Abstract
The recent upgrade of nucleic acid–protein interaction database (NPIDB, http://npidb.belozersky.msu.ru/) includes a newly elaborated classification of complexes of protein domains with double-stranded DNA and a classification of families of related complexes. Our classifications are based on contacting structural elements of both DNA: the major groove, the minor groove and the backbone; and protein: helices, beta-strands and unstructured segments. We took into account both hydrogen bonds and hydrophobic interaction. The analyzed material contains 1942 structures of protein domains from 748 PDB entries. We have identified 97 interaction modes of individual protein domain–DNA complexes and 17 DNA–protein interaction classes of protein domain families. We analyzed the sources of diversity of DNA–protein interaction modes in different complexes of one protein domain family. The observed interaction mode is sometimes influenced by artifacts of crystallization or diversity in secondary structure assignment. The interaction classes of domain families are more stable and thus possess more biological sense than a classification of single complexes. Integration of the classification into NPIDB allows the user to browse the database according to the interacting structural elements of DNA and protein molecules. For each family, we present average DNA shape parameters in contact zones with domains of the family.
Highlights
About 3000 3D structures of DNA–protein complexes are known
We describe an updated version of NPIDB, which includes a new classification of complexes of double-stranded DNA with proteins
We updated NPIDB, adding a new classification of DNA–protein complexes and their families. These classifications take into account contacting structural elements of both DNA and protein. This allows users to navigate through NPIDB in less formal way, using titles of PDB files or protein or nucleic acid sequences, and structural features of DNA–protein complexes
Summary
About 3000 3D structures of DNA–protein complexes are known. Variety of DNA–protein interactions can be described in quite different terms attributed to, for example, specific and nonspecific recognition; interaction with the major or the minor DNA grooves; interaction via alpha-helices, beta-structures or unstructured regions of protein; interactions of different kinds: hydrogen bonds, water-mediated contacts or hydrophobic interaction; etc. Luscombe with co-authors [7] divided 240 DNA–protein complexes into 8 functional groups and further into 54 structural families on the basis of the structural similarity of DNAbinding motifs of proteins. It was shown that the similarity of structures of DNA-binding motifs does not necessarily provide the similarity of modes of DNA–protein recognition In this regard, the authors emphasize that the properties of a DNA-binding protein but some general parameters of interaction should be considered in classification procedure. Schneider with co-authors [15] analyzed DNA–protein complexes on the basis of classification of interacting protein blocks of five consecutive amino acid residues, on the one hand, and structures of dinucleotide conformers, on the other hand. Our classification may simplify navigation through numerous structures of DNA–protein complexes considering peculiarities of DNA–protein interaction
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