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Generation of a flexible loop structural ensemble and its application to induced-fit structural changes following ligand binding

View Article: PubMed Central - PubMed

ABSTRACT

Molecular recognition is often mediated by flexible loops that have widely fluctuating structures and are sometimes disordered, but that form particular complex structures following ligand binding. In fact, many loop structures found in the PDB database are too flexible to be determined precisely. A new loop modeling method was therefore developed using force-biased multicanonical molecular dynamics with the implicit solvent model to generate an ensemble of putative loop structures with low free energy values. The method was then used to create ensembles for several flexible loops that were compared with the corresponding NMR and X-ray structures. The induced-fit structural change of dihydrofolate reductase (DHFR) was also predicted from a structural ensemble of ligand-free M20 loop conformations and successive docking simulations.

No MeSH data available.


The ligand-binding pocket of DHFR and the folate molecule generated from a docking simulation with NADP+ and structural optimization. The dotted lines correspond to intermolecular hydrogen bonds. Semi-circles represent the protein residues involved in the hydrophobic interaction. Numbers in italics represent the interatomic distance between the interacting heavy atom pairs (Å). (A) Binding pocket in the X-ray crystal structure of the closed form of the M20 loop in DHFR, with NADP+ and folate (1RX2). (B) Binding pocket in the X-ray crystal structure of the open form of the M20 loop in DHFR, with NADP+ and folate (1RA2). (C) Binding pocket in the docked structure between the center structure of the M20α cluster and folate. (D) Binding pocket in the docked structure between the center structure of the M20β cluster and folate.
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f8-2_1: The ligand-binding pocket of DHFR and the folate molecule generated from a docking simulation with NADP+ and structural optimization. The dotted lines correspond to intermolecular hydrogen bonds. Semi-circles represent the protein residues involved in the hydrophobic interaction. Numbers in italics represent the interatomic distance between the interacting heavy atom pairs (Å). (A) Binding pocket in the X-ray crystal structure of the closed form of the M20 loop in DHFR, with NADP+ and folate (1RX2). (B) Binding pocket in the X-ray crystal structure of the open form of the M20 loop in DHFR, with NADP+ and folate (1RA2). (C) Binding pocket in the docked structure between the center structure of the M20α cluster and folate. (D) Binding pocket in the docked structure between the center structure of the M20β cluster and folate.

Mentions: For the M20α and M20γ center loop structures, the docking scores were rather high, −3.99 and −3.45, respectively. The docking score is a measure of the binding energy, with a lower score corresponding to higher affinity. Consequently, the high docking scores suggest low affinity of the folate ligand for the M20α and M20γ center loop structures. In addition, the docked structures show different binding schemes from the complexed X-ray crystal structues. In the closed M20 loop crystal structure (1RX2), four hydrogen bonds and a hydrophobic interaction between DHFR and the folate ligand are observed, in addition to hydrophobic interactions between NADP+ and the ligand (Fig. 8A). The open M20 loop crystal structure (1RA2) shows a binding mode almost identical to that of the closed loop structure, but fewer interactions between the M20 loop and the ligand are observed (Fig. 8B)22. In contrast, the predicted ternary structure in Fig. 8C has quite a different hydrogen bond network between DHFR and folate from that of the closed and open loops. Here, the docking scheme of folate bound to DHFR with NADP+ is displayed for the M20α center structure. The corresponding RMSD values of the folate against the X-ray crystal structure in 1RX2 and 1RA2 were very large, 4.34 Å and 4.25 Å, respectively.


Generation of a flexible loop structural ensemble and its application to induced-fit structural changes following ligand binding
The ligand-binding pocket of DHFR and the folate molecule generated from a docking simulation with NADP+ and structural optimization. The dotted lines correspond to intermolecular hydrogen bonds. Semi-circles represent the protein residues involved in the hydrophobic interaction. Numbers in italics represent the interatomic distance between the interacting heavy atom pairs (Å). (A) Binding pocket in the X-ray crystal structure of the closed form of the M20 loop in DHFR, with NADP+ and folate (1RX2). (B) Binding pocket in the X-ray crystal structure of the open form of the M20 loop in DHFR, with NADP+ and folate (1RA2). (C) Binding pocket in the docked structure between the center structure of the M20α cluster and folate. (D) Binding pocket in the docked structure between the center structure of the M20β cluster and folate.
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC5036648&req=5

f8-2_1: The ligand-binding pocket of DHFR and the folate molecule generated from a docking simulation with NADP+ and structural optimization. The dotted lines correspond to intermolecular hydrogen bonds. Semi-circles represent the protein residues involved in the hydrophobic interaction. Numbers in italics represent the interatomic distance between the interacting heavy atom pairs (Å). (A) Binding pocket in the X-ray crystal structure of the closed form of the M20 loop in DHFR, with NADP+ and folate (1RX2). (B) Binding pocket in the X-ray crystal structure of the open form of the M20 loop in DHFR, with NADP+ and folate (1RA2). (C) Binding pocket in the docked structure between the center structure of the M20α cluster and folate. (D) Binding pocket in the docked structure between the center structure of the M20β cluster and folate.
Mentions: For the M20α and M20γ center loop structures, the docking scores were rather high, −3.99 and −3.45, respectively. The docking score is a measure of the binding energy, with a lower score corresponding to higher affinity. Consequently, the high docking scores suggest low affinity of the folate ligand for the M20α and M20γ center loop structures. In addition, the docked structures show different binding schemes from the complexed X-ray crystal structues. In the closed M20 loop crystal structure (1RX2), four hydrogen bonds and a hydrophobic interaction between DHFR and the folate ligand are observed, in addition to hydrophobic interactions between NADP+ and the ligand (Fig. 8A). The open M20 loop crystal structure (1RA2) shows a binding mode almost identical to that of the closed loop structure, but fewer interactions between the M20 loop and the ligand are observed (Fig. 8B)22. In contrast, the predicted ternary structure in Fig. 8C has quite a different hydrogen bond network between DHFR and folate from that of the closed and open loops. Here, the docking scheme of folate bound to DHFR with NADP+ is displayed for the M20α center structure. The corresponding RMSD values of the folate against the X-ray crystal structure in 1RX2 and 1RA2 were very large, 4.34 Å and 4.25 Å, respectively.

View Article: PubMed Central - PubMed

ABSTRACT

Molecular recognition is often mediated by flexible loops that have widely fluctuating structures and are sometimes disordered, but that form particular complex structures following ligand binding. In fact, many loop structures found in the PDB database are too flexible to be determined precisely. A new loop modeling method was therefore developed using force-biased multicanonical molecular dynamics with the implicit solvent model to generate an ensemble of putative loop structures with low free energy values. The method was then used to create ensembles for several flexible loops that were compared with the corresponding NMR and X-ray structures. The induced-fit structural change of dihydrofolate reductase (DHFR) was also predicted from a structural ensemble of ligand-free M20 loop conformations and successive docking simulations.

No MeSH data available.