An updated version of NPIDB includes new classifications of DNA-protein complexes and their families.
Nucleic Acids Res
; 44(D1): D144-53, 2016 Jan 04.
Article
em En
| MEDLINE
| ID: mdl-26656949
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.
Texto completo:
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Base de dados:
MEDLINE
Assunto principal:
DNA
/
Bases de Dados Genéticas
/
Proteínas de Ligação a DNA
Idioma:
En
Ano de publicação:
2016
Tipo de documento:
Article