1/9/2013
Atomic scale modeling of
plasma-bacterial cell wall interactions
for plasma medicine applications
M. Yusupov, E. Neyts and A. Bogaerts
Research group PLASMANT, University of Antwerp
Aim of the work
Interaction between plasma species and bacterial cell walls
→ Mechanism of bacteria killing (bacterial cell wall damage)
Different interaction mechanisms for different plasma species?
Effect of liquid layer around cell?
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1/9/2013
Model system:
Peptidoglycan (PG)
Gram-negative bacteria
e.g. Escherichia coli
(E. coli)
PG = 6-7 nm thick
Gram-positive bacteria
e.g. Staphylococcus aureus
(S. aureus)
PG = 20-30 nm thick
Model system:
Peptidoglycan (PG)
Disaccharide
Stem
Gram-positive bacteria
e.g. Staphylococcus aureus
(S. aureus)
PG = 20-30 nm thick
Bridge
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Model system:
Peptidoglycan (PG)
PG structure of S. aureus:
•
•
Disaccharide (NAM‐NAG)
Stem (tetrapeptide, i.e., L‐Ala‐D‐iso‐Gln‐L‐Lys‐D‐Ala)
Bridge (pentaglycine, i.e., Gly‐Gly‐Gly‐Gly‐Gly)
•
Important bonds in PG:
• C‐C
• C‐N
• C‐O (in disaccharides, i.e., 4 ether bonds in each disaccharide)
Molecular Dynamics (MD) method
•
Trajectory of particles: by integrating equations of motion
•
Forces on the atoms: from suitable interatomic potential
Fi = −∇ ri U
In this work:
Force field: ReaxFF
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Prior to the particle impacts
Impinging plasma species:
•
•
•
Initial positions: random, at distance of 10 Å around PG
and from each other
Initial energies: room temperature (i.e. 300 K)
Velocity directions: random
Reaction mechanisms:
•
•
•
Reflection
H‐abstraction
Breaking of important bonds (i.e. C‐N, C‐O, C‐C)
Initial positions of 10 OH radicals around PG
= interesting! Cell wall damage
Bond breaking events
Simulation:
•
•
50 runs for each plasma species
Simulation time: 300 ps
= 3x106 iterations
= long enough to chemically destruct the PG Note: No bond breaking
events
observed
in
pentaglycine interpeptide,
even when H‐abstraction
reactions take place.
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1/9/2013
Impinging plasma species
Reactive oxygen species (ROS):
•
O3, O2, O (published in New J. Phys. 14, 093043, 2012)
•
OH, H2O2, H2O (submitted to J. Phys. Chem. C)
Bond breaking mechanisms:
•
Same for O3, O and OH → H‐abstraction from the PG by plasma species •
Different for H2O2
•
No bond breaking for O2, H2O: long distance interaction (i.e., H bridge formation)
→ H‐abstraction from HO2• (product of H2O2) by PG Breaking mechanism of C-O bonds
Consecutive breaking of 3 important ether C‐O bonds (black dashed circles) upon O atom impact
(a) First O atom abstracts H
(b) Another H is abstracted from
from GlcNAc
MurNAc by a second O atom
→ formation of an OH radical
(c) The OH radical abstracts another H atom,
connected to C1 → H2O molecule created
→ Some double C‐O and C‐C bonds are formed
→ breaking of 3 C‐O ether bonds
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Breaking mechanism of C-O bonds
Breaking of 4th important ether C‐O bonds (black dashed circles) upon O atom impact
(a) O atom abstracts H
from GlcNAc → OH formed
(b) Another H abstracted from methyl
residue of MurNAc
→ formation of double C‐C and C‐O bonds
→ cleavage of 4th ether bond.
Breaking mechanism of C-O bonds
Consecutive breaking of 3 important ether C‐O bonds (black dashed circles) upon OH radical impact
(a) The OH radical first
approaches the H1 atom,
connected to C2.
(b)
→
→
→
The OH radical abstracts the H1.
H2O molecule is created
Some double C‐O and C‐C bonds are formed breaking of 3 C‐O ether bonds
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Breaking mechanism of C-O bonds
Breaking of important ether C‐O bond in GlcNAc
upon H2O2 molecule impact
(a) First 3 H2O2 molecules
(indicated in purple (O)
and light blue (H) colors)
assemble around the PG.
(b) H2O2 molecules react with
each other, dissociating
into HO2• and H2O
molecules.
(c) H abstracted from HO2•
→ formation of double C‐C and C‐O bonds
→ cleavage of C3‐O4 ether bond
Summarizing results
Incident plasma
species
O atoms
O3 molecules
OH radicals
H2O2 molecules
1.
2.
3.
4.
5.
C‐N bond breaking events, %
Ether C‐O bond breaking events, %
C‐C bond breaking events, %
26 ± 6
8 ± 4
8 ± 4
0 78 ± 6
56 ± 7
54 ± 7
44 ± 7 38 ± 7
26 ± 6
14 ± 5
12 ± 5 O3, OH, H2O2 and O: breaking of structurally important bonds in PG
O atoms: more effective in bond cleavage than OH, H2O2 and O3
Ether C‐O bonds: more easily broken (consecutive breaking events)
O2 and H2O molecules: no structural damage to the PG
Bond breaking mechanisms: different for H2O2 compared to others
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PG surrounded with water layer
Preliminary results
PG surrounded with water layer
Preliminary results
After 100 ps
500 H2O molecules around PG
PG with surrounding water layer
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Example: OH impact:
New OH formed during trajectory through H2O layer
But no bond breaking of PG (yet)
Preliminary results
(+ compared with no water layer)
Incident plasma
species
C‐N bond Ether C‐O bond C‐C bond breaking events, breaking events, breaking events, %
%
%
O atoms
O3 molecules
OH radicals
H2O2 molecules
2 (vs. 26)
2 (vs. 8)
0 (vs. 8)
0 (vs. 0) 18 (vs. 78)
12 (vs. 56)
0 (vs. 54)
14 (vs. 44) 6 (vs. 38)
6 (vs. 26)
0 (vs. 14)
2 (vs. 12) Lower reactivity of all species
•
OH radicals → maybe not long enough simulation time (i.e., 300 ps) •
O, O3, H2O2 : sometimes direct interaction with PG due to holes in water layer
•
Indirect interaction occurs as well: creation of OH (O + H2O → OH + OH
→ Not enough water molecules around PG ?
OH + H2O → H2O + OH): interacts with PG
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Conclusions
MD simulations: interaction of O, OH, H2O2, O3, O2, H2O with PG:
• O2 , H2O molecules: no structural damage to the PG
• O, OH, O3, H2O2: breaking of structurally important bonds in PG
• Bond breaking mechanisms:
‐ O, OH, O3: initiated by H‐abstraction from PG by incident species
‐ H2O2: H‐abstraction from HO2• (= product of H2O2) by PG
• O atoms: more effective in bond cleavage than OH, H2O2 and O3
• C‐O bonds: more easily broken (4 consecutive events)
• Effect water layer (preliminary results): species less reactive,
but bond breaking still possible
• Future work: study in detail behavior of species with liquid H2O
(without PG)
Future work
• Experimental validation ! (input needed from experimentalists)
• Behavior of species in liquid water layer
• Interaction with spores, viruses,… ?
→ human cells/tissue probably too complicated for atomic simulations
• Interaction with lipid bilayer
→ develop force field for P (does not exist yet)
• All suggestions for good model systems welcome !
(to study the most biomedically relevant + ‘realistic’ systems)
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