Ribbon model (proteins)

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Protein structures, from primary to quaternary structure.

Ribbon models are molecular models of protein structures . They visualize elements of the secondary structure such as an α-helix or a β-sheet and allow a representation of the tertiary structure . Different polypeptides can be marked in different colors for better differentiation. Ribbon models are used in molecular modeling , e.g. B. in protein engineering . The ribbon model was established in 1980/81 by Jane Richardson . However, similar approaches have existed before.

Structural representations

Triosephosphate isomerase hand drawn by Jane Richardson.
Secondary structure
α-helices Cylindrical spiral ribbons, with the ribbon plane roughly at the peptide bond plane.
β strands Arrows with a thickness of 25% of the width in the direction of the N- to the C-terminus . β-sheets consist of parallel β-strands with β-loops.
Loops and others
Non-repetitive loops Round strands along the α-C atoms of the amino acids that become thinner from the foreground to the background.
Connections between loops and helices Round strands along the α-carbon atoms of the amino acids, which become flatter when they transition to the α-helix.
Other characteristics
N and C terminus Small arrows on one or both ends or coded with letters. For β strands, the direction of the arrow is sufficient. A color gradient along the amino acid sequence is often used for this.
Disulfide bridges With an interlaced double S or with a zigzag line
Proesthetic groups or inhibitors Stick model, ball-and-stick model
Metals Bullets
Shade and color The contrast decreases towards the background

software

Various programs for representing proteins in the ribbon model have been developed, e.g. B. Molscript by Arthur M. Lesk , Karl Hardman and John Priestle, Jmol , DeepView , MolMol , KiNG , UCSF Chimera and PyMOL by Warren DeLano .

literature

Individual evidence

  1. ↑ a b c Jane Shelby Richardson: The anatomy and taxonomy of protein structure. In: Advances in protein chemistry. Volume 34, 1981, pp. 167-339, PMID 7020376 .
  2. ↑ a b c J. S. Richardson: Schematic drawings of protein structures. In: Methods in enzymology. Volume 115, 1985, pp. 359-380, PMID 3853075 .
  3. ^ JS Richardson: Early ribbon drawings of proteins. In: Nature Structural Biology . Volume 7, Number 8, August 2000, pp. 624-625, doi : 10.1038 / 77912 . PMID 10932243 . PDF ( Memento of the original from February 1, 2014 in the Internet Archive ) Info: The archive link was inserted automatically and has not yet been checked. Please check the original and archive link according to the instructions and then remove this notice. . @1@ 2Template: Webachiv / IABot / csb.stanford.edu
  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 . Volume 36, Number 4, September 2011, pp. 571-574, PMID 21857104 . PDF .
  5. ^ PD Sun, CE Foster, JC Boyington: Overview of protein structural and functional folds. In: Current protocols in protein science / editorial board, John E. Coligan ... [et al.]. Chapter 17 May 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, pp. 121-122, doi : 10.1016 / 0263-7855 (86) 80010-8 .
  7. ^ JS Richardson: Early ribbon drawings of proteins. In: Nature structural biology. Volume 7, Number 8, August 2000, pp. 624-625, doi : 10.1038 / 77912 . PMID 10932243 . PDF ( Memento of the original from February 1, 2014 in the Internet Archive ) Info: The archive link was inserted automatically and has not yet been checked. Please check the original and archive link according to the instructions and then remove this notice. . @1@ 2Template: Webachiv / IABot / csb.stanford.edu
  8. ↑ PJ Kraulis: MOLSCRIPT: a program to produce Both detailed and schematic plots of protein structures. In: Journal of Applied Crystallography. 24, p. 946, doi : 10.1107 / S0021889891004399 .
  9. ^ 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. Volume 34, Number 4, July 2006, pp. 255-261, doi : 10.1002 / bmb.2006.494034042644 , PMID 21638687 .
  10. ^ MU Johansson, V. Zoete, O. Michielin, N. Guex: Defining and searching for structural motifs using DeepView / Swiss-PdbViewer. In: BMC Bioinformatics. Volume 13, 2012, p. 173, doi : 10.1186 / 1471-2105-13-173 , PMID 22823337 , PMC 3436773 (free full text).
  11. ↑ R. Koradi, M. Billeter, K. Wüthrich: MOLMOL: a program for display and analysis of macromolecular structures. In: Journal of molecular graphics. Volume 14, Number 1, February 1996, pp. 51-5, 29, PMID 8744573 .
  12. ^ VB Chen, IW Davis, DC Richardson: KING (Kinemage, Next Generation): a versatile interactive molecular and scientific visualization program. In: Protein science: a publication of the Protein Society. Volume 18, number 11, November 2009, pp. 2403-2409, doi : 10.1002 / pro.250 , PMID 19768809 , PMC 2788294 (free full text).
  13. ↑ TD Goddard, CC Huang, TE Ferrin: Software extensions to UCSF chimera for interactive visualization of large molecular assemblies. In: Structure (London, England: 1993). Volume 13, Number 3, March 2005, pp. 473-482, doi : 10.1016 / j.str.2005.01.006 , PMID 15766548 .
  14. ↑ AT Brunger, JA Wells: Warren L. DeLano 21 June 1972 to 3 November 2009. In: Nature Structural & Molecular Biology. Volume 16, Number 12, December 2009, pp. 1202-1203, doi : 10.1038 / nsmb1209-1202 , PMID 19956203 .