ABCMdb

ABCB10 p.Leu339Cys

Predicted by SNAP2:	A: N (78%), C: N (82%), D: D (66%), E: D (63%), F: N (78%), G: D (59%), H: N (53%), I: N (97%), K: D (59%), M: N (97%), N: N (57%), P: D (66%), Q: N (66%), R: N (57%), S: N (57%), T: N (61%), V: N (93%), W: N (72%), Y: N (72%),
Predicted by PROVEAN:	A: D, C: D, D: D, E: D, F: N, G: D, H: D, I: N, K: D, M: N, N: D, P: D, Q: D, R: D, S: D, T: D, V: N, W: D, Y: D,

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[hide] Structural characterization of two metastable ATP-... PLoS One. 2014 Mar 14;9(3):e91916. doi: 10.1371/journal.pone.0091916. eCollection 2014. O'Mara ML, Mark AE
Structural characterization of two metastable ATP-bound states of P-glycoprotein.
PLoS One. 2014 Mar 14;9(3):e91916. doi: 10.1371/journal.pone.0091916. eCollection 2014., [PMID:24632881]

Abstract [show]
ATP Binding Cassette (ABC) transporters couple the binding and hydrolysis of ATP to the transport of substrate molecules across the membrane. The mechanism by which ATP binding and/or hydrolysis drives the conformational changes associated with substrate transport has not yet been characterized fully. Here, changes in the conformation of the ABC export protein P-glycoprotein on ATP binding are examined in a series of molecular dynamics simulations. When one molecule of ATP is placed at the ATP binding site associated with each of the two nucleotide binding domains (NBDs), the membrane-embedded P-glycoprotein crystal structure adopts two distinct metastable conformations. In one, each ATP molecule interacts primarily with the Walker A motif of the corresponding NBD. In the other, the ATP molecules interacts with both Walker A motif of one NBD and the Signature motif of the opposite NBD inducing the partial dimerization of the NBDs. This interaction is more extensive in one of the two ATP binding site, leading to an asymmetric structure. The overall conformation of the transmembrane domains is not altered in either of these metastable states, indicating that the conformational changes associated with ATP binding observed in the simulations in the absence of substrate do not lead to the outward-facing conformation and thus would be insufficient in themselves to drive transport. Nevertheless, the metastable intermediate ATP-bound conformations observed are compatible with a wide range of experimental cross-linking data demonstrating the simulations do capture physiologically important conformations. Analysis of the interaction between ATP and its cofactor Mg(2+) with each NBD indicates that the coordination of ATP and Mg(2+) differs between the two NBDs. The role structural asymmetry may play in ATP binding and hydrolysis is discussed. Furthermore, we demonstrate that our results are not heavily influenced by the crystal structure chosen for initiation of the simulations.

