Документ взят из кэша поисковой машины. Адрес оригинального документа : http://www.cosmos.ru/seminar/tarusa2009_3/20090604/Lujkov.pdf Дата изменения: Fri Jun 5 18:50:00 2009 Дата индексирования: Fri Oct 16 23:55:31 2009 Кодировка: Поисковые слова: m 1

, ,




, ,


- -




(A)

() () «--»

( )




M. Levitt, Nature Structural Biology, 2001



: NPT, NVT , RMSD,

1700 , 2Cl-, 5475 H2O (Rw~35 е)

- :
=300,t=10 ps, s te p s : MD=2fs, trj= 40fs




p ( i ) = e
Q
NVT

- H ( i )

/Q
d

= e

- H ( )

- i ( )

Y ( ) = p ( )Y ( )d

& H ( ) = T ( X ) + U ( X )

,

= 1 / kT



e

- ( H ( )- A)

d = 1

A = E - TS
- : , ,

ln Q )V , N T ln Q S = kT ( ) V , N + k ln Q T E = kT 2 (


. 1.

A=-

1



ln e

(

- H ( )

d =

)

1



ln e

(

+ H ( )

p( )d + const

)

, thermodynamic integration. . , . ­ 1930-

A( A( = 1) - A( = 0) = 0
1

) d =

...

A( ) 1 Q ( ) =- ... Q

=


0

1

H ( , )

d


SC-TI, MC-TI


. 2.

(-1933, -1951)

A2 = - - =- 1

1



ln(Q2 ) =
- (U 1 ( ) + U 21 ( ))



ln e

(

= A1 + U 21 ( ) 1 -


2

(

Q ' ' Q ' 2 Q' 1 d = - ln (Q1 ) + 1 + 1 - 1 ... = Q1 2Q1 Q1

)

U ( ) - U 21 ( )
2 21 1

2 1

)

+ ...


. 3.

, free energy perturbation (FEP). . - 1954

Q2 = Q1 e e

- U 2 ( ) - U1 ( )

d d

=



e

- U 21 ( ) - U 1 ( )

e

d



e

- U 1 ( )

d

=e

- U 21 ( ) 1

Q2 1 A2 - A1 = - ln = - ln e Q1 1

- U 21 ( ) 1


(FEP)

A2 - A1 = - =- 1

1



ln e

- (U 2 ( ) -U1 ( )) 1 ) -U ( ,m )) m

=
U
1




m =1

n -1

ln e

- (U ( ,

m +1

U
= 0 .5

2

= 0. 75
= 1. 0

U ( , m ) = (1 - m )U 1 ( ) + mU 2 ( )

= 0.25

m = 0 1, m = 1,..., n
= 0.0

R

direct

1

2

3

n-1

n

reverse


. 4.



,overlap sampling. - 1976

Q2 = Q1 We

We

- U 2 ( ) 1 - U1 ( ) 2

,

min(var( ( A2 - A1 )))

( A2 - A1 ) = ln

f (U 1 ( ) - U 2 ( ) + C

f (U 2 ( ) - U 1 ( ) - C

) )

2 1

+C

,

f ( x ) = 1 /(1 + e x )
Q n C = ln 1 2 Q n 21


.

Ca++ OW(TIP3P) SCAAS model, R(water)=19е

«-» 1- FEP


FEP/MD

GbAin
R R...A A
d

G G

bi nd

G = G

B bi nd R mut R ,W B

- G - G

A bi nd

= =
A

R ,W mut

= G

- G

W mut R ,W A

G
R

W mut

G
B

R mut

R...B

= -kT ln e

-(U B ( X ) -U A ( X )) / kT

GbBin

d

: - - ,

A
HH XCCH HH H H

B
d d d XNH


1998: c KcsA

17.6 kDa Streptomyces lividans

· ·

Schrempf et al. The EMBO J. 14 (1995) 5170. Doyle, MacKinnon, et al. Science 280 (1998) 69.


KcsA

· · · ·

еqvist J. Luzhkov Luzhkov Luzhkov

and V.B. V.B. V.B.

Luzhkov V. and еqvist and еqvist and еqvist

B. J. J. J.

Natur BBA BBA BBA

e 404 1481 1548 1747

(2000) (2000) (2001) (2005)

881. 360. 194. 109.










Gbind = (Vl

vdw

-s



bound

- Vl

vdw

-s



free

) + (Vl - s
el

bound

- Vl - s
el

free

)



H H C H

H H HH C HH HCCNCCH HH HH C H H C H H H

g- CH3
N CH3

g+

Luzhkov et al., Phys.Chem.Chem.Phys. 4 (2002) 4640.


D2d KcsA

Y82

TEA

Y82

D2d T KcsA (1000 ps )
Cz Y82 Cz Y82

Cz Y82

K+

Cz Y82

Luzhkov et al., FEBS Letters (2003) v.554, p.159.



-79.9
H HNH H

-52.

HHH 1H C H HCNCH H H C HHH

-

HH HC H H HHC H H C HCC HH HCNCH H H HH CCH C H CHHH H 37.2 H C H H H

-

HH HC H HH H C H HC HCNCH H CH C H CHHH H H 43.7 H

(/) (D2d)

(Amber)


- KcsA

IC50, mM

TMA

TEA

T Pr A

300 -0.7 (3.0)

2.0 -3.7 (0.0)

50 -1.8 (1.9)

(AutoDock)

-3.0

-5.1 (D2d) -4.6 ( S4 )

-5.5 ( D2d ) -5.0 ( S4 )

(FEP/MD)

2.44

0.00 (D2d) 3.79 ( S4 )

1.64 (D2d) 4.54 ( S4 )

Luzhkov et al., FEBS Letters (2003) v.554, p.159.


Kv1.2 Kv1.5
O NC H H N

O O N H O

H N


Kv1.5 "PVP­"
PVP-





Gb
4.0 /-0.7 -4.3 /-5.3 -7.2 /-9.0

in d

kcal/mol


Internal complexes of bupivacaine and TEA with potassium channels

Experiment: Gbind = -7.4 kcal/mol Calculation: Gbind = -3.3 - -9.0 kcal/mol

Experiment: Gbind = -4.8 kcal/mol Calculation: Gbind = -2.1 - -7.2 kcal/mol

Luzhkov V.B., Nilsson J., еrhem P., еqvist J. BBA 1652 (2003) 35.

Luzhkov V.B., еqvist J. FEBS Letters 495 (2001) 191.



. , , FEP ,