Limits...
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.


Related in: MedlinePlus

Stereo drawings of the modeled M20 loop conformations in DHFR. (A) The X-ray crystal structure of the M20 loop in the closed form (1RX2) is shown by a red backbone and orange side-chains. A blue backbone and cyan side-chains indicate the structure with the smallest RMSDx (1.72 Å) with 1RX2, designated as Loop M20β1 in the M20β cluster. (B) The X-ray crystal structure of the M20 loop in the open form (1RA2) is shown by a red backbone and orange side-chains. A blue backbone and cyan side-chains indicate the structure with the smallest RMSDx (2.11 Å) with 1RA2, designated as Loop M20β2 in the M20β cluster. (C) The X-ray crystal structure of the M20 loop in the occluded form (1RX5) is shown by a red backbone and orange side-chains. A blue backbone and cyan side-chains indicate the structure with the smallest RMSDx (3.10 Å) with 1RX5, designated as Loop M20β3 in the M20β cluster.
© Copyright Policy
Related In: Results  -  Collection


getmorefigures.php?uid=PMC5036648&req=5

f7-2_1: Stereo drawings of the modeled M20 loop conformations in DHFR. (A) The X-ray crystal structure of the M20 loop in the closed form (1RX2) is shown by a red backbone and orange side-chains. A blue backbone and cyan side-chains indicate the structure with the smallest RMSDx (1.72 Å) with 1RX2, designated as Loop M20β1 in the M20β cluster. (B) The X-ray crystal structure of the M20 loop in the open form (1RA2) is shown by a red backbone and orange side-chains. A blue backbone and cyan side-chains indicate the structure with the smallest RMSDx (2.11 Å) with 1RA2, designated as Loop M20β2 in the M20β cluster. (C) The X-ray crystal structure of the M20 loop in the occluded form (1RX5) is shown by a red backbone and orange side-chains. A blue backbone and cyan side-chains indicate the structure with the smallest RMSDx (3.10 Å) with 1RX5, designated as Loop M20β3 in the M20β cluster.

Mentions: As shown in Fig. 5, the conformation of the M20β cluster is widely distributed on the 2D plane by the first and the second principle axes. We attempted to search for the experimental ligand-bound loop conformations in the M20β cluster. Consequently, we found that one of the model structures in M20β shown in Fig. 7A (designated as M20β1) is comparable to the closed loop of the X-ray crystal structure (1RX2) with a RMSD value of 1.72 Å. In the same way, the M20β2 loop shown in Fig. 7B and the M20β3 loop shown in Fig. 7C are very similar to the open and occluded loops of the X-ray crystal structures (1RA2 and 1RX5) with RMSD values of 2.12 Å and 3.10 Å, respectively. Here, the RMSD values were calculated between the heavy atoms of the modeled flexible loop regions from residue 14 to 25 and those in the X-ray crystal structures, where the X-ray crystal structures of DHFR backbones were superimposed on the backbone of the current template structure. Thus, in the current structural ensemble, we can find structures similar to several different loop conformations that were observed with the ligand in the X-ray crystal structures, even when the conformational search was made for the apo-form DHFR starting from a very different initial loop conformation.


Generation of a flexible loop structural ensemble and its application to induced-fit structural changes following ligand binding
Stereo drawings of the modeled M20 loop conformations in DHFR. (A) The X-ray crystal structure of the M20 loop in the closed form (1RX2) is shown by a red backbone and orange side-chains. A blue backbone and cyan side-chains indicate the structure with the smallest RMSDx (1.72 Å) with 1RX2, designated as Loop M20β1 in the M20β cluster. (B) The X-ray crystal structure of the M20 loop in the open form (1RA2) is shown by a red backbone and orange side-chains. A blue backbone and cyan side-chains indicate the structure with the smallest RMSDx (2.11 Å) with 1RA2, designated as Loop M20β2 in the M20β cluster. (C) The X-ray crystal structure of the M20 loop in the occluded form (1RX5) is shown by a red backbone and orange side-chains. A blue backbone and cyan side-chains indicate the structure with the smallest RMSDx (3.10 Å) with 1RX5, designated as Loop M20β3 in the M20β cluster.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC5036648&req=5

f7-2_1: Stereo drawings of the modeled M20 loop conformations in DHFR. (A) The X-ray crystal structure of the M20 loop in the closed form (1RX2) is shown by a red backbone and orange side-chains. A blue backbone and cyan side-chains indicate the structure with the smallest RMSDx (1.72 Å) with 1RX2, designated as Loop M20β1 in the M20β cluster. (B) The X-ray crystal structure of the M20 loop in the open form (1RA2) is shown by a red backbone and orange side-chains. A blue backbone and cyan side-chains indicate the structure with the smallest RMSDx (2.11 Å) with 1RA2, designated as Loop M20β2 in the M20β cluster. (C) The X-ray crystal structure of the M20 loop in the occluded form (1RX5) is shown by a red backbone and orange side-chains. A blue backbone and cyan side-chains indicate the structure with the smallest RMSDx (3.10 Å) with 1RX5, designated as Loop M20β3 in the M20β cluster.
Mentions: As shown in Fig. 5, the conformation of the M20β cluster is widely distributed on the 2D plane by the first and the second principle axes. We attempted to search for the experimental ligand-bound loop conformations in the M20β cluster. Consequently, we found that one of the model structures in M20β shown in Fig. 7A (designated as M20β1) is comparable to the closed loop of the X-ray crystal structure (1RX2) with a RMSD value of 1.72 Å. In the same way, the M20β2 loop shown in Fig. 7B and the M20β3 loop shown in Fig. 7C are very similar to the open and occluded loops of the X-ray crystal structures (1RA2 and 1RX5) with RMSD values of 2.12 Å and 3.10 Å, respectively. Here, the RMSD values were calculated between the heavy atoms of the modeled flexible loop regions from residue 14 to 25 and those in the X-ray crystal structures, where the X-ray crystal structures of DHFR backbones were superimposed on the backbone of the current template structure. Thus, in the current structural ensemble, we can find structures similar to several different loop conformations that were observed with the ligand in the X-ray crystal structures, even when the conformational search was made for the apo-form DHFR starting from a very different initial loop conformation.

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.


Related in: MedlinePlus