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. 2010 Jun;135(6):555-62.
doi: 10.1085/jgp.200910373.

Exploring atomic resolution physiology on a femtosecond to millisecond timescale using molecular dynamics simulations

Ron O Dror  1 , Morten Ø Jensen, David W Borhani, David E Shaw
Affiliations

Exploring atomic resolution physiology on a femtosecond to millisecond timescale using molecular dynamics simulations

Ron O Dror et al. J Gen Physiol. 2010 Jun.
No abstract available

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Figures

Figure 1.
Figure 1.
Spatiotemporal resolution of various biophysical techniques. The temporal (abcissa) and spatial (ordinate) resolutions of each technique are indicated by colored boxes. Techniques capable of yielding data on single molecules (as opposed to only on ensembles) are shown in bold. Nuclear magnetic resonance methods can probe a wide range of timescales, but they provide limited information on motion at certain intermediate timescales, as indicated by the lighter shading and dashed lines. The timescales of some fundamental molecular processes, as well as composite physiological processes, are indicated below the abcissa. The (spatial) resolution needed to resolve certain objects is shown at right. AFM, atomic force microscopy; EM, electron microscopy; FRET, Förster resonance energy transfer; NMR, nuclear magnetic resonance.
Figure 2.
Figure 2.
Single-channel recording of ion permeation from experiment and simulation. Electrophysiological recording of current through a potassium channel (top) and recording of ion permeation from an all-atom simulation of the Kv1.2 potassium channel (bottom; cf. Jensen et al., 2010). (Bottom left) The simulated model, consisting of lipid molecules (spheres), Kv1.2 (orange; only the pore domain is shown), potassium ions (shown as green spheres within the selectivity filter [white box]; remaining K+ and Cl− ions not shown), lipid molecules (chains of spheres), and water molecules (red/white spheres and gray surface). (Bottom middle) Magnification of the selectivity filter. (Bottom right) Positions of K+ ions permeating the selectivity filter (left ordinate; drawn to scale with the selectivity filter) versus simulation time (abcissa) at a depolarizing voltage of ∼25 mV. Traces of individual ion positions are shown in various colors. Red line and circles indicate accumulated permeation events of individual K+ ions (right ordinate). The experimental channel recording was originally published by Li et al. (2006) and is reprinted here with permission from Proceedings of the National Academy of Sciences of the United States of America (PNAS). Use of this figure is gratefully acknowledged.
See this image and copyright information in PMC

References

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