Role of water in Protein Aggregation and Amyloid Polymorphism

A variety of neurodegenerative diseases are associated with the formation of amyloid plaques. Our incomplete understanding of this process underscores the need to decipher the principles governing protein aggregation. Most experimental and simulation studies have been interpreted largely from the perspective of proteins: the role of solvent has been relatively overlooked. In this Account, we provide a perspective on how interactions with water affect folding landscapes of A$\beta$ monomers, A$\beta_{16-22}$ oligomer formation, and protofilament formation in a Sup35 peptide. Simulations show that the formation of aggregation-prone structures (N$^*$) similar to the structure in the fibril requires overcoming high desolvation barrier. The mechanism of protofilament formation in a polar Sup35 peptide fragment illustrates that water dramatically slows down self-assembly. Release of water trapped in the pores as water wires creates protofilament with a dry interface. Similarly, one of the main driving force for addition of a solvated monomer to a preformed fibril is the entropy gain of released water. We conclude by postulating that two-step model for protein crystallization must also hold for higher order amyloid structure formation starting from N$^*$. Multiple N$^*$ structures with varying water content results in a number of distinct water-laden polymorphic structures. In predominantly hydrophobic sequences, water accelerates fibril formation. In contrast, water-stabilized metastable intermediates dramatically slow down fibril growth rates in hydrophilic sequences.Comment: 27 pages, 4 figures; Accounts of Chemical Research, 201

Chloride (HCl ∕ Cl⁻) dominates inorganic aerosol formation from ammonia in the Indo-Gangetic Plain during winter: modeling and comparison with observations

The Winter Fog Experiment (WiFEX) was an intensive field campaign conducted at Indira Gandhi International Airport (IGIA) Delhi, India, in the Indo-Gangetic Plain (IGP) during the winter of 2017–2018. Here, we report the first comparison in South Asia of high-temporal-resolution simulation of ammonia (NH3) along with ammonium (NH4+) and total NHx (i.e., NH3+ NH4+) using the Weather Research and Forecasting model coupled with chemistry (WRF-Chem) and measurements made using the Monitor for AeRosols and Gases in Ambient Air (MARGA) at the WiFEX research site. In the present study, we incorporated the Model for Simulating Aerosol Interactions and Chemistry (MOSAIC) aerosol scheme into WRF-Chem. Despite simulated total NHx values and variability often agreeing well with the observations, the model frequently simulated higher NH3 and lower NH4+ concentrations than the observations. Under the winter conditions of high relative humidity (RH) in Delhi, hydrogen chloride (HCl) was found to promote the increase in the particle fraction of NH4+ (which accounted for 49.5 % of the resolved aerosol in equivalent units), with chloride (Cl−) (29.7 %) as the primary anion. By contrast, the absence of chloride (HCl / Cl−) chemistry in the standard WRF-Chem model results in the prediction of sulfate (SO42-) as the dominant inorganic aerosol anion. To understand the mismatch associated with the fraction of NHx in the particulate phase (NH4+ / NHx), we added HCl / Cl− to the model and evaluated the influence of its chemistry by conducting three sensitivity experiments using the model: no HCl, base case HCl (using a published waste burning inventory), and 3 × base HCl run. We found that 3 × base HCl increased the simulated average NH4+ by 13.1 µg m−3 and NHx by 9.8 µg m−3 concentration while reducing the average NH3 by 3.2 µg m−3, which is more in accord with the measurements. Thus HCl / Cl− chemistry in the model increases total NHx concentration, which was further demonstrated by reducing NH3 emissions by a factor of 3 (−3 × NH3_EMI) in the 3 × base HCl simulation. Reducing NH3 emissions in the 3 × base HCl simulation successfully addressed the discrepancy between measured and modeled total NHx. We conclude that modeling the fate of NH3 in Delhi requires a correct chemistry mechanism accounting for chloride dynamics with accurate inventories of both NH3 and HCl emissions.</p

Orally bioavailable anti-HBV dinucleotide acyloxyalkyl prodrugs

The acyloxyalkyl derivatives of a model anti-HBV dinucleotide were synthesized and evaluated as orally bioavailable prodrugs. Our studies have led to the identification of the first orally bioavailable dinucleotide prodrugs for further therapeutic development against the hepatitis B virus (HBV)