Molecular crowding effects on the biochemical properties of amyloid β-heme, Aβ-Cu and Aβ-heme-Cu complexes

Molecular crowding effect in Hantzch pyridine synthesis in polyethylene glycol aqueous solution

In a molecular crowding environment, the kinetics and thermodynamics differ from those in a diluted solution. Although the molecular crowding effect has been extensively investigated, its fundamental kinetics and thermodynamics remain unclear. In this study, we investigated the change in the rate constant (k) of the Hantzch pyridine reaction in a molecular crowding environment using polyethylene glycol (PEG). While the k value increased to a PEG concentration (CPEG) of 10 vol%, a decreasing trend was observed for CPEG > 20 vol%. This intriguing behavior was analyzed based on the increase in reactant activity due to volume exclusion and the decrease in water activity due to osmotic pressure. Volume exclusion and osmotic pressure had opposing effects on the reaction, which were positive for volume exclusion and negative for osmotic pressure. We found that k decreased when the negative effect of the osmotic pressure surpassed the volume exclusion effect.

Silicon-Carbon Dots-Loaded Mesoporous Silica Nanocomposites (mSiO2@SiCDs): An Efficient Dual Inhibitor of Cu2+-Mediated Oxidative Stress and Aβ Aggregation for Alzheimer's Disease

The redox-active metal ions, especially Cu2+, are highly correlated to Alzheimer's disease (AD) by causing metal ion-mediated oxidative stress and toxic metal-bound β-amyloid (Aβ) aggregates. Numerous pieces of evidence have revealed that the regulation of metal homeostasis could be an effective therapeutic strategy for AD. Herein, in virtue of the interaction of both amino-containing silane and ethylenediaminetetraacetic acid disodium salt for Cu2+, the silicon-carbon dots (SiCDs) are deliberately prepared using these two raw materials as the cocarbon source; meanwhile, to realize the local enrichment of SiCDs and further maximize the chelating ability to Cu2+, the SiCDs are feasibly loaded to the biocompatible mesoporous silica nanoparticles (mSiO2) with the interaction between residual silane groups on SiCDs and silanol groups of mSiO2. Thus-obtained nanocomposites (i.e., mSiO2@SiCDs) could serve as an efficient Cu2+ chelator with satisfactory metal selectivity and further modulate the enzymic activity of free Cu2+ and the Aβ42-Cu2+ complex to alleviate the pathological oxidative stress with an anti-inflammatory effect. Besides, mSiO2@SiCDs show an inspiring inhibitory effect on Cu2+-mediated Aβ aggregation and further protect the neural cells against the toxic Aβ42-Cu2+ complex. Moreover, the transgenic Caenorhabditis elegans CL2120 assay demonstrates the protective efficacy of mSiO2@SiCDs on Cu2+-mediated Aβ toxicity in vivo, indicating its potential for AD treatment.

Insights into In Vivo Environmental Effects on Quantitative Biochemistry in Single Cells

Biomacromolecules exist and function in a crowded and spatially confined intracellular milieu. Single-cell analysis has been an essential tool for deciphering the molecular mechanisms of cell biology and cellular heterogeneity. However, a sound understanding of in vivo environmental effects on single-cell quantification has not been well established. In this study, via cell mimicking with giant unilamellar vesicles and single-cell analysis by an approach called plasmonic immunosandwich assay (PISA) that we developed previously, we investigated the effects of two in vivo environmental factors, i.e., molecular crowding and spatial confinement, on quantitative biochemistry in the cytoplasm of single cells. We find that molecular crowding greatly affects the biomolecular interactions and immunorecognition-based detection while the effect of spatial confinement in cell-sized space is negligible. Without considering the effect of molecular crowding, the results by PISA were found to be apparently under-quantitated, being only 29.5-50.0% of those by the calibration curve considering the effect of molecular crowding. We further demonstrated that the use of a calibration curve established with standard solutions containing 20% (wt) polyethylene glycol 6000 can well offset the effect of intracellular crowding and thereby provide a simple but accurate calibration for the PISA measurement. Thus, this study not only sheds light on how intracellular environmental factors influence biomolecular interactions and immunorecognition-based single-cell quantification but also provides a simple but effective strategy to make the single-cell analysis more accurate.

