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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.


Stereo drawings of Loop R8 and R12 in RNase A. (A) Loop R8: The backbone of the X-ray crystal structure of bovine RNase A (8RAT) is shown in red. Blue, cyan and green backbones correspond to center structures of the R8α, R8β and R8γ clusters, respectively. The gray backbone represents the structure with the smallest RMSDx (0.72 Å) in R8α. (B) Loop R12: The backbone of the X-ray crystal structure of bovine RNase A (8RAT) is shown in red. Blue and cyan backbones correspond to center structures of the R12α and R12β clusters, respectively. The gray backbone represents the structure with the smallest RMSDx (1.50 Å) in R12α.
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f4-2_1: Stereo drawings of Loop R8 and R12 in RNase A. (A) Loop R8: The backbone of the X-ray crystal structure of bovine RNase A (8RAT) is shown in red. Blue, cyan and green backbones correspond to center structures of the R8α, R8β and R8γ clusters, respectively. The gray backbone represents the structure with the smallest RMSDx (0.72 Å) in R8α. (B) Loop R12: The backbone of the X-ray crystal structure of bovine RNase A (8RAT) is shown in red. Blue and cyan backbones correspond to center structures of the R12α and R12β clusters, respectively. The gray backbone represents the structure with the smallest RMSDx (1.50 Å) in R12α.

Mentions: Since our method provides an ensemble of loop conformations, it is useful to have a representative structure for each structural cluster in the ensemble. For that purpose, we initially calculated an average loop structure for each cluster using the backbone heavy atoms in the loop. Following this, a loop structure was selected as the ‘center structure’, which possesses the smallest RMSD value from the aforementioned average loop structure following structural superpositioning of the backbone atoms of the three preceding residues before the loop and the three residues after the loop. The center structures are shown in Fig. 3A. Using the center structure, we further calculated the RMSDc, which represents the RMSD value of the heavy atoms in Loop R8 between the center structure of each cluster and the model structure. The correlation between RMSDc and RMSDx in the structural ensemble for the R8α cluster was very high, with a Pearson correlation coefficient of 0.892. For other clusters, there was little or no correlation. This suggests that the center structure of the R8α cluster may be a good representative of the cluster. The three center structures of the individual clusters are shown in Fig. 4A with the X-ray crystal structure.


Generation of a flexible loop structural ensemble and its application to induced-fit structural changes following ligand binding
Stereo drawings of Loop R8 and R12 in RNase A. (A) Loop R8: The backbone of the X-ray crystal structure of bovine RNase A (8RAT) is shown in red. Blue, cyan and green backbones correspond to center structures of the R8α, R8β and R8γ clusters, respectively. The gray backbone represents the structure with the smallest RMSDx (0.72 Å) in R8α. (B) Loop R12: The backbone of the X-ray crystal structure of bovine RNase A (8RAT) is shown in red. Blue and cyan backbones correspond to center structures of the R12α and R12β clusters, respectively. The gray backbone represents the structure with the smallest RMSDx (1.50 Å) in R12α.
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Related In: Results  -  Collection

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f4-2_1: Stereo drawings of Loop R8 and R12 in RNase A. (A) Loop R8: The backbone of the X-ray crystal structure of bovine RNase A (8RAT) is shown in red. Blue, cyan and green backbones correspond to center structures of the R8α, R8β and R8γ clusters, respectively. The gray backbone represents the structure with the smallest RMSDx (0.72 Å) in R8α. (B) Loop R12: The backbone of the X-ray crystal structure of bovine RNase A (8RAT) is shown in red. Blue and cyan backbones correspond to center structures of the R12α and R12β clusters, respectively. The gray backbone represents the structure with the smallest RMSDx (1.50 Å) in R12α.
Mentions: Since our method provides an ensemble of loop conformations, it is useful to have a representative structure for each structural cluster in the ensemble. For that purpose, we initially calculated an average loop structure for each cluster using the backbone heavy atoms in the loop. Following this, a loop structure was selected as the ‘center structure’, which possesses the smallest RMSD value from the aforementioned average loop structure following structural superpositioning of the backbone atoms of the three preceding residues before the loop and the three residues after the loop. The center structures are shown in Fig. 3A. Using the center structure, we further calculated the RMSDc, which represents the RMSD value of the heavy atoms in Loop R8 between the center structure of each cluster and the model structure. The correlation between RMSDc and RMSDx in the structural ensemble for the R8α cluster was very high, with a Pearson correlation coefficient of 0.892. For other clusters, there was little or no correlation. This suggests that the center structure of the R8α cluster may be a good representative of the cluster. The three center structures of the individual clusters are shown in Fig. 4A with the X-ray crystal structure.

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.