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A three dimensional visualisation approach to protein heavy-atom structure reconstruction.

Peng X, Chenani A, Hu S, Zhou Y, Niemi AJ - BMC Struct. Biol. (2014)

Bottom Line: Our method easily detects those atoms in a crystallographic protein structure which are either outliers or have been likely misplaced, possibly due to radiation damage.Our approach forms a basis for the development of a new generation, visualization based side chain construction, validation and refinement tools.The heavy atom positions are identified in a manner which accounts for the secondary structure environment, leading to improved accuracy.

View Article: PubMed Central - PubMed

Affiliation: Department of Physics and Astronomy, Uppsala University, Uppsala, Sweden. xubiaopeng@gmail.com.

ABSTRACT

Background: A commonly recurring problem in structural protein studies, is the determination of all heavy atom positions from the knowledge of the central α-carbon coordinates.

Results: We employ advances in virtual reality to address the problem. The outcome is a 3D visualisation based technique where all the heavy backbone and side chain atoms are treated on equal footing, in terms of the Cα coordinates. Each heavy atom is visualised on the surfaces of a different two-sphere, that is centered at another heavy backbone and side chain atoms. In particular, the rotamers are visible as clusters, that display a clear and strong dependence on the underlying backbone secondary structure.

Conclusions: We demonstrate that there is a clear interdependence between rotameric states and secondary structure. Our method easily detects those atoms in a crystallographic protein structure which are either outliers or have been likely misplaced, possibly due to radiation damage. Our approach forms a basis for the development of a new generation, visualization based side chain construction, validation and refinement tools. The heavy atom positions are identified in a manner which accounts for the secondary structure environment, leading to improved accuracy.

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Distribution of Cβatoms immediately after and right before a proline. (Color online) The grey-scaled background is determined by the high-density region of Figure 4a). In figure a) immediately after trans-PRO and in figure b) immediately after cis-PRO. In figure c) right before trans-PRO and in figure d) right before cis-PRO.
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Fig9: Distribution of Cβatoms immediately after and right before a proline. (Color online) The grey-scaled background is determined by the high-density region of Figure 4a). In figure a) immediately after trans-PRO and in figure b) immediately after cis-PRO. In figure c) right before trans-PRO and in figure d) right before cis-PRO.

Mentions: In Figure 9a)-d) we display the Cβ carbons that are located either immediately after or right before a proline. We observe the following:Figure 9


A three dimensional visualisation approach to protein heavy-atom structure reconstruction.

Peng X, Chenani A, Hu S, Zhou Y, Niemi AJ - BMC Struct. Biol. (2014)

Distribution of Cβatoms immediately after and right before a proline. (Color online) The grey-scaled background is determined by the high-density region of Figure 4a). In figure a) immediately after trans-PRO and in figure b) immediately after cis-PRO. In figure c) right before trans-PRO and in figure d) right before cis-PRO.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4302604&req=5

Fig9: Distribution of Cβatoms immediately after and right before a proline. (Color online) The grey-scaled background is determined by the high-density region of Figure 4a). In figure a) immediately after trans-PRO and in figure b) immediately after cis-PRO. In figure c) right before trans-PRO and in figure d) right before cis-PRO.
Mentions: In Figure 9a)-d) we display the Cβ carbons that are located either immediately after or right before a proline. We observe the following:Figure 9

Bottom Line: Our method easily detects those atoms in a crystallographic protein structure which are either outliers or have been likely misplaced, possibly due to radiation damage.Our approach forms a basis for the development of a new generation, visualization based side chain construction, validation and refinement tools.The heavy atom positions are identified in a manner which accounts for the secondary structure environment, leading to improved accuracy.

View Article: PubMed Central - PubMed

Affiliation: Department of Physics and Astronomy, Uppsala University, Uppsala, Sweden. xubiaopeng@gmail.com.

ABSTRACT

Background: A commonly recurring problem in structural protein studies, is the determination of all heavy atom positions from the knowledge of the central α-carbon coordinates.

Results: We employ advances in virtual reality to address the problem. The outcome is a 3D visualisation based technique where all the heavy backbone and side chain atoms are treated on equal footing, in terms of the Cα coordinates. Each heavy atom is visualised on the surfaces of a different two-sphere, that is centered at another heavy backbone and side chain atoms. In particular, the rotamers are visible as clusters, that display a clear and strong dependence on the underlying backbone secondary structure.

Conclusions: We demonstrate that there is a clear interdependence between rotameric states and secondary structure. Our method easily detects those atoms in a crystallographic protein structure which are either outliers or have been likely misplaced, possibly due to radiation damage. Our approach forms a basis for the development of a new generation, visualization based side chain construction, validation and refinement tools. The heavy atom positions are identified in a manner which accounts for the secondary structure environment, leading to improved accuracy.

Show MeSH
Related in: MedlinePlus