Limits...
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.

Show MeSH

Related in: MedlinePlus

Committor tests characterizing the TSE.(A) The binned distributions of the final structures after 10 ns unrestrained MD simulations (blue bars), assigned by index of the nearest MFEP image (i.e., classified by the Voronoi tessellation). The MD simulations were executed from different initial distributions (red bars) at , 33, and 34. (B) The average structures of the MFEP images at  (before the TSE), and 34 (after the TSE). The ligand and the residues of Thr31, Lys57, Arg88, Gly85, and Gln92 are represented by sticks. The hydrogen bonds are indicated by the dashed yellow lines.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC3369945&req=5

pcbi-1002555-g005: Committor tests characterizing the TSE.(A) The binned distributions of the final structures after 10 ns unrestrained MD simulations (blue bars), assigned by index of the nearest MFEP image (i.e., classified by the Voronoi tessellation). The MD simulations were executed from different initial distributions (red bars) at , 33, and 34. (B) The average structures of the MFEP images at (before the TSE), and 34 (after the TSE). The ligand and the residues of Thr31, Lys57, Arg88, Gly85, and Gln92 are represented by sticks. The hydrogen bonds are indicated by the dashed yellow lines.

Mentions: The MFEP revealed that AMP adenine enters the AMP-binding pocket around , as indicated by a rapid decrease in the accessible area (Figure 4A). This event is well correlated with the position of the PMF barrier along the MFEP (Figure 2B). This coincidence between the binding process and the domain closure suggests that the two processes are closely coupled. Before analyzing the situation in detail, however, it is necessary to assess whether the observed PMF barrier around (Figure 2B) corresponds to a TSE, because the PMF barrier is not necessarily a signature of dynamical bottleneck in high-dimensional systems [33]. TSE validation is usually performed with a committor test [4], [7], [9], [33]. In principle, the committor test launches unbiased MD simulations from structures chosen randomly from the barrier region, and tests whether the resultant trajectories reach the product state with probability 1/2. Here, since limited computational resources precluded execution of a full committor test, 40 unbiased MD simulations of 10 ns were initiated from each of , 33 or 34, a total of 120 simulations or 1.2 , and the distributions of the final structures after 10 ns were monitored [9]. Figure 5A shows the binned distributions of the final structures assigned by index of the nearest MFEP image (the blue bars). When the simulations were initiated from the image at (), the distribution biases to the open form-side (the closed form-side) relative to the initial structures. On the other hand, when starting from the image at , the distribution is roughly symmetric around the initial structures. This result suggests that the TSE is located at . In other words, it was validated that the TSE was successfully captured in the MFEP, and at the same time, the collective variables were good enough to describe 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)

Committor tests characterizing the TSE.(A) The binned distributions of the final structures after 10 ns unrestrained MD simulations (blue bars), assigned by index of the nearest MFEP image (i.e., classified by the Voronoi tessellation). The MD simulations were executed from different initial distributions (red bars) at , 33, and 34. (B) The average structures of the MFEP images at  (before the TSE), and 34 (after the TSE). The ligand and the residues of Thr31, Lys57, Arg88, Gly85, and Gln92 are represented by sticks. 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-g005: Committor tests characterizing the TSE.(A) The binned distributions of the final structures after 10 ns unrestrained MD simulations (blue bars), assigned by index of the nearest MFEP image (i.e., classified by the Voronoi tessellation). The MD simulations were executed from different initial distributions (red bars) at , 33, and 34. (B) The average structures of the MFEP images at (before the TSE), and 34 (after the TSE). The ligand and the residues of Thr31, Lys57, Arg88, Gly85, and Gln92 are represented by sticks. The hydrogen bonds are indicated by the dashed yellow lines.
Mentions: The MFEP revealed that AMP adenine enters the AMP-binding pocket around , as indicated by a rapid decrease in the accessible area (Figure 4A). This event is well correlated with the position of the PMF barrier along the MFEP (Figure 2B). This coincidence between the binding process and the domain closure suggests that the two processes are closely coupled. Before analyzing the situation in detail, however, it is necessary to assess whether the observed PMF barrier around (Figure 2B) corresponds to a TSE, because the PMF barrier is not necessarily a signature of dynamical bottleneck in high-dimensional systems [33]. TSE validation is usually performed with a committor test [4], [7], [9], [33]. In principle, the committor test launches unbiased MD simulations from structures chosen randomly from the barrier region, and tests whether the resultant trajectories reach the product state with probability 1/2. Here, since limited computational resources precluded execution of a full committor test, 40 unbiased MD simulations of 10 ns were initiated from each of , 33 or 34, a total of 120 simulations or 1.2 , and the distributions of the final structures after 10 ns were monitored [9]. Figure 5A shows the binned distributions of the final structures assigned by index of the nearest MFEP image (the blue bars). When the simulations were initiated from the image at (), the distribution biases to the open form-side (the closed form-side) relative to the initial structures. On the other hand, when starting from the image at , the distribution is roughly symmetric around the initial structures. This result suggests that the TSE is located at . In other words, it was validated that the TSE was successfully captured in the MFEP, and at the same time, the collective variables were good enough to describe 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