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Pattern similarity study of functional sites in protein sequences: lysozymes and cystatins.

Nakai S, Li-Chan EC, Dou J - BMC Biochem. (2005)

Bottom Line: Hydrogen bonding was used as the side-chain property for searching the binding sites of lysozymes.Pattern similarity and average index values of structure-related properties of side chains in short segments of three residues or longer were, for the first time, successfully applied for predicting functional sites in sequences.This new approach may be applicable to studying functional sites in un-annotated proteins, for which complete 3D structures are not yet available.

View Article: PubMed Central - HTML - PubMed

Affiliation: Food, Nutrition and Health, The University of British Columbia, 6650 Marine Drive, Vancouver, B.C., Canada. shuryo.nakai@ubc.ca

ABSTRACT

Background: Although it is generally agreed that topography is more conserved than sequences, proteins sharing the same fold can have different functions, while there are protein families with low sequence similarity. An alternative method for profile analysis of characteristic conserved positions of the motifs within the 3D structures may be needed for functional annotation of protein sequences. Using the approach of quantitative structure-activity relationships (QSAR), we have proposed a new algorithm for postulating functional mechanisms on the basis of pattern similarity and average of property values of side-chains in segments within sequences. This approach was used to search for functional sites of proteins belonging to the lysozyme and cystatin families.

Results: Hydrophobicity and beta-turn propensity of reference segments with 3-7 residues were used for the homology similarity search (HSS) for active sites. Hydrogen bonding was used as the side-chain property for searching the binding sites of lysozymes. The profiles of similarity constants and average values of these parameters as functions of their positions in the sequences could identify both active and substrate binding sites of the lysozyme of Streptomyces coelicolor, which has been reported as a new fold enzyme (Cellosyl). The same approach was successfully applied to cystatins, especially for postulating the mechanisms of amyloidosis of human cystatin C as well as human lysozyme.

Conclusion: Pattern similarity and average index values of structure-related properties of side chains in short segments of three residues or longer were, for the first time, successfully applied for predicting functional sites in sequences. This new approach may be applicable to studying functional sites in un-annotated proteins, for which complete 3D structures are not yet available.

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HSS search patterns for active sites of human lysozyme. Segment 53–57 of hen lysozyme was used as the reference. A: HSS search pattern based on charge. B: HSS search pattern based on turn propensity.
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Figure 3: HSS search patterns for active sites of human lysozyme. Segment 53–57 of hen lysozyme was used as the reference. A: HSS search pattern based on charge. B: HSS search pattern based on turn propensity.

Mentions: The search patterns illustrated in Figure 3A (charge) and 3B (turn propensity) are a trial run to validate the HSS approach, applied to human lysozyme vs. hen lysozyme, employing the five residues flanking E35 (K33FESN of hen) as a search unit. The rules herein for selecting active segments are that the greater the similarity approaching to 1.0 and the nearer the average value to that of the reference, the more likely to be active sites in the test sequence. In Figure 3A, in addition to E35 and D53, three residues of E7, S80 and D120 show about the same similarity constants (upper pattern) as well as similar average charge values (shown by arrows on the lower pattern). However, none of the above latter three positions are acceptable as the active site, as N44, I59, C65, Q86, and Q126 in Figure 3B for β-turn search do not have matching peaks in Figure 2A for charge search. Therefore, only E35 and D53 are qualified as the active positions of human lysozyme. The same result was obtained when five residues flanking D52 (S50TDYG) of hen lysozyme were used as an alternative reference segment. The two regions around E35 and D53 determined for human lysozyme are in good agreement with those being reported for the active site in the literature [13]. Despite the fact that the charge is of prime importance in defining active sites of lysozymes, the turn propensity values of the segment rather than its pattern similarity appear to play an important role in the enzyme, as exemplified in a low similarity value of 0.30 for D53 compared to 0.98 for E35, whereas similar average turn values of 1.2 and 1.1, respectively, were computed (Fig. 3B). All these results may imply that the exposure of active sites to react with the substrate binding sites is essential.


