1,721,072 research outputs found
Auger Spectrum of a Water Molecule after Single and Double Core-Ionization by Intense X-Ray Radiation
No full textEfficient Dynamic Protonation and Constant pH Simulations with Explicit Solvent: Calculation of Apparent pKa Values in Proteins
No full text
In Silico Examination Of The Influence Of Nucleotide Modifications And Magnesium Ions On tRNA Structure And Dynamics
No full textCore hole screening and decay rates of double core ionized first row hydrides
Full text linkBecause of the high intensity, X-ray free electron lasers allow one to create and probe double core ionized states in molecules. The decay of these multiple core ionized states crucially determines the evolution of radiation damage in single molecule diffractive imaging experiments. Here we have studied the Auger decay in hydrides of first row elements after single and double core ionization by quantum mechanical ab initio calculations. In our approach the continuum wave function of the emitted Auger electron is expanded into spherical harmonics on a radial grid. The obtained decay rates of double K-shell vacancies were found to be systematically larger than those for the respective single K-shell vacancies, markedly exceeding the expected factor of two. This enhancement is attributed to the screening effects induced by the core hole. We propose a simple model, which is able to predict core hole decay rates in molecules with low Z elements based on the electron density in the vicinity of the core hole
Anomalous Surface Diffusion of Protons on Lipid Membranes
Full text linkAbstract:
The cellular energy machinery depends crucially on the presence and properties
of protons at or in the vicinity of lipid membranes. To asses the energetics and
mobility of a proton near a membrane, we simulated an excess proton near a sol-
vated DMPC bilayer at 323 K, using a recently developed method to include the
Grotthuss proton shuttling mechanism in classical molecular dynamics simulations.
We obtained a proton surface a nity of 13
:
0
0
:
5 kJ mol
1
. The proton interacted
strongly with both lipid head group and linker carbonyl oxygens. Furthermore, the
surface di usion of the proton was anomalous, with a subdi usive regime over the
rst few nanoseconds, followed by a superdi usive regime. The time- and distance
dependency of the proton surface di usion coe cient within these regimes may also
resolve many discrepancies between previously reported di usion coe cients. Our
simulations show that the proton anomalous surface di usion originates from re-
stricted di usion in two di erent surface-bound states, interrupted by the occasional
bulk-mediated long-range surface di usion. Although only a DMPC membrane was
considered in this work, we speculate that the restrictive character of the on-surface
di usion is highly sensitive to the speci c membrane conditions, which can alter
the relative contributions of the surface and bulk pathways to the overall di usion
process.peerReviewe
Constant pH Molecular Dynamics in Explicit Solvent with λ-Dynamics
No full textpH is an important parameter in condensed-phase systems, because it determines the protonation state of titratable groups and thus influences the structure, dynamics, and function of molecules in solution. In most force field simulation protocols, however, the protonation state of a system (rather than its pH) is kept fixed and cannot adapt to changes of the local environment. Here, we present a method, implemented within the MD package GROMACS, for constant pH molecular dynamics simulations in explicit solvent that is based on the λ-dynamics approach. In the latter, the dynamics of the titration coordinate λ, which interpolates between the protonated and deprotonated states, is driven by generalized forces between the protonated and deprotonated states. The hydration free energy, as a function of pH, is included to facilitate constant pH simulations. The protonation states of titratable groups are allowed to change dynamically during a simulation, thus reproducing average protonation probabilities at a certain pH. The accuracy of the method is tested against titration curves of single amino acids and a dipeptide in explicit solvent
Erratum: “Auger spectrum of a water molecule after single and double core ionization” [J. Chem. Phys. 136, 144304 (2012)]
No full textCharge-Neutral Constant pH Molecular Dynamics Simulations Using a Parsimonious Proton Buffer
No full textIn constant pH molecular dynamics simulations, the protonation states of titratable sites can respond to changes of the pH and of their electrostatic environment. Consequently, the number of protons bound to the biomolecule, and therefore the overall charge of the system, fluctuates during the simulation. To avoid artifacts associated with a non-neutral simulation system, we introduce an approach to maintain neutrality of the simulation box in constant pH molecular dynamics simulations, while maintaining an accurate description of all protonation fluctuations. Specifically, we introduce a proton buffer that, like a buffer in experiment, can exchange protons with the biomolecule enabling its charge to fluctuate. To keep the total charge of the system constant, the uptake and release of protons by the buffer are coupled to the titration of the biomolecule with a constraint. We find that, because the fluctuation of the total charge (number of protons) of a typical biomolecule is much smaller than the number of titratable sites of the biomolecule, the number of buffer sites required to maintain overall charge neutrality without compromising the charge fluctuations of the biomolecule, is typically much smaller than the number of titratable sites, implying markedly enhanced simulation and sampling efficiency
g_membed: Efficient insertion of a membrane protein into an equilibrated lipid bilayer with minimal perturbation
No full textTo efficiently insert a protein into an equilibrated and fully hydrated membrane with minimal membrane perturbation we present a computational tool, called g_membed, which is part of the Gromacs suite of programs. The input consists of an equilibrated membrane system, either flat or curved, and a protein structure in the right position and orientation with respect to the lipid bilayer. g_membed first decreases the width of the protein in the xy-plane and removes all molecules (generally lipids and waters) that overlap with the narrowed protein. Then the protein is grown back to its full size in a short molecular dynamics simulation (typically 1000 steps), thereby pushing the lipids away to optimally accommodate the protein in the membrane. After embedding the protein in the membrane, both the lipid properties and the hydration layer are still close to equilibrium. Thus, only a short equilibration run (less then 1 ns in the cases tested) is required to re-equilibrate the membrane. Its simplicity makes g_membed very practical for use in scripting and high-throughput molecular dynamics simulations
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