P-Loop Channels: Experimental Structures, and Physics-Based and Neural Networks-Based Models
Abstract
:1. Introduction
2. Comparative Structural Analysis of P-Loop Channels
3. Crystal and Cryo-EM Structures
4. Structures of P-Loop Channels with Drugs and Toxins
5. π-Bulges in the Inner Helices
6. AlphaFold2 Models and Experimental Structures
7. Perspectives
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
Abbreviations
AMPA | α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid |
Cryo-EM | cryo-electron microscopy |
DHP | dihydropyridines |
NMDA | N-methyl-d-aspartate |
iGluR | ionotropic glutamate receptors |
PD | pore domain |
PDB | protein data bank |
PDB ID | PDB index |
RMS | root mean square |
S1–S6 | transmembrane helices in P-loop channels |
SF | selectivity filter |
TRP | transient receptor potential |
VSD | voltage-sensing domain |
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Channel | PDB ID | Ref. | AF a | Channel | PDB ID | Ref. | AF a |
---|---|---|---|---|---|---|---|
Potassium | Calcium | ||||||
KcsA | 1bl8 | [26] | rbCav1.1 | 5gjv | [30] | ||
MthK | 6u6e | [31] | 6jpa | [32] | |||
MlotiK1 | 3beh | [33] | 6jpb | [32] | |||
Kv1.2/Kv2.1 | 2r9r | [28] | 7jpk | [34] | |||
hKv1.2 | P16389 | 7jpw | [34] | ||||
hKv1.6 | P17658 | 6jp5 | [32] | ||||
hKv2.1 | Q14721 | hCav1.1 | Q13698 | ||||
hKv3.1 | P48547 | hCav1.3 | Q01668 | ||||
hKv7.1 | 6uzz | [35] | P51787 | hCav3.1 | 6kzo | [36] | O43497 |
hERG | 5va2 | [37] | 6kzp | [36] | |||
Kir3.2 | 4kfm | [38] | hCav3.2 | O95180 | |||
GsuK | 4gx5 | [39] | hCav1.4 | O60840 | |||
Slo | 5tj6 | [40] | |||||
Sodium | iGluR | ||||||
NavAb | 3rvy | [41] | AMPA | 6dm0 | [42] | ||
5vb2 | [43] | NMDA | 6cna | [44] | |||
5vb8 | [43] | ||||||
6p6x | [45] | TRP | |||||
6pwp | [45] | TRPA1 | 3j9p | [46] | O75762 | ||
NavMs | 4f4l | [47] | TRPV1 | 3j5r | [48] | Q8NER1 | |
NavRh | 4dxw | [49] | TRPV2 | 6oo7 | [50] | Q9Y5S1 | |
NavPaS | 6a95 | [51] | TRPV3 | 6dvy | [52] | Q8NET8 | |
Nav1.2 | 6j8e | [53] | Q01118 | 6mhw | [54] | ||
hNav1.4 | 6agf | [55] | P35499 | 6mho | [54] | ||
EeNav1.4 | 5xsy | [56] | 6pvl | [57] | |||
rNav1.5 | 6uz3 | [58] | P15389 | 6dvw | [52] | ||
7fbs | [59] | 6uw9 | [60] | ||||
7k18 | [61] | 6lgp | [62] | ||||
hNav1.5 | 6lqa | [63] | Q14524 | 6uw4 | [60] | ||
hNav1.7 | 6j8j | [64] | 6mhs | [54] | |||
6n4r | [65] | TRPV6 | 5iwk | [66] | |||
hNav1.9 | Q9UI33 | 6e2g | [67] | Q9H1D0 | |||
hNav2.1 | Q01118 | TRPM2 | 6mj2 | [68] | O94759 | ||
TPC1 | 6c96 | [69] | TRPM6 | 6Bo9 | [70] |
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Tikhonov, D.B.; Zhorov, B.S. P-Loop Channels: Experimental Structures, and Physics-Based and Neural Networks-Based Models. Membranes 2022, 12, 229. https://doi.org/10.3390/membranes12020229
Tikhonov DB, Zhorov BS. P-Loop Channels: Experimental Structures, and Physics-Based and Neural Networks-Based Models. Membranes. 2022; 12(2):229. https://doi.org/10.3390/membranes12020229
Chicago/Turabian StyleTikhonov, Denis B., and Boris S. Zhorov. 2022. "P-Loop Channels: Experimental Structures, and Physics-Based and Neural Networks-Based Models" Membranes 12, no. 2: 229. https://doi.org/10.3390/membranes12020229