturation can be reversed by addition of nonionic surfactants that absorb SDS forming mixed micelles, leaving the protein free to refold. Refolding can occur in parallel tracks if only a fraction of the protein is initially stripped of SDS. SDS unfolding is nearly always reversible unless carried out at low pH, where charge neutralization can lead to superclusters of protein-surfactant complexes. With the general mechanism of SDS denaturation now firmly established, it largely remains to explore how other ionic surfactants (including biosurfactants) may diverge from this path.
Topics: Micelles; Proteins; Scattering, Small Angle; Sodium Dodecyl Sulfate; Surface-Active Agents; X-Ray Diffraction
PubMed: 36027673
DOI: 10.1016/j.cis.2022.102754 -
Drug Discovery Today Feb 2016Biologics exist in equilibrium between native, partially denatured, and denatured conformational states. The population of any of these states is dictated by their Gibbs... (Review)
Review
Biologics exist in equilibrium between native, partially denatured, and denatured conformational states. The population of any of these states is dictated by their Gibbs energy and can be altered by changes in physical and solution conditions. Some conformations have a tendency to self-associate and aggregate, an undesirable phenomenon in protein therapeutics. Conformational equilibrium and self-association are linked thermodynamic functions. Given that any associative reaction is concentration dependent, conformational stability studies performed at different protein concentrations can provide early clues to future aggregation problems. This analysis can be applied to the selection of protein variants or the identification of better formulation solutions. In this review, we discuss three different aggregation situations and their manifestation in the observed conformational equilibrium of a protein.
Topics: Biological Products; Protein Conformation; Protein Denaturation; Proteins; Thermodynamics
PubMed: 26608889
DOI: 10.1016/j.drudis.2015.11.007 -
Journal of the American Chemical Society May 2023Collagen provides mechanical and biological support for virtually all human tissues in the extracellular matrix (ECM). Its defining molecular structure, the... (Review)
Review
Collagen provides mechanical and biological support for virtually all human tissues in the extracellular matrix (ECM). Its defining molecular structure, the triple-helix, could be damaged and denatured in disease and injuries. To probe collagen damage, the concept of collagen hybridization has been proposed, revised, and validated through a series of investigations reported as early as 1973: a collagen-mimicking peptide strand may form a hybrid triple-helix with the denatured chains of natural collagen but not the intact triple-helical collagen proteins, enabling assessment of proteolytic degradation or mechanical disruption to collagen within a tissue-of-interest. Here we describe the concept and development of collagen hybridization, summarize the decades of chemical investigations on rules underlying the collagen triple-helix folding, and discuss the growing biomedical evidence on collagen denaturation as a previously overlooked ECM signature for an array of conditions involving pathological tissue remodeling and mechanical injuries. Finally, we propose a series of emerging questions regarding the chemical and biological nature of collagen denaturation and highlight the diagnostic and therapeutic opportunities from its targeting.
Topics: Humans; Collagen; Extracellular Matrix; Peptides; Peptide Hydrolases; Biology
PubMed: 37158802
DOI: 10.1021/jacs.3c00713 -
Pharmaceutics Nov 2022Maintaining the structure of protein and peptide drugs has become one of the most important goals of scientists in recent decades. Cold and thermal denaturation... (Review)
Review
Maintaining the structure of protein and peptide drugs has become one of the most important goals of scientists in recent decades. Cold and thermal denaturation conditions, lyophilization and freeze drying, different pH conditions, concentrations, ionic strength, environmental agitation, the interaction between the surface of liquid and air as well as liquid and solid, and even the architectural structure of storage containers are among the factors that affect the stability of these therapeutic biomacromolecules. The use of genetic engineering, side-directed mutagenesis, fusion strategies, solvent engineering, the addition of various preservatives, surfactants, and additives are some of the solutions to overcome these problems. This article will discuss the types of stress that lead to instabilities of different proteins used in pharmaceutics including regulatory proteins, antibodies, and antibody-drug conjugates, and then all the methods for fighting these stresses will be reviewed. New and existing analytical methods that are used to detect the instabilities, mainly changes in their primary and higher order structures, are briefly summarized.
PubMed: 36432723
DOI: 10.3390/pharmaceutics14112533 -
Frontiers in Molecular Biosciences 2022Human health depends on the correct folding of proteins, for misfolding and aggregation lead to diseases. An unfolded (denatured) protein can refold to its original...
Human health depends on the correct folding of proteins, for misfolding and aggregation lead to diseases. An unfolded (denatured) protein can refold to its original folded state. How does this occur is known as the protein folding problem. One of several related questions to this problem is that how much more stable is the folded state than the unfolded state. There are several measures of protein stability. In this article, protein stability is given a thermodynamic definition and is measured by Gibbs free energy change ( ) associated with the equilibrium, native (N) conformation ↔ denatured (D) conformation under the physiological condition usually taken as dilute buffer (or water) at 25 °C. We show that this thermodynamic quantity ( ), where subscript D represents transition between N and D states, and superscript 0 (zero) represents the fact that the transition occurs in the absence of denaturant, can be neither measured nor predicted under physiological conditions. However, can be measured in the presence of strong chemical denaturants such as guanidinium chloride and urea which are shown to destroy all noncovalent interactions responsible for maintaining the folded structure. A problem with this measurement is that the estimate of comes from the analysis of the plot of denaturant concentration, which requires a long extrapolation of values of , and all the three methods of extrapolation give three different values of for a protein. Thus, our confidence in the authentic value of is eroded. Another problem with this measurement of is that it is done on the pure protein sample in dilute buffer which is a very large extrapolation of the conditions, for the crowding effect on protein stability is ignored.
