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TIM-Finder: a new method for identifying TIM-barrel proteins.

Si JN, Yan RX, Wang C, Zhang Z, Su XD - BMC Struct. Biol. (2009)

Bottom Line: The triosephosphate isomerase (TIM)-barrel fold occurs frequently in the proteomes of different organisms, and the known TIM-barrel proteins have been found to play diverse functional roles.With the assistance of Support Vector Machine (SVM), the three descriptors were combined to obtain a new method with improved performance, which we call TIM-Finder.TIM-Finder can serve as a competitive tool for proteome-wide TIM-barrel protein identification.

View Article: PubMed Central - HTML - PubMed

Affiliation: State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China. sijingna@gmail.com

ABSTRACT

Background: The triosephosphate isomerase (TIM)-barrel fold occurs frequently in the proteomes of different organisms, and the known TIM-barrel proteins have been found to play diverse functional roles. To accelerate the exploration of the sequence-structure protein landscape in the TIM-barrel fold, a computational tool that allows sensitive detection of TIM-barrel proteins is required.

Results: To develop a new TIM-barrel protein identification method in this work, we consider three descriptors: a sequence-alignment-based descriptor using PSI-BLAST e-values and bit scores, a descriptor based on secondary structure element alignment (SSEA), and a descriptor based on the occurrence of PROSITE functional motifs. With the assistance of Support Vector Machine (SVM), the three descriptors were combined to obtain a new method with improved performance, which we call TIM-Finder. When tested on the whole proteome of Bacillus subtilis, TIM-Finder is able to detect 194 TIM-barrel proteins at a 99% confidence level, outperforming the PSI-BLAST search as well as one existing fold recognition method.

Conclusions: TIM-Finder can serve as a competitive tool for proteome-wide TIM-barrel protein identification. The TIM-Finder web server is freely accessible at http://202.112.170.199/TIM-Finder/.

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The TIM-barrel fold. (a) Cartoon representation of the 3D structure of a typical TIM-barrel protein (triosephosphate isomerase, PDB entry: 8tim). (b) The SCOP statistics on the TIM-barrel fold.
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Figure 1: The TIM-barrel fold. (a) Cartoon representation of the 3D structure of a typical TIM-barrel protein (triosephosphate isomerase, PDB entry: 8tim). (b) The SCOP statistics on the TIM-barrel fold.

Mentions: One of the top ten superfolds is the triosephosphate isomerase (TIM)-barrel fold (Figure 1A). It was first observed in triosephosphate isomerase and consists of eight α-helices on the outside and eight parallel β-strands on the inside that alternate along the peptide backbone [3]. In the past, many protein structures with the TIM-barrel fold have been determined, which allow a more complete understanding of the fold space of the TIM-barrel (Figure 1B). In the SCOP database (version 1.73) [4], the TIM-barrel fold contains 33 superfamilies and 101 families (Figure 1B). As a common fold with multiple functions, TIM-barrel proteins often function as enzymes. They can catalyze five of the six categories of biochemical reactions [5]. The evolution of the TIM-barrel fold has also received considerable attention, and it has been established that the TIM-barrel fold is one of the most ancestral folds [6].


TIM-Finder: a new method for identifying TIM-barrel proteins.

Si JN, Yan RX, Wang C, Zhang Z, Su XD - BMC Struct. Biol. (2009)

The TIM-barrel fold. (a) Cartoon representation of the 3D structure of a typical TIM-barrel protein (triosephosphate isomerase, PDB entry: 8tim). (b) The SCOP statistics on the TIM-barrel fold.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2803183&req=5

Figure 1: The TIM-barrel fold. (a) Cartoon representation of the 3D structure of a typical TIM-barrel protein (triosephosphate isomerase, PDB entry: 8tim). (b) The SCOP statistics on the TIM-barrel fold.
Mentions: One of the top ten superfolds is the triosephosphate isomerase (TIM)-barrel fold (Figure 1A). It was first observed in triosephosphate isomerase and consists of eight α-helices on the outside and eight parallel β-strands on the inside that alternate along the peptide backbone [3]. In the past, many protein structures with the TIM-barrel fold have been determined, which allow a more complete understanding of the fold space of the TIM-barrel (Figure 1B). In the SCOP database (version 1.73) [4], the TIM-barrel fold contains 33 superfamilies and 101 families (Figure 1B). As a common fold with multiple functions, TIM-barrel proteins often function as enzymes. They can catalyze five of the six categories of biochemical reactions [5]. The evolution of the TIM-barrel fold has also received considerable attention, and it has been established that the TIM-barrel fold is one of the most ancestral folds [6].

Bottom Line: The triosephosphate isomerase (TIM)-barrel fold occurs frequently in the proteomes of different organisms, and the known TIM-barrel proteins have been found to play diverse functional roles.With the assistance of Support Vector Machine (SVM), the three descriptors were combined to obtain a new method with improved performance, which we call TIM-Finder.TIM-Finder can serve as a competitive tool for proteome-wide TIM-barrel protein identification.

View Article: PubMed Central - HTML - PubMed

Affiliation: State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China. sijingna@gmail.com

ABSTRACT

Background: The triosephosphate isomerase (TIM)-barrel fold occurs frequently in the proteomes of different organisms, and the known TIM-barrel proteins have been found to play diverse functional roles. To accelerate the exploration of the sequence-structure protein landscape in the TIM-barrel fold, a computational tool that allows sensitive detection of TIM-barrel proteins is required.

Results: To develop a new TIM-barrel protein identification method in this work, we consider three descriptors: a sequence-alignment-based descriptor using PSI-BLAST e-values and bit scores, a descriptor based on secondary structure element alignment (SSEA), and a descriptor based on the occurrence of PROSITE functional motifs. With the assistance of Support Vector Machine (SVM), the three descriptors were combined to obtain a new method with improved performance, which we call TIM-Finder. When tested on the whole proteome of Bacillus subtilis, TIM-Finder is able to detect 194 TIM-barrel proteins at a 99% confidence level, outperforming the PSI-BLAST search as well as one existing fold recognition method.

Conclusions: TIM-Finder can serve as a competitive tool for proteome-wide TIM-barrel protein identification. The TIM-Finder web server is freely accessible at http://202.112.170.199/TIM-Finder/.

Show MeSH