A potassium ion channel simulated with a universal neural network potential

A potassium ion channel simulated with a universal neural network potential

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2 weeks ago 60

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A potassium ion channel simulated with a universal neural network potential

@scienceguy2 weeks ago

A potassium ion channel simulated with a
universal neural network potential.
Tim Duignan
tim@orb…

1/16

Figure 1: The KcsA potassium ion channel (PDB ID: 1K4C) and its selectivity filter
(SF). Overall s…

2/16

may be crucial for understanding the channel’s exceptional K+/Na+ selectivity and
deactivation mec…

3/16

significantly faster simulations, while maintaining high accuracy. Orb-D3 also has
remarkable tran…

4/16

ulate the whole protein with Orb-D3 were unsuccessful this is unsurprising given
that this is a me…

5/16

S1
S4
S3
S2 F
a) b) c) d) e)
Figure 3: Snapshots from a simulation trajectory showing rapid wa…

6/16

0 100 200 300 400 500 600 700
Time (ps)
15
10
5
0
5
10
15
20
25
Z position (Å)
K
Water…

7/16

0 2 4 6 8 10
Distance (Å)
0.0
0.5
1.0
1.5
2.0
2.5
RDF
O---H
Figure 5: Radial distribution…

8/16

(a) T75 Hydrogen bond. (b) Flipped G77s carbonyls.
Figure 6: Example snapshots from the simulation…

9/16

and a hard knock-on mechanism occurs. In fact, the strong positive charge in the
SF appears to cau…

10/16

2 4 6 8 10
r [Å]
0
2
4
RDF
K-O (orb-d3-v2)
K-O (DC-R
2SCAN-NNP)
(a) Potassium-oxygen RDFs
…

11/16

as well as their sensitivity to small errors in the potential energy surface. This work
demonstrat…

12/16

References
[1] D. A. Doyle, J. M. Cabral, R. A. Pfuetzner, A. Kuo, J. M. Gulbis, S. L. Cohen,
B. …

13/16

[21] W. Treptow, Y. Liu, C. A. Z. Bassetto, B. I. Pinto, J. Alves, C. Chipot, F.
Bezanilla, B. Rou…

14/16

[34] H. Yang, C. Hu, Y. Zhou, X. Liu, Y. Shi, J. Li, G. Li, Z. Chen, S. Chen,
C. Zeni, M. Horton, …

15/16

[50] K. Mita, T. Sumikama, M. Iwamoto, Y. Matsuki, K. Shigemi, S. Oiki, Proc.
Natl. Acad. Sci. U.S…

16/16

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A potassium ion channel simulated with a universal neural network potential

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