Fig 1.
Cartoon representation of a) IdeR monomer that consist of three domains, DNA binding domain [DBD, green], dimerization domain [DD, yellow], the SH3-like domain [SH3, cyan] and a 10 residue long linker region [shown in pink]. Each monomer binds to two metals ions, shown in red spheres. The cavity formed at the centre of the monomer is named as the ‘Junction region’ in this study b) IdeR dimer that binds to DNA via the DNA binding helices [DBH], c) IdeR functional unit. Two IdeR dimers bind to opposite sides of DNA to form a ‘dimer-of-dimer’ complex. The four monomeric subunits are labeled as A, B, C and D.
Table 1.
List of systems selected for simulation studies.
Fig 2.
Conformational flexibility of the monomeric systems.
Free energy landscape based on the first two eigen vectors from the simulation trajectories of monomeric units are shown for a) M (without metal ion), b) M1 (bound to one Fe+2 ion) and c) M2 (bound to two Fe+2 ions).d) Free energy landscape based on the first eigen vector for all the three system.
Fig 3.
The structural readjustments as a result of iron binding were also evident from protein structure networks.
Dynamically stable community formation in the PSNs of the three monomeric systems, a) M, b) M1 and c) M2 is illustrated. Communities are indicated by red triangles and calculated using the program PSN-Ensemble.
Fig 4.
Distance profile of the N-terminal residues between the two chains as a function of simulation time.
N-terminal stability between the two dimeric systems (with and without metal ion) is quantified by measuring distances between a) Thr7A-Met1B and b) Thr7A-Thr7B as a function of time over the entire period of simulation (100 ns).
Fig 5.
Structural superposition of the reference and final structure of a) FU-nm and b) FU-m are shown as cartoon representation.
In both cases the reference structures are shown in gray while the final structure obtained at the end of 100 ns simulations are shown in red for FU-nm and blue for FU-m. c) Panel highlights two specific regions in the structure that shows maximum deviation in the non-metallated case. The first column shows variation in the SH3 domain, while the second column represents variation in the DNA binding helix [DBH]. Each row in the panel represents the four monomeric subunits.
Fig 6.
The trajectories of the interdomain angle (the angle between the centers of mass of the three domains, as shown in the inset) for all the subunits in the two functional units, a) FU-nm and b) FU-m.
Different colours represent different chains in the system.
Fig 7.
Influence of metal on the energy landscape of IdeR-DNA complex.
Y-axis represents the statistical free energy evaluated with respect to a) number of hydrogen bonds between protein and DNA and b) the number of non-bonded contacts between the protein and DNA. These two parameters broadly define the extent of protein-DNA interaction. Profiles shown in red are for the non-metallated system [FU-nm], while those in green are for the metallated system [FU-m].
Fig 8.
Proposed model of IdeR activation and DNA binding.
A schematic representation of the various steps involved in IdeR activation as DNA binding as understood from experimental as well as simulations studies is provided. The three domains of IdeR monomer are represented in different colours, green–DNA binding domain, yellow–dimerization domain, and cyan–SH3 domain. The N-terminal region is shown in brown and the linker region is represented in magenta. The black triangles in the structure represent network connectivity as obtained from Protein Structure Network analysis. The top three panels correspond to the population distribution of the ‘open’ and ‘closed’ states of IdeR in the monomeric form, cartoon diagram of the dimeric form, and the DNA complexed with four units of IdeR, in the absence of metal ion. The three panels in the bottom row correspond to the same in the presence of metal ion.