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1
Supplementary Information
Properties
o
f DNA
-
a
nd Protein
-
Scaffolded Lipid Nanodiscs
Vishal Maingi and Paul W. K. Rothemund
Supplementary Methods
Model building
We have explained here protein and DNA scaffolds model building.
In all the cases
lipids, in the form of bilayer lattice, were inserted inside the scaffold rings using
insane.py
1
script.
NW
11
and circNW
11
protein scaffolds
c
NW11
(circular NW11)
all
-
atom model was obtained from CHARMM
-
GUI
.
2
A
ll
-
atom
protein
part in c
NW11
, without lipids,
was coarse
-
grained
(CG)
using
martinize.py
3
script
(MARTINI)
and
the
h
elical secondary structure was imposed.
This provided a starting
CG NW
11
model (not covalently
circularized
)
.
L
ipid filled simulated fi
nal snapshot is
shown in Fig. S2
A.
To
model
a CG circNW
11
(covalently circularized model)
we used
the same
CG NW11
model
but with an additional harmonic bond between
the
terminal
amino acids (G
ly
and T
hr
) backbone beads with a bond distance 0.4 nm and a force
constant
1000
kJ
mol
-
1
nm
-
2
.
In circNW11 t
erminal Gly
and
Thr residues backbone bead
type
s were
changed to N0 with charge 0
(
to represent them as
internal Gly and Thr
residues
because the scaffold is now circular).
Lipid filled simulated final snapshots are
shown in Fig.
2A
.
DNA rings and hydrophobic
modifications
First
,
all
-
atom
ds
DNA rings
were generated
in all the cases
using Nucleic Acid Builder
(NAB)
.
4
10.5 base pairs
(bp)
per turn was
used during model building.
dsDNA rings with
diameters
c.a.
11 nm
(
dec_select
-
DNA
11
and
et_all
-
DNA
11
)
,
c.a.
15 nm
(
dec_select
-
DNA
15
,
et_all
-
DNA
15
,
et_ss
-
DNA
15
,
and
et_select
-
DNA
15
)
and
c.a.
45 nm
(
et
_
all
-
DNA
45
)
were built using
100, 140 and 420
bp
respectively
.
These models are
essentially linear double helices bent to form circles. Because we did not perfectly adjust
t
wist, backbone beads at
the junction where the ends of the linear double helix meet
are
imperfe
ctly aligned, and it may appear that 5’
-
5’ or 3’
-
3’ linkages are made. This is not in
2
fact the case, the ends of the helix are simply constrained to match with imperfect twist.
Such point defects did not significantly change the density of either hydrophob
ic groups
or charges along the inner surface of the helix, and caused no apparent deformity in any
of the rings. Thus we assume that it did not significantly affect membrane properties
measured from calculations.
For a six
-
helix bundle DNA ring
(
et_all
-
hex
DNA
45
)
the
inner
most
ring
helix has a diameter of
c.a.
45 nm, and the outer
remaining five
helices
were constructed
by assuming
inter
-
helix
distance
c.a.
2.2 nm
.
Using NAB
,
s
ix rings
(all
-
atom)
were generated separately with 420
(inner
most)
, 440, 480 and
500
(outer
most)
bp
respectively
. All the six rings were
then
placed concentric
ally
.
After generating
atomic
coordinates
in all cases,
CG
MARTINI
stiff
dsDNA models were
built
using
martinize
-
dna.py
.
5
For
the
six
-
helix bundle all the rings were placed concentric before using
martinize
-
dna.py
,
which allowed
creating
intra
-
helix and inter
-
helix elastic bond
networks.
In
CG models DNA backbones (bead name BB1) were modified at specific
locations with ethyl and decyl chains. The backbone bead type at the modified sites was
changed from Q0 (
-
1
charge) to P5 (0 charge). For ethyl chain
modifi
cations
we
attached
a single
small type MARTINI
bead (
type
SC2) to DNA backbone (
name
BB1)
with a bond
distance 0.162 nm and
force constant
20,
000
kJ
mol
-
1
nm
-
2
.
We used
a
similar approach in our previous studies
.
6
DNA backbone
residues were selected based
on the radial distance criteria from the center of the ring allowing only inner facing
residu
es to be modified. This was
automated
using
our own
custom
PERL script.
This
introduced 85, 119 and 360 ethyl modifications
(SC2 type beads)
in
11 nm ring
;
et_all
-
DNA
11
,
15 nm
ring
;
et_all
-
DNA
15
and
45 nm rings
;
et
_
all
-
DNA
45
,
et_all
-
hexDNA
45
respectively.
Representative model for
ethyl modified
dsDNA
15 nm ring is shown in
Fig.
