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

Lahiri T, Mishra H, Sarkar S, Misra K - Bioinformation (2008)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Indian Institute of Information Technology, Allahabad, India. tlahiri@iiita.ac.in

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.

No MeSH data available.


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.
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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.

Mentions: Images of 3D molecular structures for each of the proteins were visualized and collected by VMD surface visualization software. VMD is designed for modeling, visualization, and analysis of biological systems such as proteins, nucleic acids and lipid bi-layer assemblies. VMD can read PDB files and display structures. VMD provides a wide variety of options for drawing and coloring a molecule. The option used by us is VDW (Van der Waals) as a drawing method, “Name” as coloring method, “Opaque” as material with sphere scale 1.0 and sphere resolution 8 [7]. VMD images of proteins were compared with images of aggregate counterpart using the following steps (illustration is given in figure 1): (1) the orientation of the VMD-viewer-image of a protein was carefully changed to find the best match with one of its corresponding aggregate image. (2) Step 1 was repeated for different aggregates of the same protein. 15 VMD images taken at various orientations for each protein were thus collected and this forms the PDB image dataset of proteins.


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

Lahiri T, Mishra H, Sarkar S, Misra K - Bioinformation (2008)

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.
© Copyright Policy - open-access
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2533056&req=5

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.
Mentions: Images of 3D molecular structures for each of the proteins were visualized and collected by VMD surface visualization software. VMD is designed for modeling, visualization, and analysis of biological systems such as proteins, nucleic acids and lipid bi-layer assemblies. VMD can read PDB files and display structures. VMD provides a wide variety of options for drawing and coloring a molecule. The option used by us is VDW (Van der Waals) as a drawing method, “Name” as coloring method, “Opaque” as material with sphere scale 1.0 and sphere resolution 8 [7]. VMD images of proteins were compared with images of aggregate counterpart using the following steps (illustration is given in figure 1): (1) the orientation of the VMD-viewer-image of a protein was carefully changed to find the best match with one of its corresponding aggregate image. (2) Step 1 was repeated for different aggregates of the same protein. 15 VMD images taken at various orientations for each protein were thus collected and this forms the PDB image dataset of proteins.

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Indian Institute of Information Technology, Allahabad, India. tlahiri@iiita.ac.in

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.

No MeSH data available.