2 research outputs found
REMD Simulations Reveal the Dynamic Profile and Mechanism of Action of Deleterious, Rescuing, and Stabilizing Perturbations to NBD1 from CFTR
Cystic
Fibrosis (CF) is a lethal, genetic disease caused by mutations
to the CFTR chloride channel. The most common CF causing mutation
is the deletion of F508 from the first Nucleotide Binding Domain (F508del-NBD1).
This mutation leads to a thermally unstable domain and a misfolded,
nonfunctioning CFTR. Replica Exchange MD simulations were used to
simulate seven NBD1 constructs including wt and F508del-NBD1 both
alone and in the presence of known rescuing mutations as well as F508del-NBD1
in complex with a known small (ligand) stabilizer. Analyzing the resulting
trajectories suggests that differences in the biochemical properties
of the constructs result from local and coupled differences in their
dynamic profiles. A comparative analysis of these profiles as well
as of the resulting trajectories reveals how the different perturbations
exert their deleterious, rescuing, and stabilizing effects on NBD1.
These simulations may therefore be useful for the design and mechanism-of-action
analysis of new NBD1 stabilizers
Design of Compact Biomimetic Cellulose Binding Peptides as Carriers for Cellulose Catalytic Degradation
The
conversion of biomass into biofuels can reduce the strategic
vulnerability of petroleum-based systems and at the same time have
a positive effect on global climate issues. Lignocellulose is the
cheapest and most abundant source of biomass and consequently has
been widely considered as a source for liquid fuel. However, despite
ongoing efforts, cellulosic biofuels are still far from commercial
realization, one of the major bottlenecks being the hydrolysis of
cellulose into simpler sugars. Inspired by the structural and functional
modularity of cellulases used by many organisms for the breakdown
of cellulose, we propose to mimic the cellulose binding domain (CBD)
and the catalytic domain of these proteins by small molecular entities.
Multiple copies of these mimics could subsequently be tethered together
to enhance hydrolytic activity. In this work, we take the first step
toward achieving this goal by applying computational approaches to
the design of efficient, cost-effective mimetics of the CBD. The design
is based on low molecular weight peptides that are amenable to large-scale
production. We provide an optimized design of four short (i.e., ∼18
residues) peptide mimetics based on the three-dimensional structure
of a known CBD and demonstrate that some of these peptides bind cellulose
as well as or better than the full CBD. The structures of these peptides
were studied by circular dichroism and their interactions with cellulose
by solid phase NMR. Finally, we present a computational strategy for
predicting CBD/peptide–cellulose binding free energies and
demonstrate its ability to provide values in good agreement with experimental
data. Using this computational model, we have also studied the dissociation
pathway of the CBDs/peptides from the surface of cellulose