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The Protein-DNA Interface database

BMC Bioinformatics (2010) 11
DOI: 10.1186/1471-2105-11-262
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Abstract

The Protein-DNA Interface database (PDIdb) is a repository containing relevant structural information of Protein-DNA complexes solved by X-ray crystallography and available at the Protein Data Bank. The database includes a simple functional classification of the protein-DNA complexes that consists of three hierarchical levels: Class, Type and Subtype. This classification has been defined and manually curated by humans based on the information gathered from several sources that include PDB, PubMed, CATH, SCOP and COPS. The current version of the database contains only structures with resolution of 2.5 Å or higher, accounting for a total of 922 entries. The major aim of this database is to contribute to the understanding of the main rules that underlie the molecular recognition process between DNA and proteins. To this end, the database is focused on each specific atomic interface rather than on the separated binding partners. Therefore, each entry in this database consists of a single and independent protein-DNA interface. We hope that PDIdb will be useful to many researchers working in fields such as the prediction of transcription factor binding sites in DNA, the study of specificity determinants that mediate enzyme recognition events, engineering and design of new DNA binding proteins with distinct binding specificity and affinity, among others. Finally, due to its friendly and easy-to-use web interface, we hope that PDIdb will also serve educational and teaching purposes. © 2010 Norambuena and Melo; licensee BioMed Central Ltd.

Figures

  • Figure 1 PDB complexes and interfaces definition. (A) Example of a structure whose asymmetric unit contained half of the known biological unit (left). For each entry of this type, the complete biological unit was obtained from the specialized ftp site of PDB at ftp://ftp.wwpdb.org. (B) Each entry of the database consists of a single and independent protein-DNA interface, which is isolated from the whole PDB complex. Here, two examples that illustrate this feature are shown. (Top) 1am9, which PDB file contains two separable complexes, each having a single protein-DNA interface; (Bottom) 1h89, which has one complex, but with two independent protein-DNA interfaces. Each interface has assigned a unique ID in the database.
  • Table 1: Description of protein features classes and types
  • Table 1: Description of protein features classes and types (Continued)
  • Figure 2 Protein-protein interaction modes with DNA. Three modes of protein-protein interaction with DNA are defined, according to the direction and the axis of the DNA helix. (A) Mode 1, the direction of the protein interaction and the double helix axis are orthogonal. (B) Mode 2, the direction of the interaction is parallel to the double helix axis. (C) Mode 3, both previous modes are observed at the same time. In the Mode 3 example, the histone core shown is the only instance of this case in the current version of the database. The histone core presents a set of proteins interacting with each other, thus making up a continuous interface with DNA. Additionally, a Mode 0 to assign those interfaces with only one protein has also been defined (not shown).
  • Figure 3 DNA features. Several DNA features has been defined. (A) Double strand or single strand in the asymmetric unit. This is useful to identify those interfaces coming from the reconstruction of the biological unit. (B) Sticky ends were defined based on the specific strands and the number of free bases at their ends. (C) Presence of flipped bases. (C) Existance of nicked DNA. (E) Existance of gapped DNA. (F) Presence of modified or non-standard DNA bases. (G) Presence of opened or unpaired bases at the DNA ends. Although not depicted here, left-handed DNA conformation was also recorded (Z-DNA).
  • Figure 4 Definition of effective atomic interactions. (A) To determine if the interaction between DNA atom X and protein atom Y is effective, all other atoms inside the X interacting sphere (Zi atoms) are evaluated by comparing each ωi angle (i.e. the angle between atoms X, Zi and Y) with a defined shielding angle value Ω. If all the ωi angles observed are smaller than Ω, then the interaction between X and Y is defined as effective. (B) Threedimensional view of three example interacting spheres of X, which only differ in the value of Ω. Red balls represent those protein atoms interacting effectively with DNA atom X. Pink balls represent protein atoms not interacting effectively with X, since they are shielded by other atoms inside the interacting sphere of X, according to the Ω value defined and used. A definition of Ω = 90° commonly captures the first interacting atom shell, while using Ω = 180° all the interactions observed inside the contacting sphere are considered as effective. To build this database a value of 90° for Ω was adopted.
  • Table 2: Definition of interaction classes and types
  • Figure 5 Classification of DNA atoms. All the interactions occurring in an effective interface were classified according to the chemical/ structural/groove position of the DNA atoms. Pink-highlighted atoms were classified as being part of the major groove, green-highlighted atoms belong to the minor groove, blue-highlighted atoms belong to the backbone and sugar, and yellow-highlighted atoms were classified as not assigned since they are in an ambiguous location.

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Norambuena, T., & Melo, F. (2010). The Protein-DNA Interface database. BMC Bioinformatics, 11. https://doi.org/10.1186/1471-2105-11-262

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