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Minimum free energy path of ligand-induced transition in adenylate kinase.

Matsunaga Y, Fujisaki H, Terada T, Furuta T, Moritsugu K, Kidera A - PLoS Comput. Biol. (2012)

Bottom Line: It was found that the LID domain was able to partially close without the ligand, while the closure of the AMPbd domain required the ligand binding.It was also found that complete closure of the LID domain required the dehydration of solvents around the P-loop.These findings suggest that the interplay of the two different types of domain motion is an essential feature in the conformational transition of the enzyme.

View Article: PubMed Central - PubMed

Affiliation: Computational Science Research Program, RIKEN, Wako, Japan. ymatsunaga@riken.jp

ABSTRACT
Large-scale conformational changes in proteins involve barrier-crossing transitions on the complex free energy surfaces of high-dimensional space. Such rare events cannot be efficiently captured by conventional molecular dynamics simulations. Here we show that, by combining the on-the-fly string method and the multi-state Bennett acceptance ratio (MBAR) method, the free energy profile of a conformational transition pathway in Escherichia coli adenylate kinase can be characterized in a high-dimensional space. The minimum free energy paths of the conformational transitions in adenylate kinase were explored by the on-the-fly string method in 20-dimensional space spanned by the 20 largest-amplitude principal modes, and the free energy and various kinds of average physical quantities along the pathways were successfully evaluated by the MBAR method. The influence of ligand binding on the pathways was characterized in terms of rigid-body motions of the lid-shaped ATP-binding domain (LID) and the AMP-binding (AMPbd) domains. It was found that the LID domain was able to partially close without the ligand, while the closure of the AMPbd domain required the ligand binding. The transition state ensemble of the ligand bound form was identified as those structures characterized by highly specific binding of the ligand to the AMPbd domain, and was validated by unrestrained MD simulations. It was also found that complete closure of the LID domain required the dehydration of solvents around the P-loop. These findings suggest that the interplay of the two different types of domain motion is an essential feature in the conformational transition of the enzyme.

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Related in: MedlinePlus

Two-dimensional PMF surface of the motion of the ligand along the MFEP.(A) PMF is projected onto the MFEP images and onto the 1st PC of the xyz-coordinates of the mass center of the AMP adenine. The PMF is represented by the colored contour lines. (B) Tens of the MD snapshots are superimposed at  (left image), and 4 snapshots shows the misbinding between the AMP ribose and Asp84 at  (right image). The hydrogen bonds are indicated by the dashed yellow lines.
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pcbi-1002555-g004: Two-dimensional PMF surface of the motion of the ligand along the MFEP.(A) PMF is projected onto the MFEP images and onto the 1st PC of the xyz-coordinates of the mass center of the AMP adenine. The PMF is represented by the colored contour lines. (B) Tens of the MD snapshots are superimposed at (left image), and 4 snapshots shows the misbinding between the AMP ribose and Asp84 at (right image). The hydrogen bonds are indicated by the dashed yellow lines.

Mentions: The origin of the double-well profile in holo-AK was investigated via the ligand-protein interactions. The motion of the ligand along the MFEP was firstly analyzed by focusing on the AMP adenine dynamics, since the release of the AMP moiety from the AMP-binding pocket was observed in the open state. It is again emphasized that the ligand is completely free from any restraint during the simulations. PCA was performed for the three-dimensional Cartesian coordinates of the center of mass of AMP adenine, and the coordinates were projected onto the resultant 1st PC in Figure 4A. The AMP adenine is observed to move as much as 10 Å in the open state (; Figure 4B), while it is confined to a narrow region of width 1–2 Å (the binding pocket) in the closed state (). Such a reduction of the accessible space of the AMP adenine might generate a drastic decrease in entropy or an increase in the PMF barrier of the open-to-closed transition. Furthermore, close inspection of the PMF surface reveals the existence of a misbinding event at (Figure 4B), in which the AMP ribose misbinds to Asp84 in the CORE domain, and is prevented from entering the AMP-binding pocket. This event further increases the barrier-height of the transition.


