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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.

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Cross sections of the four HAMP domain hydrophobic core layers (layer 1–layer 4), viewed from the N-terminal sides (from the top of the structures in Fig. 4). (a) NMR structure of Af1503 (PDBid: 2asw). (b) Simulated structure of Af1503 at 100 ns. (c) Simulated structure of HtrII at 100 ns. AS1 and AS2 helices are colored in green and yellow, respectively. The two helices at bottom represent chain A and those at top are chain B. The side-chain atoms of the x-positions are represented by red spheres, and those of the da positions by blue spheres. The knobs-into-holes packing form is achieved by rotations of the helices by +26° for AS1 (green) and −26° for AS2 (yellow).
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f6-6_27: Cross sections of the four HAMP domain hydrophobic core layers (layer 1–layer 4), viewed from the N-terminal sides (from the top of the structures in Fig. 4). (a) NMR structure of Af1503 (PDBid: 2asw). (b) Simulated structure of Af1503 at 100 ns. (c) Simulated structure of HtrII at 100 ns. AS1 and AS2 helices are colored in green and yellow, respectively. The two helices at bottom represent chain A and those at top are chain B. The side-chain atoms of the x-positions are represented by red spheres, and those of the da positions by blue spheres. The knobs-into-holes packing form is achieved by rotations of the helices by +26° for AS1 (green) and −26° for AS2 (yellow).

Mentions: The inter-helical contacts in the coiled-coil structure serve as the main source of stability in the HAMP domains. The coiled-coil packing in the NMR structure and the simulation results for Af1503 and HtrII are shown in Fig. 6. Hulko et al. argued that the Af1503 HAMP domain is characterized by unusual knobs-to-knobs (x-da) packing, which is related to canonical knobs-into-holes packing by a 26° rotation of each helix12. The NMR structure indicates that the side-chains of I284 and L315 at the x-position in layers 1 and 2, respectively, point toward the center of the coiled-coil (Fig. 6a). This is the characteristic form of knobs-to-knobs (x-da) packing. On the other hand, in the layer 4, L322 appears to be inserted into the pocket formed by I294 and A295 of the other chain. This feature is typical of knobs-into-holes (a-d) packing. Therefore, our data suggest that layers 1 and 2 exhibit x-da packing as argued by Hulko et al.12, while layer 4 is clearly in the a–d packing state. However, the packing form cannot be rigorously determined by eye, particularly in the case of residues with small side-chains, such as A291 in layer 3. To overcome this limitation, we calculated the side-chain crick angle using TWISTER program17.


Molecular modeling of the HAMP domain of sensory rhodopsin II transducer from Natronomonas pharaonis
Cross sections of the four HAMP domain hydrophobic core layers (layer 1–layer 4), viewed from the N-terminal sides (from the top of the structures in Fig. 4). (a) NMR structure of Af1503 (PDBid: 2asw). (b) Simulated structure of Af1503 at 100 ns. (c) Simulated structure of HtrII at 100 ns. AS1 and AS2 helices are colored in green and yellow, respectively. The two helices at bottom represent chain A and those at top are chain B. The side-chain atoms of the x-positions are represented by red spheres, and those of the da positions by blue spheres. The knobs-into-holes packing form is achieved by rotations of the helices by +26° for AS1 (green) and −26° for AS2 (yellow).
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f6-6_27: Cross sections of the four HAMP domain hydrophobic core layers (layer 1–layer 4), viewed from the N-terminal sides (from the top of the structures in Fig. 4). (a) NMR structure of Af1503 (PDBid: 2asw). (b) Simulated structure of Af1503 at 100 ns. (c) Simulated structure of HtrII at 100 ns. AS1 and AS2 helices are colored in green and yellow, respectively. The two helices at bottom represent chain A and those at top are chain B. The side-chain atoms of the x-positions are represented by red spheres, and those of the da positions by blue spheres. The knobs-into-holes packing form is achieved by rotations of the helices by +26° for AS1 (green) and −26° for AS2 (yellow).
Mentions: The inter-helical contacts in the coiled-coil structure serve as the main source of stability in the HAMP domains. The coiled-coil packing in the NMR structure and the simulation results for Af1503 and HtrII are shown in Fig. 6. Hulko et al. argued that the Af1503 HAMP domain is characterized by unusual knobs-to-knobs (x-da) packing, which is related to canonical knobs-into-holes packing by a 26° rotation of each helix12. The NMR structure indicates that the side-chains of I284 and L315 at the x-position in layers 1 and 2, respectively, point toward the center of the coiled-coil (Fig. 6a). This is the characteristic form of knobs-to-knobs (x-da) packing. On the other hand, in the layer 4, L322 appears to be inserted into the pocket formed by I294 and A295 of the other chain. This feature is typical of knobs-into-holes (a-d) packing. Therefore, our data suggest that layers 1 and 2 exhibit x-da packing as argued by Hulko et al.12, while layer 4 is clearly in the a–d packing state. However, the packing form cannot be rigorously determined by eye, particularly in the case of residues with small side-chains, such as A291 in layer 3. To overcome this limitation, we calculated the side-chain crick angle using TWISTER program17.

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.


Related in: MedlinePlus