Analisis of Protein-DNA interactions of complexes of SCOP families are created by Olga Zanegina
New classification of Protein-DNA interactions was suggested and integrated to NPIDB. All interacting with DNA SCOP families were divided to 20 types of protein-DNA interactions based on recognizing elements of protein (helix, sheet, strand, turn) and DNA (the major/minor groove, sugar-phosphate backbone). http://npidb.belozersky.msu.ru/contacttypes.html This classification allows to find proteins combined by different SCOP domains but interact with DNA in similar ways.
Each SCOP domain family which interacts with DNA complex was analyzed by structure. All structures from one family were superimposed and all their sequences were aligned. Relies on DSSP secondary structure and H-bond determination between element of protein and DNA list of protein-DNA contacts were defined. Overall type of protein-DNA interaction for the whole SCOP family was defined basing on all lists of contacts.
One can find all data for each SCOP family on corresponding page (ex.: http://npidb.belozersky.msu.ru/scopfm/scop.html?46903) which contain:
- Contact Type
- Method of 3-D alignment
- Quality of 3-D alignment
- Number of analized complexes
- Number of complexes with DNA
- Sequence alignment and structures superimposition files
Method is a tool that was used for structural alignment:
SSM (PDBeFold) is an interactive service for comparing protein structures in 3D. SSM algorithm of protein structure comparison in three dimensions includes an original procedure of matching graphs built on the protein's secondary-structure elements, followed by an iterative three-dimensional alignment of protein backbone C-alpha atoms. http://www.ebi.ac.uk/msd-srv/ssm/
CE is a method for calculating pairwise structure alignments. CE aligns two polypeptide chains using characteristics of their local geometry as defined by vectors between C alpha positions. Matches are termed aligned fragment pairs (AFPs). Heuristics are used in defining a set of optimal paths joining AFPs with gaps as needed. The path with the best RMSD is subject to dynamic programming to achieve an optimal alignment. http://cl.sdsc.edu/
Quality is an expert assessment of a structural alignment.
High: all structures fits together so tight as they were one structure.
Good: proteins/DNAs fits together rather good, while DNAs/proteins overlap each other only in parts.
Middle: structures lay near each other and form an average shape of protein-DNA complex.
Low: the structural alignment looks like Flying Spaghetti Monster