Dataset Information

GIANT: pattern analysis of molecular interactions in 3D structures of protein-small ligand complexes.

ABSTRACT: BACKGROUND:Interpretation of binding modes of protein-small ligand complexes from 3D structure data is essential for understanding selective ligand recognition by proteins. It is often performed by visual inspection and sometimes largely depends on a priori knowledge about typical interactions such as hydrogen bonds and ?-? stacking. Because it can introduce some biases due to scientists' subjective perspectives, more objective viewpoints considering a wide range of interactions are required. DESCRIPTION:In this paper, we present a web server for analyzing protein-small ligand interactions on the basis of patterns of atomic contacts, or "interaction patterns" obtained from the statistical analyses of 3D structures of protein-ligand complexes in our previous study. This server can guide visual inspection by providing information about interaction patterns for each atomic contact in 3D structures. Users can visually investigate what atomic contacts in user-specified 3D structures of protein-small ligand complexes are statistically overrepresented. This server consists of two main components: "Complex Analyzer", and "Pattern Viewer". The former provides a 3D structure viewer with annotations of interacting amino acid residues, ligand atoms, and interacting pairs of these. In the annotations of interacting pairs, assignment to an interaction pattern of each contact and statistical preferences of the patterns are presented. The "Pattern Viewer" provides details of each interaction pattern. Users can see visual representations of probability density functions of interactions, and a list of protein-ligand complexes showing similar interactions. CONCLUSIONS:Users can interactively analyze protein-small ligand binding modes with statistically determined interaction patterns rather than relying on a priori knowledge of the users, by using our new web server named GIANT that is freely available at http://giant.hgc.jp/.

SUBMITTER: Kasahara K

PROVIDER: S-EPMC3897944 | biostudies-literature | 2014 Jan

REPOSITORIES: biostudies-literature

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GIANT: pattern analysis of molecular interactions in 3D structures of protein-small ligand complexes.

Kasahara Kota K Kinoshita Kengo K

BMC bioinformatics 20140114

<h4>Background</h4>Interpretation of binding modes of protein-small ligand complexes from 3D structure data is essential for understanding selective ligand recognition by proteins. It is often performed by visual inspection and sometimes largely depends on a priori knowledge about typical interactions such as hydrogen bonds and π-π stacking. Because it can introduce some biases due to scientists' subjective perspectives, more objective viewpoints considering a wide range of interactions are requ ...[more]

PMID: 24423161

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Project description:BackgroundShape complementarity and non-covalent interactions are believed to drive protein-ligand interaction. To date protein-protein, protein-DNA, and protein-RNA interactions were systematically investigated, which is in contrast to interactions with small ligands. We investigate the role of covalent and non-covalent bonds in protein-small ligand interactions using a comprehensive dataset of 2,320 complexes.Methodology and principal findingsWe show that protein-ligand interactions are governed by different forces for different ligand types, i.e., protein-organic compound interactions are governed by hydrogen bonds, van der Waals contacts, and covalent bonds; protein-metal ion interactions are dominated by electrostatic force and coordination bonds; protein-anion interactions are established with electrostatic force, hydrogen bonds, and van der Waals contacts; and protein-inorganic cluster interactions are driven by coordination bonds. We extracted several frequently occurring atomic-level patterns concerning these interactions. For instance, 73% of investigated covalent bonds were summarized with just three patterns in which bonds are formed between thiol of Cys and carbon or sulfur atoms of ligands, and nitrogen of Lys and carbon of ligands. Similar patterns were found for the coordination bonds. Hydrogen bonds occur in 67% of protein-organic compound complexes and 66% of them are formed between NH- group of protein residues and oxygen atom of ligands. We quantify relative abundance of specific interaction types and discuss their characteristic features. The extracted protein-organic compound patterns are shown to complement and improve a geometric approach for prediction of binding sites.Conclusions and significanceWe show that for a given type (group) of ligands and type of the interaction force, majority of protein-ligand interactions are repetitive and could be summarized with several simple atomic-level patterns. We summarize and analyze 10 frequently occurring interaction patterns that cover 56% of all considered complexes and we show a practical application for the patterns that concerns interactions with organic compounds.

Dataset Information

GIANT: pattern analysis of molecular interactions in 3D structures of protein-small ligand complexes.

Publications

GIANT: pattern analysis of molecular interactions in 3D structures of protein-small ligand complexes.

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