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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.


Sequence alignment between the HAMP domains of Af1503 and HtrII. Two different alignments (model 1 and model 2) were constructed. The gray shaded region delineates the difference between the two alignments. AS1 and AS2 denote the helices observed in the NMR structure. The positions noted by x and da, and a and d, are according to references 5 and 12, respectively.
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f1-6_27: Sequence alignment between the HAMP domains of Af1503 and HtrII. Two different alignments (model 1 and model 2) were constructed. The gray shaded region delineates the difference between the two alignments. AS1 and AS2 denote the helices observed in the NMR structure. The positions noted by x and da, and a and d, are according to references 5 and 12, respectively.

Mentions: A model of the N-terminal HAMP domain of Natronomonas pharaonis HtrII (residues 84–136) was built using homology modeling based on the NMR structure of Archaeoglobus fulgidus Af1503 (residues 278–331; PDBid: 2asw)12. We evaluated two different sequence alignments; one obtained by a Needleman and Wunsch type algorithm18 with BLOSUM6219 (Fig. 1, model 1), and the other obtained with PAM7020 (model 2). Both alignments were obtained with gap opening (=11) and extension (=1) penalties. The alignments differ only in three residues and a gap, but this resulted in a large change in the stability of the connector loop (described below). The common part of the two alignments was confirmed by the x-da pattern in the NMR structure12, and the heptad sequence repeats of the helices predicted for the secondary structures5. The coordinates of the homology model were generated using MODELLER (version 8.2)21, followed by refinement of the side-chain conformations using SCWRL (version 3.0)22. The N-terminal and C-terminal residues were acetylated and amidated, respectively, to avoid the influence of charges. The model was validated by WHAT_CHECK23 and PROCHECK24. The HAMP domain model was then relaxed in an explicit water environment by molecular dynamics simulations, using the MD program MARBLE25 according to the protocol described below. The model was solvated in a periodic boundary box of water26 and subject to energy minimization, followed by equilibration. Product runs were then performed without restraints. The simulation system for HtrII consists of a box of 64 Å×55 Å×44 Å containing 4,300 water molecules and 14 Na+ ions (14,600 atoms in total). The reference system for Af1503 was contained in a box of 66 Å×50 Å×45 Å with 4,200 water molecules and 2 Na+ ions (14,200 atoms in total).


Molecular modeling of the HAMP domain of sensory rhodopsin II transducer from Natronomonas pharaonis
Sequence alignment between the HAMP domains of Af1503 and HtrII. Two different alignments (model 1 and model 2) were constructed. The gray shaded region delineates the difference between the two alignments. AS1 and AS2 denote the helices observed in the NMR structure. The positions noted by x and da, and a and d, are according to references 5 and 12, respectively.
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Related In: Results  -  Collection

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f1-6_27: Sequence alignment between the HAMP domains of Af1503 and HtrII. Two different alignments (model 1 and model 2) were constructed. The gray shaded region delineates the difference between the two alignments. AS1 and AS2 denote the helices observed in the NMR structure. The positions noted by x and da, and a and d, are according to references 5 and 12, respectively.
Mentions: A model of the N-terminal HAMP domain of Natronomonas pharaonis HtrII (residues 84–136) was built using homology modeling based on the NMR structure of Archaeoglobus fulgidus Af1503 (residues 278–331; PDBid: 2asw)12. We evaluated two different sequence alignments; one obtained by a Needleman and Wunsch type algorithm18 with BLOSUM6219 (Fig. 1, model 1), and the other obtained with PAM7020 (model 2). Both alignments were obtained with gap opening (=11) and extension (=1) penalties. The alignments differ only in three residues and a gap, but this resulted in a large change in the stability of the connector loop (described below). The common part of the two alignments was confirmed by the x-da pattern in the NMR structure12, and the heptad sequence repeats of the helices predicted for the secondary structures5. The coordinates of the homology model were generated using MODELLER (version 8.2)21, followed by refinement of the side-chain conformations using SCWRL (version 3.0)22. The N-terminal and C-terminal residues were acetylated and amidated, respectively, to avoid the influence of charges. The model was validated by WHAT_CHECK23 and PROCHECK24. The HAMP domain model was then relaxed in an explicit water environment by molecular dynamics simulations, using the MD program MARBLE25 according to the protocol described below. The model was solvated in a periodic boundary box of water26 and subject to energy minimization, followed by equilibration. Product runs were then performed without restraints. The simulation system for HtrII consists of a box of 64 Å×55 Å×44 Å containing 4,300 water molecules and 14 Na+ ions (14,600 atoms in total). The reference system for Af1503 was contained in a box of 66 Å×50 Å×45 Å with 4,200 water molecules and 2 Na+ ions (14,200 atoms in total).

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.