1B
, and ethyl model six
-
helix hexago
n bundle ring is shown in Fig.
1C
.
Additionally,
15
nm dsDNA rings
et_select
-
DNA
15
and
et_ss
-
DNA
15
with 14 and 60,
respectively, et
hyl modifications were designed
(Fig. S9
)
. Modification sites in
et_select
-
DNA
15
are
chosen based
on experimental
7
designs.
To model a
CG
MARTINI
decyl chain we used three
attached
b
eads: one
bead with SC2 type (representing two
carbons) and two beads with C1 type (representi
ng 2
x
4
carbons). This three
-
bead chain
(
representing
decyl) was attached to
DNA backbone (bead name
BB1
) with the SC2 bead
type with a bond distance 0.
162
nm and force constant 20,
000 kJ mol
-
1
nm
-
2
. SC2 bead
was
next
attached to C1 type bead with a bond distanc
e 0.235 nm and force constant
10,
000
kJ mol
-
1
nm
-
2
. Finally
,
this
middle C1
bead type was attached to the
terminal
C1
bead type with a bond distance 0.47 nm and force constant 10,000 kJ mol
-
1
nm
-
2
.
A
ngle
between DNA backbone bead, SC2 (type) and C1 (type)
was set to 170
°
with
force
constant
250
kJ
mol
-
1
rad
-
2
and
the
angle between SC2 (type), C1 (type) and C1 (type)
was set to 180° with force constant 250 kJ mol
-
1
rad
-
2
.
These parameters were partly
taken from MARTINI sodium dodecyl sulfate molecule
but wit
h a higher force
constant
preventing
backward flips
of decyl chains
.
Specific DNA backbone residues were
determined based on the experimental design
7
and using
cus
tom
PERL scripts
select
3
residues were attached with CG decyl chains. For 11 nm
(100 bp)
and 15 nm
(140 bp)
dsDNA ring model
s
20 and 26 decyl modifications were done, respectively.
Representative model for a
decyl modified
15 nm ring is shown in Fig
.
1B
.
DNA
-
protein hybrid scaffold
DNA
part
.
Here a different sized six
-
helix bundle ring CG model was built with six
concentric rings. The inner
most ring has a diameter
c.a.
51.6 nm, and the outer remaining
five helices were constructed by assuming inter
-
helix distance
c.a.
2.2 nm. Six rings w
ere
generated separately with 480
(inner
most)
, 500, 540 and 56
0
(outer
most)
bp
using NAB
and
rings were
then placed concentric. The rin
gs
were
converted to CG
stiff dsDNA
model
s
using
martinize
-
dna.py
.
This provided intra
-
helix
and inter
-
helix
elastic bond
networks.
Protein
part
. We used
CG
NW
11
protein scaffold
in this case
, and
the CG model was
obtained as explained above.
CG
NW
11
is a double belt
scaffold
and circular in shape.
From this double belt scaffold we took a single scaffold and opened it by pulling the
amino acid residue
s
towards the
dummy beads (no interaction)
positioned in
a
c
ircular
arc shape (diameter of
c.a.
45 nm)
; Fig. S1
A
.
A replica of the same
open
scaffold was
placed in an antiparallel direction
, Fig. S1
B,
and
c.a.
1.2 nm apart taking care of the
proximity
helix registries
between the
antiparallel scaffolds
as present in the original
c
NW11 CHARMM
-
GUI model
.
This antiparallel double belt open configuration was
replicated four times so that i
t
finally
encloses a circular scaffold
c.a.
41
nm
(Fig. S1
C)
.
To summarise
,
there are in total 8 protein scaffolds; 4 at top and 4 at bottom where the
top and bottom scaff
olds are placed in an antiparallel fashion.
Thus, this can be
considered as a 4 double belts protein scaffold model.
Combining DNA and protein parts
.
The
six
-
helix bundle DNA ring and the 4 double belt
s
protein scaffold ring
were
placed concentric.
Then
the
central amino acid residue in
each
of the four protein scaffolds on top
was
connect
ed to
a
DNA back
bone bead
(innermost
dsDNA helix) at four
almost equidistant
location
s
.
The
initial
distance
(bond)
between
the connecting points was maintained
, during
MD runs,
using
harmonic
potential
with
force constant 1000 kJ mol
-
1
nm
-
2
. This
was achieved using the pull code implement
ed
in
GROMACS
v2019.4
(in
mdp
file settings).
T
he remaining 4
bottom scaffolds
have
no
connection
points
with the DNA scaffold.
In Fig.
6
B,
6
C the red
lines
represent the
harmonic
bonds
connecting protein scaffolds to DNA ring.
There are 4 harmonic bonds
in hexDNA::NW
11
and only two in hexDNA:NW
11
.