Conserved features of protein-DNA interaction in all X-ray characterized families of DNA-binding proteins

Olga Zanegina(M) / Andrey Alexeevski (M)

Introductionbbb

Figure 1Nucleic Acid – Protein Interaction DataBase

Figure 2 SCOP family characteristic

Figure 3 Classification of protein-DNA interactions

Figure 4 Type example

Summary & OutlookAll 110 well-represented by structural data protein domain families were characterized and conserved features were identified. Proposed classification into types of protein-DNA interaction allows revealing specific features of interaction with DNA within protein families.The results are included into NPIDB. Thus, NPIDB provides users with comprehensive information on structural features of protein domains interacting with DNA. Review of types of protein-DNA interactions basing on the obtained information will be done in forthcoming publication.

All these results are publicly available at NPIDB site (http://mouse.belozersky.msu.su/NPIDB/index.html)

№ Protein recognizing element(s)

DNA (groove /backbone)

Protein recognizing element(s)

DNA (groove /backbone)

1 Helixes Major grv.

2 Helixes +Loops Major grv.

3 Sheets + Loops Major grv.

4 Loops Major grv.

5 Helixes Minor grv.

6 Helixes +Loops Minor grv.

7 Sheets + Loops Minor grv.

8 Loops Minor grv.

9 Helixes Major grv.

Any element(s) Minor grv.

10 Helixes +Loops Major grv.

Any element(s) Minor grv.

11 Sheets + Loops Major grv.

Any element(s) Minor grv.

12 Helixes +Sheets +Loops Major grv.

Any element(s) Minor grv.

13 Loops Major grv.

Any element(s) Minor grv.

14 Any element(s) Major grv.

Helixes Minor grv.

15 Any element(s) Major grv.

Helixes +Loops Minor grv.

16 Any element(s) Major grv.

Sheets + Loops Minor grv.

17 Any element(s) Major grv.

Helixes +Sheets +Loops Minor grv.

18 Any element(s) Major grv.

Loops Minor grv.

19 Any element(s) Major grv.

Any element(s) Minor grv.

20 Non-specific interaction with backbone

Major groove:14,15,16,17,18) Any element

Minor groove:14)Helices

15)Helices +Loops

16)Sheets + Loops

17)Helices + Sheets +Loops

18)Loops

AND

-sheet in minor groove

Prokaryotic DNA-bending protein

1owf_A

"Histone-like" proteins from Archaea

1azp_A

DNA repair protein MutS, domain I

1w7a_A2-116

TATA-box binding protein (TBP), C-terminal domain

1cdw_A155-252

Introduction  At the moment more than 1500 structures of protein-DNA complexes are available. Among them there are complexes with proteins that specifically or non-specifically interact with DNA. Proteins interact with DNA in different ways: using helixes, sheets, strands and turns of protein; via major/minor groove, sugar-phosphate backbone of DNA; different combinations of interactions are possible. Development of approaches in systematization of protein-DNA complexes is necessary for understanding mechanisms of protein-DNA interaction.

 Results In our group, Nucleic Acid – Protein Interaction DataBase (NPIDB; Spirin,S. et.al. Bioinformatics 2007, 23 (23):3247-8) was created. NPIDB contains 2 747 structures of DNA-protein and RNA-protein complexes supported with search, navigation and analysis tools. For each structure from NPIDB it is possible to download the PDB-structure, find hydrophobic clusters, hydrogen bonds, potential water bridges between protein and DNA; view sequence, view the 3D structure in Jmol, explore link to Pfam and SCOP [fig.1].Systematization of structural data is performed by classification of protein-DNA interactions. As units of classification, we used structural SCOP (release 1.73, November 2007) domains {fig2}. Basing on interacting elements of protein (helix, sheet, strand, turn) and DNA (the major/minor groove, sugar-phosphate backbone), 20 types of protein-DNA interaction were suggested [fig.3].Specific contacts and the type of protein-DNA interaction are determined for each DNA-binding protein [fig.4]. Also 110 SCOP domain families containing more than one structure of protein in contact with DNA in PDB files were characterized. For each family, a sequence alignment and a structural alignment were constructed; conserved features including conserved protein-DNA interaction were identified [fig.2].

Types of protein-DNA interaction Examples of some types of protein-DNA interaction

Distribution of SCOP families by interaction types