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. 2009 Sep;28(2):131-9.
doi: 10.1016/j.jmgm.2009.04.010. Epub 2009 May 4.

Visualisation of cyclic and multi-branched molecules with VMD

Simon Cross  1 , Michelle M Kuttel, John E Stone, James E Gain
Affiliations

Visualisation of cyclic and multi-branched molecules with VMD

Simon Cross et al. J Mol Graph Model. 2009 Sep.

Abstract

We report the addition of two visualisation algorithms, termed PaperChain and Twister, to the freely available Visual Molecular Dynamics (VMD) package. These algorithms produce visualisations of complex cyclic molecules and multi-branched polysaccharides and are a generalization and optimization of those we previously developed in a standalone package for carbohydrates. PaperChain highlights each ring in a molecular structure with a polygon, which is coloured according to the ring pucker. Twister traces glycosidic bonds with a ribbon that twists according to the relative orientation of successive sugar residues. Combination of these novel algorithms and new ring selection statements with the large set of visualisations already available in VMD allows for unprecedented flexibility in the level of detail displayed for glycoconjugate, glycoprotein and carbohydrate-binding protein structures, as well as other cyclic structures. We highlight the efficacy of these algorithms with selected illustrative examples, clearly demonstrating the value of the new visualisations, not only for structure validation, but also for facilitating insights into molecular structure and mechanism.

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Figures

Fig. 1
Fig. 1
Sample ring structures for cycloalkanes shown with a combination of the VMD Licorice and our new PaperChain visualisation, illustrating the default hot-to-cold colour scale based on the Cremer-Pople ring puckering amplitude.[13] (a) Cyclopropane, (b) cyclobutane, (c) cyclopentane , (d) cyclohexane in boat (top), twist-boat (middle) and chair (bottom) conformations, (e) cycloheptane and (f) cyclooctane in a crown conformation.
Fig. 2
Fig. 2
The SIV GP120 glycoprotein structure determined by Chen et al.[19] (PDB code 2BF1). (a) The protein displayed in the VMD NewCartoon visualisation and the carbohydrate rings displayed with a combination of our PaperChain and the standard VMD Licorice visualisations, (b) The same view of the structure, showing the carbohydrate components only. Only rings with puckering amplitudes less than 0.49 or greater than 0.6 are visualised with PaperChain.
Fig. 3
Fig. 3
A goat secretory glycoprotein (SPG-40) chilotelectin binding a hexasaccharide N-acetylglucosamine, GlcNAc6 (PDB code 2DT3).[20] Inset shows SPG-40 binding (a) pentasaccharide GlcNAc5 (PDB code 2DT2), (b) GlcNAc4 (PDB code 2DT1) and (c) G1CNAC3 (PDB code 2DT0). In each case, the carbohydrate substrate is depicted with a combination of our new PaperChain and the standard VMD Licorice visualisations, while the surface of the protein is shown in gray using the VMD Surf[31] visualisation. The image was rendered with the ambient occlusion lighting feature provided by the Tachyon [32] program included with the VMD distribution.
Fig. 4
Fig. 4
A further visualisation of the goat secretory glycoprotein (SPG-40) chilotelectin binding a hexasaccharide N-acetylglucosamine, GlcNAc6. Here, all cyclic residues are highlighted with both PaperChain and the Licorice visualization. (Cyclic rings in the protein were selected for display in the Licorice representation using “select maxringsize 6 from protein”.) The inset shows interaction of the hexasaccharide substrate with the aromatic residues located in the binding groove, with CH-π stacking interactions between aromatic protein residues and the C-H groups of bound sugar rings indicated by dashed arrows.
Fig. 5
Fig. 5
The six-unit N-acetylglucosamine substrate from Figs. 4 and 5 depicted with (a) PaperChain and Twister and (b) Twister only. Here the relative 180° flip of successive sugar rings is highlighted by the twists in the connecting ribbon.
Fig. 6
Fig. 6
A variety of cyclic molecules visualized with PaperChain and Twister, (a) Sucrose shown with PaperChain and the standard VMD Licorice visualisation, (b) Morphine shown with PaperChain and Licorice visualisations, (c) PaperChain visualisation of a haem structure in two orientations. (d) Buckminsterfullerene in the PaperChain visualisation. (e) α-cyclodextrin shown with PaperChain. (f) Cyclotetradecaamylose[33] and (g) amylopectin branch point viewed with both the PaperChain and Twister conformations, and the ring oxygens shown as balls (CPK). Here the top and bottom of the ribbon (defined according to IUPAC convention for saccharides) are coloured white and blue, respectively, (h) A-DNA structure visualized with Twister for the DNA backbone, PaperChain for the rings and Licorice for the bonds connecting the rings.
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