Heme-Aβ in SDS micellar environment: Active site environment and reactivity

Alzheimer's disease (AD), the most common cause of dementia, is a progressive neurodegenerative disorder that causes brain cell death. Oxidative stress derived from the accumulation of redox cofactors like heme in amyloid plaques originating from amyloid β (Aβ) peptides has been implicated in the pathogenesis of AD. In the past our group has studied the interactions and reactivities of heme with soluble oligomeric and aggregated forms of Aβ. In this manuscript we report the interaction of heme with Aβ that remains membrane bound using membrane mimetic SDS (sodium dodecyl sulfate) micellar medium. Employing different spectroscopic techniques viz. circular dichroism (CD), absorption (UV-Vis), electron paramagnetic resonance (EPR) and resonance Raman (rR) we find that Aβ binds heme using one of its three His (preferentially His13) in SDS micellar medium. We also find that Arg5 is an essential distal residue responsible for higher peroxidase activity of heme bound Aβ in this membrane mimetic environment than free heme. This peroxidase activity exerted by even membrane bound heme-Aβ can potentially be more detrimental as the active site remains close to membranes and can hence oxidise the lipid bilayer of the neuronal cell, which can induce cell apoptosis. Thus, heme-Aβ in solution as well as in membrane-bound form are detrimental.

J-aggregation of 5, 10, 15, 20-tetraphenyl-21H, 23H-porphinetetrasulfonic acid in a molecular crowding environment simulated using dextran

In a molecular crowding environment, different thermodynamics is often observed in a dilute solution. One such example is the promotion of the formation of amyloids, which are causal agents of Alzheimer's disease. Although a considerable number of molecular crowding studies have been reported, its effect remains unclear. In this study, we investigated a J-aggregation of a porphyrin derivative, 5, 10, 15, 20-tetraphenyl-21H,23H-porphinetetrasulfonic acid (TPPS), in a molecular crowding environment simulated by dextran (Dex) in HClO₄, HCl, and NaCl solutions. The changes in the number of monomers in the J-aggregate (n) with the concentration of Dex (C_Dex) depended on the type of solution. No change in n was observed in the NaCl solution, which indicated that the Dex solution did not affect the J-aggregation because of the ionic strength effect. In the HCl solution, the aggregation behavior changed with the pH. Further, at a low pH, the electrostatic interactions promoted J-aggregation by the volume exclusion of Dex, while the aggregation was suppressed at a high pH owing to steric hindrance. A different aggregation mechanism, involving the hydrogen bonding between NH in the center of the TPPS macrocyclic frame and the SO₃H and ClO₄^- functional groups, was responsible for the J-aggregation in the HClO₄ solution. Moreover, the n value increased owing to the volume exclusion effect. We expect that this study will be useful for further elucidation of the molecular crowding effect.

DNA origami nanocalipers for pH sensing at the nanoscale

A DNA origami nanocaliper is employed as a shape-resolved nanomechanical device, with pH-responsive triplex DNA integrated into the two arms. The shape transition of the nanocaliper results in a subtle difference depending on the local pH that is visible via TEM imaging, demonstrating the potential of these nanocalipers to act as a universal platform for pH sensing at the nanoscale.

Large Amino Acid Mimicking Selenium-Doped Carbon Quantum Dots for Multi-Target Therapy of Alzheimer's Disease

Multi-target intervention and synergistic treatment are critical for the drug development of Alzheimer’s disease (AD) due to its complex and multifactional nature. Oxidative stress and amyloid β peptides (Aβ) accumulation have been recognized as therapeutic targets for AD. Herein, with ability to inhibit Aβ aggregation and the broad-spectrum antioxidant properties, the large amino acid mimicking selenium-doped carbon quantum dots (SeCQDs) are presented as novel nanoagents for multi-target therapy of AD. Compared with the precursor, selenocystine, SeCQDs which maintain the intrinsic properties of both selenium and carbon quantum dots (CQDs) possess good biocompatibility and a remarkable ROS-scavenging activity. Moreover, the functionalized α-carboxyl and amino groups on edge of SeCQDs can trigger multivalent interactions with Aβ, leading to the ability of SeCQDs to inhibit Aβ aggregation. In vivo study demonstrated that SeCQDs can significantly ameliorate the Aβ induced memory deficits, reduce Aβ accumulation and inhibit neuron degeneration in AD model rats. The versatility of functionalization and potential ability to cross the blood-brain barrier (BBB) make SeCQDs as prospective nanodrugs for treating AD.

Effect of Molecular Crowding on Complexation of Metal Ions and 8-Quinolinol-5-Sulfonic Acid

The effect of molecular crowding on macromolecular reactions has been revealed by many researchers. In this study, we investigate the complexation of metal ions (Zn, Co, and Cd) with 8-quinolinol-5-sulfonic acid as a model of small-molecular reactions in molecular crowding. The complexation constants for 1:1, 1:2, and total complexation in the presence of polyethylene glycol (PEG, a molecular crowding reagent) are evaluated based on the increase in the reactant activity by volume exclusion and the decrease in the water activity due to the change in osmotic pressure. All complexation constants are enhanced by increasing the concentration of PEG. Its mechanisms differ for 1:1, 1:2, and total complexation. The 1:1 complexation is promoted only by the influence of the water activity, while the reactant and water activities influence the increase in the 1:2 complexation constant. Increasing the molecular weight of PEG further increases the complexation constants, as dehydration of the complex is promoted by a higher hydration number of PEG. Because this study gives the fundamental knowledge for the protein-metal interaction, in which solvation is an important factor, in molecular crowding, it provides new insights into molecular crowding studies and should attract the attention of a broad spectrum of biochemistry researchers.

