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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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Examples of rotamers in level-ε atoms. (Color online) The black circles have the same radius in a) and b), in c) and d), and in e) and f). In figure a) the α-helix and in b) the β-strand rotamers for for CE in MET and LYS; the structures outside the circle are LYS, those inside are MET. In figure c) the α-helix and in d) the β-strand rotamers for CE1 in PHE and TYR. In figure e) the α-helix rotamers for OE1 in GLU and GLN, and in f) the α-helix rotamers for OE2 in GLU (there is no GLN).
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Fig17: Examples of rotamers in level-ε atoms. (Color online) The black circles have the same radius in a) and b), in c) and d), and in e) and f). In figure a) the α-helix and in b) the β-strand rotamers for for CE in MET and LYS; the structures outside the circle are LYS, those inside are MET. In figure c) the α-helix and in d) the β-strand rotamers for CE1 in PHE and TYR. In figure e) the α-helix rotamers for OE1 in GLU and GLN, and in f) the α-helix rotamers for OE2 in GLU (there is no GLN).

Mentions: In Figure 17a) - f) we show various examples of level-ε atoms. We observe that in addition of rotamers in the longitude, there are also rotamer-like variations in the latitude angle, as shown in black circles in each figure.Figure 17


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)

Examples of rotamers in level-ε atoms. (Color online) The black circles have the same radius in a) and b), in c) and d), and in e) and f). In figure a) the α-helix and in b) the β-strand rotamers for for CE in MET and LYS; the structures outside the circle are LYS, those inside are MET. In figure c) the α-helix and in d) the β-strand rotamers for CE1 in PHE and TYR. In figure e) the α-helix rotamers for OE1 in GLU and GLN, and in f) the α-helix rotamers for OE2 in GLU (there is no GLN).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig17: Examples of rotamers in level-ε atoms. (Color online) The black circles have the same radius in a) and b), in c) and d), and in e) and f). In figure a) the α-helix and in b) the β-strand rotamers for for CE in MET and LYS; the structures outside the circle are LYS, those inside are MET. In figure c) the α-helix and in d) the β-strand rotamers for CE1 in PHE and TYR. In figure e) the α-helix rotamers for OE1 in GLU and GLN, and in f) the α-helix rotamers for OE2 in GLU (there is no GLN).
Mentions: In Figure 17a) - f) we show various examples of level-ε atoms. We observe that in addition of rotamers in the longitude, there are also rotamer-like variations in the latitude angle, as shown in black circles in each figure.Figure 17

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