Molecular Dynamics
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- Contributed by Simone Furini
When calculating the free-energy of ions permeating membrane proteins, an initial decision to make is how many ions needs to be included in the calculation. This decision is usually based on previous knowledge (both experiments and simulations), and on the intuition of the researcher. But intuition might be wrong… And taking the number of ions wrong might render free-energy profiles that are ...
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- Published in Molecular Dynamics
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- Contributed by Simone Furini
Periodic Boundary Conditions are almost universally adopted in simulations of biological systems at the microscopic scale, in order to replicate as close as possible the experimental environment, while keeping the number of particles to a minimum. While PBC are generally great, they do not allow to simulate gradients in-between the two sides of the simulation box, as these are actually the same ...
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- Published in Molecular Dynamics
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- Contributed by Simone Furini
Na+ channels have high-conductivity to sodium ions, while at the same time being almost completely impermeable to potassium ion. The first characteristic suggests loose atomic interactions between the permeating particles and the channel. On the other hand, it is hard to imagine how selectivity between two similar ion species might be possible under these loose atomic interactions. ...
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- Published in Molecular Dynamics
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- Contributed by Simone Furini
The selectivity of ion channels to different ion species is crucial for important biological processes, as nerve transmission and muscular contraction. Thanks to the availability of experimental atomic structures of several ion channels, including K+-channels, Na+-channels and Ca2+-channels, it is now possible to investigate the microscopic details of conduction ...
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- Published in Molecular Dynamics
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- Contributed by Simone Furini
The binding of proteins to DNA controls many cellular events, including gene expression. In order to work properly, DNA binding proteins need to find their target sequences on DNA with high speed and accuracy. The recognition of the specific DNA binding site requires intimate contacts between the protein and the DNA molecule. However, strong atomic interactions between the two molecules are ...
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- Published in Molecular Dynamics
