2 research outputs found
Asymmetric DNA-Search Dynamics by Symmetric Dimeric Proteins
We focus on dimeric DNA-binding proteins
from two well-studied
families: orthodox type II restriction endonucleases (REs) and transcription
factors (TFs). Interactions of the protein’s recognition sites
with the DNA and, particularly, the contribution of each of the monomers
to one-dimensional (1D) sliding along nonspecific DNA were studied
using computational tools. Coarse-grained molecular dynamics simulations
of DNA scanning by various TFs and REs provide insights into how the
symmetry of a homodimer can be broken while they nonspecifically interact
with DNA. The characteristics of protein sliding along DNA, such as
the average sliding length, partitioning between 1D and 3D search,
and the one-dimensional diffusion coefficient <i>D</i><sub>1</sub>, strongly depend on the salt concentration, which in turn
affects the probability of the two monomers adopting a cooperative
symmetric sliding mechanism. Indeed, we demonstrate that maximal DNA
search efficiency is achieved when the protein adopts an asymmetric
search mode in which one monomer slides while its partner hops. We
find that proteins classified as TFs have a higher affinity for the
DNA, longer sliding lengths, and an increased probability of symmetric
sliding in comparison with REs. Moreover, TFs can perform their biological
function over a much wider range of salt concentrations than REs.
Our results demonstrate that the different biological functions of
DNA-binding proteins are related to the different nonspecific DNA
search mechanisms they adopt
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