Improved data visualization techniques for analyzing macromolecule structural changes.
The empirical phase diagram (EPD) is a colored representation of overall structural integrity and conformational stability of macromolecules in response to various environmental perturbations. Numerous proteins and macromolecular complexes have been analyzed by EPDs to summarize results from large data sets from multiple biophysical techniques. The current EPD method suffers from a number of deficiencies including lack of a meaningful relationship between color and actual molecular features, difficulties in identifying contributions from individual techniques, and a limited ability to be interpreted by color-blind individuals. In this work, three improved data visualization approaches are proposed as techniques complementary to the EPD. The secondary, tertiary, and quaternary structural changes of multiple proteins as a function of environmental stress were first measured using circular dichroism, intrinsic fluorescence spectroscopy, and static light scattering, respectively. Data sets were then visualized as (1) RGB colors using three-index EPDs, (2) equiangular polygons using radar charts, and (3) human facial features using Chernoff face diagrams. Data as a function of temperature and pH for bovine serum albumin, aldolase, and chymotrypsin as well as candidate protein vaccine antigens including a serine threonine kinase protein (SP1732) and surface antigen A (SP1650) from S. pneumoniae and hemagglutinin from an H1N1 influenza virus are used to illustrate the advantages and disadvantages of each type of data visualization technique.
Bioengineering Graduate Program, University of Kansas, Lawrence, Kansas 66045, USA.
Jae Hyun
JH
Kim
Vidyashankara
V
Iyer
Sangeeta B
SB
Joshi
David B
DB
Volkin
C Russell
CR
Middaugh
D000818:Animals; D002417:Cattle; D002942:Circular Dichroism; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods*; D003196:Computer Graphics; D005145:Face / Q000033:anatomy & histology; D006801:Humans; D006863:Hydrogen-Ion Concentration; D008954:Models, Biological; D008958:Models, Molecular; D011506:Proteins / Q000737:chemistry*; D012815:Signal Processing, Computer-Assisted; D013696:Temperature
D011506:Proteins