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Дата изменения: Wed Oct 24 19:28:16 2007
Дата индексирования: Mon Oct 1 20:19:22 2012
Кодировка:

F . ., . ., . ., . ., . ., . . . .
(, )

- . , [10, 9] . f ( ) . f.

. . ( ) . 1, 2, b6f -. 1 b6f . , -- (. 1).

8. , Part 8. Mathematical methods in biology, ecology and chemistry

. 1. . . 1, 2, b6/f . (), (PQ).

f 1, ( ) [11, 4, 3]. (410 [6]) (402830 е). [5]. , : , .

956

. . . -- -- 2005, . 3, . 955 957 Kovalenko I. B. et. al. -- MCE -- 2005, vol. 3, p. 955 957

, , , , -- . (, ). f ( ) . . . , [10]. . . Pc cyt f , , , f (. 2). . , , - , . [8], , .
957

8. , Part 8. Mathematical methods in biology, ecology and chemistry

. 2. f .

: x dx tr = f x (t ) + Fx , dt x -- , x , tr -- , fx(t) Fx -- x, . : d x ro t = m x (t ) + M x ,
dt

x rot -- x, mx(t) Mx -- x, . fx(t) x 2kT tr . k -- , T , t -- . f 2a, 2b 2c (2a -- , b = c). Protein Data Bank. , ( 2a) . (. 3).

958

. . . -- -- 2005, . 3, . 955 959 Kovalenko I. B. et. al. -- MCE -- 2005, vol. 3, p. 955 959

[1]:
a tr =

8 R ( p 2 - 1)
3

3/ 2

p [(2 p 2 - 1) ln( p + p [(2 p 2 - 3) ln( p +

p 2 - 1) - p p 2 - 1]
3/ 2

,

b tr =

16 R ( p 2 - 1)
3

p 2 - 1) + p p 2 - 1]
3/ 2

,

a rot

= =

16 R 3 ( p 2 - 1)

3 p [ p p 2 - 1 - ln( p + 16 R 3 ( p 2 - 1) 3 p [(2 p 2 - 1) ln( p +

p 2 - 1)]
3/ 2

,

b rot

( p 2 + 1)

p 2 - 1) - p p 2 - 1]

.

a b a b tr , tr rot , rot -- a b , , -- , 2a -- ,

b = c, p = a / b , R = 3 a * b * b . ( ) . . (.. -- ) () . . , . , : .

959

8. , Part 8. Mathematical methods in biology, ecology and chemistry

. 3. () f ()

. , . - , () . . , , . (1050) , , , , , ( , ) -- . . () [3, 5, 12]. . , . 960

. . . -- -- 2005, . 3, . 955 961 Kovalenko I. B. et. al. -- MCE -- 2005, vol. 3, p. 955 961

, , . =2 . = 80 (). ( 100 е) - . , . , , . ( ) pH . , . 2 е. , . MacroDox. , , 2; 80; - 40; . (1), - (2) [7]:
961

8. , Part 8. Mathematical methods in biology, ecology and chemistry

. n-

0 =

(

(
6

i =1

h ii + 4 q0 h
i

6
i =1

) )+

h3

2 0

, 2 =

8 N A e2 I I= k BT

1 2

i =1

K

cibulk Z

2 i

= -4 + 2

(2)

-- , -- , -- bulk -- i- , i , Zi -- i-, e -- , T -- , NA -- , I -- , h -- . . 4 . . , ( ) . , , , , , . , . , , , .

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. . . -- -- 2005, . 3, . 955 963 Kovalenko I. B. et. al. -- MCE -- 2005, vol. 3, p. 955 963

. 4. 6.5 +6.5 f 300 M, pH = 7, - = 80

. . , , . f . - . , . f, , - . , f. 1, -- . , [5] f 25 е.
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8. , Part 8. Mathematical methods in biology, ecology and chemistry

. f . 100 1000 . . 5 [2] f . 0.02, 100 , 14 е. .

. 5. f . -- , -- [2]

. f, , - , f. . f.
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, . 1 .

. .. .
, 03-0449048 04-07-90278.

: 1. Bloomfield V.A. Chapter 1. Survey of Biomolecular Hydrodynamics // On-Line Biophysics Textbook. Separations and Hydrodynamics. / Edited by T. M. Schuster, 2000. 2. Crowley P., Hunter D., Sato K., McFarlane W., Dennison C. The complex of parsley plastocyanin and turnip cytochrome f -- a structurally distorted but kinetically functional acidic patch. // Biochem. J. 2003. V.1423. 3. Gross E. L. Plastocyanin: structure, location, diffusion and electron transfer mechanisms // Biochemistry & Molecular Biology of Plants. V. V. / Edited by R. Jones, Kluwer Academic Publishers, 1996. P.413429. 4. Hope A.B. The chloroplast cytochrome bf complex: a critical focus on function // Biochim. Biophys. Acta. 1993. V.1143. P.122. 5. Hope A.B. Electron transfers amongst cytochrome f, plastocyanin and photosystem I: kinetics and mechanisms // Biochim. Biophys. Acta. 2000. V.1456. P.526. 6. Mehta M., Sarafis V., Critchley C. Thylakoid membrane architecture // Aust. J. Plant Physiol. 1999. V.26. P.709716. 7. Ullmann G.M. Macromolecular Electrostatics -- University Heidelberg, 2004. 8. , -- .: , 1999. 9. .., .., .., .., .., .., .. 1 // .
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8. , Part 8. Mathematical methods in biology, ecology and chemistry

". . ". -- . : - " ", 2004. 10. . ., . ., . ., . ., . ., . ., .., . . 1 // . 2003. .48. 4. .656665. 11. .., .. . -- .: - . -, 1992. 12. . . -- .: "", 2000.

DIRECT SIMULATION OF INTERACTION OF THE PROTEINS PLASTOCYANIN AND CYTOCHROME F Kovalenko I. B., Abaturova A. M., Gromov P. A., Ustinin D. M., Grachev E. A., Riznichenko G. Yu., Rubin A. B.
(Russia, Moscow)
The paper is devoted to a novel approach for direct computer simulation of protein diffusion and interaction in a 3D space. The interacting molecules are considered as rigid bodies with spatial fixed partial charges. We consider 3D translational and rotational Brownian motion of proteins and electrostatic interactions. This approach is a further development of the method of direct 3D simulation of electron transport in photosynthetic membrane [1, 2]. We built a 3D computer model for the interaction of mobile electron carrier protein plastocyanin with cytochrome f, one of the subunits of cytochrome bf complex, in solution. Using this model we studied the dependence of the kinetic parameters of protein-protein interactions on the ionic strength.

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