10 research outputs found
Redox Potentials of Protein Disulfide Bonds from Free-Energy Calculations
Thiol/disulfide
exchange in proteins is a vital process in all
organisms. To ensure specificity, the involved thermodynamics and
kinetics are believed to be tailored by the structure and dynamics
of the protein hosting the thiol/disulfide pair. We here aim at predicting
the thermodynamics of thiol/disulfide pairs in proteins. We devise
a free-energy calculation scheme, which makes use of the Crooks Gaussian
intersection method to estimate the redox potential of thiol/disulfide
pairs in 12 proteins belonging to the thioredoxin superfamily, namely,
thioredoxins, glutaredoxins, and thiolâdisulfide oxidoreductases
in disulfide bond formation systems. We obtained a satisfying correlation
of computed with experimental redox potentials (varying by 160 mV),
with a residual error of âŒ40 mV (8 kJ/mol), which drastically
reduces when considering a less diverse set of only thioredoxins.
Our simple and transferrable approach provides a route toward estimating
redox potentials of any disulfide-containing protein given that its
(reduced or oxidized) structure is known and thereby represents a
step toward a rational design of redox proteins
Macromolecular Entropy Can Be Accurately Computed from Force
A method
is presented to evaluate a moleculeâs entropy from
the atomic forces calculated in a molecular dynamics simulation. Specifically,
diagonalization of the mass-weighted force covariance matrix produces
eigenvalues which in the harmonic approximation can be related to
vibrational frequencies. The harmonic oscillator entropies of each
vibrational mode may be summed to give the total entropy. The results
for a series of hydrocarbons, dialanine and a ÎČ hairpin are
found to agree much better with values derived from thermodynamic
integration than results calculated using quasiharmonic analysis.
Forces are found to follow a harmonic distribution more closely than
coordinate displacements and better capture the underlying potential
energy surface. The methodâs accuracy, simplicity, and computational
similarity to quasiharmonic analysis, requiring as input force trajectories
instead of coordinate trajectories, makes it readily applicable to
a wide range of problems
Stress Propagation through Biological Lipid Bilayers in Silico
Membrane
tension plays various critical roles in the cell. We here
asked how fast and how far localized pulses of mechanical stress dynamically
propagate through biological lipid bilayers. In both coarse-grained
and all-atom molecular dynamics simulations of a dipalmitoylphosphatidylcholine
lipid bilayer, we observed nanometer-wide stress pulses, propagating
very efficiently longitudinally at a velocity of approximately 1.4
± 0.5 nm/ps (km/s), in close agreement
with the expected speed of sound from experiments. Remarkably, the
predicted characteristic attenuation time of the pulses was in the
order of tens of picoseconds, implying longitudinal stress propagation
over length scales up to several tens of nanometers before damping.
Furthermore, the computed dispersion relation leading to such damping
was consistent with proposed continuum viscoelastic models of propagation.
We suggest this mode of stress propagation as a potential ultrafast
mechanism of signaling that may quickly couple mechanosensitive elements
in crowded biological membranes
On the Cis to Trans Isomerization of ProlylâPeptide Bonds under Tension
The cis peptide bond is a characteristic feature of turns
in protein
structures and can play the role of a hinge in protein folding. Such
cis conformations are most commonly found at peptide bonds immediately
preceding proline residues, as the cis and trans states for such bonds
are close in energy. However, isomerization over the high rotational
barrier is slow. In this study, we investigate how mechanical force
accelerates the cis to trans isomerization of the prolylâpeptide
bond in a stretched backbone. We employ hybrid quantum mechanical/molecular
mechanical force-clamp molecular dynamics simulations in order to
describe the electronic effects involved. Under tension, the bond
order of the prolylâpeptide bond decreases from a partially
double toward a single bond, involving a reduction in the electronic
conjugation around the peptide bond. The conformational change from
cis to extended trans takes place within a few femtoseconds through
a nonplanar state of the nitrogen of the peptide moiety in the transition
state region, whereupon the partial double-bond character and planarity
of the peptide bond in the final trans state is restored. Our findings
give insight into how prolylâpeptide bonds might act as force-modulated
mechanical timers or switches in the refolding of proteins
On the Cis to Trans Isomerization of ProlylâPeptide Bonds under Tension
The cis peptide bond is a characteristic feature of turns
in protein
structures and can play the role of a hinge in protein folding. Such
cis conformations are most commonly found at peptide bonds immediately
preceding proline residues, as the cis and trans states for such bonds
are close in energy. However, isomerization over the high rotational
barrier is slow. In this study, we investigate how mechanical force
accelerates the cis to trans isomerization of the prolylâpeptide
bond in a stretched backbone. We employ hybrid quantum mechanical/molecular
mechanical force-clamp molecular dynamics simulations in order to
describe the electronic effects involved. Under tension, the bond
order of the prolylâpeptide bond decreases from a partially
double toward a single bond, involving a reduction in the electronic
conjugation around the peptide bond. The conformational change from
cis to extended trans takes place within a few femtoseconds through
a nonplanar state of the nitrogen of the peptide moiety in the transition
state region, whereupon the partial double-bond character and planarity
of the peptide bond in the final trans state is restored. Our findings
give insight into how prolylâpeptide bonds might act as force-modulated
mechanical timers or switches in the refolding of proteins
Exploring the Multidimensional Free Energy Surface of Phosphoester Hydrolysis with Constrained QM/MM Dynamics
The mechanism of the hydrolysis of phosphate monoesters,
a ubiquitous
biological reaction, has remained under debate. We here investigated
the hydrolysis of a nonenzymatic model system, the monomethyl phosphate
dianion, by hybrid quantum mechanical and molecular mechanical simulations.
