Bändermodell (Proteine)

Proteinstrukturen, von der primären zur quartären Struktur.

Bändermodelle sind Molekülmodelle von Proteinstrukturen.[1][2][3][4] Sie visualisieren Elemente der Sekundärstruktur wie eine α-Helix oder ein β-Faltblatt und erlauben eine Darstellung der Tertiärstruktur. Verschiedene Polypeptide können zur besseren Unterscheidung farblich unterschiedlich markiert sein. Bändermodelle werden bei der molekularen Modellierung eingesetzt,[5][6] z. B. beim Protein-Engineering. Das Bändermodell wurde 1980/81 durch Jane Richardson etabliert.[1][2][3] Ähnliche Ansätze gab es aber schon früher.

Strukturdarstellungen

Triosephosphatisomerase, handgezeichnet von Jane Richardson.
Sekundärstruktur[1][2]
α-Helices Zylindrische spiralförmige Bänder, mit der Bänderebene ungefähr auf der Peptidbindungsebene.
β-Stränge Pfeile mit einer Dicke von 25 % der Breite in Richtung von N- zu C-Terminus. β-Faltblätter bestehen aus parallel angeordneten β-Strängen mit β-Schleifen.
Schleifen und andere
Nichtrepetitive Schleifen Runde Stränge entlang der α-C-Atome der Aminosäuren, die vom Vordergrund zum Hintergrund dünner werden.
Verbindungen zwischen Schleifen und Helices Runde Stränge entlang der α-C-Atome der Aminosäuren, die beim Übergang zur α-Helix flacher werden.
Andere Merkmale
N- und C-Terminus Kleine Pfeile an einem oder beiden Enden oder mit Buchstaben codiert. Für β-Stränge ist die Richtung des Pfeils ausreichend. Oftmals wird hierfür ein Farbgradient entlang der Aminosäuresequenz verwendet.
Disulfidbrücken Mit verschränktem Doppel-S oder mit einem Zick-Zack-Strich
Prosthetische Gruppen oder Inhibitoren Stabmodell, Kugel-und-Stabmodell
Metalle Kugeln
Schattierung und Farbe Der Kontrast nimmt zum Hintergrund hin ab

Software

Verschiedene Programme zur Darstellung von Proteinen im Bändermodell wurden entwickelt, z. B. Molscript von Arthur M. Lesk, Karl Hardman und John Priestle,[7] Jmol,[8] DeepView,[9] MolMol,[10] KiNG,[11] UCSF Chimera[12] und PyMOL von Warren DeLano.[13]

Literatur

Einzelnachweise

  1. ↑ a b c Jane Shelby Richardson: The anatomy and taxonomy of protein structure. In: Advances in protein chemistry. Band 34, 1981, S. 167–339, PMID 7020376.
  2. ↑ a b c J. S. Richardson: Schematic drawings of protein structures. In: Methods in enzymology. Band 115, 1985, S. 359–380, PMID 3853075.
  3. ↑ a b Jane S. Richardson: Early ribbon drawings of proteins (Memento vom 1. Februar 2014 im Internet Archive; PDF; 227 KB). In: Nature Structural Biology, Band 7, Nummer 8, August 2000, S. 624–625, doi:10.1038/77912. PMID 10932243.
  4. ↑ M. Morange: What history tells us XXV. Construction of the ribbon model of proteins (1981). The contribution of Jane Richardson. In: Journal of Biosciences. Band 36, Nummer 4, September 2011, S. 571–574, PMID 21857104. PDF.
  5. ↑ P. D. Sun, C. E. Foster, J. C. Boyington: Overview of protein structural and functional folds. In: Current protocols in protein science / editorial board, John E. Coligan ... [et al.]. Chapter 17, Mai 2004, S. Unit 17.1, doi:10.1002/0471140864.ps1701s35. PMID 18429251.
  6. ↑ Mike Carson, Charles E Bugg: Algorithm for ribbon models of proteins. In: Journal of Molecular Graphics. 4, 1986, S. 121–122, doi:10.1016/0263-7855(86)80010-8.
  7. ↑ P. J. Kraulis: MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. In: Journal of Applied Crystallography. 24, S. 946, doi:10.1107/S0021889891004399.
  8. ↑ A. Herráez: Biomolecules in the computer: Jmol to the rescue. In: Biochemistry and molecular biology education : a bimonthly publication of the International Union of Biochemistry and Molecular Biology. Band 34, Nummer 4, Juli 2006, S. 255–261, doi:10.1002/bmb.2006.494034042644, PMID 21638687.
  9. ↑ M. U. Johansson, V. Zoete, O. Michielin, N. Guex: Defining and searching for structural motifs using DeepView/Swiss-PdbViewer. In: BMC Bioinformatics. Band 13, 2012, S. 173, doi:10.1186/1471-2105-13-173, PMID 22823337, PMC 3436773 (freier Volltext).
  10. ↑ R. Koradi, M. Billeter, K. Wüthrich: MOLMOL: a program for display and analysis of macromolecular structures. In: Journal of molecular graphics. Band 14, Nummer 1, Februar 1996, S. 51–5, 29, PMID 8744573.
  11. ↑ V. B. Chen, I. W. Davis, D. C. Richardson: KING (Kinemage, Next Generation): a versatile interactive molecular and scientific visualization program. In: Protein science : a publication of the Protein Society. Band 18, Nummer 11, November 2009, S. 2403–2409, doi:10.1002/pro.250, PMID 19768809, PMC 2788294 (freier Volltext).
  12. ↑ T. D. Goddard, C. C. Huang, T. E. Ferrin: Software extensions to UCSF chimera for interactive visualization of large molecular assemblies. In: Structure (London, England : 1993). Band 13, Nummer 3, März 2005, S. 473–482, doi:10.1016/j.str.2005.01.006, PMID 15766548.
  13. ↑ A. T. Brunger, J. A. Wells: Warren L. DeLano 21 June 1972-3 November 2009. In: Nature structural & molecular biology. Band 16, Nummer 12, Dezember 2009, S. 1202–1203, doi:10.1038/nsmb1209-1202, PMID 19956203.

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