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.
Highlights
The study of protein surface is emerging as a novel approach in the field of protein-ligand interactions [1] where part of the surface plays the dominant role of binding site in such interactions
For large molecules like DNA, interaction occurs through convex surface or elevations on the protein surface
The description of this surface as indexed surface parameter is possible only through the availability of 3D structures of protein derived by X-ray crystallography or nuclear magnetic resonance (NMR) or molecular modeling
Summary
The study of protein surface is emerging as a novel approach in the field of protein-ligand interactions [1] where part of the surface plays the dominant role of binding site in such interactions. The importance of studies on protein surface roughness mainly lies in defining functional sites of proteins from their surface The description of this surface as indexed surface parameter is possible only through the availability of 3D structures of protein derived by X-ray crystallography or nuclear magnetic resonance (NMR) or molecular modeling. These studies are helpful for further extraction of active or functional site of proteins. Power Shot S50) at its optical zoom 2× This forms HDPA protein aggregation can influence specific structure of image dataset for proteins. If RLHS + RRHS < d, the members of the variant-pair are well-separated and if RLHS + RRHS > d, the variant clusters of the variant-pair are overlapped
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