32 research outputs found
Mechanism of lignin inhibition of enzymatic biomass deconstruction
Background
The conversion of plant biomass to ethanol via enzymatic cellulose hydrolysis offers a potentially sustainable route to biofuel production. However, the inhibition of enzymatic activity in pretreated biomass by lignin severely limits the efficiency of this process. Results
By performing atomic-detail molecular dynamics simulation of a biomass model containing cellulose, lignin, and cellulases (TrCel7A), we elucidate detailed lignin inhibition mechanisms. We find that lignin binds preferentially both to the elements of cellulose to which the cellulases also preferentially bind (the hydrophobic faces) and also to the specific residues on the cellulose-binding module of the cellulase that are critical for cellulose binding of TrCel7A (Y466, Y492, and Y493). Conclusions Lignin thus binds exactly where for industrial purposes it is least desired, providing a simple explanation of why hydrolysis yields increase with lignin removal
Memory, gender and anti-fascism in France and Britain in the 1930s
Synaptotagmin
(Syt) is a membrane-associated protein involved in
vesicle fusion through the SNARE complex that is found throughout
the human body in 17 different isoforms. These isoforms have two membrane-binding
C2 domains, which sense Ca<sup>2+</sup> and thereby promote anionic
membrane binding and lead to vesicle fusion. Through molecular dynamics
simulations using the highly mobile membrane mimetic acclerated bilayer
model, we have investigated how small protein sequence changes in
the Ca<sup>2+</sup>-binding loops of the C2 domains may give rise
to the experimentally determined difference in binding kinetics between
Syt-1 and Syt-7 isoforms. Syt-7 C2 domains are found to form more
close contacts with anionic phospholipid headgroups, particularly
in loop 1, where an additional positive charge in Syt-7 draws the
loop closer to the membrane and causes the anchoring residue F167
to insert deeper into the bilayer than the corresponding methionine
in Syt-1 (M173). By performing additional replica exchange umbrella
sampling calculations, we demonstrate that these additional contacts
increase the energetic cost of unbinding the Syt-7 C2 domains from
the bilayer, causing them to unbind more slowly than their counterparts
in Syt-1
Reversible Unwrapping Algorithm for Constant-Pressure Molecular Dynamics Simulations
Molecular
simulation technologies have afforded researchers a unique
look into the nanoscale interactions driving physical processes. However,
a limitation for molecular dynamics (MD) simulations is that they
must be performed on finite-sized systems in order to map onto computational
resources. To minimize artifacts arising from finite-sized simulation
systems, it is common practice for MD simulations to be performed
with periodic boundary conditions (PBCs). However, in order to calculate
specific physical properties, such as mean square displacements to
calculate diffusion coefficients, continuous particle trajectories
where the atomic movements are continuous and do not jump between
cell faces are required. In these cases, modifying atomic coordinates
through unwrapping schemes is an essential post-processing tool to
remove these jumps. Here, two established trajectory unwrapping schemes
are applied to 1 μs wrapped trajectories for a small water box
and lysozyme in water. The existing schemes can result in spurious
diffusion coefficients, long bonds within unwrapped molecules, and
inconsistent atomic coordinates when coordinates are rewrapped after
unwrapping. We determine that prior unwrapping schemes do not account
for changing periodic box dimensions and introduce an additional correction
term to the existing displacement unwrapping scheme to correct for
these artifacts. We also demonstrate that the resulting algorithm
is a hybrid between the existing heuristic and displacement unwrapping
schemes. After treatment using this new unwrapping scheme, molecular
geometries are correct even after long simulations. In anticipation
for longer MD trajectories, we develop implementations for this new
scheme in multiple PBC handling tools
LongBondEliminator: A Molecular Simulation Tool to Remove Ring Penetrations in Biomolecular Simulation Systems
