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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.


Polar and hydrophobic contacts involved in the HAMP domain connector loops. (a) A tube model of the Af1503 HAMP domain (taken from a snapshot of the trajectory at 100 ns). The color scheme of the chain is the same as that in Fig. 4, but the difference in the alignments of models 1 and 2 (residues 110–112; the gray shaded region in Fig. 1) is colored in dark gray. (b) Schematic representation of the contacts in Af1503. Magenta and gray lines represent polar and hydrophobic contacts, respectively. Solid lines indicate the contacts between the corresponding pairs of residues in Af1503 and HtrII. Broken lines represent contacts appearing in either of the two molecules. (c) Tube model of the HtrII HAMP domain (taken from a snapshot of the trajectory at 160 ns). (d) Schematic representation of the contacts in HtrII.
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f5-6_27: Polar and hydrophobic contacts involved in the HAMP domain connector loops. (a) A tube model of the Af1503 HAMP domain (taken from a snapshot of the trajectory at 100 ns). The color scheme of the chain is the same as that in Fig. 4, but the difference in the alignments of models 1 and 2 (residues 110–112; the gray shaded region in Fig. 1) is colored in dark gray. (b) Schematic representation of the contacts in Af1503. Magenta and gray lines represent polar and hydrophobic contacts, respectively. Solid lines indicate the contacts between the corresponding pairs of residues in Af1503 and HtrII. Broken lines represent contacts appearing in either of the two molecules. (c) Tube model of the HtrII HAMP domain (taken from a snapshot of the trajectory at 160 ns). (d) Schematic representation of the contacts in HtrII.

Mentions: Structural stability is represented better by the RMSF values than the RMSD data. Figure 4a shows the RMSF values for Cα atoms of the Af1503 HAMP domain calculated for the last 50 ns of the trajectory. The stability of the Af1503 HAMP domain was confirmed by the small RMSF values, except for the flexible terminal residues. There are two minima in the RMSF values for the connector loop region, corresponding to L299 and V303. These two residues are stabilized during the simulation by hydrophobic contacts, L299-L326 and V303-I319/E320 (Fig. 5a). Hulko et al. pointed out that these residues are conserved during evolution and their contacts contribute to the stability of the connector loop12.


Molecular modeling of the HAMP domain of sensory rhodopsin II transducer from Natronomonas pharaonis
Polar and hydrophobic contacts involved in the HAMP domain connector loops. (a) A tube model of the Af1503 HAMP domain (taken from a snapshot of the trajectory at 100 ns). The color scheme of the chain is the same as that in Fig. 4, but the difference in the alignments of models 1 and 2 (residues 110–112; the gray shaded region in Fig. 1) is colored in dark gray. (b) Schematic representation of the contacts in Af1503. Magenta and gray lines represent polar and hydrophobic contacts, respectively. Solid lines indicate the contacts between the corresponding pairs of residues in Af1503 and HtrII. Broken lines represent contacts appearing in either of the two molecules. (c) Tube model of the HtrII HAMP domain (taken from a snapshot of the trajectory at 160 ns). (d) Schematic representation of the contacts in HtrII.
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Related In: Results  -  Collection

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f5-6_27: Polar and hydrophobic contacts involved in the HAMP domain connector loops. (a) A tube model of the Af1503 HAMP domain (taken from a snapshot of the trajectory at 100 ns). The color scheme of the chain is the same as that in Fig. 4, but the difference in the alignments of models 1 and 2 (residues 110–112; the gray shaded region in Fig. 1) is colored in dark gray. (b) Schematic representation of the contacts in Af1503. Magenta and gray lines represent polar and hydrophobic contacts, respectively. Solid lines indicate the contacts between the corresponding pairs of residues in Af1503 and HtrII. Broken lines represent contacts appearing in either of the two molecules. (c) Tube model of the HtrII HAMP domain (taken from a snapshot of the trajectory at 160 ns). (d) Schematic representation of the contacts in HtrII.
Mentions: Structural stability is represented better by the RMSF values than the RMSD data. Figure 4a shows the RMSF values for Cα atoms of the Af1503 HAMP domain calculated for the last 50 ns of the trajectory. The stability of the Af1503 HAMP domain was confirmed by the small RMSF values, except for the flexible terminal residues. There are two minima in the RMSF values for the connector loop region, corresponding to L299 and V303. These two residues are stabilized during the simulation by hydrophobic contacts, L299-L326 and V303-I319/E320 (Fig. 5a). Hulko et al. pointed out that these residues are conserved during evolution and their contacts contribute to the stability of the connector loop12.

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.