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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.


Schematic representation of the definition of the side-chain crick angle.
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f2-6_27: Schematic representation of the definition of the side-chain crick angle.

Mentions: The crick angle is defined in TWISTER for two helices (A and B) in a coiled-coil by the average of the angles COAXA and COBXB, where OA is a point on the central axis of helix A, C is the center of the coiled-coil defined by (OA+OB)/2, and XA represents the position of Cα in helix A at which the crick angle is defined (Fig. 2). However, the original definition, based on the position of Cα, is not necessarily appropriate for rigorously defining the direction of a side-chain forming core packing in coiled-coil. To solve this problem, we defined the side-chain crick angle by changing the definition of XA to the center of mass of nonhydrogen atoms in the side-chain projected onto the plane defined by OAOB and an axis perpendicular to the coiled-coil axis.


Molecular modeling of the HAMP domain of sensory rhodopsin II transducer from Natronomonas pharaonis
Schematic representation of the definition of the side-chain crick angle.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC5036668&req=5

f2-6_27: Schematic representation of the definition of the side-chain crick angle.
Mentions: The crick angle is defined in TWISTER for two helices (A and B) in a coiled-coil by the average of the angles COAXA and COBXB, where OA is a point on the central axis of helix A, C is the center of the coiled-coil defined by (OA+OB)/2, and XA represents the position of Cα in helix A at which the crick angle is defined (Fig. 2). However, the original definition, based on the position of Cα, is not necessarily appropriate for rigorously defining the direction of a side-chain forming core packing in coiled-coil. To solve this problem, we defined the side-chain crick angle by changing the definition of XA to the center of mass of nonhydrogen atoms in the side-chain projected onto the plane defined by OAOB and an axis perpendicular to the coiled-coil axis.

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.