PubMed: 35992266
DOI: 10.3389/fmolb.2022.880358 -
Nature Communications Nov 2023The dense stroma of desmoplastic tumor limits nanotherapeutic penetration and hampers the antitumor immune response. Here, we report a denaturation-and-penetration...
The dense stroma of desmoplastic tumor limits nanotherapeutic penetration and hampers the antitumor immune response. Here, we report a denaturation-and-penetration strategy and the use of tin monosulfide nanoparticles (SnSNPs) as nano-sonosensitizers that can overcome the stromal barrier for the management of desmoplastic triple-negative breast cancer (TNBC). SnSNPs possess a narrow bandgap (1.18 eV), allowing for efficient electron (e)-hole (h) pair separation to generate reactive oxygen species under US activation. More importantly, SnSNPs display mild photothermal properties that can in situ denature tumor collagen and facilitate deep penetration into the tumor mass upon near-infrared irradiation. This approach significantly enhances sonodynamic therapy (SDT) by SnSNPs and boosts antitumor immunity. In mouse models of malignant TNBC and hepatocellular carcinoma (HCC), the combination of robust SDT and enhanced cytotoxic T lymphocyte infiltration achieves remarkable anti-tumor efficacy. This study presents an innovative approach to enhance SDT and antitumor immunity using the denaturation-and-penetration strategy, offering a potential combined sono-immunotherapy approach for the cancer nanomedicine field.
Topics: Humans; Animals; Mice; Ultrasonic Therapy; Carcinoma, Hepatocellular; Triple Negative Breast Neoplasms; Liver Neoplasms; Neoplasms; Reactive Oxygen Species; Nanoparticles; Cell Line, Tumor
PubMed: 37914681
DOI: 10.1038/s41467-023-42509-7 -
International Journal of Food Science 2021Heating milk for yoghurt preparation has a significant effect on the structural properties of yoghurt. Milk heated at elevated temperature causes denaturation of whey... (Review)
Review
Heating milk for yoghurt preparation has a significant effect on the structural properties of yoghurt. Milk heated at elevated temperature causes denaturation of whey protein, aggregation, and some case gelation. It is important to understand the mechanism involved in each state of stabilization for tailoring the final product. We review the formation of these complexes and their consequence on the physical, rheological, and microstructural properties of acid milk gels. To investigate the interactions between denatured whey protein and casein, the formation of covalent and noncovalent bonds, localization of the complexes, and their impact on ultimate gelation and final yoghurt texture are reviewed. The information regarding this fundamental mechanism will be beneficial to develop uniform quality yoghurt texture and potential interest of future research.
PubMed: 34604378
DOI: 10.1155/2021/5569917 -
Journal of Controlled Release :... Oct 2016As the most abundant protein in mammals and a major structural component in extracellular matrix, collagen holds a pivotal role in tissue development and maintaining the... (Review)
Review
As the most abundant protein in mammals and a major structural component in extracellular matrix, collagen holds a pivotal role in tissue development and maintaining the homeostasis of our body. Persistent disruption to the balance between collagen production and degradation can cause a variety of diseases, some of which can be fatal. Collagen remodeling can lead to either an overproduction of collagen which can cause excessive collagen accumulation in organs, common to fibrosis, or uncontrolled degradation of collagen seen in degenerative diseases such as arthritis. Therefore, the ability to monitor the state of collagen is crucial for determining the presence and progression of numerous diseases. This review discusses the implications of collagen remodeling and its detection methods with specific focus on targeting native collagens as well as denatured collagens. It aims to help researchers understand the pathobiology of collagen-related diseases and create novel collagen targeting therapeutics and imaging modalities for biomedical applications.
Topics: Collagen; Diagnostic Imaging; Drug Delivery Systems; Extracellular Matrix; Humans; Peptides; Protein Binding; Protein Denaturation
PubMed: 26773768
DOI: 10.1016/j.jconrel.2016.01.007 -
Journal of the Royal Society, Interface Oct 2018Although it is now relatively well understood how sequence defines and impacts global protein stability in specific structural contexts, the question of how sequence... (Review)
Review
Although it is now relatively well understood how sequence defines and impacts global protein stability in specific structural contexts, the question of how sequence modulates the configurational landscape of proteins remains to be defined. Protein configurational equilibria are generally characterized by using various chemical denaturants or by changing temperature or pH. Another thermodynamic parameter which is less often used in such studies is high hydrostatic pressure. This review discusses the basis for pressure effects on protein structure and stability, and describes how the unique mechanisms of pressure-induced unfolding can provide unique insights into protein conformational landscapes.
Topics: Animals; Pressure; Protein Denaturation; Protein Stability; Proteins; Thermodynamics
PubMed: 30282759
DOI: 10.1098/rsif.2018.0244