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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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Crystal structures of E. coli AK.(A) Open conformation without ligand (PDBid: 4ake). The position of P-loop is indicated. (b) Closed conformation with Ap5A represented by sticks (PDBid: 1ake). The ATP and AMP moieties are encircled. Three relatively rigid domains, designated CORE, AMPbd, and LID, are colored by green, cyan, and magenta, respectively.
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pcbi-1002555-g001: Crystal structures of E. coli AK.(A) Open conformation without ligand (PDBid: 4ake). The position of P-loop is indicated. (b) Closed conformation with Ap5A represented by sticks (PDBid: 1ake). The ATP and AMP moieties are encircled. Three relatively rigid domains, designated CORE, AMPbd, and LID, are colored by green, cyan, and magenta, respectively.

Mentions: Here, we applied the above proposed methods to the conformational change in Escherichia coli adenylate kinase (AK), the best-studied of enzymes exhibiting a large conformational transition [12]–[23]. AK is a ubiquitous monomeric enzyme that regulates cellular energy homeostasis by catalyzing the reversible phosphoryl transfer reaction: ATP+AMP↔2ADP. According to the analysis of the crystal structures by the domain motion analysis program DynDom [24], AK is composed of three relatively rigid domains (Figure 1); the central domain (CORE: residues 1–29, 68–117, and 161–214), an AMP-binding domain (AMPbd: 30–67), and a lid-shaped ATP-binding domain (LID: 118–167). Inspection of the crystal structures suggests that, upon ligand binding, the enzyme undergoes a transition from the inactive open form to the catalytically competent closed structure [25] (Figure 1). This transition is mediated by large-scale closure motions of the LID and AMPbd domains insulating the substrates from the water environment, while occluding some catalytically relevant water molecules. The ATP phosphates are bound to the enzyme through the P-loop (residues 7–13), a widely-distributed ATP-binding motif.


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)

Crystal structures of E. coli AK.(A) Open conformation without ligand (PDBid: 4ake). The position of P-loop is indicated. (b) Closed conformation with Ap5A represented by sticks (PDBid: 1ake). The ATP and AMP moieties are encircled. Three relatively rigid domains, designated CORE, AMPbd, and LID, are colored by green, cyan, and magenta, respectively.
© Copyright Policy
Related In: Results  -  Collection

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

pcbi-1002555-g001: Crystal structures of E. coli AK.(A) Open conformation without ligand (PDBid: 4ake). The position of P-loop is indicated. (b) Closed conformation with Ap5A represented by sticks (PDBid: 1ake). The ATP and AMP moieties are encircled. Three relatively rigid domains, designated CORE, AMPbd, and LID, are colored by green, cyan, and magenta, respectively.
Mentions: Here, we applied the above proposed methods to the conformational change in Escherichia coli adenylate kinase (AK), the best-studied of enzymes exhibiting a large conformational transition [12]–[23]. AK is a ubiquitous monomeric enzyme that regulates cellular energy homeostasis by catalyzing the reversible phosphoryl transfer reaction: ATP+AMP↔2ADP. According to the analysis of the crystal structures by the domain motion analysis program DynDom [24], AK is composed of three relatively rigid domains (Figure 1); the central domain (CORE: residues 1–29, 68–117, and 161–214), an AMP-binding domain (AMPbd: 30–67), and a lid-shaped ATP-binding domain (LID: 118–167). Inspection of the crystal structures suggests that, upon ligand binding, the enzyme undergoes a transition from the inactive open form to the catalytically competent closed structure [25] (Figure 1). This transition is mediated by large-scale closure motions of the LID and AMPbd domains insulating the substrates from the water environment, while occluding some catalytically relevant water molecules. The ATP phosphates are bound to the enzyme through the P-loop (residues 7–13), a widely-distributed ATP-binding motif.

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