(x)(y)

1
?????????? ???????? ????????????? ? ?????????

• ?????? ????????? ?????
• ???, ????????????? ?????????
• ???. ?????????

2
????????? ? ?????????

????????? ??? ?? ? ?6?? ??? ? (x) (y)
 
3
?????? ?????????.??????? ???????? ? ????????
???????? ????????? ????????????
????????-6-??????? (?) ? ????????????????? (?)
(??????) ? ??????? ??????? ??????? (?????) ???
?????? ????????? ?????????? ???????, ? -
???????????????? ??????? (???? ?? ???????
????????? ??????? ???????). ? ????????? ?
?????????? ?????????? ? ????? (?????????? ???? ??
??????? ????????? ???????? ??????).
4
Photosynthetic pathways in chloroplasts
NADPH
NADP
PS II
PS I
bf
hn
hn
2H
2H
fluorescence
QA
Fd
bh
FeSI
PQ
PQ
PQ
P680
Chl
bl
Chl
Chl
PQH2
P700
FeSR
H2O
Pc
f
2H
-OOC
Q-cycle
2H
1/2O2
R-COO-
DpH
-OOC
3H
K
H
R-COO-

lumen

Thylakoid membrane
_
_
F
stroma
ADP Pi
Cl-
Fm
F0
ATP
ATP-synthase
Calvin cycle
0 1 10 t, c
5
Scheme of the states of Photosystem
2Cl-chlirophyllPhe-pheophytitnQA,Qb quinone
acceptors
z
z
z
z
z
z
z
1
2
3
4
5
6
7
Hl
15
16
17
19
20
14
18







2H
2H
2H
2H
2H
2H
2H
s
s
s
s
s
s
s
21
22
23
24
25
26
27
PQH
PQH
PQH
PQH
PQH
PQH
PQH
2
2
2
2
2
2
2
g
g
g
g
g
g
g
1
2
3
4
5
6
7
Hl
33
32
30
29
28
41
31
34
35
36
37
38
39
40
x
x
x
x
x
x
x
1
2
3
4
5
6
7
1
5
6
7
y
1
Hl
Chl
8
Phe
Q
A
11
-
Q
B
6

• The photosystem II model block considers electron
  transfer processes at the donor and acceptor
  sides of PSII taking into account the
  recombination processes including non-radiative
  recombination in PS II (arrows)