The solvation effects were taken into account with explicit water.
Detailed free energy landscapes in two-dimensional and three-dimensional
space were resolved using the multidimensional potential of mean constraint
force, a newly developed method that was demonstrated to be powerful
for free energy calculations along multiple coordinates. As in previous
theoretical studies, the associative and dissociative pathways were
indistinguishable. Furthermore, the associative pathway was investigated
in great detail. We propose a rotation of an OâH bond in the
transition between two pentacoordinated structures, during which an
overall transition state was identified with an activation energy
of 50 kcal/mol. This is consistent with experimental data. The results
support a concerted proton transfer from the nucleophilic water to
the phosphate group, and then to the leaving group
Stability of Biological Membranes upon Mechanical Indentation
Mechanical
perturbations are ubiquitous in living cells, and many
biological functions are dependent on the mechanical response of lipid
membranes. Recent force-spectroscopy studies have captured the stepwise
fracture of stacks of bilayers, avoiding substrate effects. However,
the effect of stacking bilayers, as well as the exact molecular mechanism
of the fracture process, is unknown. Here, we use atomistic and coarse-grained
force-clamp molecular dynamics simulation to assess the effects of
mechanical indentation on stacked and single bilayers. Our simulations
show that the rupture process obeys the laws of force-activated barrier
crossing, and stacking multiple membranes stabilizes them. The rupture
times follow a log-normal distribution which allows the interpretation
of membrane rupture as a pore-growth process. Indenter hydrophobicity
determines the type of pore formation, the preferred dwelling region,
and the resistance of the bilayer against rupture. Our results provide
a better understanding of the nanomechanics underlying the plastic
rupture of lipid membranes
Stability of Biological Membranes upon Mechanical Indentation
Mechanical
perturbations are ubiquitous in living cells, and many
biological functions are dependent on the mechanical response of lipid
membranes. Recent force-spectroscopy studies have captured the stepwise
fracture of stacks of bilayers, avoiding substrate effects. However,
the effect of stacking bilayers, as well as the exact molecular mechanism
of the fracture process, is unknown. Here, we use atomistic and coarse-grained
force-clamp molecular dynamics simulation to assess the effects of
mechanical indentation on stacked and single bilayers. Our simulations
show that the rupture process obeys the laws of force-activated barrier
crossing, and stacking multiple membranes stabilizes them. The rupture
times follow a log-normal distribution which allows the interpretation
of membrane rupture as a pore-growth process. Indenter hydrophobicity
determines the type of pore formation, the preferred dwelling region,
and the resistance of the bilayer against rupture. Our results provide
a better understanding of the nanomechanics underlying the plastic
rupture of lipid membranes
Sampling Long- versus Short-Range Interactions Defines the Ability of Force Fields To Reproduce the Dynamics of Intrinsically Disordered Proteins
Molecular dynamics (MD) simulations
have valuably complemented
experiments describing the dynamics of intrinsically disordered proteins
(IDPs), particularly since the proposal of models to solve the artificial
collapse of IDPs <i>in silico</i>. Such models suggest redefining
nonbonded interactions, by either increasing water dispersion forces
or adopting the Kirkwood-Buff force field. These approaches yield
extended conformers that better comply with experiments, but it is
unclear if they all sample the same intrachain dynamics of IDPs. We
have tested this by employing MD simulations and single-molecule FoÌrster
resonance energy transfer spectroscopy to sample the dimensions of
systems with different sequence compositions, namely strong and weak
polyelectrolytes. For strong polyelectrolytes in which charge effects
dominate, all the proposed solutions equally reproduce the expected
ensembleâs dimensions. For weak polyelectrolytes, at lower
cutoffs, force fields abnormally alter intrachain dynamics, overestimating
excluded volume over chain flexibility or reporting no difference
between the dynamics of different chains. The TIP4PD water model alone
can reproduce experimentally observed changes in extensions (dimensions),
but not quantitatively and with only weak statistical significance.
Force field limitations are reversed with increased interaction cutoffs,
showing that chain dynamics are critically defined by the presence
of long-range interactions. Force field analysis aside, our study
provides the first insights into how long-range interactions critically
define IDP dimensions and raises the question of which length range
is crucial to correctly sample the overall dimensions and internal
dynamics of the large group of weakly charged yet highly polar IDPs
KirkwoodâBuff Approach Rescues Overcollapse of a Disordered Protein in Canonical Protein Force Fields
Understanding the function of intrinsically
disordered proteins
is intimately related to our capacity to correctly sample their conformational
dynamics. So far, a gap between experimentally and computationally
derived ensembles exists, as simulations show overcompacted conformers.
Increasing evidence suggests that the solvent plays a crucial role
in shaping the ensembles of intrinsically disordered proteins and
has led to several attempts to modify water parameters and thereby
favor proteinâwater over proteinâprotein interactions.
This study tackles the problem from a different perspective, which
is the use of the KirkwoodâBuff theory of solutions to reproduce
the correct conformational ensemble of intrinsically disordered proteins
(IDPs). A protein force field recently developed on such a basis was
found to be highly effective in reproducing ensembles for a fragment
from the FG-rich nucleoporin 153, with dimensions matching experimental
values obtained from small-angle X-ray scattering and single molecule
FRET experiments. KirkwoodâBuff theory presents a complementary
and fundamentally different approach to the recently developed four-site
TIP4P-D water model, both of which can rescue the overcollapse observed
in IDPs with canonical protein force fields. As such, our study provides
a new route for tackling the deficiencies of current protein force
fields in describing protein solvation