Resolving the Structure of Viral Genomes with Atomic ...
Transcript of Resolving the Structure of Viral Genomes with Atomic ...
Resolving the Structure of Viral Genomes with Atomic
ResolutionAleksei Aksimentiev
Department of PhysicsUniversity of Illinois at Urbana-Champaign
I use Blue Waters to …
… understand molecular underpinnings of life … build biologically inspired systems
DNA, the blueprint
Viral genome, the program of infection
Cryoem reconstruction with concentric rings (Evilevitch et al, UIUC)
http://darwin.bio.uci.edu/~faculty/wagner/hsv2f.html
Herpes virus (HSV)
Open questions:- What is the 3D structure of the genome?- How genome ejection is triggered and sustained?- Can it be used as a drug target?
DNA is a highly
charged polymer!
Samesigncharges….
- -Samesignchargescana0ract(inamedium)
FF
- -Samesignchargesrepel
(invacuum)
FF
DNAissurroundedbycounterions +1e, sodium or potassium
+2e, magnesium or calcium
+4e,spermine
+3e,spermidine
EffecBvea0racBonbetweenDNAisobservedwhencounterionshavecharge≥2e
All-Atom Molecular Dynamics Simulation of DNA Condensates
Classical Force Field
U(r) =X
bonds
kb(b� b0)2 +
X
angles
k✓(✓ � ✓0)2 +
X
dihedrals
k�(1 + cos(n�� �0))
U(r) =X
bonds
kb(b� b0)2 +
X
angles
k✓(✓ � ✓0)2 +
X
dihedrals
k�(1 + cos(n�� �0))
+X
non-bonded pairs i,j
4✏ij
"✓�ij
rij
◆12
�✓�ij
rij
◆6#
+X
non-bonded pairs i,j
qiqj4⇡✏0rij
�
✓b
Bonded parameters from quantum mechanics
} LJ parameters from
experiments
U(r) =X
bonds
kb(b� b0)2 +
X
angles
k✓(✓ � ✓0)2 +
X
dihedrals
k�(1 + cos(n�� �0))
U(r) =X
bonds
kb(b� b0)2 +
X
angles
k✓(✓ � ✓0)2 +
X
dihedrals
k�(1 + cos(n�� �0))
+X
non-bonded pairs i,j
4✏ij
"✓�ij
rij
◆12
�✓�ij
rij
◆6#
+X
non-bonded pairs i,j
qiqj4⇡✏0rij
�
✓b
U(r) =X
bonds
kb(b� b0)2 +
X
angles
k✓(✓ � ✓0)2 +
X
dihedrals
k�(1 + cos(n�� �0))
U(r) =X
bonds
kb(b� b0)2 +
X
angles
k✓(✓ � ✓0)2 +
X
dihedrals
k�(1 + cos(n�� �0))
+X
non-bonded pairs i,j
4✏ij
"✓�ij
rij
◆12
�✓�ij
rij
◆6#
+X
non-bonded pairs i,j
qiqj4⇡✏0rij
�
✓b
}Partial charges from quantum
mechanics
Add 64 DNA helices
Add polyamine cations (+4)
Add 150 mM NaCl
Add explicit water
Solve the equation of motion (F= ma) under periodic
boundary condition in all directions
DNA-confining wall of radius RApply a half-harmonic wall
potential only to DNA
y (n
m)
15-ns MDCross-sectional view of MD using CHARMM27 Na
Standard CHARMM & AMBER Force Fields Are Not Perfect for the Simulation of DNA Condensates
x (nm)
1
2
46
10
2
46
100
Pres
sure
(ba
r)
3025DNA-DNA distance (Å)
Rau et al. AMBER99 CHARMM
1
2
46
10
2
46
100Pr
essu
re (
bar)
323028262422DNA-DNA distance (Å)
Rau et al. AMBER99 CHARMM
[Na] = 250 mM [Mg] = 20 mM
Rau et al.Rau et al.
