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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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RMSD from experimental structures and helical rotation.The negative log of the probability distributions are shown for (A) the WT system as a function of the number of helical hydrogen bonds  and the RMSD with respect to the NMR structure of WT,  and (B) the WT* system as a function of the RMSD with respect to the NMR structure of the A291F mutant,  and . Labels indicate stable states. Contour lines are rendered every 1. The stars indicate the starting point of the simulations. (C) Time evolution of helical rotation in the WT* system. The helical rotation for each helix is plotted as a function of simulation time, as a running average of 10 ps for a typical WT* simulation. The helical rotation is calculated as the angle between a reference point on the helix, the center of mass of the helix and the reference point on an aligned reference structure, see Methods for details. The MD simulations show that HAMP can visit additional conformational states.
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pcbi-1002913-g002: RMSD from experimental structures and helical rotation.The negative log of the probability distributions are shown for (A) the WT system as a function of the number of helical hydrogen bonds and the RMSD with respect to the NMR structure of WT, and (B) the WT* system as a function of the RMSD with respect to the NMR structure of the A291F mutant, and . Labels indicate stable states. Contour lines are rendered every 1. The stars indicate the starting point of the simulations. (C) Time evolution of helical rotation in the WT* system. The helical rotation for each helix is plotted as a function of simulation time, as a running average of 10 ps for a typical WT* simulation. The helical rotation is calculated as the angle between a reference point on the helix, the center of mass of the helix and the reference point on an aligned reference structure, see Methods for details. The MD simulations show that HAMP can visit additional conformational states.

Mentions: Mutagenesis studies have shown that Af1503-HAMP has reduced activity upon altering the alanine at position 291. Increasing the volume of the hydrophobic sidechain at this position changes the packing in the hydrophobic packing from complementary to (knobs-into-holes) [7]. In this section, we perform MD simulations on wild-type and the mutant A291F Af1503-HAMP domains, to investigate the differences in structure and dynamics of these conformations. First we performed four 40 ns and four 60 ns MD simulations of the wild-type Af1503-HAMP domain, called WT hereafter, using the NMR structure (PDB code 2ASW [3]) as a starting point. Visual inspection revealed no dissociation of the complex or unfolding of the -helical regions. As a quantitative measure we calculated the RMSD of the helices with respect to the NMR structure, , and the number of helical hydrogen bonds, , shown in FIG. 2-A as a contour plot of the negative natural logarithm of the probability distribution of these two measures. The profile displays a single minimum at  = 0.7 Å and around 50. In other representations, including the helical rotation, , the inter-helical tilt angles , and the helical piston motion , the WT simulations also display a single minimum. The values of these collective variables are listed in TAB. 1. The helices within one monomer have a tilt angle with respect to each other, while tilting angles between monomers are around . These angles are consistent with typical values observed in Ref. [3] and reflect that the monomers are not exactly parallel, but have a tilted orientation with respect to each other. Consequently, the HAMP domain resembles a cone with the tip at the C-terminal side, see FIG. 1-B. Finally, the helical piston shift in the WT system is very small. All these observations indicate that the structure resolved by NMR for the Af1503 HAMP domain is very stable as a single unit at room temperature.


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)

RMSD from experimental structures and helical rotation.The negative log of the probability distributions are shown for (A) the WT system as a function of the number of helical hydrogen bonds  and the RMSD with respect to the NMR structure of WT,  and (B) the WT* system as a function of the RMSD with respect to the NMR structure of the A291F mutant,  and . Labels indicate stable states. Contour lines are rendered every 1. The stars indicate the starting point of the simulations. (C) Time evolution of helical rotation in the WT* system. The helical rotation for each helix is plotted as a function of simulation time, as a running average of 10 ps for a typical WT* simulation. The helical rotation is calculated as the angle between a reference point on the helix, the center of mass of the helix and the reference point on an aligned reference structure, see Methods for details. The MD simulations show that HAMP can visit additional conformational states.
© Copyright Policy
Related In: Results  -  Collection

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

pcbi-1002913-g002: RMSD from experimental structures and helical rotation.The negative log of the probability distributions are shown for (A) the WT system as a function of the number of helical hydrogen bonds and the RMSD with respect to the NMR structure of WT, and (B) the WT* system as a function of the RMSD with respect to the NMR structure of the A291F mutant, and . Labels indicate stable states. Contour lines are rendered every 1. The stars indicate the starting point of the simulations. (C) Time evolution of helical rotation in the WT* system. The helical rotation for each helix is plotted as a function of simulation time, as a running average of 10 ps for a typical WT* simulation. The helical rotation is calculated as the angle between a reference point on the helix, the center of mass of the helix and the reference point on an aligned reference structure, see Methods for details. The MD simulations show that HAMP can visit additional conformational states.
Mentions: Mutagenesis studies have shown that Af1503-HAMP has reduced activity upon altering the alanine at position 291. Increasing the volume of the hydrophobic sidechain at this position changes the packing in the hydrophobic packing from complementary to (knobs-into-holes) [7]. In this section, we perform MD simulations on wild-type and the mutant A291F Af1503-HAMP domains, to investigate the differences in structure and dynamics of these conformations. First we performed four 40 ns and four 60 ns MD simulations of the wild-type Af1503-HAMP domain, called WT hereafter, using the NMR structure (PDB code 2ASW [3]) as a starting point. Visual inspection revealed no dissociation of the complex or unfolding of the -helical regions. As a quantitative measure we calculated the RMSD of the helices with respect to the NMR structure, , and the number of helical hydrogen bonds, , shown in FIG. 2-A as a contour plot of the negative natural logarithm of the probability distribution of these two measures. The profile displays a single minimum at  = 0.7 Å and around 50. In other representations, including the helical rotation, , the inter-helical tilt angles , and the helical piston motion , the WT simulations also display a single minimum. The values of these collective variables are listed in TAB. 1. The helices within one monomer have a tilt angle with respect to each other, while tilting angles between monomers are around . These angles are consistent with typical values observed in Ref. [3] and reflect that the monomers are not exactly parallel, but have a tilted orientation with respect to each other. Consequently, the HAMP domain resembles a cone with the tip at the C-terminal side, see FIG. 1-B. Finally, the helical piston shift in the WT system is very small. All these observations indicate that the structure resolved by NMR for the Af1503 HAMP domain is very stable as a single unit at room temperature.

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