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Molecular modeling of the HAMP domain of sensory rhodopsin II transducer from Natronomonas pharaonis

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ABSTRACT

The halobacterial transducer of sensory rhodopsin II (HtrII) is a photosignal transducer associated with phototaxis in extreme halophiles. The HAMP domain, a linker domain in HtrII, is considered to play an important role in transferring the signal from the membrane to the cytoplasmic region, although its structure in the complex remains undetermined. To establish the structural basis for understanding the mechanism of signal transduction, we present an atomic model of the structure of the N-terminal HAMP domain from Natronomonas pharaonis (HtrII: 84–136), based on molecular dynamics (MD) simulations. The model was built by homology modeling using the NMR structure of Af1503 from Archaeoglobus fulgidus as a template. The HAMP domains of Af1503 and HtrII were stable during MD simulations over 100 ns. Quantitative analyses of inter-helical packing indicated that the Af1503 HAMP domain stably maintained unusual knobs-to-knobs packing, as observed in the NMR structure, while the bulky side-chains of HtrII shifted the packing state to canonical knobs-into-holes. The role of the connector loop in maintaining structural stability was also discussed using MD simulations of loop deletion mutants.

No MeSH data available.


Side-chain crick angles of the residues located in the four hydrophobic core layers plotted against simulation time. (a) Af1503 and (b) HtrII. Top: x-positions; middle: da-positions in the intra-chain interactions; bottom: da-positions in the inter-chain interactions. Coloring scheme: Layer 1 (blue), Layer 2 (red), Layer 3 (cyan), and Layer 4 (magenta). The spheres at time 0 indicate the average angles of the NMR structure. As a reference, the side-chain crick angles of a typical knobs-into-holes packing of a parallel coiled-coil of GCN4 leucine zipper (PDBid: 1gcl33) are given by horizontal lines (top and middle: a at 19° and d at −21°; bottom: e at 88° and g at −79°). The calculated values for GCN4 leucine zipper are shown in Supplementary Fig. S5. A typical knobs-to-knobs packing of a parallel, coiled-coil may give 0° for x-position and ±52° for da-position. Detailed values are shown in Supplementary Tab. S1.
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f7-6_27: Side-chain crick angles of the residues located in the four hydrophobic core layers plotted against simulation time. (a) Af1503 and (b) HtrII. Top: x-positions; middle: da-positions in the intra-chain interactions; bottom: da-positions in the inter-chain interactions. Coloring scheme: Layer 1 (blue), Layer 2 (red), Layer 3 (cyan), and Layer 4 (magenta). The spheres at time 0 indicate the average angles of the NMR structure. As a reference, the side-chain crick angles of a typical knobs-into-holes packing of a parallel coiled-coil of GCN4 leucine zipper (PDBid: 1gcl33) are given by horizontal lines (top and middle: a at 19° and d at −21°; bottom: e at 88° and g at −79°). The calculated values for GCN4 leucine zipper are shown in Supplementary Fig. S5. A typical knobs-to-knobs packing of a parallel, coiled-coil may give 0° for x-position and ±52° for da-position. Detailed values are shown in Supplementary Tab. S1.

Mentions: Figure 7 shows the side-chain crick angles of the NMR structure and the simulation results, along with the average values of the GCN4 leucine zipper (PDBid: 1gcl33) as an example of typical knobs-into-holes packing of parallel four-helix coiled-coil (the calculated side-chain crick angles for GCN4 are given in Supplementary Fig. S5). Typical knobs-to-knobs packing in a parallel coiled-coil may yield 0° for the x-position and ±52° for the da-position. The side-chain crick angles were stable during the simulations, maintained to within about ±3°. A deviation of the magnitude is much smaller than the difference between the two sets of side-chain crick angles for knobs-to-knobs and knobs-into-holes packing. Assuming that the signal transduction hypothesis of Hulko et al.’s 12 is true, or assuming that the HAMP domain interconverts the coiled-coil structure between knobs-to-knobs and knobs-into-holes packing states upon signal reception, the side-chain crick angles would be expected to fluctuate to a greater extent between the knobs-to-knobs and knobs-into-holes forms even in the equilibrium state. The small amplitudes of rotational motion of the four helices observed in the simulations suggest that any transition between the two packing forms requires an external stimulation much larger than the thermal fluctuations.