7
Fluorescence induction curve
Photosynthetic efficiency
P
F
D
S
O
Fo
0 0.05 0.7
Time (s) 5
8
???.6. ???????????? ???????, ???????????? ?
??????? ?????? ????????? ????????? ???????????
??? ???? ?????? ?????????????? ????????? ???????
1000, 100 ? 10 (1) ????2. ???????,
????????????? ? ????? ???????, ?????????????
??????????? ?????? ????????????. ??????????
???????? ?? ??????????????? ????? ???????. ?)
????????????? ????? ????????????? (F) ? ????????
???????????????? ?????????????? ??????????
(??) ?) ???????????? ????????? ????????????
????????? ?? II ?) ???????? ?????????,
???????????? ? ???????????? ????????????? ????? ?
?????? ????????? Hbf ????? ???????? ? ?????
??? ????????? ???????????? ?? ??????????? ???????
??????? bf ????????? H??? ????? ???????? ?
????? ?? ??????????????????? ????????? ?? II
H??? ???????? ??????????? ???????? ?????? ?
???-????????? ??????? Kleak ???????? ??????
????? K ?? ?????? ?????????.
9
????????? Chara corallina
?
?) ???????????? ????????? ??? ?? ?????? ?????? C.
corallina (14 ???) ????? ????????? (0 ???)
???????? ????? ?????? ????? (8 ???) ???????????
????????? ??????? (75 ???) ?? ????? 6.5, ??
???????? ??? 8.5
?
???.2. ?) ??????? ??? ????????? C. corallina
???. 3 ????????? ?????? Chara corallina (????
?????? ????? ??????? ???)
10
????? ?????????????????? ????????? ?????
????????? ?????????. (???????? ?? ?????????)
??????? ?????
?m
?m
7
8
pH
pH
?????? ????????? ????? (K, Na, Cl- ? ?.?.)
H
hout
?
4
??????????
hin
H
pH
5
AT?
A???i
H
????
3
?m
6
pH
h?
1.???? ?????????? ???????? ???????????, ??
????????? ??????????, ?? ???????????
??????????. 2. ????????? ?? ?????? ????????????
?????????? ????? ???????? ?? ?????????? ?
???????????. 3.?o??? ???????? ?? ?????????? ?
??????????? ???????? ? ????????? ?? ??????????
(???). 4. ????????? ????????? ???????
?????????????????? ????????. 5. ?????????? ??????
???????? ????? ?????? ???????? ? ????????? ??
(???) ?????????? ? ????????????? ???????????
?????????? (?m?). 6. ????????? ?????????
???-???. 7. ?????????? ?????? ???????? ?????
???-??? ???????? ? ????????? ?? (???) ???????
?????? ? ???????????????? ??????????? ??????????
(?m?).. 8. ????????? ????????? ???????. ????
????? ??????????? (?? ?????? 5)
2
H
pH
pH
0
1
????????
??????????
???????
11
???????????? ????? ?????? ???????? ? ?????????,
??????????? ???????????? ????????? ????????? ?
????????? ???????????? ???????? ??????
??????????? ??????
(1)
H0- ???????????? ???????? ?? ??????? ???????, ?i
?? ?????????? ??????? ?????????????? ????????
,
12
????? ?????????? ????????
??? ????? ATP
C ??????? g - ????????????
??? ??????
13
???????????? ????????? ??? ???????????? ????????
??? ?????????????? ???????? ( h0 ) ? ??????????
?? ????????
,
,
,
,
,
,
,
,L ????? ?????? (?).
.
14
???????????? ?????????????? ???????
?
?
hout
8.1
1.0
300
0.5
r
?
0.0
?) pH ??????? ????? ?????? ????????? ?????
????????? Bulychev et al., J.Theor. Biol., 2001,
212, 275-294 ?) ????????? ??????????? ?????????
??????? g0.08, ?0-1.335, n0.9, z1, ?0.025,
q0.001, D5, I0.04
15
????? ?????????????????? ????????? ?????
????????? ?????????. (???????? ?? ?????????)
??????? ?????
?m
?m
7
8
pH
pH
?????? ????????? ????? (K, Na, Cl- ? ?.?.)
H
hout
?
4
??????????
hin
H
pH
5
AT?
A???i
H
????
3
?m
6
pH
h?
1.???? ?????????? ???????? ???????????, ??
????????? ??????????, ?? ???????????
??????????. 2. ????????? ?? ?????? ????????????
?????????? ????? ???????? ?? ?????????? ?
???????????. 3.?o??? ???????? ?? ?????????? ?
??????????? ???????? ? ????????? ?? ??????????
(???). 4. ????????? ????????? ???????
?????????????????? ????????. 5. ?????????? ??????
???????? ????? ?????? ???????? ? ????????? ??
(???) ?????????? ? ????????????? ???????????
?????????? (?m?). 6. ????????? ?????????
???-???. 7. ?????????? ?????? ???????? ?????
???-??? ???????? ? ????????? ?? (???) ???????
?????? ? ???????????????? ??????????? ??????????
(?m?).. 8. ????????? ????????? ???????. ????
????? ??????????? (?? ?????? 5)
2
H
pH
pH
0
1
????????
??????????
???????
16
????? ???????????? ??????
17
??????? ????????? ? ??????????? ??????
18
The scheme of time scales of protein molecular
dynamics

• Primary events in photosynthesis and vision
  10-13 10-12 s
• Local dynamics of atoms and small groups
  10-12 10-11 s
• of side chains and polypeptide chain segments
  10-11 10-7 s
• Motions of domains and subunits
  10-8 10-5 s
• Release of bound ligand molecules
  10-6 10-3 s
• Folding-unfolding kinetics
  10-4 102 s

