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Дата изменения: Wed Oct 24 19:28:42 2007
Дата индексирования: Mon Oct 1 20:17:54 2012
Кодировка:

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

, . -, . , . . , - MNDO PM3 . ( ) . PRECISE NOMM . , , , , , . , N-H [5] . , , . . ,
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. , . , - , . , : , , , , .
1. ( , )
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1 1 1 1 1 1 0

. . . . . . .

00 45 08 51 20 36 96

1 7 1 4 3 4 6

0. 1. 1. 1. 1. 1. 0.

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NCC CC=O CC-O CO-H CNH CCH HNH HCH NCH

113. 126. 110. 112. 113. 107. 110. 107. 110.

28 41 62 28 27 87 29 04 27

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. . 1. . , , c . . , 1 [6] . , 901

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

. 2. , Hof (298.15 ) 2. [712]. .
2. (Hof) 20 L-
. . Gly Ala Val Leu Ile Phe Tyr Trp Ser Cys PM3 -95.968 -101.1 -110.015 -116.786 -115.032 -71.8732 -117.929 -54.8358 -141.146 -91.0534 -93.3 -99.1 -108.78 -116.34 -74.8 . . Glu Asp Gln Asn Arg His Met Pro Tre Lys PM3 -193.575 -188.069 -142.623 -136.872 -101.733 -66.2796 -102.199 -100.645 -146.992 -110.487

-98.83 -87.52

: 1) , Glu, Asp, (180/190 /) 2) OH-, Gln, Asp, Ser, Thr, (115/ 143 /) 3) , Gly, Ala, Leu, Ile, (93/112 /) 4) , Phe, Trp, Tyr, His (52/70 /). . 3. , ,
902

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-- , ' = Ic (Ia + Ib). ( Ic(a,b) -- ) [13]. . , , .. , «» , -- , (. 1).
- ' 300 250 200 150 100 50 0 Ile Phe Ty r Trp Met Pro Thr Ly s Gln Asn Arg His Gly Ala Va l Leu Ser Cy s Glu Asp

. 1. (') 20 L-

, , ' = -200.0 (u·е2). , «» , , ' = 30.0 (u·е2). 4. , , , , . , , ,
903

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

. , , , (. 3). , , , , , 1.0 D (). , , .. , ( , .), 2 , (, ..).
3. () - 20 L- . . . . Gly 1.03026 10.52817 Glu 5.06432 9.60867 Ala 1.10794 10.26942 Asp 4.04556 8.52295 Val 2.19506 10.12114 Gln 6.08022 10.59024 Leu 2.43389 10.22481 Asn 3.38476 8.23761 Ile 2.26971 10.07875 Arg 2.25159 13.20473 Phe 1.09337 10.42243 His 2.93442 8.54344 Tyr 2.81399 10.24546 Met 1.05073 10.14214 Trp 3.59592 11.73135 Pro 1.58181 10.65372 Ser 0.78912 9.15332 Tre 2.03808 9.27117 Cys 1.31203 8.64691 Lys 1.33412 10.9495

5. , , , - , , . , , , . , , ,
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S0 . 4, , , 20 L. , -, ( ), -, . , S0 , .. , (. 4).
4. () (1) (S0) - (ZI)
.. Gly Ala Val Leu Ile Phe Tyr Trp Ser Cys Glu Asp Gln Asn Arg His Met Pro Tre Lys 1 47.26 40.31 52.93 38.07 51.74 28.79 29.22 33.65 37.28 35.86 39.96 41.43 48.81 36.89 20.88 32.16 30.44 28.76 45.61 34.83 2 234.02 168.3 70.93 52.04 61.61 36 36.76 39.37 88.14 68.73 71.82 81.01 85.67 50.68 27.3 40.98 38.29 47.69 85.65 42.88 3 257.19 225.76 172.83 99.97 129.46 46.9 48.05 67.81 202.96 179.65 84.17 134.24 122.64 68.64 40.48 54.79 56.81 98.88 162.6 49.27 S0 76.0873 83.01 94.8681 102.6758 100.3409 108.7924 114.8393 117.0938 88.5751 92.5332 100.7194 94.7338 99.8991 95.9226 128.2829 105.2406 110.1749 90.711 93.9593 113.0279 1 Z-I 86.22 60.4 43.11 49.84 60.64 38.29 34.86 36.45 60.93 43.21 43.51 43.96 24.80 44.99 20.59 29.56 28.41 60.10 60.94 40.38 2 Z-I 259.29 178.1 85.13 63.70 83.30 67.57 47.38 49.94 93.07 77.05 52.63 70.35 48.58 71.6 27.82 47.50 48.97 97.10 74.10 51.00 3 Z-I 410.12 242.3 181.5 97.40 116.16 86.58 58.54 67.65 198.42 124.98 62.77 82.7 86.15 85.21 51.51 58.71 61.88 142.76 165.10 55.91 S0 Z-I 75.47 82.68 93.57 100.48 98.77 106.54 112.47 115.71 86.15 91.23 99.24 93.01 98.42 94.61 126.87 104.37 108.49 85.602 92.08 111.14

905

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

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. . . -- -- 2005, . 3, . 899 907 Kondratiev M. S. et. al. -- MCE -- 2005, vol. 3, p. 899 907

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125 117 117 110 112 110 111 1.27 1.26 1.53 1.51 1.42 1.49 129.7 111.0 119.0 110.7 111.1 104.5 113.0 1.26 1.22 1.62 1.52 1.41 1.5