We develop a workflow, implemented as a plugin to the molecular visualization program VMD, that can fix ring penetrations with minimal user input. LongBondEliminator, detects ring piercing artifacts by the long, strained bonds that are the local minimum energy conformation during minimization for some assembled simulation system. The LongBondEliminator tool then automatically treats regions near these long bonds using multiple biases applied through NAMD. By combining biases implemented through the collective variables module, density-based forces, and alchemical techniques in NAMD, LongBondEliminator will iteratively alleviate long bonds found within molecular simulation systems. Through three concrete examples with increasing complexity, a lignin polymer, an viral capsid assembly, and a large, highly glycosylated protein aggrecan, we demonstrate the utility for this method in eliminating ring penetrations from classical MD simulation systems. The tool is available via gitlab as a VMD plugin, and has been developed to be generically useful across a variety of biomolecular simulations
A Microscopic View of Phospholipid Insertion into Biological Membranes
Understanding the process of membrane
insertion is an essential
step in developing a detailed mechanism, for example, for peripheral
membrane protein association and membrane fusion. The highly mobile
membrane mimetic (HMMM) has been used to accelerate the membrane association
and binding of peripheral membrane proteins in simulations by increasing
the lateral diffusion of phospholipid headgroups while retaining an
atomistic description of the interface. Through a comparative study,
we assess the difference in insertion rate of a free phospholipid
into an HMMM as well as into a conventional phospholipid bilayer and
develop a detailed mechanistic model of free phospholipid insertion
into biological membranes. The mechanistic insertion model shows that
successful irreversible association of the free phospholipid to the
membrane interface, which results in its insertion, is the rate-limiting
step. Association is followed by independent, sequential insertion
of the acyl tails of the free phospholipid into the membrane, with
splayed acyl tail intermediates. Use of the HMMM is found to replicate
the same intermediate insertion states as in the full phospholipid
bilayer; however, it accelerates overall insertion by approximately
a factor of 3, with the probability of successful association of phospholipid
to the membrane being significantly enhanced
Differential Membrane Binding Mechanics of Synaptotagmin Isoforms Observed in Atomic Detail
Synaptotagmin
(Syt) is a membrane-associated protein involved in
vesicle fusion through the SNARE complex that is found throughout
the human body in 17 different isoforms. These isoforms have two membrane-binding
C2 domains, which sense Ca<sup>2+</sup> and thereby promote anionic
membrane binding and lead to vesicle fusion. Through molecular dynamics
simulations using the highly mobile membrane mimetic acclerated bilayer
model, we have investigated how small protein sequence changes in
the Ca<sup>2+</sup>-binding loops of the C2 domains may give rise
to the experimentally determined difference in binding kinetics between
Syt-1 and Syt-7 isoforms. Syt-7 C2 domains are found to form more
close contacts with anionic phospholipid headgroups, particularly
in loop 1, where an additional positive charge in Syt-7 draws the
loop closer to the membrane and causes the anchoring residue F167
to insert deeper into the bilayer than the corresponding methionine
in Syt-1 (M173). By performing additional replica exchange umbrella
sampling calculations, we demonstrate that these additional contacts
increase the energetic cost of unbinding the Syt-7 C2 domains from
the bilayer, causing them to unbind more slowly than their counterparts
in Syt-1
Differential Membrane Binding Mechanics of Synaptotagmin Isoforms Observed in Atomic Detail
Synaptotagmin
(Syt) is a membrane-associated protein involved in
vesicle fusion through the SNARE complex that is found throughout
the human body in 17 different isoforms. These isoforms have two membrane-binding
C2 domains, which sense Ca<sup>2+</sup> and thereby promote anionic
membrane binding and lead to vesicle fusion. Through molecular dynamics
simulations using the highly mobile membrane mimetic acclerated bilayer
model, we have investigated how small protein sequence changes in
the Ca<sup>2+</sup>-binding loops of the C2 domains may give rise
to the experimentally determined difference in binding kinetics between
Syt-1 and Syt-7 isoforms. Syt-7 C2 domains are found to form more
close contacts with anionic phospholipid headgroups, particularly
in loop 1, where an additional positive charge in Syt-7 draws the