Molecular modeling of the HAMP domain of sensory rhodopsin II transducer from Natronomonas pharaonis
Side-chain crick angles of the residues located in the four hydrophobic core layers plotted against simulation time. (a) Af1503 and (b) HtrII. Top: x-positions; middle: da-positions in the intra-chain interactions; bottom: da-positions in the inter-chain interactions. Coloring scheme: Layer 1 (blue), Layer 2 (red), Layer 3 (cyan), and Layer 4 (magenta). The spheres at time 0 indicate the average angles of the NMR structure. As a reference, the side-chain crick angles of a typical knobs-into-holes packing of a parallel coiled-coil of GCN4 leucine zipper (PDBid: 1gcl33) are given by horizontal lines (top and middle: a at 19° and d at −21°; bottom: e at 88° and g at −79°). The calculated values for GCN4 leucine zipper are shown in Supplementary Fig. S5. A typical knobs-to-knobs packing of a parallel, coiled-coil may give 0° for x-position and ±52° for da-position. Detailed values are shown in Supplementary Tab. S1.
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getmorefigures.php?uid=PMC5036668&req=5

f7-6_27: Side-chain crick angles of the residues located in the four hydrophobic core layers plotted against simulation time. (a) Af1503 and (b) HtrII. Top: x-positions; middle: da-positions in the intra-chain interactions; bottom: da-positions in the inter-chain interactions. Coloring scheme: Layer 1 (blue), Layer 2 (red), Layer 3 (cyan), and Layer 4 (magenta). The spheres at time 0 indicate the average angles of the NMR structure. As a reference, the side-chain crick angles of a typical knobs-into-holes packing of a parallel coiled-coil of GCN4 leucine zipper (PDBid: 1gcl33) are given by horizontal lines (top and middle: a at 19° and d at −21°; bottom: e at 88° and g at −79°). The calculated values for GCN4 leucine zipper are shown in Supplementary Fig. S5. A typical knobs-to-knobs packing of a parallel, coiled-coil may give 0° for x-position and ±52° for da-position. Detailed values are shown in Supplementary Tab. S1.
Mentions: Figure 7 shows the side-chain crick angles of the NMR structure and the simulation results, along with the average values of the GCN4 leucine zipper (PDBid: 1gcl33) as an example of typical knobs-into-holes packing of parallel four-helix coiled-coil (the calculated side-chain crick angles for GCN4 are given in Supplementary Fig. S5). Typical knobs-to-knobs packing in a parallel coiled-coil may yield 0° for the x-position and ±52° for the da-position. The side-chain crick angles were stable during the simulations, maintained to within about ±3°. A deviation of the magnitude is much smaller than the difference between the two sets of side-chain crick angles for knobs-to-knobs and knobs-into-holes packing. Assuming that the signal transduction hypothesis of Hulko et al.’s 12 is true, or assuming that the HAMP domain interconverts the coiled-coil structure between knobs-to-knobs and knobs-into-holes packing states upon signal reception, the side-chain crick angles would be expected to fluctuate to a greater extent between the knobs-to-knobs and knobs-into-holes forms even in the equilibrium state. The small amplitudes of rotational motion of the four helices observed in the simulations suggest that any transition between the two packing forms requires an external stimulation much larger than the thermal fluctuations.

View Article: PubMed Central - PubMed

ABSTRACT

The halobacterial transducer of sensory rhodopsin II (HtrII) is a photosignal transducer associated with phototaxis in extreme halophiles. The HAMP domain, a linker domain in HtrII, is considered to play an important role in transferring the signal from the membrane to the cytoplasmic region, although its structure in the complex remains undetermined. To establish the structural basis for understanding the mechanism of signal transduction, we present an atomic model of the structure of the N-terminal HAMP domain from Natronomonas pharaonis (HtrII: 84–136), based on molecular dynamics (MD) simulations. The model was built by homology modeling using the NMR structure of Af1503 from Archaeoglobus fulgidus as a template. The HAMP domains of Af1503 and HtrII were stable during MD simulations over 100 ns. Quantitative analyses of inter-helical packing indicated that the Af1503 HAMP domain stably maintained unusual knobs-to-knobs packing, as observed in the NMR structure, while the bulky side-chains of HtrII shifted the packing state to canonical knobs-into-holes. The role of the connector loop in maintaining structural stability was also discussed using MD simulations of loop deletion mutants.

No MeSH data available.