Minimum free energy path of ligand-induced transition in adenylate kinase.

Matsunaga Y, Fujisaki H, Terada T, Furuta T, Moritsugu K, Kidera A - PLoS Comput. Biol. (2012)

Two-dimensional PMF surface of the motion of the ligand along the MFEP.(A) PMF is projected onto the MFEP images and onto the 1st PC of the xyz-coordinates of the mass center of the AMP adenine. The PMF is represented by the colored contour lines. (B) Tens of the MD snapshots are superimposed at  (left image), and 4 snapshots shows the misbinding between the AMP ribose and Asp84 at  (right image). The hydrogen bonds are indicated by the dashed yellow lines.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3369945&req=5

pcbi-1002555-g004: Two-dimensional PMF surface of the motion of the ligand along the MFEP.(A) PMF is projected onto the MFEP images and onto the 1st PC of the xyz-coordinates of the mass center of the AMP adenine. The PMF is represented by the colored contour lines. (B) Tens of the MD snapshots are superimposed at (left image), and 4 snapshots shows the misbinding between the AMP ribose and Asp84 at (right image). The hydrogen bonds are indicated by the dashed yellow lines.
Mentions: The origin of the double-well profile in holo-AK was investigated via the ligand-protein interactions. The motion of the ligand along the MFEP was firstly analyzed by focusing on the AMP adenine dynamics, since the release of the AMP moiety from the AMP-binding pocket was observed in the open state. It is again emphasized that the ligand is completely free from any restraint during the simulations. PCA was performed for the three-dimensional Cartesian coordinates of the center of mass of AMP adenine, and the coordinates were projected onto the resultant 1st PC in Figure 4A. The AMP adenine is observed to move as much as 10 Å in the open state (; Figure 4B), while it is confined to a narrow region of width 1–2 Å (the binding pocket) in the closed state (). Such a reduction of the accessible space of the AMP adenine might generate a drastic decrease in entropy or an increase in the PMF barrier of the open-to-closed transition. Furthermore, close inspection of the PMF surface reveals the existence of a misbinding event at (Figure 4B), in which the AMP ribose misbinds to Asp84 in the CORE domain, and is prevented from entering the AMP-binding pocket. This event further increases the barrier-height of the transition.

Bottom Line: It was found that the LID domain was able to partially close without the ligand, while the closure of the AMPbd domain required the ligand binding.It was also found that complete closure of the LID domain required the dehydration of solvents around the P-loop.These findings suggest that the interplay of the two different types of domain motion is an essential feature in the conformational transition of the enzyme.

View Article: PubMed Central - PubMed

Affiliation: Computational Science Research Program, RIKEN, Wako, Japan. ymatsunaga@riken.jp

ABSTRACT
Large-scale conformational changes in proteins involve barrier-crossing transitions on the complex free energy surfaces of high-dimensional space. Such rare events cannot be efficiently captured by conventional molecular dynamics simulations. Here we show that, by combining the on-the-fly string method and the multi-state Bennett acceptance ratio (MBAR) method, the free energy profile of a conformational transition pathway in Escherichia coli adenylate kinase can be characterized in a high-dimensional space. The minimum free energy paths of the conformational transitions in adenylate kinase were explored by the on-the-fly string method in 20-dimensional space spanned by the 20 largest-amplitude principal modes, and the free energy and various kinds of average physical quantities along the pathways were successfully evaluated by the MBAR method. The influence of ligand binding on the pathways was characterized in terms of rigid-body motions of the lid-shaped ATP-binding domain (LID) and the AMP-binding (AMPbd) domains. It was found that the LID domain was able to partially close without the ligand, while the closure of the AMPbd domain required the ligand binding. The transition state ensemble of the ligand bound form was identified as those structures characterized by highly specific binding of the ligand to the AMPbd domain, and was validated by unrestrained MD simulations. It was also found that complete closure of the LID domain required the dehydration of solvents around the P-loop. These findings suggest that the interplay of the two different types of domain motion is an essential feature in the conformational transition of the enzyme.

Show MeSH
Related in: MedlinePlus