Thermostable D-amino acid decarboxylases derived from Thermotoga maritima diaminopimelate decarboxylase

Diaminopimelate decarboxylases (DAPDCs) are highly selective enzymes that catalyze the common final step in different lysine biosynthetic pathways, i.e. the conversion of meso-diaminopimelate (DAP) to L-lysine. We examined the modification of the substrate specificity of the thermostable decarboxylase from Thermotoga maritima with the aim to introduce activity with 2-aminopimelic acid (2-APA) since its decarboxylation leads to 6-aminocaproic acid (6-ACA), a building block for the synthesis of nylon-6. Structure-based mutagenesis of the distal carboxylate binding site resulted in a set of enzyme variants with new activities toward different D-amino acids. One of the mutants (E315T) had lost most of its activity toward DAP and primarily acted as a 2-APA decarboxylase. We next used computational modeling to explain the observed shift in catalytic activities of the mutants. The results suggest that predictive computational protocols can support the redesign of the catalytic properties of this class of decarboxylating PLP-dependent enzymes

In Silico Study of Full-Length Amyloid β 1-42 Tri- and Penta-Oligomers in Solution

Amyloid oligomers are considered to play causal roles in the pathogenesis of amyloid-related degenerative diseases including Alzheimer’s disease. Using MD simulation techniques, we explored the contributions of the different structural elements of trimeric and pentameric full-length Aβ1-42 aggregates in solution to their stability and conformational dynamics. We found that our models are stable at a temperature of 310 K, and converge toward an interdigitated side-chain packing for intermolecular contacts within the two β-sheet regions of the aggregates: β1 (residues 18-26) and β2 (residues 31-42). MD simulations reveal that the β-strand twist is a characteristic element of Aβ-aggregates, permitting a compact, interdigitated packing of side chains from neighboring β-sheets. The β2 portion formed a tightly organized β-helix, whereas the β1 portion did not show such a firm structural organization, although it maintained its β-sheet conformation. Our simulations indicate that the hydrophobic core comprising the β2 portion of the aggregate is a crucial stabilizing element in the Aβ aggregation process. On the basis of these structure-stability findings, the β2 portion emerges as an optimal target for further antiamyloid drug design.

In Silico Study of Full-Length Amyloid β 1-42 Tri- and Penta-Oligomers in Solution

Amyloid oligomers are considered to play causal roles in the pathogenesis of amyloid-related degenerative diseases including Alzheimer's disease. Using MD simulation techniques, we explored the contributions of the different structural elements of trimeric and pentameric full-length A beta(1-42) aggregates in solution to their stability and conformational dynamics. We found that Our models are stable at a temperature of 3 10 K, and converge toward an interdigitated side-chain packing for intermolecular contacts within the two beta-sheet regions of the aggregates: beta(1) (residues 18-26) and beta(2) (residues 31-42). MD simulations reveal that the beta-strand twist is a characteristic element of A beta-aggregates, permitting a compact, interdigitated packing of side chains from neighboring beta-sheets. The beta(2) portion formed a tightly organized beta-helix, whereas the beta(1) portion did not show such a firm Structural organization, although it maintained its beta-sheet conformation. Our simulations indicate that the hydrophobic core comprising the beta(2) portion of the aggregate is a crucial stabilizing element in the A beta aggregation process. On the basis of these structure-stability findings, the beta(2) portion emerges as an optimal target for further antiamyloid drug design

Penetratin and derivatives acting as antifungal agents

The synthesis, in vitro evaluation, and conformational study of RQIKIWFQNRRMKWKK-NH2 (penetratin) and related derivatives acting as antifungal agents are reported. Penetratin and some of its derivatives displayed antifungal activity against the human opportunistic pathogenic standardized ATCC strains Candida albicans and Cryptococcus neoformans as well as clinical isolates of C. neoformans. Among the compounds tested, penetratin along with the nonapeptide RKWRRKWKK-NH2 and the tetrapeptide RQKK-NH2 exhibited significant antifungal activities against the Cryptococcus species. A comprehensive conformational analysis on the peptides reported here using three different approaches, molecular mechanics, simulated annealing and molecular dynamics simulations, was carried out. The experimental and theoretical results allow us to identify a topographical template which may provide a guide for the design of new compounds with antifungal characteristics against C. neoformans.