TY  - JOUR
AB  - Amyloid-β (Aβ) and islet amyloid polypeptide (IAPP) are small peptides that have the potential to not only self-assemble but also cross-assemble and form cytotoxic amyloid aggregates. Recently, we experimentally investigated the nature of Aβ-IAPP coaggregation and its inhibition by small polyphenolic molecules. Notably, we found that epigallocatechin gallate (EGCG) had the ability to reduce heteroaggregate formation. However, the precise molecular mechanism behind the reduction of heteroaggregates remains unclear. In this study, the dimerization processes of Aβ40 and IAPP peptides with and without EGCG were characterized by the enhanced sampling technique. Our results showed that these amyloid peptides exhibited a tendency to form a stable heterodimer, which represented the first step toward coaggregation. Furthermore, we also found that the EGCG regulated the dimerization process. In the presence of EGCG, well-tempered metadynamics simulation indicated a notable shift in the bound state toward a greater center of mass (COM) distance. Additionally, the presence of EGCG led to a significant increase in the free energy barrier height (∼15kBT) along the COM distance, and we observed a transition state between the bound and unbound states. Our findings also unveiled that the EGCG formed a greater number of hydrogen bonds with Aβ40, effectively obstructing the dimer formation. In addition, we carried out microseconds of all-atom conventional molecular dynamics (cMD) simulations to investigate the formation of both hetero- and homo-oligomer states by these peptides. MD simulations illustrated that EGCG played a significant role in preventing oligomer formation by reducing the content of β-sheets in the peptide. Collectively, our results offered valuable insight into the mechanism of cross-amyloid aggregation between Aβ40 and IAPP and the inhibition effect of EGCG on the heteroaggregation process.
AU  - Srivastava, A.*
AU  - Al Adem, K.
AU  - Shanti, A.*
AU  - Lee, S.*
AU  - Abedrabbo, S.*
AU  - Homouz, D.*
C1  - 71250
C2  - 55957
CY  - 1155 16th St, Nw, Washington, Dc 20036 Usa
SP  - 30256-30269
TI  - Inhibition of the early-stage cross-amyloid aggregation of amyloid-β and IAPP via EGCG: Insights from molecular dynamics simulations.
JO  - ACS Omega
VL  - 9
IS  - 28
PB  - Amer Chemical Soc
PY  - 2024
SN  - 2470-1343
ER  - 

TY  - JOUR
AB  - Uncharacterized proteins have been underutilized as targets for the development of novel therapeutics for difficult-to-treat bacterial infections. To facilitate the exploration of these proteins, 2819 predicted, uncharacterized proteins (19.1% of the total) from reference strains of multidrug Acinetobacter baumannii, Klebsiella pneumoniae, and Pseudomonas aeruginosa species were organized using an unsupervised k-means machine learning algorithm. Classification using normalized values for protein length, pI, hydrophobicity, degree of conservation, structural disorder, and %AT of the coding gene rendered six natural clusters. Cluster proteins showed different trends regarding operon membership, expression, presence of unknown function domains, and interactomic relevance. Clusters 2, 4, and 5 were enriched with highly disordered proteins, nonworkable membrane proteins, and likely spurious proteins, respectively. Clusters 1, 3, and 6 showed closer distances to known antigens, antibiotic targets, and virulence factors. Up to 21.8% of proteins in these clusters were structurally covered by modeling, which allowed assessment of druggability and discontinuous B-cell epitopes. Five proteins (4 in Cluster 1) were potential druggable targets for antibiotherapy. Eighteen proteins (11 in Cluster 6) were strong B-cell and T-cell immunogen candidates for vaccine development. Conclusively, we provide a feature-based schema to fractionate the functional dark proteome of critical pathogens for fundamental and biomedical purposes.
AU  - Sicilia, C.*
AU  - Corral-Lugo, A.*
AU  - Smialowski, P.
AU  - McConnell, M.J.*
AU  - Martín-Galiano, A.J.*
C1  - 67036
C2  - 53407
SP  - 46131–46145
TI  - Unsupervised machine learning organization of the functional dark proteome of gram-negative "superbugs": Six protein clusters amenable for distinct scientific applications.
JO  - ACS Omega
VL  - 7
IS  - 50
PY  - 2022
SN  - 2470-1343
ER  - 

TY  - JOUR
AB  - Volatile and semivolatile organic compounds in ambient air and occupational settings are of great concern due to their associated adverse human health and environmental impacts. Novel graphene wool samplers have been developed and tested to overcome limitations of commercially available sorbents that can only be used once and typically require solvent extraction. Graphene wool (GW) was synthesized by non-catalytic chemical vapor deposition with optimized conditions, resulting in a novel fibrous graphene wool that is very easy to manage and less rigid than other forms of graphene, lending itself to a wide range of potential applications. Here, the air pollutant sampling capabilities of the GW were of interest. The optimal packing weight of GW inside a glass tube (length 178 mm, i.d. 4 mm, o.d. 6 mm) was investigated by the adsorption of vaporized alkane standards on the GW, using a condensation aerosol generator in a temperature-controlled chamber and subsequent detection using a flame ionization detector. The optimized GW packing density was found to be 0.19 mg mm-3 at a flow rate of 500 mL min-1, which provided a gas collection efficiency of >90% for octane, decane, and hexadecane. The humidity uptake of the sampler is less than 1% (m/m) for ambient humidities <70%. Breakthrough studies showed the favorable adsorption of polar molecules, which is attributed to the defective nature of the graphene and the inhomogeneous coating of the graphene layers on the quartz wool, suggesting that the polar versus non-polar uptake potential of the GW can be tuned by varying the graphene layering on the quartz wool substrate during synthesis. Oxidized domains at the irregular edges of the graphene layers, due to a broken, non-pristine sp2 carbon network, allow for adsorption of polar molecules. The GW was applied and used in a combustion sampling campaign where the samplers proved to be comparable to frequently used polydimethylsiloxane sorbents in terms of sampling and thermal desorption of non-polar semivolatile organic compounds. The total alkane concentrations detected after thermal desorption of GW and PDMS samplers were found to be 17.96 ± 13.27 and 18.30 ± 16.42 μg m-3, respectively; thus, the difference in the alkane sampling concentration between the two sorbent systems was negligible. GW provides a new, exciting possibility for the monitoring of organic air pollutants with numerous advantages, including high sampling efficiencies, simple and cost-effective synthesis of the thermally stable GW, solvent-free and environmentally friendly analysis, and, importantly, the reusability of samplers.
AU  - Geldenhuys, G.L.*
AU  - Mason, Y.*
AU  - Dragan, G.-C.
AU  - Zimmermann, R.
AU  - Forbes, P.*
C1  - 63176
C2  - 51368
SP  - 24765-24776
TI  - Novel graphene wool gas adsorbent for volatile and semivolatile organic compounds.
JO  - ACS Omega
VL  - 6
IS  - 38
PY  - 2021
SN  - 2470-1343
ER  -