Limits...
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.

Show MeSH

Related in: MedlinePlus

Effects of mutating the strand domain of human cystatin C (mutated 21 residues). A: Strand index, B: Helix index. The numbers show multiples of activity increases from wild-type. 1 shows no increase of inhibitory activity. 5* is the reference mutant 12W86V with the highest inhibitory activity.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC1173080&req=5

Figure 7: Effects of mutating the strand domain of human cystatin C (mutated 21 residues). A: Strand index, B: Helix index. The numbers show multiples of activity increases from wild-type. 1 shows no increase of inhibitory activity. 5* is the reference mutant 12W86V with the highest inhibitory activity.

Mentions: Heat treatment of HCC induced its dimer formation at an early stage of separation, resulting in a complete loss of its activity [25]. Based on a dramatic decrease in the monomer form as shown by its CD spectrum, polymerization such as amyloidosis could be a cause of the loss of papain inhibitory activity of mutated HCC [14]. Of 35 residues (positions 1–35) of the helix domain of HCC, 17 residues were mutated in the 22 single-site mutants using the RCG program [14 (Table 1)]. When 33 mutants obtained by adding one extra residue each in both side of the original 17 residues after eliminating duplication were used for PCS computation, the resultant PCS demonstrated that helix propensity and bulkiness were playing important roles in thermostability (data not shown). Employment of three residues flanking the mutated residue was important in pattern similarity computation. This conclusion is in good agreement with Hall et al. [26] who did an exhaustive study showing that mutations at positions 8–10 enhanced thermostability of cystatin. With regard to the papain inhibitory activity, the importance of hydrophobicity and bulkiness was demonstrated (the PCS scattergrams, similar to Fig. 7, are not shown here).


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

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

Effects of mutating the strand domain of human cystatin C (mutated 21 residues). A: Strand index, B: Helix index. The numbers show multiples of activity increases from wild-type. 1 shows no increase of inhibitory activity. 5* is the reference mutant 12W86V with the highest inhibitory activity.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 7: Effects of mutating the strand domain of human cystatin C (mutated 21 residues). A: Strand index, B: Helix index. The numbers show multiples of activity increases from wild-type. 1 shows no increase of inhibitory activity. 5* is the reference mutant 12W86V with the highest inhibitory activity.
Mentions: Heat treatment of HCC induced its dimer formation at an early stage of separation, resulting in a complete loss of its activity [25]. Based on a dramatic decrease in the monomer form as shown by its CD spectrum, polymerization such as amyloidosis could be a cause of the loss of papain inhibitory activity of mutated HCC [14]. Of 35 residues (positions 1–35) of the helix domain of HCC, 17 residues were mutated in the 22 single-site mutants using the RCG program [14 (Table 1)]. When 33 mutants obtained by adding one extra residue each in both side of the original 17 residues after eliminating duplication were used for PCS computation, the resultant PCS demonstrated that helix propensity and bulkiness were playing important roles in thermostability (data not shown). Employment of three residues flanking the mutated residue was important in pattern similarity computation. This conclusion is in good agreement with Hall et al. [26] who did an exhaustive study showing that mutations at positions 8–10 enhanced thermostability of cystatin. With regard to the papain inhibitory activity, the importance of hydrophobicity and bulkiness was demonstrated (the PCS scattergrams, similar to Fig. 7, are not shown here).

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