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Normal Mode Flexible Fitting of High-Resolution Structures of Biological Molecules Toward SAXS Data.

Gorba C, Tama F - Bioinform Biol Insights (2010)

Bottom Line: We present a method to reconstruct a three-dimensional protein structure from an atomic pair distribution function derived from the scattering intensity profile from SAXS data by flexibly fitting known x-ray structures.For computational efficiency, the protein and water molecules included in the protein first hydration shell are coarse-grained.Illustrative results of our flexible fitting studies on simulated SAXS data from five different proteins are presented.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry and Biochemistry, The University of Arizona, 1041 E. Lowell Street, Tucson, AZ, 85721.

ABSTRACT
We present a method to reconstruct a three-dimensional protein structure from an atomic pair distribution function derived from the scattering intensity profile from SAXS data by flexibly fitting known x-ray structures. This method uses a linear combination of low-frequency normal modes from an elastic network description of the molecule in an iterative manner to deform the structure to conform optimally to the target pair distribution function derived from SAXS data. For computational efficiency, the protein and water molecules included in the protein first hydration shell are coarse-grained. In this paper, we demonstrate the validity of our coarse-graining approach to study SAXS data. Illustrative results of our flexible fitting studies on simulated SAXS data from five different proteins are presented.

No MeSH data available.


(a) The initial structure of EF2, (b) the target structure from which the simulated experimental data is created and (c) the modeled structure predicted from the fitting algorithm. Domain 2 has a different placement in target and modeled structure compared to the initial structure.
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f4-bbi-2010-043: (a) The initial structure of EF2, (b) the target structure from which the simulated experimental data is created and (c) the modeled structure predicted from the fitting algorithm. Domain 2 has a different placement in target and modeled structure compared to the initial structure.

Mentions: Figure 4 shows two different conformations of the Elongation Factor along with the modeled structure (Fig. 4c). In the two known X-ray structures, domains 2 and 5 have different positions. In the modeled structure, domains 2 and 5 are close to each other, which is comparable to their position in the target structure. Although our method only predicts the structure within ∼5 Å RMSD (see Table 1), most of the conformational change is accurately described by correctly predicting major rearrangements between domains.


Normal Mode Flexible Fitting of High-Resolution Structures of Biological Molecules Toward SAXS Data.

Gorba C, Tama F - Bioinform Biol Insights (2010)

(a) The initial structure of EF2, (b) the target structure from which the simulated experimental data is created and (c) the modeled structure predicted from the fitting algorithm. Domain 2 has a different placement in target and modeled structure compared to the initial structure.
© Copyright Policy - open-access
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2901630&req=5

f4-bbi-2010-043: (a) The initial structure of EF2, (b) the target structure from which the simulated experimental data is created and (c) the modeled structure predicted from the fitting algorithm. Domain 2 has a different placement in target and modeled structure compared to the initial structure.
Mentions: Figure 4 shows two different conformations of the Elongation Factor along with the modeled structure (Fig. 4c). In the two known X-ray structures, domains 2 and 5 have different positions. In the modeled structure, domains 2 and 5 are close to each other, which is comparable to their position in the target structure. Although our method only predicts the structure within ∼5 Å RMSD (see Table 1), most of the conformational change is accurately described by correctly predicting major rearrangements between domains.

Bottom Line: We present a method to reconstruct a three-dimensional protein structure from an atomic pair distribution function derived from the scattering intensity profile from SAXS data by flexibly fitting known x-ray structures.For computational efficiency, the protein and water molecules included in the protein first hydration shell are coarse-grained.Illustrative results of our flexible fitting studies on simulated SAXS data from five different proteins are presented.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry and Biochemistry, The University of Arizona, 1041 E. Lowell Street, Tucson, AZ, 85721.

ABSTRACT
We present a method to reconstruct a three-dimensional protein structure from an atomic pair distribution function derived from the scattering intensity profile from SAXS data by flexibly fitting known x-ray structures. This method uses a linear combination of low-frequency normal modes from an elastic network description of the molecule in an iterative manner to deform the structure to conform optimally to the target pair distribution function derived from SAXS data. For computational efficiency, the protein and water molecules included in the protein first hydration shell are coarse-grained. In this paper, we demonstrate the validity of our coarse-graining approach to study SAXS data. Illustrative results of our flexible fitting studies on simulated SAXS data from five different proteins are presented.

No MeSH data available.