Pattern similarity study of functional sites in protein sequences: lysozymes and cystatins.

Nakai S, Li-Chan EC, Dou J - BMC Biochem. (2005)

HSS search patterns for active sites of human lysozyme. Segment 53–57 of hen lysozyme was used as the reference. A: HSS search pattern based on charge. B: HSS search pattern based on turn propensity.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC1173080&req=5

Figure 3: HSS search patterns for active sites of human lysozyme. Segment 53–57 of hen lysozyme was used as the reference. A: HSS search pattern based on charge. B: HSS search pattern based on turn propensity.
Mentions: The search patterns illustrated in Figure 3A (charge) and 3B (turn propensity) are a trial run to validate the HSS approach, applied to human lysozyme vs. hen lysozyme, employing the five residues flanking E35 (K33FESN of hen) as a search unit. The rules herein for selecting active segments are that the greater the similarity approaching to 1.0 and the nearer the average value to that of the reference, the more likely to be active sites in the test sequence. In Figure 3A, in addition to E35 and D53, three residues of E7, S80 and D120 show about the same similarity constants (upper pattern) as well as similar average charge values (shown by arrows on the lower pattern). However, none of the above latter three positions are acceptable as the active site, as N44, I59, C65, Q86, and Q126 in Figure 3B for β-turn search do not have matching peaks in Figure 2A for charge search. Therefore, only E35 and D53 are qualified as the active positions of human lysozyme. The same result was obtained when five residues flanking D52 (S50TDYG) of hen lysozyme were used as an alternative reference segment. The two regions around E35 and D53 determined for human lysozyme are in good agreement with those being reported for the active site in the literature [13]. Despite the fact that the charge is of prime importance in defining active sites of lysozymes, the turn propensity values of the segment rather than its pattern similarity appear to play an important role in the enzyme, as exemplified in a low similarity value of 0.30 for D53 compared to 0.98 for E35, whereas similar average turn values of 1.2 and 1.1, respectively, were computed (Fig. 3B). All these results may imply that the exposure of active sites to react with the substrate binding sites is essential.

Bottom Line: Hydrogen bonding was used as the side-chain property for searching the binding sites of lysozymes.Pattern similarity and average index values of structure-related properties of side chains in short segments of three residues or longer were, for the first time, successfully applied for predicting functional sites in sequences.This new approach may be applicable to studying functional sites in un-annotated proteins, for which complete 3D structures are not yet available.

View Article: PubMed Central - HTML - PubMed

Affiliation: Food, Nutrition and Health, The University of British Columbia, 6650 Marine Drive, Vancouver, B.C., Canada. shuryo.nakai@ubc.ca

ABSTRACT

Background: Although it is generally agreed that topography is more conserved than sequences, proteins sharing the same fold can have different functions, while there are protein families with low sequence similarity. An alternative method for profile analysis of characteristic conserved positions of the motifs within the 3D structures may be needed for functional annotation of protein sequences. Using the approach of quantitative structure-activity relationships (QSAR), we have proposed a new algorithm for postulating functional mechanisms on the basis of pattern similarity and average of property values of side-chains in segments within sequences. This approach was used to search for functional sites of proteins belonging to the lysozyme and cystatin families.

Results: Hydrophobicity and beta-turn propensity of reference segments with 3-7 residues were used for the homology similarity search (HSS) for active sites. Hydrogen bonding was used as the side-chain property for searching the binding sites of lysozymes. The profiles of similarity constants and average values of these parameters as functions of their positions in the sequences could identify both active and substrate binding sites of the lysozyme of Streptomyces coelicolor, which has been reported as a new fold enzyme (Cellosyl). The same approach was successfully applied to cystatins, especially for postulating the mechanisms of amyloidosis of human cystatin C as well as human lysozyme.

Conclusion: Pattern similarity and average index values of structure-related properties of side chains in short segments of three residues or longer were, for the first time, successfully applied for predicting functional sites in sequences. This new approach may be applicable to studying functional sites in un-annotated proteins, for which complete 3D structures are not yet available.

Show MeSH
Related in: MedlinePlus