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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.


Pattern generated by DA (fragmented line and circle) and DI (solid line and circle) for all possible pairs of proteins (as shown in Table 1 under supplementary material) omitting data for 2 protein-pairs.
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Related In: Results  -  Collection


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

Mentions: Table 1 (see supplementary material) contains DD-values, DA for the protein-aggregates and DI for the individual native protein-pairs. Cells on both sides of the diagonal show the same combinations or pairs of proteins. The cells with un-bold values on left side of diagonal are used to represent DD values for PDB images (DI) and cells on the right side of the diagonal with bold values represent DD values for aggregate images (DA). Both of these values show overall efficiency of the ILMFD feature in differentiating one protein from another. As we have already discussed in methodology, the average values of (DAVA= 0.4015) and DI (DAVI = 0.2356) are indicative of differentiating capability of the feature of our concern namely ILMFD. The mean DD values greater than or equal to 1 indicate full differentiation (methodology section) which was not fully satisfied in this case. The significance in fulfilling the goal was followed from the comparative analysis. In our bid to find the correspondence of protein-aggregates with their native form, we compared their DD values, DA and DI for different combinations or pairs as marked by their different indices, omitting the data for two pairs (shown in Figure 2).


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

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

Pattern generated by DA (fragmented line and circle) and DI (solid line and circle) for all possible pairs of proteins (as shown in Table 1 under supplementary material) omitting data for 2 protein-pairs.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 2: Pattern generated by DA (fragmented line and circle) and DI (solid line and circle) for all possible pairs of proteins (as shown in Table 1 under supplementary material) omitting data for 2 protein-pairs.
Mentions: Table 1 (see supplementary material) contains DD-values, DA for the protein-aggregates and DI for the individual native protein-pairs. Cells on both sides of the diagonal show the same combinations or pairs of proteins. The cells with un-bold values on left side of diagonal are used to represent DD values for PDB images (DI) and cells on the right side of the diagonal with bold values represent DD values for aggregate images (DA). Both of these values show overall efficiency of the ILMFD feature in differentiating one protein from another. As we have already discussed in methodology, the average values of (DAVA= 0.4015) and DI (DAVI = 0.2356) are indicative of differentiating capability of the feature of our concern namely ILMFD. The mean DD values greater than or equal to 1 indicate full differentiation (methodology section) which was not fully satisfied in this case. The significance in fulfilling the goal was followed from the comparative analysis. In our bid to find the correspondence of protein-aggregates with their native form, we compared their DD values, DA and DI for different combinations or pairs as marked by their different indices, omitting the data for two pairs (shown in Figure 2).

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.