loop closer to the membrane and causes the anchoring residue F167
to insert deeper into the bilayer than the corresponding methionine
in Syt-1 (M173). By performing additional replica exchange umbrella
sampling calculations, we demonstrate that these additional contacts
increase the energetic cost of unbinding the Syt-7 C2 domains from
the bilayer, causing them to unbind more slowly than their counterparts
in Syt-1
Passive permeability controls synthesis for the allelochemical sorgoleone in sorghum root exudate
Input structures for a manuscript, along with selected output data and structures. This directory structure contains a cut-down copy of the directories used to generate the simulation data and the analysis. In order to make this fit into the 50GB Zenodo limit, it was constructed with the following tar command: tar -zcvf sorgoleonepermeability.tar.gz --exclude="*BAK" --exclude="*#" --exclude="*log" --exclude="*xsc" --exclude="*coor" --exclude="*vel" --exclude="*[0-9].out" --exclude="*old" --exclude="*dcd" --exclude="*tmp" --exclude="*ppm" --exclude="*png" --exclude="*pdf" --exclude="*catchy*" --exclude="*svg" --exclude="*restart*" --exclude="*history" --exclude="core.*" --exclude="FFTW_NAMD*" --exclude="*avi" --exclude="*mp4" sorgoleone-permeability, which intentionally excludes large files. The full dataset that includes trajectories is available upon request.
The data is split into two directories initially "build" and "Simulations"
"build" directory is the part where initial system for unbiased and biased simulation were build using "resolvate.tcl" and "smd-single-build-system.tcl" respectively.
"Simulations" directory has the different namd files for running unbiased simulation, steered molecular dynamics and replica exchange umbrella sampling.
The folder structure was generated using "gendirs*.py".
The unbiased simulations were run using "run.namd".
Steered molecular dynamics namd files were with name "step*.namd" and colvars configuration file are named "step*.conf".
Replica exchange moleuclar dynamics (REUS) system was generated using "buildreplicas*.tcl".
Replica windows size and force constant were written into a namd configuration file using "reus-genscript*.py".
REUS general configuration file containing the parameters and forcefield is named as "base.namd".
Colvars for leaflet exchange REUS are in "replicadistZcolvars.conf".
Colvars for absorption into water REUS are in "replicadistcoordNumclovar.conf".
Colvars for absorption into organic phase REUS are in "replica-blob-run4.conf"
Umbrella sampling is performed with "umbrella.namd".
For visualizing trajectories in VMD "load*.tcl" scripts were used
Extension of the Highly Mobile Membrane Mimetic to Transmembrane Systems through Customized <i>in Silico</i> Solvents
The
mechanics of the protein–lipid interactions of transmembrane
proteins are difficult to capture with conventional atomic molecular
dynamics, due to the slow lateral diffusion of lipids restricting
sampling to states near the initial membrane configuration. The highly
mobile membrane mimetic (HMMM) model accelerates lipid dynamics by
modeling the acyl tails nearest to the membrane center as a fluid
organic solvent while maintaining an atomic description of the lipid
headgroups and short acyl tails. The HMMM has been applied to many
peripheral protein systems; however, the organic solvent used to date
caused deformations in transmembrane proteins by intercalating into
the protein and disrupting interactions between individual side chains.
We ameliorate the effect of the solvent on transmembrane protein structure
through the development of two new <i>in silico</i> Lennard-Jones
solvents. The parameters for the new solvents were determined through
an extensive parameter search in order to match the bulk properties
of alkanes in a highly simplified model. Using these new solvents,
we substantially improve the insertion free energy profiles of 10
protein side chain analogues across the entire bilayer. In addition,
we reduce the intercalation of solvent into transmembrane systems,
resulting in native-like transmembrane protein structures from five
different topological classes within a HMMM bilayer. The parametrization
of the solvents, in addition to their computed physical properties,
is discussed. By combining high lipid lateral diffusion with intact
transmembrane proteins, we foresee the developed solvents being useful
to efficiently identify membrane composition inhomogeneities and lipid
binding caused by the presence of membrane proteins