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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.


(A) Structural overview of DHFR: The magenta pipe (residues 1–13 and 26–149) of DHFR (1RX2) was drawn using INSIGHT II (Accelrys Inc., San Diego, CA, USA). The thick red pipe, dotted orange sphere and dotted gray sphere correspond to residues 14–25 of the M20 loop of DHFR, NADP+ and folate, respectively. (B) The center structures for Loop M20: Stereo drawings of the ligand-free M20 loop and the closed M20 loop of ternary complex conformations. The blue, cyan, green, yellow and red pipes correspond to center structures of the M20α, M20β, M20γ and M20δ clusters, and the X-ray crystal structure (1RX2), respectively. The dotted orange sphere is NADP+, and the dotted gray sphere is folate. The loop of the X-ray crystal structure of the closed form is close to NADP+.
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f6-2_1: (A) Structural overview of DHFR: The magenta pipe (residues 1–13 and 26–149) of DHFR (1RX2) was drawn using INSIGHT II (Accelrys Inc., San Diego, CA, USA). The thick red pipe, dotted orange sphere and dotted gray sphere correspond to residues 14–25 of the M20 loop of DHFR, NADP+ and folate, respectively. (B) The center structures for Loop M20: Stereo drawings of the ligand-free M20 loop and the closed M20 loop of ternary complex conformations. The blue, cyan, green, yellow and red pipes correspond to center structures of the M20α, M20β, M20γ and M20δ clusters, and the X-ray crystal structure (1RX2), respectively. The dotted orange sphere is NADP+, and the dotted gray sphere is folate. The loop of the X-ray crystal structure of the closed form is close to NADP+.

Mentions: The center structures of the four clusters and the closed loop crystal structures including the cofactor, Nicotinamide Adenine Dinucleotide Phosphate (NADP+), and the ligand are shown in Figs. 6A and B. The backbone of the center structures of M20α and M20γ penetrated the ligand pocket. The backbone of the M20β center structure made slight contact with the ligand, similar to the case of the M20 closed loop that contacted the ligand. The M20δ center structure is located far from the active site, and did not interact with the ligand at all. The RMSDx values of the four center structures for the heavy atoms in Loop M20 are listed in Table 2.


Generation of a flexible loop structural ensemble and its application to induced-fit structural changes following ligand binding
(A) Structural overview of DHFR: The magenta pipe (residues 1–13 and 26–149) of DHFR (1RX2) was drawn using INSIGHT II (Accelrys Inc., San Diego, CA, USA). The thick red pipe, dotted orange sphere and dotted gray sphere correspond to residues 14–25 of the M20 loop of DHFR, NADP+ and folate, respectively. (B) The center structures for Loop M20: Stereo drawings of the ligand-free M20 loop and the closed M20 loop of ternary complex conformations. The blue, cyan, green, yellow and red pipes correspond to center structures of the M20α, M20β, M20γ and M20δ clusters, and the X-ray crystal structure (1RX2), respectively. The dotted orange sphere is NADP+, and the dotted gray sphere is folate. The loop of the X-ray crystal structure of the closed form is close to NADP+.
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC5036648&req=5

f6-2_1: (A) Structural overview of DHFR: The magenta pipe (residues 1–13 and 26–149) of DHFR (1RX2) was drawn using INSIGHT II (Accelrys Inc., San Diego, CA, USA). The thick red pipe, dotted orange sphere and dotted gray sphere correspond to residues 14–25 of the M20 loop of DHFR, NADP+ and folate, respectively. (B) The center structures for Loop M20: Stereo drawings of the ligand-free M20 loop and the closed M20 loop of ternary complex conformations. The blue, cyan, green, yellow and red pipes correspond to center structures of the M20α, M20β, M20γ and M20δ clusters, and the X-ray crystal structure (1RX2), respectively. The dotted orange sphere is NADP+, and the dotted gray sphere is folate. The loop of the X-ray crystal structure of the closed form is close to NADP+.
Mentions: The center structures of the four clusters and the closed loop crystal structures including the cofactor, Nicotinamide Adenine Dinucleotide Phosphate (NADP+), and the ligand are shown in Figs. 6A and B. The backbone of the center structures of M20α and M20γ penetrated the ligand pocket. The backbone of the M20β center structure made slight contact with the ligand, similar to the case of the M20 closed loop that contacted the ligand. The M20δ center structure is located far from the active site, and did not interact with the ligand at all. The RMSDx values of the four center structures for the heavy atoms in Loop M20 are listed in Table 2.

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.