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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.


Time evolution of the root mean square displacement (RMSD= 〈(ri – Ri) 2〉1/2 where ri is the coordinates of atom i of the target structure superimposed upon the reference structure Ri, and 〈 〉 denotes the average) for Cα atoms of the Af1503 HAMP domains from the NMR structure (PDBid: 2asw) during the simulation. The RMSD values were obtained by superimposition of the helix regions, AS1 and AS2 (Af1503: 278–296 and 310–331; HtrII: 84–102 and 115–136). The values presented here is the average for the two chains. (a) Af1503, (b) the Af1503 loop deletion mutant, (c) HtrII, and (d) the HtrII loop deletion mutant. Blue: RMSD for the entire HAMP domain; Red: RMSD for the helices only; Gray: RMSD for the connector loops only (Af1503: 297–309; HtrII: 103–114).
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f3-6_27: Time evolution of the root mean square displacement (RMSD= 〈(ri – Ri) 2〉1/2 where ri is the coordinates of atom i of the target structure superimposed upon the reference structure Ri, and 〈 〉 denotes the average) for Cα atoms of the Af1503 HAMP domains from the NMR structure (PDBid: 2asw) during the simulation. The RMSD values were obtained by superimposition of the helix regions, AS1 and AS2 (Af1503: 278–296 and 310–331; HtrII: 84–102 and 115–136). The values presented here is the average for the two chains. (a) Af1503, (b) the Af1503 loop deletion mutant, (c) HtrII, and (d) the HtrII loop deletion mutant. Blue: RMSD for the entire HAMP domain; Red: RMSD for the helices only; Gray: RMSD for the connector loops only (Af1503: 297–309; HtrII: 103–114).

Mentions: The root-mean-square-displacements (RMSD) of the HAMP domain from the NMR structure (PDBid: 2asw) are plotted against the simulation time in Figs. 3a and 3c. The Af1503 HAMP domain was stable over a period of 100 ns, maintaining the original NMR structure even in the loop region. The RMSD value for the helices and the loop region averaged over the last 50 ns were 1.32 Å, and 1.67 Å, respectively. The HtrII HAMP domain was also stable in the helical regions (RMSD=1.61 Å), but in the loop region the structure appeared to change considerably compared to the template structure based on the NMR structure (RMSD= 2.96 Å). As discussed in more detail below, the large RMSD value for the HtrII HAMP domain was caused by the process of optimizing the template structure rather than flexibility of the loop region.


Molecular modeling of the HAMP domain of sensory rhodopsin II transducer from Natronomonas pharaonis
Time evolution of the root mean square displacement (RMSD= 〈(ri – Ri) 2〉1/2 where ri is the coordinates of atom i of the target structure superimposed upon the reference structure Ri, and 〈 〉 denotes the average) for Cα atoms of the Af1503 HAMP domains from the NMR structure (PDBid: 2asw) during the simulation. The RMSD values were obtained by superimposition of the helix regions, AS1 and AS2 (Af1503: 278–296 and 310–331; HtrII: 84–102 and 115–136). The values presented here is the average for the two chains. (a) Af1503, (b) the Af1503 loop deletion mutant, (c) HtrII, and (d) the HtrII loop deletion mutant. Blue: RMSD for the entire HAMP domain; Red: RMSD for the helices only; Gray: RMSD for the connector loops only (Af1503: 297–309; HtrII: 103–114).
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Related In: Results  -  Collection

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f3-6_27: Time evolution of the root mean square displacement (RMSD= 〈(ri – Ri) 2〉1/2 where ri is the coordinates of atom i of the target structure superimposed upon the reference structure Ri, and 〈 〉 denotes the average) for Cα atoms of the Af1503 HAMP domains from the NMR structure (PDBid: 2asw) during the simulation. The RMSD values were obtained by superimposition of the helix regions, AS1 and AS2 (Af1503: 278–296 and 310–331; HtrII: 84–102 and 115–136). The values presented here is the average for the two chains. (a) Af1503, (b) the Af1503 loop deletion mutant, (c) HtrII, and (d) the HtrII loop deletion mutant. Blue: RMSD for the entire HAMP domain; Red: RMSD for the helices only; Gray: RMSD for the connector loops only (Af1503: 297–309; HtrII: 103–114).
Mentions: The root-mean-square-displacements (RMSD) of the HAMP domain from the NMR structure (PDBid: 2asw) are plotted against the simulation time in Figs. 3a and 3c. The Af1503 HAMP domain was stable over a period of 100 ns, maintaining the original NMR structure even in the loop region. The RMSD value for the helices and the loop region averaged over the last 50 ns were 1.32 Å, and 1.67 Å, respectively. The HtrII HAMP domain was also stable in the helical regions (RMSD=1.61 Å), but in the loop region the structure appeared to change considerably compared to the template structure based on the NMR structure (RMSD= 2.96 Å). As discussed in more detail below, the large RMSD value for the HtrII HAMP domain was caused by the process of optimizing the template structure rather than flexibility of the loop region.

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.