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The HAMP signal relay domain adopts multiple conformational states through collective piston and tilt motions.

Zhu L, Bolhuis PG, Vreede J - PLoS Comput. Biol. (2013)

Bottom Line: These simulations revealed additional conformational states that differ in the tilt angles between the helices as well as the relative piston shifts of the helices relative to each other.Our results indicate that HAMP can access additional conformational states characterized by piston motion.Our results provide insights into the conformational changes that underlie the signaling mechanism involving HAMP.

View Article: PubMed Central - PubMed

Affiliation: Van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam, The Netherlands.

ABSTRACT
The HAMP domain is a linker region in prokaryotic sensor proteins and relays input signals to the transmitter domain and vice versa. Functional as a dimer, the structure of HAMP shows a parallel coiled-coil motif comprising four helices. To date, it is unclear how HAMP can relay signals from one domain to another, although several models exist. In this work, we use molecular simulation to test the hypothesis that HAMP adopts different conformations, one of which represents an active, signal-relaying configuration, and another an inactive, resting state. We first performed molecular dynamics simulation on the prototype HAMP domain Af1503 from Archaeoglobus fulgidus. We explored its conformational space by taking the structure of the A291F mutant disabling HAMP activity as a starting point. These simulations revealed additional conformational states that differ in the tilt angles between the helices as well as the relative piston shifts of the helices relative to each other. By enhancing the sampling in a metadynamics set up, we investigated three mechanistic models for HAMP signal transduction. Our results indicate that HAMP can access additional conformational states characterized by piston motion. Furthermore, the piston motion of the N-terminal helix of one monomer is directly correlated with the opposite piston motion of the C-terminal helix of the other monomer. The change in piston motion is accompanied by a change in tilt angle between the monomers, thus revealing that HAMP exhibits a collective motion, i.e. a combination of changes in tilt angles and a piston-like displacement. Our results provide insights into the conformational changes that underlie the signaling mechanism involving HAMP.

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One-dimensional bias on tilt angle, piston shift and rotation angle.In the metadynamics simulations the biasing potential was applied to (A) Intermonomer tilt angle  (B) rotation angle  (C) piston shift . For each simulation the free energy evolution is given in panels A0,B0,C0, with the reweighted free energy profiles in (A1,B1,C1)  versus ; (A2,B2,C2)  versus ; (A3,B3,C3)  versus ; (A4,B4,C4)  versus ; (A5,B5,C5)  versus ; (A6,B6,C6)  versus . Stars indicate the CV on which the bias was applied. Labels indicate stable states. Contour lines are rendered every . The metadynamics simulations show that biasing the piston shift reveals an additional conformational state and that the piston and tilt motions are correlated.
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pcbi-1002913-g005: One-dimensional bias on tilt angle, piston shift and rotation angle.In the metadynamics simulations the biasing potential was applied to (A) Intermonomer tilt angle (B) rotation angle (C) piston shift . For each simulation the free energy evolution is given in panels A0,B0,C0, with the reweighted free energy profiles in (A1,B1,C1) versus ; (A2,B2,C2) versus ; (A3,B3,C3) versus ; (A4,B4,C4) versus ; (A5,B5,C5) versus ; (A6,B6,C6) versus . Stars indicate the CV on which the bias was applied. Labels indicate stable states. Contour lines are rendered every . The metadynamics simulations show that biasing the piston shift reveals an additional conformational state and that the piston and tilt motions are correlated.

Mentions: FIG. 5-A0 shows the time evolution of the biasing potential along . After 35 ns, the shape of the profile does not change anymore. At this point the negative biasing potential represents the free energy profile along and shows one broad free energy minimum. The width of the minimum is consistent with the results from the conventional MD simulations. Even though the biasing potential acts on one CV, we can obtain the free energy surface along other CVs by using a reweighting procedure [25]. The resulting profiles are shown in FIG. 5-A1–A6. The patterns of piston motions as observed in the WT* simulations are partially reproduced. Only the pair of helices N1-C2 exhibits piston motions, while does not change (see FIG. 5-A1,A2). When reaches , becomes more negative, see FIG. 5-A3 (accordingly reaches 1.5 Å, see FIG. 5-A1). This shows that even though we bias the inter-monomer tilt angle, a spontaneous transition to the state can occur as well. The reweighted free energy surface as a function of and for N1 in FIG. 5-A6 does not show such correlated motions.


