Supporting information
Molecular modelling
Apo-HiC: The three runs of apo-HiC in a water box, each originated from the
crystal structure determined for the apo-form, deposited in the PDB with code 4oyy.
There are twelve independent HiC monomers in the unit cell, all closely similar in
fold and chain A was chosen as the starting structure for these simulations. The model
lacked the side chains of two arginine residues (Arg-51 and Arg-141), which were
built on using PRIME1. The N-terminal and C-terminal ends were acetylated and Nmethylated, respectively. Protonation states were examined by PROPKA3.12.
Protonation states of the two histidine residues were chosen based on surrounding
residues, giving rise to His49 being modeled as the Nε-tautomer while His173, which
is part of the catalytic triad, is modeled as the Nδ-tautomer. The setups were solvated
by the TIP3P water model3 and two chloride ions were added to neutralize the
systems. Three replicates of the system, containing 19968 atoms, were simulated for
40 ns and are referred to as HiC(1), HiC(2), and HiC(3).
Apo-HiC with four SDS molecules. Three new systems containing one apo-HiC
from either HiC(1), HiC(2) or HiC(3) were supplied with four SDS molecules placed
20 Å away from the protein surface along the x- and y-axes, preventing interactions
between HiC and SDS at the intuition of the simulation. The parameters for SDS can
be found in the CHARMM27 lipid parameter and topology file4. These three systems
were run for 40 ns in four replicas, yielding 12 simulations with a total simulation
time of 480 ns. These simulations will be referred to as H4S(1.1)-H4S(1.4),
H4S(2.1)-H4S(2.4) and H4S(3.1)-H4S(3.4).
Simulations. Each system was initially minimized by the conjugated gradient method
for 15,000 steps followed by simulation using the NPT ensemble at 310 K with 1 fs
time step. All simulations were run in NAMD2.85, utilizing the CHARMM276 force
field with CMAP corrections7,8. Constant pressure at 1 atm was maintained by
employing the Langevin piston method9,10 with a damping coefficient of 0.5 ps-1 and a
piston period of 100 fs. PME was used to treat full electrostatics11 while van der
Waals interactions were truncated at a cut-off distance of 12 Å using a switching
function from 10 Å.
Analysis. The RMSD and RMSF calculations as well as the volumetric maps,
created from the build in VolMap tool, were calculated utilizing VMD1.9.112.
VolMap divides the simulation box into a grid, where every grid point is separated by
1 Å. Each grid point is set to either 0 or 1 in each frame depending on the location of
SDS. If one of the atoms in one of the SDS molecules overlays a grid point it is given
the value 1 else 0. The numbers from each frame is summed together and divided by
the number of frames giving a fraction of time where the grid point is occupied. This
fraction is plotted in figure 9 as isosurfaces.
Supporting figure legends:
Figure S1: [15N-1H]-HSQC of HiC with assignments: Peaks in red are negative
(folded) peaks, presumably Arg Hε/Nε peaks (HiC contains 12 Arg residues). Peaks
denoted with “*” are unassigned: they come from side chain Asn and Gln amide
peaks (HiC contains 13 Asn and 7 Gln residues each potentially showing two side
chain peaks) or from impurities or from some of the unassigned residues of HiC (none
of them showed useful correlations in the triple resonance spectra that would allow an
assignment).
Figure S2: Overlay of [15N-1H]-HSQC of HiC without SDS (red) and with SDS
(blue). Inserts illustrate chemical shift changes of selected residues during titration:
SDS concentrations: black: 0 μM, blue: 37 μM, green: 74 μM, red: 111 μM, orange:
148 μM, brown: 185 μM.
Figure S3: A: RMSD of HiC(1)-HiC(3). B: RMSF of apo-HiC.
Figure S4: A and B: RMSD and RMSF of H4S(1.1)-H4S(1.4), respectively. C and D:
RMSD and RMSF of H4S(2.1)-H4S(2.4), respectively. E and F: RMSD and RMSF
of H4S(3.1)-H4S(3.4), respectively.
Table S1. Data and refinement statistics
Data set
PDB Code
Wavelength (Å)
Space group
Cell parameters (Å,º)
Native
4oyy
1.54
P212121
a = 125.55
b = 127.0
c = 134.51
MEP complex
4oyl
0.89
P21
a = 71.63
b = 66.40
c = 71.98
 = 119.3
99,112
36,132
20-2.05 (2.09–2.05)
0.058 (0.115)
97.4 (89.3)
2.8 (1.9)
10.5 (2.6)
2.33
3
0.143
0.184
4599
337
19.9
19.2
Total reflections
195,605
Unique reflections
43,331
Resolution (Å)
20-3.0 (3.16-3.0)
Rmerge
0.118 (0.324)
Completeness (%)
99.5 (97.5)
Redundancy
4.5 (3.6)
5.9 (2.3)
<I/(I)>
VM (Å3/Da)
3.14
Mol. per asymmetric unit
12
Rcryst
0.172
Rfree
0.193
No. of non-hydrogen atoms
16996
No. of water molecules
106
Mean B value (Å2)
28.1
2
Mean B value protein (Å )
28.1
RMS deviation from ideality
Bonds (Å)
0.011
0.017
Angles (º)
1.5
1.7
Values in parenthesis correspond to the high resolution shell.
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