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At least 19 recordsLinked to original sources
PubMed2025

Prediction and Evaluation of Protein Aggregation with Computational Methods.

Protein and peptide aggregation has recently become one of the most studied biomedical problems due to its central role in several neurodegenerative disorders and of biotechnological importance. Multiple in silico methods, databases, tools, and algorithms have been developed to predict aggregation of proteins and peptides to better understand fundamental mechanisms of various aggregation diseases. Here, we attempt to provide a brief overview of bioinformatic methods and tools to better understand molecular mechanisms of aggregation disorders. Furthermore, through a better understanding of protein aggregation mechanisms, it might be possible to design novel therapeutic agents to treat and hopefully prevent protein aggregation diseases.

Computational Biology↗
PubMed2026

Colorimetric gold nanosensors for monitoring protein aggregation: implications for Alzheimer's disease.

Alzheimer's disease (AD) is the leading cause of dementia worldwide. It remains a major public health challenge due to the lack of early diagnostic tools and effective disease-modifying therapies. Molecularly, AD is characterized by extracellular amyloid-β (Aβ) plaques and intracellular Tau tangles, as well as soluble oligomers that are likely the neurotoxic species. However, the transient and heterogeneous nature of these oligomers makes them difficult to detect using conventional biosensing approaches. Nanomaterial-based colorimetric biosensors have emerged as promising platforms for detecting protein aggregates and discovering aggregation inhibitors. Specifically, the localized surface plasmon resonance properties of metallic nanomaterials can enable rapid, label-free, and visually detectable colorimetric sensing of molecular interactions. These features can be leveraged to monitor protein aggregation processes in real time and achieve high-throughput screening of aggregation inhibitors, which may collectively enable early detection and timely intervention of AD progression. This Review Article presents the design and engineering of gold-nanomaterial-based colorimetric biosensors for monitoring protein aggregation and highlights the current challenges and emerging opportunities for applying these nanosensors to combat AD.

Journal Article↗
PubMed1978

Cross-linking of lipid bilayers by central nervous system myelin basic protein: aggregation of free and vesicle-bound protein.

Central nervous system myelin basic protein binds to the zwitterionic lipid, egg diacylphosphatidylcholine, over a wide range of pH and ionic strength. Lipid vesicles containing the protein have been observed to increase in size and to aggregate. The size increase is most marked at very low ionic strengths whereas aggregation is evident at ionic strengths from 0.001 to 0.35. The pH and ionic-strength dependence of this aggregation closely follows that of the self-association of the protein, suggesting that vesicle association is mediated by binding between polypeptides attached to different vesicles. Basic protein is monomeric at low pH but above pH 6 self-associates yielding primarily small oligomers (probably dimers) and minor amounts of higher species. It is envisaged that each protein molecule possesses two distinct binding sites, one capable of association with lipid bilayers and the second with another protein molecule. Basic protein is found predominantly on the intracellular surface of the myelin membrane. Given the ability of the protein to act as a bridge between lipid bilayer vesicles in vitro it is proposed that it may perform a similar function in vivo, serving to cross-link the inner surfaces of the oligodendroglial cell membrane. This protein function could lead to formation of the long cellular processes which encircle the nerve cell axon and could assist in stabilizing the highly ordered myelin structure which results.

Animals↗
PubMed2025

Benchmark for Quantitative Global and Redox Proteomics Analysis by Combining Protein-Aggregation Capture and Data Independent Acquisition.

Oxidative damage plays a critical role in various diseases including cardiovascular and neurological disorders. Thiol redox reactions, acting as oxidative stress sensors, influence protein structure and function. Redox proteomics, based on the differential alkylation of cysteine sites followed by mass spectrometry, enables the comprehensive analysis of thiol redox status in cells and tissues. However, these approaches require extensive sample manipulation and are not compatible with data-independent acquisition techniques. Here, we introduce PACREDOX, an innovative strategy based on protein aggregation capture (PAC), and demonstrate its compatibility with library-free DIA. Compared with traditional methods such as FASILOX, PACREDOX reduces preparation time and costs while maintaining thiol and proteome coverage. To enable library-free DIA, we corrected in silico spectral libraries in DIA-NN using experimental retention time data from methylthiolated-Cys peptides. PACREDOX with DIA was benchmarked against FASILOX in a myocardial infarction model, yielding the same biological insights, while enhancing peptide and protein coverage. Our results underscore the potential and efficiency of this methodology for studying oxidative damage. Overall, PACREDOX offers an automatable, high-throughput, and cost-effective strategy for redox proteomics.

Proteomics↗
PubMed2026

Influence of protein aggregates, extracellular vesicles, and lipoprotein fusion on ionizable lipid nanoparticles protein corona analysis.

