Insights into Allosteric Mechanisms of the Lung-Enriched p53 Mutants V157F and R158L

Lung cancer is a leading fatal malignancy in humans. p53 mutants exhibit not only loss of tumor suppressor capability but also oncogenic gain-of-function, contributing to lung cancer initiation, progression and therapeutic resistance. Research shows that p53 mutants V157F and R158L occur with high frequency in lung squamous cell carcinomas. Revealing their conformational dynamics is critical for developing novel lung therapies. Here, we used all-atom molecular dynamics (MD) simulations to investigate the effect of V157F and R158L substitutions on the structural properties of the p53 core domain (p53C). Compared to wild-type (WT) p53C, both V157F and R158L mutants display slightly lesser β-sheet structure, larger radius of gyration, larger volume and larger exposed surface area, showing aggregation-prone structural characteristics. The aggregation-prone fragments (residues 249–267 and 268–282) of two mutants are more exposed to water solution than that of WT p53C. V157F and R158L mutation sites can affect the conformation switch of loop 1 through long-range associations. Simulations also reveal that the local structure and conformation around the V157F and R158L mutation sites are in a dynamic equilibrium between the misfolded and properly folded conformations. These results provide molecular mechanistic insights into allosteric mechanisms of the lung-enriched p53 mutants.

The Interplay between Whey Protein Fibrils with Carbon Nanotubes or Carbon Nano-Onions

Whey protein isolate (WPI) fibrils were prepared using an acid hydrolysis induction process. Carbon nanotubes (CNTs) and carbon nano-onions (CNOs) were made via the catalytic chemical vapor deposition (CVD) of methane. WPI fibril-CNTs and WPI fibril-CNOs were prepared via hydrothermal synthesis at 80 °C. The composites were characterized by SEM, TEM, FTIR, XRD, Raman, and TG analyses. The interplay between WPI fibrils and CNTs and CNOs were studied. The WPI fibrils with CNTs and CNOs formed uniform gels and films. CNTs and CNOs were highly dispersed in the gels. Hydrogels of WPI fibrils with CNTs (or CNOs) could be new materials with applications in medicine or other fields. The CNTs and CNOs shortened the WPI fibrils, which might have important research value for curing fibrosis diseases such as Parkinson's and Alzheimer's diseases. The FTIR revealed that CNTs and CNOs both had interactions with WPI fibrils. The XRD analysis suggested that most of the CNTs were wrapped in WPI fibrils, while CNOs were partially wrapped. This helped to increase the biocompatibility and reduce the cytotoxicity of CNTs and CNOs. HR-TEM and Raman spectroscopy studies showed that the graphitization level of CNTs was higher than for CNOs. After hybridization with WPI fibrils, more defects were created in CNTs, but some original defects were dismissed in CNOs. The TG results indicated that a new phase of WPI fibril-CNTs or CNOs was formed.

Protein aggregation detection with fluorescent macromolecular and nanostructured probes: challenges and opportunities

Nanoprobes based on various nanomaterials, polymers or AIEgens are overcoming previous limitations for diagnosis and therapy of early-stage protein aggregation.

Clustering and Fibril Formation during GNNQQNY Aggregation: A Molecular Dynamics Study

The precise kinetic pathways of peptide clustering and fibril formation are not fully understood. Here we study the initial clustering kinetics and transient cluster morphologies during aggregation of the heptapeptide fragment GNNQQNY from the yeast prion protein Sup35. We use a mid-resolution coarse-grained molecular dynamics model of Bereau and Deserno to explore the aggregation pathways from the initial random distribution of free monomers to the formation of large clusters. By increasing the system size to 72 peptides we could follow directly the molecular events leading to the formation of stable fibril-like structures. To quantify those structures we developed a new cluster helicity parameter. We found that the formation of fibril-like structures is a cooperative processes that requires a critical number of monomers, M⋆≈25, in a cluster. The terminal tyrosine residue is the structural determinant in the formation of helical fibril-like structures. This work supports and quantifies the two-step aggregation model where the initially formed amorphous clusters grow and, when they are large enough, rearrange into mature twisted structures. However, in addition to the nucleated fibrillation, growing aggregates undergo further internal reorganization, which leads to more compact structures of large aggregates.

Anti-amyloid activities of three different types of water-soluble fullerene derivatives

Anti-amyloid activity, aggregation behaviour, cytotoxicity and acute toxicity were investigated for three water-soluble fullerene derivatives with different types of solubilizing addends. All investigated compounds showed a strong anti-amyloid effect in vitrocaused by interaction of the water-soluble fullerene derivatives with the Ab(1-42)-peptide and followed by destruction of the amyloid fibrils. Notably, all of the studied fullerene derivatives showed very low cytotoxicity and low acute toxicity in mice (most promising compound 3 was more than four times less toxic than aspirin). Strong anti-amyloid effect of the fullerene derivatives together with low toxicity reveals high potential of these compounds as drug candidates for treatment of neurodegenerative diseases.

