92 research outputs found
Molecular Simulations of Liquid Jet Explosions and Shock Waves Induced by X-Ray Free-Electron Lasers
X-ray free-electron lasers (XFELs) produce X-ray pulses with high brilliance
and short pulse duration. These properties enable structural investigations of
biomolecular nanocrystals, and they allow resolving the dynamics of
biomolecules down to the femtosecond timescale. Liquid jets are widely used to
deliver samples into the XFEL beam. The impact of the X-ray pulse leads to
vaporization and explosion of the liquid jet, while the expanding gas triggers
the formation of shock wave trains traveling along the jet, which may affect
biomolecular samples before they have been probed. Here, we used molecular
dynamics simulations to reveal the structural dynamics of shock waves after an
X-ray impact. Analysis of the density in the jet revealed shock waves that form
close to the explosion center, travel along the jet with supersonic velocities
and decay exponentially with an attenuation length proportional to the jet
diameter. A trailing shock wave formed after the first shock wave, similar to
the shock wave trains in experiments. Although using purely classical models in
the simulations, the resulting explosion geometry and shock wave dynamics
closely resemble experimental findings, and they highlight the importance of
atomistic details for modeling shock wave attenuation.Comment: 16 pages, 11 figure
An allosteric interaction controls the activation mechanism of SHP2 tyrosine phosphatase
SHP2 is a protein tyrosine phosphatase (PTP) involved in multiple signaling pathways. Mutations of SHP2 can result in Noonan syndrome or pediatric malignancies. Inhibition of wild-type SHP2 represents a novel strategy against several cancers. SHP2 is activated by binding of a phosphopeptide to the N-SH2 domain of SHP2, thereby favoring dissociation of the N-SH2 domain and exposing the active site on the PTP domain. The conformational transitions controlling ligand affinity and PTP dissociation remain poorly understood. Using molecular simulations, we revealed an allosteric interaction restraining the N-SH2 domain into a SHP2-activating and a stabilizing state. Only ligands selecting for the activating N-SH2 conformation, depending on ligand sequence and binding mode, are effective activators. We validate the model of SHP2 activation by rationalizing modified basal activity and responsiveness to ligand stimulation of several N-SH2 variants. This study provides mechanistic insight into SHP2 activation and may open routes for SHP2 regulation
Atomistic ensemble of active SHP2 phosphatase
SHP2 phosphatase plays an important role in regulating several intracellular signaling pathways. Pathogenic mutations of SHP2 cause developmental disorders and are linked to
hematological malignancies and cancer. SHP2 comprises two tandemly-arranged SH2
domains, a catalytic PTP domain, and a disordered C-terminal tail. Under physiological, nonstimulating conditions, the catalytic site of PTP is occluded by the N-SH2 domain, so that the
basal activity of SHP2 is low. Whereas the autoinhibited structure of SHP2 has been known
for two decades, its active, open structure still represents a conundrum. Since the oncogenic
mutant SHP2E76K almost completely populates the active, open state, this mutant has been
extensively studied as a model for activated SHP2. By molecular dynamics simulations and
accurate explicit-solvent SAXS curve predictions, we present the heterogeneous atomistic
ensemble of constitutively active SHP2E76K in solution, encompassing a set of conformational
arrangements and radii of gyration in agreement with experimental SAXS data
Scrutinizing the protein hydration shell from molecular dynamics simulations against consensus small-angle scattering data
Biological macromolecules in solution are surrounded by a hydration shell, whose structure
differs from the structure of bulk solvent. While the importance of the hydration shell for
numerous biological functions is widely acknowledged, it remains unknown how the hydration shell is regulated by macromolecular shape and surface composition, mainly because a
quantitative probe of the hydration shell structure has been missing. We show that smallangle scattering in solution using X-rays (SAXS) or neutrons (SANS) provide a proteinspecific probe of the protein hydration shell that enables quantitative comparison with
molecular simulations. Using explicit-solvent SAXS/SANS predictions, we derived the effect
of the hydration shell on the radii of gyration Rg of five proteins using 18 combinations of
protein force field and water model. By comparing computed Rg values from SAXS relative to
SANS in D2O with consensus SAXS/SANS data from a recent worldwide community effort,
we found that several but not all force fields yield a hydration shell contrast in remarkable
agreement with experiments. The hydration shell contrast captured by Rg values depends
strongly on protein charge and geometric shape, thus providing a protein-specific footprint of
protein–water interactions and a novel observable for scrutinizing atomistic hydration shell
models against experimental data
Continuous millisecond conformational cycle of a DEAH box helicase reveals control of domain motions by atomic-scale transitions
Helicases are motor enzymes found in every living organism and viruses, where they maintain
the stability of the genome and control against false recombination. The DEAH-box helicase
Prp43 plays a crucial role in pre-mRNA splicing in unicellular organisms by translocating
