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

PMFs of the domain motions and the RMSF along the MFEP.(Top) PMF along the MFEP as a function of the inter-domain distances between (A) the LID-CORE and (B) AMPbd-CORE domains. The blue and red curves illustrate the results for apo-AK and holo-AK, respectively. The error bars are the statistical uncertainties relative to the PMF minimum. Note that the uncertainties are small because the domains were restricted to the regions around the MFEP. (Bottom) The RMSF of the  atoms along the MFEP is shown as a function of the MFEP images for (C) apo and (D) holo-AK. The “cracked” regions with large RMSF values, around the LID-CORE hinge and P-loop, are encircled.
© Copyright Policy
Related In: Results  -  Collection

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

pcbi-1002555-g003: PMFs of the domain motions and the RMSF along the MFEP.(Top) PMF along the MFEP as a function of the inter-domain distances between (A) the LID-CORE and (B) AMPbd-CORE domains. The blue and red curves illustrate the results for apo-AK and holo-AK, respectively. The error bars are the statistical uncertainties relative to the PMF minimum. Note that the uncertainties are small because the domains were restricted to the regions around the MFEP. (Bottom) The RMSF of the atoms along the MFEP is shown as a function of the MFEP images for (C) apo and (D) holo-AK. The “cracked” regions with large RMSF values, around the LID-CORE hinge and P-loop, are encircled.

Mentions: To more clearly illustrate the energetics along the MFEP in terms of the domain motions, we separately plot the PMF as a function of the two inter-domain distances defined above (Figures 3A and 3B). We observe that the PMF of apo-AK has a double-well profile for the LID-CORE distance (indicated by the blue line in Figure 3A), whereas the PMF in terms of the AMPbd-CORE distance is characterized by a single-well (Figure 3B). The single-molecule FRET experiments monitoring the distances between specific residue pairs involving the LID domain (LID-CORE (Ala127-Ala194) [15] and LID-AMPbd (Lys145- Ile52) [16]) revealed the presence of double-well profiles in the ligand-free form. On the other hand, an electron transfer experiment probing the distance between the AMPbd and CORE domains (Ala55-Val169) [30] showed only that the distance between the two domains decreased upon ligand binding. Considering the PMF profiles in the context of these experimental results, we suggest that the partially closed state () in apo-AK (Figure 2A) can be ascribed to the LID-CORE interactions but not to the AMPbd-CORE interactions.


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)

PMFs of the domain motions and the RMSF along the MFEP.(Top) PMF along the MFEP as a function of the inter-domain distances between (A) the LID-CORE and (B) AMPbd-CORE domains. The blue and red curves illustrate the results for apo-AK and holo-AK, respectively. The error bars are the statistical uncertainties relative to the PMF minimum. Note that the uncertainties are small because the domains were restricted to the regions around the MFEP. (Bottom) The RMSF of the  atoms along the MFEP is shown as a function of the MFEP images for (C) apo and (D) holo-AK. The “cracked” regions with large RMSF values, around the LID-CORE hinge and P-loop, are encircled.
© Copyright Policy
Related In: Results  -  Collection

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

pcbi-1002555-g003: PMFs of the domain motions and the RMSF along the MFEP.(Top) PMF along the MFEP as a function of the inter-domain distances between (A) the LID-CORE and (B) AMPbd-CORE domains. The blue and red curves illustrate the results for apo-AK and holo-AK, respectively. The error bars are the statistical uncertainties relative to the PMF minimum. Note that the uncertainties are small because the domains were restricted to the regions around the MFEP. (Bottom) The RMSF of the atoms along the MFEP is shown as a function of the MFEP images for (C) apo and (D) holo-AK. The “cracked” regions with large RMSF values, around the LID-CORE hinge and P-loop, are encircled.
Mentions: To more clearly illustrate the energetics along the MFEP in terms of the domain motions, we separately plot the PMF as a function of the two inter-domain distances defined above (Figures 3A and 3B). We observe that the PMF of apo-AK has a double-well profile for the LID-CORE distance (indicated by the blue line in Figure 3A), whereas the PMF in terms of the AMPbd-CORE distance is characterized by a single-well (Figure 3B). The single-molecule FRET experiments monitoring the distances between specific residue pairs involving the LID domain (LID-CORE (Ala127-Ala194) [15] and LID-AMPbd (Lys145- Ile52) [16]) revealed the presence of double-well profiles in the ligand-free form. On the other hand, an electron transfer experiment probing the distance between the AMPbd and CORE domains (Ala55-Val169) [30] showed only that the distance between the two domains decreased upon ligand binding. Considering the PMF profiles in the context of these experimental results, we suggest that the partially closed state () in apo-AK (Figure 2A) can be ascribed to the LID-CORE interactions but not to the AMPbd-CORE interactions.

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