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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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Piston shift, tilting and rotation of helices in WT* trajectories.The negative log of the probability distributions are plotted for (A)  versus ; (B)  versus ; (C)  versus ; (D)  versus ; (E)  versus ; (F)  versus . The labels indicate stable states. Contour lines are rendered every . The stars indicate the starting point of the simulations. The WT* simulations reveal that the different conformational states of HAMP can be distinguished by differences in piston shift and tilt angle.
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pcbi-1002913-g003: Piston shift, tilting and rotation of helices in WT* trajectories.The negative log of the probability distributions are plotted for (A) versus ; (B) versus ; (C) versus ; (D) versus ; (E) versus ; (F) versus . The labels indicate stable states. Contour lines are rendered every . The stars indicate the starting point of the simulations. The WT* simulations reveal that the different conformational states of HAMP can be distinguished by differences in piston shift and tilt angle.

Mentions: The new conformations in / differ from the WT conformation in the values for the piston shifts, as shown in FIG. 3-A,B. FIG. 4 shows a schematic representation of the piston-shifted states. indicates the conformations close to WT, without any piston shifts;  = 0 Å. The new conformational state / is split up in two symmetrically related states. Focusing on , this state exhibits an upward piston shift of 1 Å for the N-helix in monomer 1 (N1), and a downward piston motion of 1.5 Å of the C-helix in monomer 2 (C2). Similarly, state reveals a downshift of C1 in combination with an upshift of N2. We show all possible piston combinations in FIG. S2 in Text S1. The piston shifts fall within the range of 1–2 Å, as experimentally determined [14]. Strikingly, a piston shift of N1 is not correlated to piston shifts occurring for N2 (see FIG. 3-A). Similarly, the piston motions of the two C-helices are not correlated.


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)

Piston shift, tilting and rotation of helices in WT* trajectories.The negative log of the probability distributions are plotted for (A)  versus ; (B)  versus ; (C)  versus ; (D)  versus ; (E)  versus ; (F)  versus . The labels indicate stable states. Contour lines are rendered every . The stars indicate the starting point of the simulations. The WT* simulations reveal that the different conformational states of HAMP can be distinguished by differences in piston shift and tilt angle.
© Copyright Policy
Related In: Results  -  Collection

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

pcbi-1002913-g003: Piston shift, tilting and rotation of helices in WT* trajectories.The negative log of the probability distributions are plotted for (A) versus ; (B) versus ; (C) versus ; (D) versus ; (E) versus ; (F) versus . The labels indicate stable states. Contour lines are rendered every . The stars indicate the starting point of the simulations. The WT* simulations reveal that the different conformational states of HAMP can be distinguished by differences in piston shift and tilt angle.
Mentions: The new conformations in / differ from the WT conformation in the values for the piston shifts, as shown in FIG. 3-A,B. FIG. 4 shows a schematic representation of the piston-shifted states. indicates the conformations close to WT, without any piston shifts;  = 0 Å. The new conformational state / is split up in two symmetrically related states. Focusing on , this state exhibits an upward piston shift of 1 Å for the N-helix in monomer 1 (N1), and a downward piston motion of 1.5 Å of the C-helix in monomer 2 (C2). Similarly, state reveals a downshift of C1 in combination with an upshift of N2. We show all possible piston combinations in FIG. S2 in Text S1. The piston shifts fall within the range of 1–2 Å, as experimentally determined [14]. Strikingly, a piston shift of N1 is not correlated to piston shifts occurring for N2 (see FIG. 3-A). Similarly, the piston motions of the two C-helices are not correlated.

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