title: An updated version of NPIDB includes new classifications of DNA-protein complexes and their families.
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.
authors.affiliation: Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia.
authors.forename: Olga
authors.initials: O
authors.lastname: Zanegina
authors.affiliation: OOO Lexpro Soft, Moscow 119019, Russia.
authors.forename: Dmitriy
authors.initials: D
authors.lastname: Kirsanov
authors.affiliation: Laboratory of Applied Mathematics, Institute of Mathematical Problems in Biology, Puschino 142290, Russia.
authors.forename: Eugene
authors.initials: E
authors.lastname: Baulin
authors.affiliation: Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia Laboratory of Biologically Active Nanostructures, Gamaleya Center of Epidemiology and Microbiology, Moscow 123098, Russia Laboratory of Genome Analysis, Institute of Agricultural Biotechnology, Moscow 127550, Russia.
authors.forename: Anna
authors.initials: A
authors.lastname: Karyagina
authors.affiliation: Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia Sector of Applied Informatics, Research Institute for System Studies, Moscow 117218, Russia.
authors.forename: Andrei
authors.initials: A
authors.lastname: Alexeevski
authors.affiliation: Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia Sector of Applied Informatics, Research Institute for System Studies, Moscow 117218, Russia sas@belozersky.msu.ru.
authors.forename: Sergey
authors.initials: S
authors.lastname: Spirin
mesh_terms: D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000737:chemistry* / Q000145:classification / Q000378:metabolism; D030541:Databases, Genetic; D009690:Nucleic Acid Conformation; D017434:Protein Structure, Tertiary
chemical_list: D004268:DNA-Binding Proteins; D004247:DNA