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Similarity search for local protein structures at atomic resolution by exploiting a database management system.

ABSTRACT: A method to search for local structural similarities in proteins at atomic resolution is presented. It is demonstrated that a huge amount of structural data can be handled within a reasonable CPU time by using a conventional relational database management system with appropriate indexing of geometric data. This method, which we call geometric indexing, can enumerate ligand binding sites that are structurally similar to sub-structures of a query protein among more than 160,000 possible candidates within a few hours of CPU time on an ordinary desktop computer. After detecting a set of high scoring ligand binding sites by the geometric indexing search, structural alignments at atomic resolution are constructed by iteratively applying the Hungarian algorithm, and the statistical significance of the final score is estimated from an empirical model based on a gamma distribution. Applications of this method to several protein structures clearly shows that significant similarities can be detected between local structures of non-homologous as well as homologous proteins.

SUBMITTER: Kinjo AR

PROVIDER: S-EPMC5036654 | biostudies-literature | 2007

REPOSITORIES: biostudies-literature

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Similarity search for local protein structures at atomic resolution by exploiting a database management system.

Kinjo Akira R AR Nakamura Haruki H

Biophysics (Nagoya-shi, Japan) 20071228

A method to search for local structural similarities in proteins at atomic resolution is presented. It is demonstrated that a huge amount of structural data can be handled within a reasonable CPU time by using a conventional relational database management system with appropriate indexing of geometric data. This method, which we call geometric indexing, can enumerate ligand binding sites that are structurally similar to sub-structures of a query protein among more than 160,000 possible candidates ...[more]

PMID: 27857569

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Project description:Structural studies of proteins usually rely on a model obtained from one crystal. By investigating the details of this model, crystallographers seek to obtain insight into the function of the macromolecule. It is therefore important to know which details of a protein structure are reproducible or to what extent they might differ. To address this question, the high-resolution structures of five crystals of bovine trypsin obtained under analogous conditions were compared. Global parameters and structural details were investigated. All of the models were of similar quality and the pairwise merged intensities had large correlation coefficients. The C(?) and backbone atoms of the structures superposed very well. The occupancy of ligands in regions of low thermal motion was reproducible, whereas solvent molecules containing heavier atoms (such as sulfur) or those located on the surface could differ significantly. The coordination lengths of the calcium ion were conserved. A large proportion of the multiple conformations refined to similar occupancies and the residues adopted similar orientations. More than three quarters of the water-molecule sites were conserved within 0.5?Å and more than one third were conserved within 0.1?Å. An investigation of the protonation states of histidine residues and carboxylate moieties was consistent for all of the models. Radiation-damage effects to disulfide bridges were observed for the same residues and to similar extents. Main-chain bond lengths and angles averaged to similar values and were in agreement with the Engh and Huber targets. Other features, such as peptide flips and the double conformation of the inhibitor molecule, were also reproducible in all of the trypsin structures. Therefore, many details are similar in models obtained from different crystals. However, several features of residues or ligands located in flexible parts of the macromolecule may vary significantly, such as side-chain orientations and the occupancies of certain fragments.

Dataset Information

Similarity search for local protein structures at atomic resolution by exploiting a database management system.

Publications

Similarity search for local protein structures at atomic resolution by exploiting a database management system.

Similar Datasets

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