CHARMM27
AMBER99
CHARMM27
AMBER99
Long-lasting contact ion pairs (CIP) between Na+ and phosphate stabilize contact DNA pairs.
2
4
12
4
102
4
100
Pres
sure
(ba
r)
3028262422DNA-DNA distance (Å)
Todd et al. AMBER99 CHARMM
[spermine] = 2 mM
Todd et al.
CHARMM27
AMBER99
Due to excessive CIP formation, the simulations
underestimate both inter-DNA distance and pressure in DNA
array systems.
[Na] = 250 mM outside
Yoo & Aksimentiev, JPCL 2012
Harmonic wall
Rau et al, PNAS 1984 Todd et al, BJ 2008
Champaign-Urbana Non-Bonded FIX (CUFIX): Improved Lennard-Jones Parameters for CHARMM & AMBER
• “Much of what is known about association and dissociation of solutes and ions comes from measurements of colligative properties” — Molecular driving forces by Dill & Bromberg.
-4 -2 0 2 41.21.00.80.60.40.20.0
Density (g/cm3)
Na Acetate Water Total
Na ≈
Dimethylphosphate Acetate
Yoo & Aksimentiev, JPCL 2012 Yoo & Aksimentiev, JCTC 2016
Yoo, Wilson & Aksimentiev, Biopolymers 2016
200
150
100
50
0
OSM
pre
ssur
e (b
ar)
43210molal conc (m)
200
150
100
50
0
OSM
pre
ssur
e (b
ar)
43210molal conc (m)
Murad & Powles, JCP 1993 Luo & Roux, JPCL 2010
0.20
0.15
0.10
0.05
0.00
-0.05
-0.10
U LJ (
kcal
/mol
)
4.03.63.22.8
Na–O distance (Å)
0.20
0.15
0.10
0.05
0.00
-0.05
-0.10
U LJ (
kcal
/mol
)
4.03.63.22.8
d (Å)
Standard rmin = 3.11 Å
rmin = 3.20 Å
Standard
NBFIX
CUFIX for CHARMM36 & AMBER99
Effectively infinite slab under PBC
Exp. from Robinson 1959
http://bionano.physics.illinois.edu/CUFIX
Yoo & Aksimentiev, JPCL 2012
1
2
46
10
2
46
100
Pres
sure
(ba
r)323028262422
DNA-DNA distance (Å)
Rau et al. AMBER99+CUFIX AMBER99 CHARMM
1
2
46
10
2
46
100
Pres
sure
(ba
r)
3025DNA-DNA distance (Å)
Rau et al. AMBER99+CUFIX AMBER99 CHARMM
CUFIX Improves Simulations of DNA Condensates
-120
-80
-40
0
40
80
120
y (Å
)
-120 -80 -40 0 40 80 120x (Å)
3
2
1
0
Charge conc. (M)
3210M
-120
-80
-40
0
40
80
120
y (Å
)
-120 -80 -40 0 40 80 120x (Å)
3
2
1
0
M
3210M
-120
-80
-40
0
40
80
120
y (Å
)-120 -80 -40 0 40 80 120
x (Å)
3
2
1
0
M
[Na] = 250 mM [Mg] = 20 mM [spermine] = 2 mM
AMBER99 AMBER99
2
4
12
4
102
4
100
Pres
sure
(ba
r)
3028262422DNA-DNA distance (Å)
Todd et al. AMBER99+CUFIX AMBER99 CHARMM
AMBER99
AMBER99 + CUFIX
AMBER99 + CUFIX
Yoo & Aksimentiev, NAR 2016
AMBER99 + CUFIX (MD included 200 mM Na)
CHARMM27
CHARMM27
CHARMM27
DNAispackagedbyamotor
At higher forces, DNA will deformPackaging process is slow (~min), all-atom simulation at physiological forces is not possible
Can one simulate the process?
Takes about 3 minutes to pack DNA 130 times longer than the capsid !
