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2016 ; 67
(ä): 44-53
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Visualizing ensembles in structural biology
#MMPMID27179343
Melvin RL
; Salsbury FR Jr
J Mol Graph Model
2016[Jun]; 67
(ä): 44-53
PMID27179343
show ga
Displaying a single representative conformation of a biopolymer rather than an
ensemble of states mistakenly conveys a static nature rather than the actual
dynamic personality of biopolymers. However, there are few apparent options due
to the fixed nature of print media. Here we suggest a standardized methodology
for visually indicating the distribution width, standard deviation and
uncertainty of ensembles of states with little loss of the visual simplicity of
displaying a single representative conformation. Of particular note is that the
visualization method employed clearly distinguishes between isotropic and
anisotropic motion of polymer subunits. We also apply this method to ligand
binding, suggesting a way to indicate the expected error in many high throughput
docking programs when visualizing the structural spread of the output. We provide
several examples in the context of nucleic acids and proteins with particular
insights gained via this method. Such examples include investigating a
therapeutic polymer of FdUMP (5-fluoro-2-deoxyuridine-5-O-monophosphate) - a
topoisomerase-1 (Top1), apoptosis-inducing poison - and nucleotide-binding
proteins responsible for ATP hydrolysis from Bacillus subtilis. We also discuss
how these methods can be extended to any macromolecular data set with an
underlying distribution, including experimental data such as NMR structures.
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