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Composite structural motifs of binding sites for delineating biological functions of proteins.

Kinjo AR, Nakamura H - PLoS ONE (2012)

Bottom Line: It is demonstrated that function similarity can be better inferred from composite motif similarity compared to the similarity of protein sequences or of individual binding sites.By integrating the composite motifs associated with each protein function, we define meta-composite motifs each of which is regarded as a time-independent diagrammatic representation of a biological process.The present results serve as a basis for bridging atomic structures to higher-order biological phenomena by classification and integration of binding site structures.

View Article: PubMed Central - PubMed

Affiliation: Institute for Protein Research, Osaka University, Suita, Osaka, Japan. akinjo@protein.osaka-u.ac.jp

ABSTRACT
Most biological processes are described as a series of interactions between proteins and other molecules, and interactions are in turn described in terms of atomic structures. To annotate protein functions as sets of interaction states at atomic resolution, and thereby to better understand the relation between protein interactions and biological functions, we conducted exhaustive all-against-all atomic structure comparisons of all known binding sites for ligands including small molecules, proteins and nucleic acids, and identified recurring elementary motifs. By integrating the elementary motifs associated with each subunit, we defined composite motifs that represent context-dependent combinations of elementary motifs. It is demonstrated that function similarity can be better inferred from composite motif similarity compared to the similarity of protein sequences or of individual binding sites. By integrating the composite motifs associated with each protein function, we define meta-composite motifs each of which is regarded as a time-independent diagrammatic representation of a biological process. It is shown that meta-composite motifs provide richer annotations of biological processes than sequence clusters. The present results serve as a basis for bridging atomic structures to higher-order biological phenomena by classification and integration of binding site structures.

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Characterization of composite motifs.A: Histogram of the number of elementary motifs comprising composite motifs. B: Histograms of the average and minimum sequence identities (%) between pairs of subunits within each composite motif. C: Composite motif similarity as a function of minimum sequence identity between pairs of composite motifs. Sequence identity between two composite motifs is defined as the sequence identity between two protein sequences, one belonging to the one motif, the other to the other motif.
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pone-0031437-g002: Characterization of composite motifs.A: Histogram of the number of elementary motifs comprising composite motifs. B: Histograms of the average and minimum sequence identities (%) between pairs of subunits within each composite motif. C: Composite motif similarity as a function of minimum sequence identity between pairs of composite motifs. Sequence identity between two composite motifs is defined as the sequence identity between two protein sequences, one belonging to the one motif, the other to the other motif.

Mentions: The number of elementary motifs that comprise a composite motif ranges from 1 to 20 (Fig. 2A). Approximately one third of the composite motifs (1975 out of 5738) consist of only one elementary motif and more than 90% of the composite motifs are composed of less than or equal to 5 elementary motifs. The number of composite motifs appears exponentially decreasing as the number of constitutive elementary motifs increases.


Composite structural motifs of binding sites for delineating biological functions of proteins.

Kinjo AR, Nakamura H - PLoS ONE (2012)

Characterization of composite motifs.A: Histogram of the number of elementary motifs comprising composite motifs. B: Histograms of the average and minimum sequence identities (%) between pairs of subunits within each composite motif. C: Composite motif similarity as a function of minimum sequence identity between pairs of composite motifs. Sequence identity between two composite motifs is defined as the sequence identity between two protein sequences, one belonging to the one motif, the other to the other motif.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3275580&req=5

pone-0031437-g002: Characterization of composite motifs.A: Histogram of the number of elementary motifs comprising composite motifs. B: Histograms of the average and minimum sequence identities (%) between pairs of subunits within each composite motif. C: Composite motif similarity as a function of minimum sequence identity between pairs of composite motifs. Sequence identity between two composite motifs is defined as the sequence identity between two protein sequences, one belonging to the one motif, the other to the other motif.
Mentions: The number of elementary motifs that comprise a composite motif ranges from 1 to 20 (Fig. 2A). Approximately one third of the composite motifs (1975 out of 5738) consist of only one elementary motif and more than 90% of the composite motifs are composed of less than or equal to 5 elementary motifs. The number of composite motifs appears exponentially decreasing as the number of constitutive elementary motifs increases.

Bottom Line: It is demonstrated that function similarity can be better inferred from composite motif similarity compared to the similarity of protein sequences or of individual binding sites.By integrating the composite motifs associated with each protein function, we define meta-composite motifs each of which is regarded as a time-independent diagrammatic representation of a biological process.The present results serve as a basis for bridging atomic structures to higher-order biological phenomena by classification and integration of binding site structures.

View Article: PubMed Central - PubMed

Affiliation: Institute for Protein Research, Osaka University, Suita, Osaka, Japan. akinjo@protein.osaka-u.ac.jp

ABSTRACT
Most biological processes are described as a series of interactions between proteins and other molecules, and interactions are in turn described in terms of atomic structures. To annotate protein functions as sets of interaction states at atomic resolution, and thereby to better understand the relation between protein interactions and biological functions, we conducted exhaustive all-against-all atomic structure comparisons of all known binding sites for ligands including small molecules, proteins and nucleic acids, and identified recurring elementary motifs. By integrating the elementary motifs associated with each subunit, we defined composite motifs that represent context-dependent combinations of elementary motifs. It is demonstrated that function similarity can be better inferred from composite motif similarity compared to the similarity of protein sequences or of individual binding sites. By integrating the composite motifs associated with each protein function, we define meta-composite motifs each of which is regarded as a time-independent diagrammatic representation of a biological process. It is shown that meta-composite motifs provide richer annotations of biological processes than sequence clusters. The present results serve as a basis for bridging atomic structures to higher-order biological phenomena by classification and integration of binding site structures.

Show MeSH
Related in: MedlinePlus