single-stranded RNA. The molecular mechanisms and conformational transitions of helicases
are not understood at the atomic level. We present a complete conformational cycle of RNA
translocation by Prp43 in atomic detail based on molecular dynamics simulations. To enable
the sampling of such complex transition on the millisecond timescale, we combined two
enhanced sampling techniques, namely simulated tempering and adaptive sampling guided
by crystallographic data. During RNA translocation, the center-of-mass motions of the RecAlike domains followed the established inchworm model, whereas the domains crawled along
the RNA in a caterpillar-like movement, suggesting an inchworm/caterpillar model. However,
this crawling required a complex sequence of atomic-scale transitions involving the release of
an arginine finger from the ATP pocket, stepping of the hook-loop and hook-turn motifs along
the RNA backbone, and several others. These findings highlight that large-scale domain
dynamics may be controlled by complex sequences of atomic-scale transitions
Free energies of membrane stalk formation from a lipidomics perspective
Many biological membranes are asymmetric and exhibit complex lipid composition, comprising hundreds of distinct chemical species. Identifying the biological function and advantage of this complexity is a central goal of membrane biology. Here, we study how membrane complexity controls the energetics of the first steps of membrane fusions, that is, the formation of a stalk. We first present a computationally efficient method for simulating thermodynamically reversible pathways of stalk formation at coarse-grained resolution. The method reveals that the inner leaflet of a typical plasma membrane is far more fusogenic than the outer leaflet, which is likely an adaptation to evolutionary pressure. To rationalize these findings by the distinct lipid compositions, we computed ~200 free energies of stalk formation in membranes with different lipid head groups, tail lengths, tail unsaturations, and sterol content. In summary, the simulations reveal a drastic influence of the lipid composition on stalk formation and a comprehensive fusogenicity map of many biologically relevant lipid classes
Cooperative Effects of an Antifungal Moiety and DMSO on Pore Formation over Lipid Membranes Revealed by Free Energy Calculations
Itraconazole is a triazole drug widely used in the treatment of fungal infections, and it is in clinical trials for treatment of several cancers. However, the drug suffers from poor solubility, while experiments have shown that itraconazole delivery in liposome nanocarriers improves both circulation half-life and tissue distribution. The drug release mechanism from the nanocarrier is still unknown, and it depends on several factors including membrane stability against defect formation. In this work, we used molecular dynamics simulations and potential of mean force (PMF) calculations to quantify the influence of itraconazole on pore formation over lipid membranes, and we compared the effect by itraconazole with a pore-stabilizing effect by the organic solvent dimethyl sulfoxide (DMSO). According to the PMFs, both itraconazole and DMSO greatly reduce the free energy of pore formation, by up to similar to 20 kJ mol(-1). However, whereas large concentrations of itraconazole of 8 mol % (relative to lipid) were required, only small concentrations of a few mole % DMSO (relative to water) were sufficient to stabilize pores. In addition, itraconazole and DMSO facilitate pore formation by different mechanisms. Whereas itraconazole predominantly aids the formation of a partial defect with a locally thinned membrane, DMSO mainly stabilizes a transmembrane water needle by shielding it from the hydrophobic core. Notably, the two distinct mechanisms act cooperatively upon adding both itraconazole and DMSO to the membrane, as revealed by an additional reduction of the pore free energy. Overall, our simulations reveal molecular mechanisms and free energies of membrane pore formation by small molecules. We suggest that the stabilization of a locally thinned membrane as well as the shielding of a transmembrane water needle from the hydrophobic membrane core may be a general mechanism by which amphiphilic molecules facilitate pore formation over lipid membranes at sufficient concentrations.Peer reviewe
Ion-induced transient potential fluctuations facilitate pore formation and cation transport through lipid membranes
Unassisted ion transport through lipid membranes plays a crucial role in many
cell functions without which life would not be possible, yet the precise
mechanism behind the process remains unknown due to its molecular complexity.
Here, we demonstrate a direct link between membrane potential fluctuations and
divalent ion transport. High-throughput wide-field second harmonic (SH)
microscopy shows that membrane potential fluctuations are universally found in
lipid bilayer systems. Molecular dynamics simulations reveal that such
variations in membrane potential reduce the free energy cost of transient pore
formation and increase the ion flux across an open pore. These transient pores
can act as conduits for ion transport, which we SH image for a series of
divalent cations (Cu, Ca, Ba, Mg) passing through
GUV membranes. Combining the experimental and computational results, we show
that permeation through pores formed via an ion-induced electrostatic field is
a viable mechanism for unassisted ion transport.Comment: 8 pages, 2 figure
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