Alternative structural models determined experimentally are available for an increasing number of …

• Abstract
• Introduction
• Methods
• Results and Discussion
• Conclusions
• Acknowledgements
• References
• Figures

Biology Articles » Bioinformatics » Conformational analysis of alternative protein structures » Figures

Figures

- Conformational analysis of alternative protein structures

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Fig. 1. Backbone conformational analysis of human transferrin set. Dendrogram obtained by hierarchical clustering is shown on top left. Models labelled according to SCOP sid code. Two main clusters A and B are observed, cluster B is further subdivided into C and D. Total SD matrix T is shown on middle row left, values in legend are in Å. S, R and X matrices are shown on the bottom, enlarged plots are available in the Supplementary Material. Comparison matrices U^AB and U^CD are shown in the middle row right and bottom right. Blue colours for values larger than 5.0, orange colour for values less than –5.0, and grey for undefined values (lack of samples at that position in the alignment). Axes in the matrices correspond to alignment positions. The superpositions of the transferrin models according to the two invariant regions identified in T are shown at the top right. Inv1 is the superposition according to the first invariant region that includes N and C terminal segments. Inv2 is the superposition according to the second invariant region, which includes the middle segments of the protein. Iron and carbonate from model d1d3ka_ are represented as CPK. Models from cluster A are in blue, models from cluster C are in dark orange and models from cluster D are in light orange. The invariant regions used for superposition are shown in thicker backbone representation.

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Fig. 2. Conformational analysis of ligand binding site of -amylase. The ligand binding site consists of all residues with at least one atom within 6.0 Å of inhibitor V-1532 in model 1pig. The dendrogram on the left was obtained based on side-chain centroid distances at the ligand binding site. The T matrix on the middle is also based on side-chain centroid distances at the ligand binding site. Using s_cutoff = 0.5, the largest invariant region is: 58–63,98,101,103–105,162–165,195,197–201,233,235,236–238,298–299. Residues positions with considerable variability are marked with arrows. The superposition on the right shows the ligand V-1532 from 1pig in ball and stick representation. Variable residues 300, 305–308 are shown in orange (cluster B) and blue (clusters E₁ and E₂). Other variable residues (151, 163, 238, 240) are labelled and shown in black thicker sticks.

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