Aggregation kinetics of short peptides: All-atom and coarse-grained molecular dynamics study

Peptides can aggregate into ordered structures with different morphologies. The aggregation mechanism and evolving structures are the subject of intense research. In this paper we have used molecular dynamics to examine the sequence-dependence of aggregation kinetics for three short peptides: octaalanine (Ala8), octaasparagine (Asn8), and the heptapeptide GNNQQNY (abbreviated as GNN). First, we compared the aggregation of 20 randomly distributed peptides using the coarse-grained MARTINI force field and the atomistic OPLS-AA force field. We found that the MARTINI and OPLS-AA aggregation kinetics are similar for Ala8, Asn8, and GNN. Second, we used the MARTINI force field to study the early stages of aggregation kinetics for a larger system with 72 peptides. In the initial stage of aggregation small clusters grow by monomer addition. In the second stage, when the free monomers are depleted, the dominant cluster growth path is cluster-cluster coalescence. We quantified the aggregation kinetics in terms of rate equations. Our study shows that the initial aggregation kinetics are similar for Ala8, Asn8, and GNN but the molecular details can be different, especially for MARTINI Ala8. We hypothesize that peptide aggregation proceed in two steps. In the first step amorphous aggregates are formed, and then, in the second step, they reorganize into ordered structures. We conclude that sequence-specific differences show up in the second step of aggregation.

Norepinephrine Inhibits Alzheimer's Amyloid-β Peptide Aggregation and Destabilizes Amyloid-β Protofibrils: A Molecular Dynamics Simulation Study

The abnormal self-assembly of amyloid-β (Aβ) peptides into toxic fibrillar aggregates is associated with the pathogenesis of Alzheimer's disease (AD). The inhibition of β-sheet-rich oligomer formation is considered as the primary therapeutic strategy for AD. Previous experimental studies reported that norepinephrine (NE), one of the neurotransmitters, is able to inhibit Aβ aggregation and disaggregate the preformed fibrils. Moreover, exercise can markedly increase the level of NE. However, the underlying inhibitory and disruptive mechanisms remain elusive. In this work, we performed extensive replica-exchange molecular dynamic (REMD) simulations to investigate the conformational ensemble of Aβ_1-42 dimer with and without NE molecules. Our results show that without NE molecules, Aβ_1-42 dimer transiently adopts a β-hairpin-containing structure, and the β-strand regions of this β-hairpin (residues 15QKLVFFA21 and 33GLMVGGVV40) strongly resemble those of the Aβ fibril structure (residues 15QKLVFFA21 and 30AIIGLMVG37) reported in an electron paramagnetic resonance spectroscopy study. NE molecules greatly reduce the interpeptide β-sheet content and suppress the formation of the above-mentioned β-hairpin, leading to a more disordered coil-rich Aβ dimer. Five dominant binding sites are identified, and the central hydrophobic core 16KLVFFA21 site and C-terminal 31IIGLMV36 hydrophobic site are the two most favorable ones. Our data reveal that hydrophobic, aromatic stacking, hydrogen-bonding and cation-π interactions synergistically contribute to the binding of NE molecules to Aβ peptides. MD simulations of Aβ_1-42 protofibril show that NE molecules destabilize Aβ protofibril by forming H-bonds with residues D1, A2, D23, and A42. This work reveals the molecular mechanism by which NE molecules inhibit Aβ_1-42 aggregation and disaggregate Aβ protofibrils, providing valuable information for developing new drug candidates and exercise therapy against AD.

Fullerene-based delivery systems

With the development of new drugs, there have been many attempts to explore innovative delivery routes. Targeted delivery systems are a desired solution designed to overcome the deficiency of routine methods. To transform this idea into reality, a wide range of nanoparticles has been proposed and studied. These nanoparticles should interact well with biological environments and pass through cell membranes to deliver therapeutic molecules. One of the pioneer classes of carbon-based nanoparticles for targeted delivery is the fullerenes. Fullerenes have a unique structure and possess suitable properties for interaction with the cellular environment. This short review concentrates on newly developed fullerene derivatives and their potential as advanced delivery systems for pharmaceutical applications.

The Inhibitory Effect of Hydroxylated Carbon Nanotubes on the Aggregation of Human Islet Amyloid Polypeptide Revealed by a Combined Computational and Experimental Study

Fibrillar deposits formed by the aggregation of the human islet amyloid polypeptide (hIAPP) are the major pathological hallmark of type 2 diabetes mellitus (T2DM). Inhibiting the aggregation of hIAPP is considered the primary therapeutic strategy for the treatment of T2DM. Hydroxylated carbon nanoparticles have received great attention in impeding amyloid protein fibrillation owing to their reduced cytotoxicity compared to the pristine ones. In this study, we investigated the influence of hydroxylated single-walled carbon nanotubes (SWCNT-OHs) on the first step of hIAPP aggregation: dimerization by performing explicit solvent replica exchange molecular dynamics (REMD) simulations. Extensive REMD simulations demonstrate that SWCNT-OHs can dramatically inhibit interpeptide β-sheet formation and completely suppress the previously reported β-hairpin amyloidogenic precursor of hIAPP. On the basis of our simulation results, we proposed that SWCNT-OH can hinder hIAPP fibrillation. This was further confirmed by our systematic turbidity measurements, thioflavin T fluorescence, circular dichroism (CD), transmission electron microscope (TEM), and atomic force microscopy (AFM) experiments. Detailed analyses of hIAPP-SWCNT-OH interactions reveal that hydrogen bonding, van der Waals, and π-stacking interactions between hIAPP and SWCNT-OH significantly weaken the inter- and intrapeptide interactions that are crucial for β-sheet formation. Our collective computational and experimental data reveal not only the inhibitory effect but also the inhibitory mechanism of SWCNT-OH against hIAPP aggregation, thus providing new clues for the development of future drug candidates against T2DM.