Limits...
Prediction of temperature factors from protein sequence.

Sonavane S, Jaybhaye AA, Jadhav AG - Bioinformation (2013)

Bottom Line: On an average, the normalized Bvalue decreases by 0.1055 with every 0.5Å increase in the distance of the residue from protein surface.The residues in the loop regions have higher B-values as compared to the residues present in other regular secondary structural elements.Our result shows that, the SVR model achieved the correlation coefficient of 0.47 which is comparable to existing methods.

View Article: PubMed Central - PubMed

Affiliation: Department of Microbiology, Institute of Science, Caves Roed, Aurangabad, India-431004.

ABSTRACT
Protein flexibility is useful in structural and functional aspect of proteins. We have analyzed the local primary protein sequence features that in combination can predict the B-value of amino acid residues directly from the protein sequence. We have also analyzed the distribution of B-value in different regions of protein three dimensional structures. On an average, the normalized Bvalue decreases by 0.1055 with every 0.5Å increase in the distance of the residue from protein surface. The residues in the loop regions have higher B-values as compared to the residues present in other regular secondary structural elements. Buried residues which are present in the protein core are more rigid (lower B-values) than the residues present on the protein surface. Similarly, the hydrophobic residues which tend to be present in the protein core have lower average B-value than the polar residues. Finally, we have proposed the method based on Support Vector Regression (SVR) to predict the B-value from protein primary sequence. Our result shows that, the SVR model achieved the correlation coefficient of 0.47 which is comparable to existing methods.

No MeSH data available.


Related in: MedlinePlus

Frequency distribution of normalized B-value in bins of 0.5. The plot showing (A) overall distribution; (B) distribution insolvent accessible and buried residues; (C) residues lining the cavities and the pockets, and; (D) the residues associated with thedifferent secondary structural elements in the whole dataset.
© Copyright Policy - open-access
Related In: Results  -  Collection


getmorefigures.php?uid=PMC3569600&req=5

Figure 1: Frequency distribution of normalized B-value in bins of 0.5. The plot showing (A) overall distribution; (B) distribution insolvent accessible and buried residues; (C) residues lining the cavities and the pockets, and; (D) the residues associated with thedifferent secondary structural elements in the whole dataset.

Mentions: The B-value distributions of the residues vary depending ontheir positions in the protein tertiary structure. Datasetconsidered in this study consists of 63771 residues across 240protein structures. The normalized B-value ranges from -2.29 to11.96. Figure 1 shows the frequency distribution of B-values foramino acid residues in overall dataset and present in differentposition in protein tertiary structure. The frequency distributionof normalized B-value in overall dataset (Figure 1A) shows theskewed distribution with the flat peak having two maximas at -0.5 and 1.


Prediction of temperature factors from protein sequence.

Sonavane S, Jaybhaye AA, Jadhav AG - Bioinformation (2013)

Frequency distribution of normalized B-value in bins of 0.5. The plot showing (A) overall distribution; (B) distribution insolvent accessible and buried residues; (C) residues lining the cavities and the pockets, and; (D) the residues associated with thedifferent secondary structural elements in the whole dataset.
© Copyright Policy - open-access
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3569600&req=5

Figure 1: Frequency distribution of normalized B-value in bins of 0.5. The plot showing (A) overall distribution; (B) distribution insolvent accessible and buried residues; (C) residues lining the cavities and the pockets, and; (D) the residues associated with thedifferent secondary structural elements in the whole dataset.
Mentions: The B-value distributions of the residues vary depending ontheir positions in the protein tertiary structure. Datasetconsidered in this study consists of 63771 residues across 240protein structures. The normalized B-value ranges from -2.29 to11.96. Figure 1 shows the frequency distribution of B-values foramino acid residues in overall dataset and present in differentposition in protein tertiary structure. The frequency distributionof normalized B-value in overall dataset (Figure 1A) shows theskewed distribution with the flat peak having two maximas at -0.5 and 1.

Bottom Line: On an average, the normalized Bvalue decreases by 0.1055 with every 0.5Å increase in the distance of the residue from protein surface.The residues in the loop regions have higher B-values as compared to the residues present in other regular secondary structural elements.Our result shows that, the SVR model achieved the correlation coefficient of 0.47 which is comparable to existing methods.

View Article: PubMed Central - PubMed

Affiliation: Department of Microbiology, Institute of Science, Caves Roed, Aurangabad, India-431004.

ABSTRACT
Protein flexibility is useful in structural and functional aspect of proteins. We have analyzed the local primary protein sequence features that in combination can predict the B-value of amino acid residues directly from the protein sequence. We have also analyzed the distribution of B-value in different regions of protein three dimensional structures. On an average, the normalized Bvalue decreases by 0.1055 with every 0.5Å increase in the distance of the residue from protein surface. The residues in the loop regions have higher B-values as compared to the residues present in other regular secondary structural elements. Buried residues which are present in the protein core are more rigid (lower B-values) than the residues present on the protein surface. Similarly, the hydrophobic residues which tend to be present in the protein core have lower average B-value than the polar residues. Finally, we have proposed the method based on Support Vector Regression (SVR) to predict the B-value from protein primary sequence. Our result shows that, the SVR model achieved the correlation coefficient of 0.47 which is comparable to existing methods.

No MeSH data available.


Related in: MedlinePlus