Limits...
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.

Show MeSH
Definition of helical motions.(A) Positions of four consecutive  atoms, indicated by colored spheres (black N1; red C1; green N2; blue C2) are used to define the head and tail groups. The arrow points at the head. (B) Three collective variables (CVs) describing helical motions: rotation , piston shift  and tilt . Reference vectors are indicated in gray. The CV definitions are indicated in red. See main text for an explanation of the definitions.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC3585426&req=5

pcbi-1002913-g008: Definition of helical motions.(A) Positions of four consecutive atoms, indicated by colored spheres (black N1; red C1; green N2; blue C2) are used to define the head and tail groups. The arrow points at the head. (B) Three collective variables (CVs) describing helical motions: rotation , piston shift and tilt . Reference vectors are indicated in gray. The CV definitions are indicated in red. See main text for an explanation of the definitions.

Mentions: Metadynamics is an enhanced sampling method that performs history-dependent sampling in a reduced collective variable (CV) space [23]. We encoded three new CVs in PLUMED [37], a package that contains the metadynamics algorithm for the tilt angle, the helical rotation and the piston shift. Rotation of a helix and tilt angles between two helices are measured via the CV and respectively. Piston motions of a single helix are quantified through the CV . As the CV and involve a reference structure, we must align the reference structure with respect to the current frame throughout the simulation. We used the NMR strcture of wild-type Af1503-HAMP as a reference, PDB-code 2ASW. These CVs can only be used under the condition that the helices under study are relatively stable without severe bending or twisting. We tested our implementation of these three new CVs by comparing the analytically calculated values of the derivative of the CVs implemented in PLUMED and those of a numerically computed derivative via a very small change in the CVs. FIG. 8 shows a schematic representation of the definitions for the three CVs.


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)

Definition of helical motions.(A) Positions of four consecutive  atoms, indicated by colored spheres (black N1; red C1; green N2; blue C2) are used to define the head and tail groups. The arrow points at the head. (B) Three collective variables (CVs) describing helical motions: rotation , piston shift  and tilt . Reference vectors are indicated in gray. The CV definitions are indicated in red. See main text for an explanation of the definitions.
© Copyright Policy
Related In: Results  -  Collection

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

pcbi-1002913-g008: Definition of helical motions.(A) Positions of four consecutive atoms, indicated by colored spheres (black N1; red C1; green N2; blue C2) are used to define the head and tail groups. The arrow points at the head. (B) Three collective variables (CVs) describing helical motions: rotation , piston shift and tilt . Reference vectors are indicated in gray. The CV definitions are indicated in red. See main text for an explanation of the definitions.
Mentions: Metadynamics is an enhanced sampling method that performs history-dependent sampling in a reduced collective variable (CV) space [23]. We encoded three new CVs in PLUMED [37], a package that contains the metadynamics algorithm for the tilt angle, the helical rotation and the piston shift. Rotation of a helix and tilt angles between two helices are measured via the CV and respectively. Piston motions of a single helix are quantified through the CV . As the CV and involve a reference structure, we must align the reference structure with respect to the current frame throughout the simulation. We used the NMR strcture of wild-type Af1503-HAMP as a reference, PDB-code 2ASW. These CVs can only be used under the condition that the helices under study are relatively stable without severe bending or twisting. We tested our implementation of these three new CVs by comparing the analytically calculated values of the derivative of the CVs implemented in PLUMED and those of a numerically computed derivative via a very small change in the CVs. FIG. 8 shows a schematic representation of the definitions for the three CVs.

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