Max Force: 100pN
Movie: Carlos Bustamante Lab
Strategy: change resolution for speed and detail
Strategy: change resolution for speed and detail
Strategy: change resolution for speed and detail
Strategy: change resolution for speed and detail
Strategy: change resolution for speed and detail
Strategy: change resolution for speed and detail
500 bp dsDNA fragment modeled at different resolutions
24 bp/2 beads 12 bp/2 beads 6 bp/2 beads 3 bp/2 beads 1 bp/2 beads All-atom, ~100 bp
Interactions in a simple coarse-grained DNA model
Interactions in a simple coarse-grained DNA model
Bond potentialr0 = nbp ⇥ 3.4 A
f0 = 1000pN
kspring = f0/r0
Elastic constant
r0 Force
Exte
nsio
n
http://www.phys.ens.fr/~cocco/Art/24physworld.pdf
Interactions in a simple coarse-grained DNA model
Angle potentialPersistence length
s
Lp = 50 nm
e−s/Lp = ⟨cos θ⟩ =∫
𝕏d𝕏 cos θ δ(θ′�[𝕏] − θ)e−βU[𝕏]
∫𝕏
d𝕏 e−βU[𝕏]=
∫ π0
sin θ dθ cos θe−β 12 kspringθ2
∫ π0
sin θ dθ e−β 12 kspringθ2
Interactions in a simple coarse-grained DNA model
90°
�
Dihedral angle potential
Twist persistence lengthLtw = 90 nm
hcos�i = e�s/Ltw
Z ⇡
0d� cos� e�
kdihed(���0)2
2kBT = e�s/Ltw
�0 = s⇥ 10.14�/A
Interactions in a simple coarse-grained DNA model
4 nmcutoff
DNA-DNA distance (Å)
Pres
sure
(bar
)
a) c)
Atomistic capsidAtomistic DNA
Grid-based capsidAtomistic DNA
z z zGrid-based capsid
coarse-grained DNA
F
F
F
z
Periodic in axial axis
Pr
b)
6.8
nm
~28 nm
'1$�FRQÀQLQJ�ZDOO�RI�UDGLXV�5
,RQV
F
F
F
F
F
F
Interactions in a simple coarse-grained DNA model
4 nmcutoff
80 80
4 bp/
Optimized to reproduce Rau & Parsegian pressureHalf-harmonic
wall to preventstrand crossing
Mapping between coarse-grained resolutions
For each helix, fit a 3D spline through bead coordinates
at end of simulation
coordinate1D spline
Fit a spline between quaternion representation of
rotations
Packaging viruses with ARBD
ARBD: Atomic Resolution Brownian Dynamics (multi-resolution)
Package DNA (CG) with ARBD, into CryoEM reconstruction of a HK97 bacteriophage capsid. A cryoEM map of the portal is fitted into the original capsid reconstruction, and DNA is
packaged through the portal.
Smooth, purely repulsive grid-based potential obtained by blurring cryoEM density and adding the portal
MulB-resoluBonpackagingdsDNAviruses
Internalpressureduringpackaging
�27Pressure (atm)
Perc
ent o
f DN
A
outs
ide
caps
id, % Evilevitch et
al, PNAS
Comparisontostructuraldata
�28
Simulation ExperimentJ. Mol. Biol. (2009) 391, 471-483, Hendrix et al
Cryo-electron microscopy
q [Å−1]
experiment simulation
I(q)
[a.u
.]
Small Angle X-ray Scattering
Experiment: Journal of molecular biology, 408: 541 (2011)
Simulation SAXS data were generated from CRYSOL, using an atomistic PDB of the protein coat and packaged DNA
Conclusionsandoutlook
�29
Obtained first atomic-resolution structure of packaged viral particle
Developed accurate multi-resolution representation of DNA—DNA and DNA—protein interactions
To do: Extend the model to ssRNA and ssDNA viruses
Acknowledgements
• Funding through CPLC
• Computations
Jejoong Yoo David Winogradoff
Chris Maffeo Kush Coshic