Since 2018, ionizable lipid nanoparticles (LNPs) have revolutionized nucleic acid therapeutics. However, achieving potent extrahepatic delivery remains a formidable challenge, primarily due to rapid hepatic uptake driven by apolipoprotein adsorption. While analyzing the LNP protein corona is essential for engineering organ-specific tropism, these soft materials present unique analytical hurdles. Co-isolation of blood-borne contaminants, such as extracellular vesicles and lipoproteins, often masks the true corona composition. This perspective examines the critical need for refined proteomic strategies to distinguish genuine corona proteins from impurities. We propose tailored investigative approaches, suggesting the LNP protein corona significantly differs from the rigid shells observed on inorganic nanoparticles.

Nanoparticles↗
PubMed1979

Further investigation of the role of calcium in human lens protein aggregation.

High-molecular-weight (HMW) protein from human cataractous lenses, isolated by differential centrifugation, was deaggregated in 7M urea and then reaggregated in either the presence or absence of 10 mM CaCl2. Over 90% of the material reaggregated in the presence of calcium appears to have a size greater than 50 X 10(6) daltons. By contrast, only 20% to 25% of the material reaggregated in the absence of calcium has molecular weight greater than 50 X 10(6) daltons. Disulfide formation during reaggregation is unlikely in the latter experiment, since the addition of 50 mM mercaptoethanol caused no change in results. About 60% to 70% of the low-molecular-weight (LMW) protein fraction deaggregated in 7M urea buffer can be converted to HMW species in the presence of 10 mM CaCl2, when the deaggregating agent is removed. However, only 5% to 10% of this protein is converted to HMW species if the deaggregation step is eliminated. Experiments with 45 Ca indicate that whereas calcium is necessary for the formation of the HMW aggregates, only one calcium per approximately 5 X 10(5) daltons remains bound in the reaggregated material. The data suggest that although calcium may be required to induce aggregation to HMW species, it is not required to stabilize such macromolecules. SDS-polyacrylamide gel electrophoresis of the HMW species formed upon reaggregation of the dissociated HMW species with calcium indicates the presence of all the major polypeptide subunits of the original HMW species present in the lens; however, reaggregation in the absence of calcium yields HMW species lacking in the 9600 dalton component.

Calcium Chloride↗
PubMed1975

The effect of manipulation of reticuloendothelial system activity on glomerular deposition of aggregated protein and immune complexes in two different strains of mice.

Glomerular uptake of intravenously administered aggregated albumen or immune complexes in mice appears to be inversely related to the activity of the reticuloendothelial system (RES). Stimulation of RES activity diminishes the amount of material appearing in the glomerulus whereas RES blockade enhances glomerular uptake. The possible relevance of these observations to experimental models of immune complex disease is discussed.

Anaphylaxis↗
PubMed1977

Anaphylactoid reactions due to non-immune complex serum protein aggregates.

The infusion of aggregate-containing i.v. human gamma-globulin as well as human serum albumin can lead to severe anaphylactoid reactions with decrease in mean arterial pressure, increase in pulmonary artery pressure and decrease in cardiac output in unsensitized dogs, while the deaggregated solutions are well tolerated. During these anaphylactoid reactions, no significant changes in the serum complement activity of the dogs were observed. In clinical human serum albumin incompatibility, stimulation with albumin aggregates led to a high response in the lymphocyte culture, whereas deaggregated albumin had no stimulatory effect. By deaggregation of horse anti-human lymphocyte globulin prior to clinical administration, the compatibility of ALG therapy was improved.

Anaphylaxis↗
PubMed1977

Comparison of hydrophobic and strongly hydrophilic cleavable crosslinking reagents in intermolecular bond formation in aggregates of proteins or protein-RNA.

Most of the bifunctional reagents in protein chemistry possess a strongly hydrophobic backbone, derived from aliphatic or aromatic hydrocarbons. Even bifunctionals of more than 30 A in length of this sort form intramolecular bridges preferentially. In recent years, the intermolecular crosslinking of physiological protein aggregates has gained in importance. As shown in the crosslinking of hemoglobin with two sets of hydrophobic and strongly hydrophilic reagents, derived from azo dyes and tartaric acid, respectively, in this case it is not primarily the length of the bifunctional, but the hydrophilic structure that will enhance intermolecular crosslinking. Artificial dimers of native structure may be obtained. For the crosslinking of RNA to protein, we have synthesized a new reagent, 3-(2-bromo-3-oxobutane-1-sulphonyl)-propionic acid p-nitrophenyl ester. In a two step reaction, it is attached to adenine and cytosine moieties at pH 6 first, and to lysine side chains at pH 7,5. The reagent has been applied to the poly-A sequence of globin messenger RNA nucleoprotein.

Adenosine↗
PubMed1975

The effect of ADP, calcium and some inhibitors of platelet aggregation on protein phosphokinases from human blood platelets.

