5 research outputs found
A simple and consistent quantum-chemical fragmentation scheme for proteins that includes two-body contributions
The Molecular Fractionation with Conjugate Caps (MFCC) method is a popular fragmentation method for the quantum-chemical treatment of proteins. However, it does not account for interactions between the amino acid fragments, such as intramolecular hydrogen bonding. Here, we present a combination of the MFCC fragmentation scheme with a second-order many-body expansion (MBE) that consistently accounts for all fragment--fragment, fragment--cap, and cap--cap interactions, while retaining the overall simplicity of the MFCC scheme with its chemically meaningful fragments. We show that with the resulting MFCC-MBE(2) scheme, the errors in the total energies of selected polypeptides and proteins can be reduced by up to one order of magnitude and relative energies of different protein conformers can be predicted accurately
Accurate quantum-chemical fragmentation calculations for ion-water clusters with the density-based many-body expansion
The many-body expansion (MBE) provides an attractive fragmentation method for the efficient quantum-chemical treatment of molecular clusters. However, its convergence with the many-body order is generally slow for molecular clusters that exhibit large intermolecular polarization effects. Ion--water clusters are thus a particularly challenging test case for quantum-chemical fragmentation methods based on the MBE. Here, we assess the accuracy of both the conventional, energy-based MBE and the recently developed density-based MBE [Schmitt-Monreal and Jacob, Int. J. Quantum Chem, 120, e26228 (2020)] for ion--water clusters. As test cases, we consider hydrated Ca^2+, F^-, OH^-, and H3O^+, and compare both total interaction energies and the relative interaction energies of different structural isomers. We show that an embedded density-based two-body expansion yields highly accurate results compared to supermolecular calculations. Already at the two-body level, the density-based MBE clearly outperforms a conventional, energy-based embedded three-body expansion. We compare different embedding schemes and find that a relaxed frozen-density embedding potential yields the most accurate results. This opens the door to accurate and efficient quantum-chemical calculations for large ion--water clusters as well as condensed-phase systems
Biomimetic Enterobactin Analogue Mediates Iron-Uptake and Cargo Transport into E. coli and P. aeruginosa
The design, synthesis
and biological evaluation of the artificial enterobactin analogue EntKL
and several fluorophore-conjugates thereof are described. EntKL
provides an attachment point for cargos such as fluorophores
or antimicrobial payloads. Corresponding conjugates are recognized by outer
membrane siderophore receptors of Gram-negative pathogens and retain the
natural hydrolyzability of the tris-lactone backbone, known to be key
for uptake into the cytosol. Initial density-functional theory (DFT)
calculations of the free energies of solvation (ÎG(sol)) and relaxed Fe-O force constants of the
corresponding [Fe-EntKL]3- complexes indicated a similar iron binding
constant compared to natural enterobactin (Ent). The synthesis of EntKL
was achieved via an iterative assembly based on a 3-hydroxylysine building block over 14 steps with an overall yield of
3%. A series of growth recovery assays under iron-limiting conditions with Escherichia coli
and Pseudomonas aeruginosa mutant strains that are defective in natural
siderophore synthesis revealed a potent concentration-dependent growth
promoting effect of EntKL similar to natural Ent.
Additionally, four cargo-conjugates differing in molecular size were able to
restore growth of E. coli indicating an uptake into the cytosol. P. aeruginosa
displayed a stronger uptake promiscuity as six different cargo-conjugates
were found to restore growth under iron-limiting conditions. Imaging studies utilizing
BODIPYFL-conjugates, demonstrated the ability of EntKL
to overcome the Gram-negative outer membrane permeability barrier and thus deliver
molecular cargos via the bacterial iron transport machinery of E. coli
and P. aeruginosa
Biomimetic enterobactin analogue mediates iron-uptake and cargo transport into E. coli and P. aeruginosa
The design, synthesis and biological evaluation of the artificial enterobactin analogue Ent(KL) and several fluorophore-conjugates thereof are described. Ent(KL) provides an attachment point for cargos such as fluorophores or antimicrobial payloads. Corresponding conjugates are recognized by outer membrane siderophore receptors of Gram-negative pathogens and retain the natural hydrolyzability of the tris-lactone backbone. Initial density-functional theory (DFT) calculations of the free energies of solvation (Delta G(sol)) and relaxed Fe-O force constants of the corresponding [Fe-Ent(KL)](3-) complexes indicated a similar iron binding constant compared to natural enterobactin (Ent). The synthesis of Ent(KL) was achieved via an iterative assembly based on a 3-hydroxylysine building block over 14 steps with an overall yield of 3%. A series of growth recovery assays under iron-limiting conditions with Escherichia coli and Pseudomonas aeruginosa mutant strains that are defective in natural siderophore synthesis revealed a potent concentration-dependent growth promoting effect of Ent(KL) similar to natural Ent. Additionally, four cargo-conjugates differing in molecular size were able to restore growth of E. coli indicating an uptake into the cytosol. P. aeruginosa displayed a stronger uptake promiscuity as six different cargo-conjugates were found to restore growth under iron-limiting conditions. Imaging studies utilizing BODIPYFL-conjugates, demonstrated the ability of Ent(KL) to overcome the Gram-negative outer membrane permeability barrier and thus deliver molecular cargos via the bacterial iron transport machinery of E. coli and P. aeruginosa
A novel SPINK5 donor splice site variant in a child with Netherton syndrome
Abstract Background Netherton syndrome (NS) is a genodermatosis caused by lossâofâfunction mutations in SPINK5, resulting in aberrant LEKTI expression. Method Nextâgeneration sequencing of SPINK5 (NM_001127698.1) was carried out and functional studies were performed by immunofluorescence microscopy of a lesional skin biopsy using antiâLEKTI antibodies. Results We describe a novel SPINK5 likely pathogenic donor splice site variant (NM_001127698.1:c.2015+5G>A) in a patient with NS and confirm its functional significance by demonstrating complete loss of LEKTI expression in lesional skin by immunofluorescence analysis. Conclusion The 2015+5G>A is a novel, likely pathogenic variant in NS. Herein we review and assimilate documented SPINK5 pathogenic variants and discuss possible genotypeâphenotype associations in NS