The HAMP signal relay domain adopts multiple conformational states through collective piston and tilt motions.

Zhu L, Bolhuis PG, Vreede J - PLoS Comput. Biol. (2013)

One-dimensional bias on tilt angle, piston shift and rotation angle.In the metadynamics simulations the biasing potential was applied to (A) Intermonomer tilt angle  (B) rotation angle  (C) piston shift . For each simulation the free energy evolution is given in panels A0,B0,C0, with the reweighted free energy profiles in (A1,B1,C1)  versus ; (A2,B2,C2)  versus ; (A3,B3,C3)  versus ; (A4,B4,C4)  versus ; (A5,B5,C5)  versus ; (A6,B6,C6)  versus . Stars indicate the CV on which the bias was applied. Labels indicate stable states. Contour lines are rendered every . The metadynamics simulations show that biasing the piston shift reveals an additional conformational state and that the piston and tilt motions are correlated.
© Copyright Policy
Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC3585426&req=5

pcbi-1002913-g005: One-dimensional bias on tilt angle, piston shift and rotation angle.In the metadynamics simulations the biasing potential was applied to (A) Intermonomer tilt angle (B) rotation angle (C) piston shift . For each simulation the free energy evolution is given in panels A0,B0,C0, with the reweighted free energy profiles in (A1,B1,C1) versus ; (A2,B2,C2) versus ; (A3,B3,C3) versus ; (A4,B4,C4) versus ; (A5,B5,C5) versus ; (A6,B6,C6) versus . Stars indicate the CV on which the bias was applied. Labels indicate stable states. Contour lines are rendered every . The metadynamics simulations show that biasing the piston shift reveals an additional conformational state and that the piston and tilt motions are correlated.
Mentions: FIG. 5-A0 shows the time evolution of the biasing potential along . After 35 ns, the shape of the profile does not change anymore. At this point the negative biasing potential represents the free energy profile along and shows one broad free energy minimum. The width of the minimum is consistent with the results from the conventional MD simulations. Even though the biasing potential acts on one CV, we can obtain the free energy surface along other CVs by using a reweighting procedure [25]. The resulting profiles are shown in FIG. 5-A1–A6. The patterns of piston motions as observed in the WT* simulations are partially reproduced. Only the pair of helices N1-C2 exhibits piston motions, while does not change (see FIG. 5-A1,A2). When reaches , becomes more negative, see FIG. 5-A3 (accordingly reaches 1.5 Å, see FIG. 5-A1). This shows that even though we bias the inter-monomer tilt angle, a spontaneous transition to the state can occur as well. The reweighted free energy surface as a function of and for N1 in FIG. 5-A6 does not show such correlated motions.

Bottom Line: These simulations revealed additional conformational states that differ in the tilt angles between the helices as well as the relative piston shifts of the helices relative to each other.Our results indicate that HAMP can access additional conformational states characterized by piston motion.Our results provide insights into the conformational changes that underlie the signaling mechanism involving HAMP.

View Article: PubMed Central - PubMed

Affiliation: Van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam, The Netherlands.

ABSTRACT
The HAMP domain is a linker region in prokaryotic sensor proteins and relays input signals to the transmitter domain and vice versa. Functional as a dimer, the structure of HAMP shows a parallel coiled-coil motif comprising four helices. To date, it is unclear how HAMP can relay signals from one domain to another, although several models exist. In this work, we use molecular simulation to test the hypothesis that HAMP adopts different conformations, one of which represents an active, signal-relaying configuration, and another an inactive, resting state. We first performed molecular dynamics simulation on the prototype HAMP domain Af1503 from Archaeoglobus fulgidus. We explored its conformational space by taking the structure of the A291F mutant disabling HAMP activity as a starting point. These simulations revealed additional conformational states that differ in the tilt angles between the helices as well as the relative piston shifts of the helices relative to each other. By enhancing the sampling in a metadynamics set up, we investigated three mechanistic models for HAMP signal transduction. Our results indicate that HAMP can access additional conformational states characterized by piston motion. Furthermore, the piston motion of the N-terminal helix of one monomer is directly correlated with the opposite piston motion of the C-terminal helix of the other monomer. The change in piston motion is accompanied by a change in tilt angle between the monomers, thus revealing that HAMP exhibits a collective motion, i.e. a combination of changes in tilt angles and a piston-like displacement. Our results provide insights into the conformational changes that underlie the signaling mechanism involving HAMP.

Show MeSH
Related in: MedlinePlus