A protein phosphokinase (ATP: protein phosphotransferase EC 2.7.1.37) which is stimulated by 3',5'-cyclic adenosine monophosphate (cyclic AMP) has been partially purified from both the cytoplasmic and membrane fractions of human platelets. The kinetics of both enzymes preparations are similar in respect to cyclic AMP, ATP, ADP and AMP. 5-10-minus 7 M cyclic AMP stimulated both preparations by approximately 100%. Both ADP and AMP at a concentration of 5-10-minus 5 M inhibited protein phosphokinase activity of the soluble and membrane preparation by between 50% and 70%. The response of the two enzyme preparations to calcium differed. 10 mM Ca-2+ inhibited soluble protein phosphokinase activity approximately 80% both in the presence and absence of 5-10 minus 7 M cyclic AMP whereas the same concentrations of Ca-2+ inhibited the membrane-bound enzyme by approximately 60% in the presence of 5-10-minus 7 M cyclic AMP and 40% in the absence of cyclic AMP. This observation may be of importance in understanding the mechanism of platelet aggregation.

Adenosine↗
PubMed1976

Electron spin resonance analysis of irreversible changes induced by calcium perturbation of erythrocyte membranes.

Introduction of calcium during hemolysis of erythrocytes causes irreversible membrane changes, including protein aggregation. These changes have been investigated by incorporation of one protein and three fatty acid spin label probes into washed membranes from erythrocytes hemolyzed with a range of Ca2+ concentrations. Electron spin resonance spectra of the lipid probes were analyzed for changes in the order parameters, isotropic coupling constants and mean angular deviations of the lipid hydrocarbon chains. The results generally indicated an increased freedom of mobility of the probes with increased Ca2+ concentration during hemolysis, but the response of each probe showed a different concentration dependence. The maximal response was obtained with the I(5, 10) probe. Variations in the responses were interpreted to reflect different modes of protein-lipid or protein-probe interactions arising from Ca2+ -induced membrane protein alterations. Spectra from membranes treated with the protein spin label showed an increased ratio of immobilized to mobile label with increased Ca2+ concentrations at hemolysis. This is consistent with the membrane protein aggregation phenomena previously observed. It is suggested that the increased protein-protein interactions formed as a result of calcium treatment permit an increased lipid mobility in the membrane regions monitored by the fatty acid probes.

Calcium↗
PubMed1977

[Experimental analysis of the complement-binding activity of gamma-globulin].

It was experimentally demonstrated that the anticomplimentary characteristics of gamma-globulin perparations was associated with disturbances of the colloid condition of the serum system and the absence of any stabilizing action of albumin and other serum proteins. It is also expressed as a result of a high complement-binding activity of protein aggregates. The anticomplementary characteristics of the nonaggregated part of protein in commercial preparations of gamma-globulin could be depressed by the addition of albumin or fresh serum; as to the anticomplementary characteristics of protein aggregates -- it remains unchanged. An intermolecular electrostatic interaction exists between albumin and gamma-globulin; it prevents sorption of the complement on Fc-fragment of IgG, whose destruction leads to the manifestation of the gamma-globulin complement-binding activity.

Blood Proteins↗
PubMed1975

Effects of denaturants on the sweet-tasting protein monellin.

Effects of the denaturants urea and guanidine-HCl on the sweet-tasting protein monellin have been studied. The pH at which monellin is initially treated with denaturant is an important factor in retention of sweetness, but the pH maintained during subsequent removal of denaturant by dialysis has no effect on activity. Recovery of sweetness of denaturant-treated monellin is favored when denaturation occurs at acid pH. Monellin treated with either 6 M guanidine-HCl or 8 M urea at acid pH retains all of its sweetness following removal of denaturant, but urea treatment at neutral pH leads to some irreversible loss of sweetness. Monellin precipitates from solution under some conditions during removal of denaturant by dialysis, and the precipitated protein is no longer sweet. Precipitation is least under acid conditions. Aggregated protein was demonstrated by gel filtration chromatography. The single sulfhydryl group of monellin was not demonstrable in the precipitated protein, having apparently become oxidized during denaturation and formation of the aggregated protein. The data support the hypothesis that the tertiary structure is important in the ability of monellin to elicit a sweet sensation.

Guanidines↗
PubMedDate not supplied

[Radiation-induced aggregation of proteins: binding of amino acids to myoglobin (author's transl)].

When myoglobin is irradiated in the presence of amino acids, the most radiation-reactive species, like the aromatic and sulfur-containing amino acids, will bind preferentially to the protein. The radiation-induced binding is strongly dependent on the concentration of protein and amino acid. Subsequent to irradiation of myoglobin in the presence of radioactively labelled tryptophan followed by tryptic hydrolysis, only a single radioactive spot was detected on the fingerprint. The binding of amino acids is thus not randomly distributed over the protein molecule but occurs at specific reactive sites.

Amino Acids↗