Effects of applied surface-tension on membrane-assisted Aβ aggregation

Pore Formation by Amyloid-like Peptides: Effects of the Nonpolar-Polar Sequence Pattern

One of the mechanisms accounting for the toxicity of amyloid peptides in diseases like Alzheimer's and Parkinson's is the formation of pores on the plasma membrane of neurons. Here, we perform unbiased all-atom simulations of the full membrane damaging pathway, which includes adsorption, aggregation, and perforation of the lipid bilayer accounting for pore-like structures. Simulations are performed using four peptides made with the same amino acids. Differences in the nonpolar-polar sequence pattern of these peptides prompt them to adsorb into the membrane with the extended conformations oriented either parallel [peptide labeled F1, Ac-(FKFE)2-NH2], perpendicular (F4, Ac-FFFFKKEE-NH2), or with an intermediate orientation (F2, Ac-FFKKFFEE-NH2, and F3, Ac-FFFKFEKE-NH2) in regard to the membrane surface. At the water-lipid interface, only F1 fully self-assembles into β-sheets, and F2 peptides partially fold into an α-helical structure. The β-sheets of F1 emerge as electrostatic interactions attract neighboring peptides to intermediate distances where nonpolar side chains can interact within the dry core of the bilayer. This complex interplay between electrostatic and nonpolar interactions is not observed for the other peptides. Although β-sheets of F1 peptides are mostly parallel to the membrane, some of their edges penetrate deep inside the bilayer, dragging water molecules with them. This precedes pore formation, which starts with the flow of two water layers through the membrane that expand into a stable cylindrical pore delimited by polar faces of β-sheets spanning both leaflets of the bilayer.

Cholesterol imbalance and neurotransmission defects in neurodegeneration

The brain contains the highest concentration of cholesterol in the human body, which emphasizes the importance of cholesterol in brain physiology. Cholesterol is involved in neurogenesis and synaptogenesis, and age-related reductions in cholesterol levels can lead to synaptic loss and impaired synaptic plasticity, which potentially contribute to neurodegeneration. The maintenance of cholesterol homeostasis in the neuronal plasma membrane is essential for normal brain function, and imbalances in cholesterol distribution are associated with various neurodegenerative disorders, including Alzheimer's disease, Parkinson's disease, and Huntington's disease. This review aims to explore the molecular and pathological mechanisms by which cholesterol imbalance can lead to neurotransmission defects and neurodegeneration, focusing on four key mechanisms: (1) synaptic dysfunction, (2) alterations in membrane structure and protein clustering, (3) oligomers of amyloid beta (Aβ) protein, and (4) α-synuclein aggregation.

Modulation of Aβ 16-22 aggregation by glucose

The self-assembly of amyloid-beta (Aβ) peptides into fibrillar structures in the brain is a signature of Alzheimer's disease. Recent studies have reported correlations between Alzheimer's disease and type-2 diabetes. Structurally, hyperglycemia induces covalent protein crosslinkings by advanced glycation end products (AGE), which can affect the stability of Aβ oligomers. In this work, we leverage physics-based coarse-grained molecular simulations to probe alternate thermodynamic pathways that affect peptide aggregation propensities at varying concentrations of glucose molecules. Similar to previous experimental reports, our simulations show a glucose concentration-dependent increase in Aβ aggregation rates, without changes in the overall secondary structure content. We discovered that glucose molecules prefer partitioning onto the aggregate-water interface at a specific orientation, resulting in a loss of molecular rotational entropy. This effectively hastens the aggregation rates, as peptide self-assembly can reduce the available surface area for peptide-glucose interactions. This work introduces a new thermodynamic-driven pathway, beyond chemical cross-linking, that can modulate Aβ aggregation.

Aggregation, structure and water permeability of membrane-embedded helical Aβ oligomers

It is widely recognized that membranes can facilitate the aggregation of amyloid-β (Aβ) peptides, while Aβ can in turn cause membrane damage. Many studies focus on the peptide-membrane interactions of Aβ oligomers with β-rich structures. However, the exact aggregation and toxicity mechanism of the membrane-embedded helical Aβ oligomers remain ambiguous. Herein, the molecular dynamics simulations were performed on membrane-embedded helical Aβ42 peptides. Initiated by eight Aβ42 monomers embedded in a lipid bilayer, the monomers aggregate into oligomers with stable transmembrane helix structures. With the aggregation of peptides, the membrane perturbations caused by Aβ aggregates decrease. The molecular architectures of oligomers were characterized and a helix-rich octamer stabilized by an annular network of hydrogen bonds was observed. The oligomers demonstrate the capability to assist transmembrane water transport. Our study may provide new insights for the investigation of transmembrane Aβ oligomers.

Transferable and Polarizable Coarse Grained Model for Proteins─ProMPT

The application of classical molecular dynamics (MD) simulations at atomic resolution (fine-grained level, FG), to most biomolecular processes, remains limited because of the associated computational complexity of representing all the atoms. This problem is magnified in the presence of protein-based biomolecular systems that have a very large conformational space, and MD simulations with fine-grained resolution have slow dynamics to explore this space. Current transferable coarse grained (CG) force fields in literature are either limited to only peptides with the environment encoded in an implicit form or cannot capture transitions into secondary/tertiary peptide structures from a primary sequence of amino acids. In this work, we present a transferable CG force field with an explicit representation of the environment for accurate simulations with proteins. The force field consists of a set of pseudoatoms representing different chemical groups that can be joined/associated together to create different biomolecular systems. This preserves the transferability of the force field to multiple environments and simulation conditions. We have added electronic polarization that can respond to environmental heterogeneity/fluctuations and couple it to protein's structural transitions. The nonbonded interactions are parametrized with physics-based features such as solvation and partitioning free energies determined by thermodynamic calculations and matched with experiments and/or atomistic simulations. The bonded potentials are inferred from corresponding distributions in nonredundant protein structure databases. We present validations of the CG model with simulations of well-studied aqueous protein systems with specific protein fold types─Trp-cage, Trpzip4, villin, WW-domain, and β-α-β. We also explore the applications of the force field to study aqueous aggregation of Aβ 16-22 peptides.