19
CH
QB
Mb - CO
P
QA
CL
P Bchl Bpheo QA
I
CL
P Bpheo QA QB
P
P700 A0 A1 FX FB FA
10-6s
ktunn gt kact
106
at Tlt700K
10-12s
H2O
103
Ri
D2O
R
Rf
180 K
20
1 Conf.
3 Conf.
2 Tunneling
21
Q-A
Frozen in the dark
Q-A
e-induced conform.
Frozen under illumination
P
QB
P
QB
QA
22
???????????????? ???????????? ?????????? ?
????????
23
Scene of the direct model
24
Brownian motion of the mobile carrier

• Langeven Equation

dx
? f ( t )
dt

• f(t) casual force, distributed by Gauss
• average value - zero
• dispersion 2kT?
• k Bolzmann constant, T temperature,
• ? friction coefficient of the media

25
Model trajectory of PQ in membrane filled by PS1
and cytochrome complexes
26
Ecvipotential surfaces calculated according to
Poisson-Bolzmann equations
model
Reduced cyt f
Oxidesed ??
r3
r4
r2
r1
Ion strength - 100 mM, pH7, e?-??80 e????? 2
red -6.5 ??, blue 6.5 ?? green atoms
of molecules. Dotted lines connect residueson Pc
and Cytf that were used by simulation for
calculation the distance between proteins
27
??????? ????? Pc ? cytf ? ?????? ?????????
?????? ?????????????? Pc-cyt f ? ?????? ?????????
????????????????? ?????? ??????? ???? 300 ??
(Shimoni et al, 2005) ????????? ???????????
?????????? ?? ???????? 1.3103 ??./???2
(Albertsson et al, 2001)
???????? ???????? ?????????? ?????? -???????
??????????? ??????? - 322?322 ??2 -??????????
??????? Pc ? cytf -270 ?? -?????????? ?????
?????????? 10 ?? -?????????? cytf ????????????
???????? ? ???????????? ? ??? ??????????
????????? Pc-cytf
28
The model
After the simulation is done, we need to estimate
the rate of protein complex formation rate
Reaction rate
k
Reaction that we simulate P1P2 P1P2
V kP1P2
We estimate k by fitting
The result of multiparticle direct simulation
Simulated curve
Concentration of P1P2
Fitted curve according to mass action law
P 0.01 r lt 1 ?? treac gt trand Slow reaction
Time
29
?????? ?????????????? Pc-cyt f ? ?????? ?????????
??????????? ????????? ???????? ??????? ????? Pc ?
cytf ? ?????? ????????? ?? ?????????? ?????
??????????
P 0.01 r lt 1 ?? treac gt trand Slow reaction
????? ???????? ????????? ??????????? ?? ????????
z
(??????? ??????? ????????? 322?322 ??2,
?????????? ??????? Pc ? cytf270 ??)
30
????????????? ????????? ???????????? ??????
??????? ???? ??????? ? ??????? ?????? ???????????
????
P 1 r lt 10 ?? treac lt trand Fast reaction
31
?????????? ????????

• ???????????? ???????? ? ????????? ????????, ?????
  5 ??????????? ????? ?????? ?????????

32
??????? ???????????? ???????? ? ?????? ?
????????? ????????
33
??????? ???????????? ???????? ? ?????? ?
????????? ????????
34
?????? ???

• ?????????? ??????????????? ??? ? ??????????? ??
  ???????

35
???????? ? ????????????? ????????????
?????????????????
?6?
??????????? ????????? (??? ?????????????? ???????)
36
???? ? ???????????? ??????
N
2000 1500 1000 500 10
0 4 8 12
16 t
37
(No Transcript)
38
????????
39
????????? ???? ????????
40

• Galina Riznichenko Evgeny Grachev
• Natalia Beljaeva Pavel Gromov
• Ilia Kovalenko
• Dmitry Ustinin
• Anna Abaturova
• Tatjana Plusnina
• Nastja Lavrova
• Vladimir Paschenko
• Petr Noks