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140 doi:10.1371/journal.pone.0091916.t001 Table 2. X-linking in the inward-facing ATP-bound state. Cross-linked residues (human P-gp numbering) Distance between Ca`s (nm) MD Simulations Calc. MTS spacer helices TM 1 2 Min Max Average (2690 ns) Ref. 1 & 11 M68C Y950C 0.8 1.2 1.0 +/- 0.1 0.9 a [56] 1 & 11 M68C Y953C 0.9 1.4 1.1 +/- 0.1 0.9 a [56] 1 & 11 M68C A954C 0.7 1.3 1.0 +/- 0.1 0.9 a [56] 1 & 11 M69C A954C 0.9 1.5 1.2 +/- 0.1 0.9 a [56] 1 & 12 M69C L975C 1.0 1.5 1.2 +/- 0.1 0.9 a [56] 2 & 11 V133C G939C 0.5 0.7 0.6 +/- 0.1 0.9 a [55] 2 & 11 C137C A935C 0.5 0.7 0.6 +/- 0.1 0.9 a [55] 3 & 9 L175C N820C 2.5 3.7 3.2 +/- 0.2 3.0 b [60] 4 & 12 L227C S993C 2.4 3.4 2.8 +/- 0.1 0.9 a [63] 4 & 12 V231C S993C 2.1 2.9 2.5 +/- 0.2 0.9 a [63] 4 & 12 W232C S993C 1.8 2.8 2.3 +/- 0.2 0.9 a [63] 4 & 12 A233C S993C 1.6 2.4 2.0 +/- 0.1 0.9 a [63] 4 & 12 I235C S993C 1.8 2.7 2.2 +/- 0.2 0.9 a [63] 4 & 12 L236C S993C 1.4 2.5 1.9 +/- 0.2 0.9 a [63] 5 & 12 A295C S993C 1.0 2.0 1.4 +/- 0.2 0.9 a [63] 5 & 12 I299C S993C 0.9 2.0 1.4 +/- 0.2 0.9 a [63] 6 & 7 L339C F728C 1.1 2.0 1.2 +/- 0.1 3.0 b [58] 6 & 7 L339C A729C 1.1 2.0 1.5 +/- 0.2 3.0 b [58] 6 & 7 F343C F728C 1.1 2.1 1.5 +/- 0.2 3.0 b [57,58] 6 & 10 L332C Q856C 2.3 2.9 2.6 +/- 0.1 2.2 c [65] 6 & 10 P350C V874C 2.2 4.1 3.2 +/- 0.4 0.9 a [63] 6 & 10 P350C E875C 1.8 3.8 2.9 +/- 0.5 0.9 a [63] 6 & 10 P350C M876C 1.7 3.9 2.9 +/- 0.5 0.9 a [63] 6 & 12 L332C L975C 0.9 1.5 1.2 +/- 0.1 2.2 c [61,62] 6 & 12 L332C L976C 1.2 1.8 1.5 +/- 0.1 2.2 c [64] 6 & 12 F343C V982C 1.5 2.3 1.9 +/- 0.1 3.0 b [58,64] 6 & 12 F343C M986C 1.3 2.4 1.8 +/- 0.2 0.9 a [62] 6 & 12 G346C G989C 1.6 3.0 2.2 +/- 0.3 0.9 a [62] 6 & 12 P350C S993C 1.4 2.8 2.0 +/- 0.2 0.9 a [62] doi:10.1371/journal.pone.0091916.t002 of P-gp obtained in previous MD simulation studies. Login to comment
150 The relative orientation of these two subdomains is Table 3. X-linking in the asymmetric ATP-bound state. Cross-linked residues (human P-gp numbering) Distance between Ca`s (nm) MD Simulations Calc. MTS spacer TM helices 1 2 Min Max Average (2690 ns) Ref. 1 & 11 M68C Y950C 0.8 1.4 1.1 +/- 0.1 0.9 a [56] 1 & 11 M68C Y953C 0.8 1.6 1.2 +/- 0.1 0.9 a [56] 1 & 11 M68C A954C 0.8 1.6 1.2 +/- 0.1 0.9 a [56] 1 & 11 M69C A954C 1.0 1.8 1.3 +/- 0.1 0.9 a [56] 1 & 12 M69C L975C 0.9 1.7 1.2 +/- 0.1 0.9 a [56] 2 & 11 V133C G939C 0.5 0.9 0.6 +/- 0.1 0.9 a [55] 2 & 11 C137C A935C 0.5 1.0 0.6 +/- 0.1 0.9 a [55] 3 & 9 L175C N820C 2.4 3.7 3.0 +/- 0.2 3.0 b [60] 4 & 12 L227C S993C 2.3 3.9 3.3 +/- 0.2 0.9 a [63] 4 & 12 V231C S993C 2.0 3.5 2.9 +/- 0.2 0.9 a [63] 4 & 12 W232C S993C 1.6 3.2 2.7 +/- 0.2 0.9 a [63] 4 & 12 A233C S993C 1.4 2.9 2.4 +/- 0.2 0.9 a [63] 4 & 12 I235C S993C 1.6 3.2 2.5 +/- 0.2 0.9 a [63] 4 & 12 L236C S993C 1.3 2.8 2.2 +/- 0.2 0.9 a [63] 5 & 12 A295C S993C 0.9 2.3 1.6 +/- 0.2 0.9 a [63] 5 & 12 I299C S993C 0.9 2.4 1.7 +/- 0.2 0.9 a [63] 6 & 7 L339C F728C 0.9 1.9 1.4 +/- 0.1 3.0 b [58] 6 & 7 L339C A729C 0.9 1.9 1.4 +/- 0.2 3.0 b [58] 6 & 7 F343C F728C 0.9 2.2 1.5 +/- 0.1 3.0 b [57,58] 6 & 10 L332C Q856C 2.5 3.4 3.1 +/- 0.2 2.2 c [65] 6 & 10 P350C V874C 1.9 4.5 3.3 +/- 0.4 0.9 a [63] 6 & 10 P350C E875C 1.6 4.1 3.0 +/- 0.4 0.9 a [63] 6 & 10 P350C M876C 1.4 4.1 3.0 +/- 0.4 0.9 a [63] 6 & 12 L332C L975C 1.1 1.9 1.5 +/- 0.1 2.2 c [61,62] 6 & 12 L332C L976C 1.4 2.2 1.8 +/- 0.1 2.2 c [64] 6 & 12 F343C V982C 1.2 2.7 2.2 +/- 0.3 3.0 b [58,64] 6 & 12 F343C M986C 1.0 2.5 2.0 +/- 0.3 0.9 a [62] 6 & 12 G346C G989C 1.1 3.3 2.4 +/- 0.4 0.9 a [62] 6 & 12 P350C S993C 1.1 3.5 2.6 +/- 0.4 0.9 a [62] NOTE: In Tables 2 and 3 the distance between Ca atoms has been estimated as follows: 26 (length of cysteine side chain + distance to spacer) + length of spacer. Login to comment