O1-C1-O2 O1-C1-C2 O2-C1-C2 C1-C2-N

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129.0 119.7 111.3 104.9

O1-C1-O2 O1-C1-C2 O2-C1-C2 C1-C2-C3 C1-C2-N N-C2-C3

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129.0 119.7 111.3 111.07 104.13 112.8

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,

,

C1-O1 C1-O2 C1-C2 C2-N

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

.
6. PM3- (Hof) (/) - 20 L- . . . . Gly -95.968 -62.5298 Glu -193.575 -164.09 Ala -101.1 -70.4641 Asp -188.069 -160.873 Val -110.015 -79.5009 Gln -142.623 -117.058 Leu -116.786 -87.1837 Asn -136.872 -112.037 Ile -115.032 -85.6522 Arg -101.733 -72.1468 Phe -71.8732 -43.4233 His -66.2796 -36.6984 Tyr -117.929 -89.5306 Met -102.199 -70.9219 Trp -54.8358 -27.1227 Pro -100.645 -67.634 Ser -141.146 -112.974 Tre -146.992 -118.217 Cys -91.0534 -61.6912 Lys -110.487 -80.7853

. , - . (). , 3 , 20 L- - - CO N (. 2).

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, . . - . , 1, . 2. , , ( 2, . 2). -- . , , , -. , , , 12 / . . 2. 5 6. - . , (.. ) . , , . . , . , - .
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8. , Part 8. Mathematical methods in biology, ecology and chemistry

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

. 3. - , 7 L

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600. Protein Data Bank [21], [22], (. 4). , , -.

Gly +

Gly - 1BDE

Ala - 1BDE . 4. 3 - PDB ( , H C) Ala +

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

.
1) ( ) ( 25%) , , . 2) , , () . , , , S0 , , 128.3 (/) 113.0 (/). , , S0 80 (/). 3) ( , ). - ( ) , . 4) 2 . , -. 12 / , -. - , , , -. 5) - , «» , . - 40 .
914

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: 1. ., ., ., ., ., . : 3- . . .-- .: , 1994. 2. .., .. . -- .: «», 2002. 3. Pauling L., Corey R.B. The structure of proteins: Two hydrogenbonded helical configurations of the polypeptide chain // Proc. Nat. Acad. Sci. US. 1951. V.37. P.205211. 4. .. . 5- . .3. . -- .: , 1997. 5. Brown, R.D., Godfrey, P.D., Kleybomer, B.K. The Conformation of Formamide // J. Molec. Spectroscopy. 1987 V.124. P.3435. 6. Sellers H.L., Schafer L. Investigations Concerning the Apparent Contradiction between the Microwave Structure and the ab Initio Calculations of Glycine // J. Am. Chem. Soc. 1978. V.78. P.77287729. 7. Cox J. and Pilcher G. Thermochemistry of Organic and Organometallic Compounds. Academic Press, New York, NY, 1970. 8. Ngauv S., Sabbah.R., Laffitte.M. Thermodynamique de composes azotes. III. Etude thermochimique de la glycine et de la L--alanine // Thermochim. Acta. 1977. V.20. P.371380. 9. Sabbah R., Laffitte M. Thermodynamique de composes azotes. IV. Etude thermochimique de la sarcosine et de la L-proline // Bull. Soc. Chim. Fr. 1978 V.1. P.5052. 10. Sabbah R., Laffitte M. Enthalpy of formation of solid L-proline // J. Chem. Thermodyn. 1978. V.10. P.100102. 11. Sabbah R., Minadakis C. Thermodynamique de substances soufrees. II. Etude thermochimique de la L-cysteine et de la Lmethionine // Thermochim. Acta. 1981. V.43. P.269277. 12. NIST http://webbook.nist.gov 13. . . . .-- .: , 1969. 14. .. . -- .: , 1966. 15. Wright L.R., Borkman R.F. Ab Initio Self-Consistent Field Calculations on Some Small Amino Acids // J. Am. Chem. Soc. 1980. V.102. P.62076210. 16. .., .. // . 2001. .35. 3. .451461.
915

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

17. ., . . 3- . .: , 1982. 18. Papoian G.A., Ulander J., and Wolynes P.G. Role of Water Mediated Interactions in Protein-Protein Recognition Landscapes // J. Am. Chem. Soc. 2003. V.125. P.91709178. 19. Papoian G.A., Ulander J., Eastwood M.P., Luthey-Schulten Z., and Wolynes P.G.Water in protein structure prediction // Proc. Nat. Acad. Sci. US. 2004. V.101. P.33523357. 20. Levy Y. and Onuchic J.N. Water and proteins: A love-hate relationship // Proc. Nat. Acad. Sci. US. 2004. V.101. P.33253326. 21. Berman H.M., Westbrook J., Feng Z., Gilliland G., Bhat T.N., Weissig H., Shindyalov I.N., Bourne P.B. The Protein Data Bank // Nucleic Acids Research. 2000. V.28. 1. P.235242. 22. Yao S., Azad A.A., Macreadie I.G., Norton R.S. ( ). 1999.

SOME ASPECTS OF STRUCTURE AND CONFORMATION LABILITY OF NATURAL L-AMINO ACIDS AND MODEL OLIGOPEPTIDES Kondratiev M. S., Samchenko A. A., Komarov V. M., Kabanov A. V.
(Russia, Pushchino)

On the basis of semi-empirical quantum-chemical calculations the organization of the form of neutral amino acids and their zwitterions, and also of short peptides in gas phase and in water environment is discussed. A special attention is given to the role of the structural and thermodynamic factors in definition of the preferable isomeric forms of amino acids in spiral organization of single oligopeptide chains.

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