Current Strategies for Modulating Aβ Aggregation with Multifunctional Agents

Alzheimer's disease (AD), as the primary cause of dementia, has seriously affected millions of people worldwide and brought a very heavy financial and social burden. With the growth of population and aging, the situation will worsen unless efficacious drugs are found to reverse, stop, or even slow down disease progression. More and more evidence has demonstrated that amyloid-β (Aβ) aggregation is an upstream causative factor in AD pathogenesis and then triggers a slew of pathological events. Furthermore, the concentrated redox metal ions in the AD brain, especially Cu(II), can significantly exacerbate Aβ aggregation and contribute to the formation of neurotoxic reactive oxygen species (ROS). Therefore, the inhibition of Aβ aggregation and relief of amyloidosis-initiated neurotoxicity play a critical role in AD treatment. Until now, several methods have been proposed to modulate Aβ aggregation, such as developing aggregation inhibitors to interfere with Aβ assembly via noncovalent interactions, copper chelators to cut off metal-accelerated Aβ aggregation and concomitant cytotoxicity, photooxidation to reduce the hydrophobicity and aggregation tendency of Aβ, thermal dissociation to disrupt amyloid aggregates susceptible to temperature, degradation with artificial protease to fracture the Aβ peptide into small fragments, and the clearance of peripheral Aβ to bypass the obstruction of the BBB and reduce the Aβ burden.In this Account, we focus on our contributions to the development of Aβ-targeted multifunctional molecules and nanoparticles, emphasizing the diversified strategies and synergistic therapeutic effects. These therapeutic agents possess the following multifunctionalities: (1) compared with frequently used aggregation inhibitors restricted by intrinsically feeble and sensitive noncovalent interactions, multifunctional agents can efficiently block Aβ aggregation by exploiting two or more Aβ-specific inhibition strategies simultaneously; (2) apart from regulating Aβ aggregation, multipronged agents can also target and modulate other pathological factors in AD pathogenesis, such as increased oxidative stress, abnormal copper accumulation, and irreversible neuron loss; (3) multifunctional platforms with both diagnostic and therapeutic modalities through integrating in situ imaging, real-time diagnostics, a multitarget direction, stimuli-responsive drug release, and the blood-brain barrier (BBB) translocation features are instrumental in improving drug levels at trouble sites, diminishing off-target adverse reactions, evaluating therapeutic effects, and averting overtreatment.Given the fact that amyloid aggregation, local inflammation, and metal dyshomeostasis are universal biomarkers shared by various neurodegenerative disorders, this Account provides a perspective for the evolution of customized therapeutic agents with multiple reactivities for other neurodegenerative diseases. In addition, recent studies have indicated that Aβ aggregates can enter the nucleus and induce DNA damage and anomalous conformational transition. We also explore the influences of DNA on the biological effects of Aβ aggregates.

Peptide sequence mediated self-assembly of molybdenum blue nanowheel superstructures

The precise control over the formation of complex nanostructures, e.g. polyoxometalates (POMs), at the sub-nanoscale is challenging but critical if non-covalent architectures are to be designed. Combining biologically-evolved systems with inorganic nanostructures could lead to sequence-mediated assembly. Herein, we exploit oligopeptides as multidentate structure-directing ligands via metal-coordination and hydrogen bonded interactions to modulate the self-assembly of POM superstructures. Six oligopeptides (GH, AH, SH, G₂H, G₄H and G₅H) are incorporated into the cavities of Molybdenum Blue (MB) POM nanowheels. It is found that the helicity of the nanowheel can be readily switched (Δ to Λ) by simply altering the N-terminal amino acid on the peptide chain rather than their overall stereochemistry. We also reveal a delicate balance between the Mo-coordination and the hydrogen bonds found within the internal cavity of the inorganic nanowheels which results in the sequence mediated formation of two unprecedented asymmetrical nanowheel frameworks: {Mo₁₂₂Ce₅} and {Mo₁₂₆Ce₄}.

Peptide sequence can be used to control the self-assembly and structures of nanoscale molybdenum blue polyoxometalate (POM) wheel-shaped clusters.