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An algorithm to enumerate all possible protein conformations verifying a set of distance constraints.

Cassioli A, Bardiaux B, Bouvier G, Mucherino A, Alves R, Liberti L, Nilges M, Lavor C, Malliavin TE - BMC Bioinformatics (2015)

Bottom Line: Whereas the most common method currently employed is simulated annealing, there have been other methods previously proposed in the literature.Most of them, however, are designed to find one solution only.The pruning devices used here are directly related to features of protein conformations.

View Article: PubMed Central - PubMed

Affiliation: LIX, Ecole Polytechnique, Palaiseau, 91128, France. cassioliandre@gmail.com.

ABSTRACT

Background: The determination of protein structures satisfying distance constraints is an important problem in structural biology. Whereas the most common method currently employed is simulated annealing, there have been other methods previously proposed in the literature. Most of them, however, are designed to find one solution only.

Results: In order to explore exhaustively the feasible conformational space, we propose here an interval Branch-and-Prune algorithm (iBP) to solve the Distance Geometry Problem (DGP) associated to protein structure determination. This algorithm is based on a discretization of the problem obtained by recursively constructing a search space having the structure of a tree, and by verifying whether the generated atomic positions are feasible or not by making use of pruning devices. The pruning devices used here are directly related to features of protein conformations.

Conclusions: We described the new algorithm iBP to generate protein conformations satisfying distance constraints, that would potentially allows a systematic exploration of the conformational space. The algorithm iBP has been applied on three α-helical peptides.

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Superimposed 2KXA and 2KSL conformations. Superimposition of 2KXA and 2KSL conformations extracted from the SOM, as the ones displaying the minimum coordinates RMSD with respect to the first conformer of the corresponding PDB structures. The N and C terminal extremities are labeled, and the conformations, drawn in cartoon, are colored from blue to red, according to the conformational index.
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Fig7: Superimposed 2KXA and 2KSL conformations. Superimposition of 2KXA and 2KSL conformations extracted from the SOM, as the ones displaying the minimum coordinates RMSD with respect to the first conformer of the corresponding PDB structures. The N and C terminal extremities are labeled, and the conformations, drawn in cartoon, are colored from blue to red, according to the conformational index.

Mentions: In 2KSL and 2KXA SOMs, the protein conformations corresponding to the region displaying the smallest coordinate RMSD values with respect to the PDB structure, were extracted (Figure 7). These sets of conformers are similar to the superimposed conformations obtained in a usual NMR calculation.Figure 7


An algorithm to enumerate all possible protein conformations verifying a set of distance constraints.

Cassioli A, Bardiaux B, Bouvier G, Mucherino A, Alves R, Liberti L, Nilges M, Lavor C, Malliavin TE - BMC Bioinformatics (2015)

Superimposed 2KXA and 2KSL conformations. Superimposition of 2KXA and 2KSL conformations extracted from the SOM, as the ones displaying the minimum coordinates RMSD with respect to the first conformer of the corresponding PDB structures. The N and C terminal extremities are labeled, and the conformations, drawn in cartoon, are colored from blue to red, according to the conformational index.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4384350&req=5

Fig7: Superimposed 2KXA and 2KSL conformations. Superimposition of 2KXA and 2KSL conformations extracted from the SOM, as the ones displaying the minimum coordinates RMSD with respect to the first conformer of the corresponding PDB structures. The N and C terminal extremities are labeled, and the conformations, drawn in cartoon, are colored from blue to red, according to the conformational index.
Mentions: In 2KSL and 2KXA SOMs, the protein conformations corresponding to the region displaying the smallest coordinate RMSD values with respect to the PDB structure, were extracted (Figure 7). These sets of conformers are similar to the superimposed conformations obtained in a usual NMR calculation.Figure 7

Bottom Line: Whereas the most common method currently employed is simulated annealing, there have been other methods previously proposed in the literature.Most of them, however, are designed to find one solution only.The pruning devices used here are directly related to features of protein conformations.

View Article: PubMed Central - PubMed

Affiliation: LIX, Ecole Polytechnique, Palaiseau, 91128, France. cassioliandre@gmail.com.

ABSTRACT

Background: The determination of protein structures satisfying distance constraints is an important problem in structural biology. Whereas the most common method currently employed is simulated annealing, there have been other methods previously proposed in the literature. Most of them, however, are designed to find one solution only.

Results: In order to explore exhaustively the feasible conformational space, we propose here an interval Branch-and-Prune algorithm (iBP) to solve the Distance Geometry Problem (DGP) associated to protein structure determination. This algorithm is based on a discretization of the problem obtained by recursively constructing a search space having the structure of a tree, and by verifying whether the generated atomic positions are feasible or not by making use of pruning devices. The pruning devices used here are directly related to features of protein conformations.

Conclusions: We described the new algorithm iBP to generate protein conformations satisfying distance constraints, that would potentially allows a systematic exploration of the conformational space. The algorithm iBP has been applied on three α-helical peptides.

Show MeSH