Photon Factory Activity Report 2014 #32 (2015) B
BL-6A/2013G732

SAXS study of iron-binding Dps protein interaction with DNA
Alexander Timchenko1, Ol’ga Ozoline2, Sergey Antipov3, Masaji Shinjo4, Hiroshi Kihara5-7*
1

Institute of Protein Research, Pushchino , Russia, 142290;
Institute of Cell Biophysics RAS, Pushchino, Russia, 142290;
3
Department of Biophysics and Biotechnology, Voronezh State University, Russia, 394006;
4Department of Physics, Kansai Medical University, Hirakata, Osaka 573-1010, Japan
5SR Center, Ritsumeikan University, 1-1-1 Noji-Higashi, Kusatsu 525-8577, Japan6Nagoya University SR Ressearch Center, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
7
Himeji-Hinomoto College, 890 Koro, Kodera-cho, Himeji 679-2151, Japan
2Introduction
Multifunctional protein Dps plays an important role in ironassimilation and a crucial role in bacterial genome
packaging. Its monomers form dodecameric sphericalparticles accumulating ~400 molecules of oxidized iron
ions within the protein cavity and applying a flexible Nterminal ends of each subunit for interaction with DNA.
Deposition of iron is a well-studied process by which cells
remove toxic Fe2+ ions from the genetic material and store
them in an easily accessible form. However, the mode ofinteraction with linear DNA remained mysterious andbinary complexes with Dps have not been characterized sofar.. Here we present SAXS patterns of DPS protein from
E.coli and its complexes with DNA.

CRYSOL program [2] (see Fig. 1b). One can see from
Fig.1 the similarity of experimental and calculated curves
for DPS. Interaction of DPS with DNA duplex
dramatically changes the DPS structure (see Fig. 1c). Forcomplex we have Rg == (42.4±0.2) Å and V=122.6 nm3 .
This value is close to half one of the whole DPS. We also
calculated SAXS pattern from one hexameric ring of DPS
molecule (1JRE.pdb). The calculated SAXS pattern isdrawn in Fig. 1d. One can see the similarity of SAXS
pattern DPS-DNA and calculated curves for half of DPS.
Thus, the interaction of DPS with DNA duplex causes
dramatic changes in DPS structure and it needs the furtherinvestigation.
10Results
SAXS pattern of DPS is presented in Fig.1a. For better
accuracy we evaluated radius of gyration (Rg) of proteinfrom the distance distribution function P(r) calculated by
GNOM program [1] in the range of Q=0.02-0.25 Å-1. It
was found that Rg == (35.7±0.2) Å. To exclude thepossible uncertainty in concentration value to calculate themolecular mass we compared volumes (V) of particles
calculated from Porod invariant. For DPS V=299.5 nm3which is closed to the value V=263.5 nm3 calculated fromthe SAXS pattern of crystal structure (1JRE.pdb) by

1

Intensity

Experimental
Recombinant DPS (Mw= 18.7 kDa for monomer) and 420
bp fragment of regulatory region of dps gene were appliedin SAXS experiments. The buffer 50 mM Tris-HCl pH 8.0,25mM NaCl, 5% glycerol was used. The protein
concentration was 1.36 mg/ml.
The molar ratio of protein-DNA complex was about 27:1.
Synchrotron X-ray measurements were done on a smallangle camera BL-6A (Photon Factory, Tsukuba) using
PILATUS 100K detector. The range of scattering vectors
Q=0.01-0.25 Å-1.

d0.1

ca0.01b0.0010.0001
0.00

0.05

0.10

0.15

0.20

0.25

0.30

-1Q(D )

Fig.1 The dependence log I versus Q for DPS (a-DPS, bDPS crystal structure, c-DPS+DNA, d- half of DPS ).
References
1) Svergun D., J.Appl.Cryst., 25, 495, 1992.
2) Svergun D. et al., J.Appl.Cryst., 28, 768, 1995.
* E-mail:kiharah1234@gmail.com