Surface characterization of proteins using multi-fractal property of heat-denatured aggregates

Abstract

Multi-fractal property of heat-denatured protein aggregates (HDPA) is characteristic of its individual form. The visual similarity between digitally generated microscopic images of HDPA with that of surface-image of its individual X-ray structures in protein databank (PDB) displayed using Visual Molecular Dynamics (VMD) viewer is the basis of the study. We deigned experiments to view the fractal nature of proteins at different aggregate scales. Intensity based multi-fractal dimensions (ILMFD) extracted from various planes of digital microscopic images of protein aggregates were used to characterize HDPA into different classes. Moreover, the ILMFD parameters extracted from aggregates show similar classification pattern to digital images of protein surface displayed by VMD viewer using PDB entry. We discuss the use of irregular patterns of heat-denatured aggregate proteins to understand various surface properties in native proteins.

Keywords: degree of differentiation; digital image processing; graphical pair-wise class comparison; light microscopy; multi-fractal dimension; protein aggregate; protein structure.

Figure 1

Representative matches of protein-aggregates with their corresponding native form are shown for six proteins. Column (a) shows the aggregate images of proteins and column (b) shows the surface map of corresponding individual native form of proteins shown by VMD viewer. The visual similarity match is obtained by manual rotation.

Figure 2

Pattern generated by D_A (fragmented line and circle) and D_I (solid line and circle) for all possible pairs of proteins (as shown in Table 1 under supplementary material) omitting data for 2 protein-pairs.