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Дата изменения: Wed Oct 24 19:28:32 2007
Дата индексирования: Mon Oct 1 20:18:21 2012
Кодировка:

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

, , , . - , , . , ; [1]. , , [2]. . I, Q, [3]. - - pH. «» , . , [4]. , , , , [510]. ,
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. . . -- -- 2005, . 3, . 923 925 Saburova E. A. et. al. -- MCE -- 2005, vol. 3, p. 923 925

. , : . 4, 5, 6, 7, 8, , . , , . -- , [1113]. , . . - , -, PDB [14, 15]. «MOLMOL 2.5.1» . [0.5, +); (0.5; +0.5), -- (; 0.5]. , : . - [4] [1113] [510] (. . 1).
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8. , Part 8. Mathematical methods in biology, ecology and chemistry

, , .. , : His = 6.6, Glu 4.5, Asp 4.5 [4]. , , . , . , , , , , , . , , 3 % . . , , .. 5.5 е . , .. [16], , , , 7 е. , , [17]. , , . . 1 4 , . , 5.5 е. . 1, -- , .
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. . . -- -- 2005, . 3, . 923 927 Saburova E. A. et. al. -- MCE -- 2005, vol. 3, p. 923 927

. . 2, 3 4.

. 1. () () 5.5 е. - ; 4, 0.1. , PDB .

, 1. , , Asp, Glu . Glu35 , , 1.3 . .

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

. 2, 3 , , 8 (. His 15 5.68 His 12 5.83 , . . 2). Asp 66 2.62 His 119 6.25 Asp 48 3.11 His 48 6.44 Asp 119 3.11 His 105 7.10 2. Asp 87 3.14 Asp 14 2.62 Asp 52 3.49 Asp 83 3.11 Asp 18 3.52 Asp 38 3.81 4, 5, 6, 8. Asp 101 4.18 Asp 121 3.92 2 . Glu 7 3.74 Asp 53 3.95 Glu 35 5.87 Glu 86 3.76 . Glu 2 3.84 Glu 49 4.34 8 Glu 111 4.37 Glu 9 4.56 , -- pI 10 11 . , . [2]. , , , , , , , . - -- -- .
, [8]

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. 2. . (0.5, +); -- (0.5; +0.5), -- (; 0.5]

. 3.

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

. 23 2, , . ( ) S S0. Glu Asp (. . 2), 4. 68 -- . 2, S S0 .
2. S S0 . f S0/ S
4.0 6.0 8.0 4.0 S0 , е
2

S

,

е2

f 1.7 1.4 1.4 1.01 1.05 1.06 1.01 1.03 1.03 1.5 1.7 1.4 1.02

1537.66 978.45 170.44 645.71 193.35 53.46 414.77 50.66 21.55 2340.19 985.41 378.07 356.54; 192.22; 645.81 318.12 16.46 155.2; 195. 6; 173.8; 339.8 169.2; 112.3 ---------

6.0

893.11 695.03 124.44 641.37 182.76 50.34 412.68 49.01 20.8 1595.9 574.39 270.05 348.31; 186.11; 481.76 175.15; 135.9 -----155.2; 195. 6; 173.8; 339.8 169.23; 112.33 ----------

8.0

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. , , (35). 6 . , . , , , , . , , . : 1. ., ., .., .., .., C .. // . 1999. .44. 5. .813820. 2. .., .., .., . . // . 2000. .65. 8. .11511161. 3. ., .., .., .. // . 2005 ( ). 4. ., . . .: «», 1984. 336. 5. Yang A.S., Gunner M.R., Sampogna R., Sharp K., Honig B. On the calculation of pKas in proteins // Proteins. 1993. .15. 3. .25265. 6. Antosiewicz J., McCammon J.A., Gilson M.K. The determinants of pKas in proteins // Biochemistry. 1996. .35. 24. .781933. 7. Elcock AH. Realistic modeling of the denatured states of proteins allows accurate calculations of the pH dependence of protein stability // J. Mol. Biol. 1999. V.294. 4. .10511062.
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8. , Part 8. Mathematical methods in biology, ecology and chemistry

8. Mehler E.L., Guarnieri F. A self-consistent, microenvironment modulated screened coulomb potential approximation to calculate pH-dependent electrostatic effects in proteins // Biophys J. 1999. V.77. 1. .322. 9. Fitch C.A., Karp D.A., Lee K.K., Stites W.E., Lattman E.E., Garcia-Moreno E.B. Experimental pK(a) values of buried residues: analysis with continuum methods and role of water penetration // Biophys J. 2002. V.82. 6. .32893304. 10. Mehler E.L., Fuxreiter M., Simon I., Garcia-Moreno E.B. The role of hydrophobic microenvironments in modulating pKa shifts in proteins // Proteins. 2002. V.48. 2. .283292. 11. Antosiewicz J., McCammon J.A., Gilson M.K. Prediction of pHdependent properties of proteins. //J. Mol. Biol. 1994. V.238. .415436. 12. Bartik K., Redfield C., Dobson C.M. Measurement of the individual pKa values of acidic residues of hen and turkey lysozymes by twodimensional NMR // Biophys. J. 1994. V.66. P.11801184. 13. Kuramitsu S., Hamaguchi K. Analysis of the acid-base titration curve of hen lysozyme // J. Biochem. 1980. V.87. P.12151219. 14. Dung M.H., Bell J.A. Structure of crystal form IX of bovine pancreatic ribonuclease // Acta Crystallogr. 1997. V.53. P.419. 15. Ramanadham M., Sieker L.C., Jensen L.H. Refinement of triclinic lysozyme: II. The method of stereochemically restrained least squares // Acta Crystallogr. 1990. V.46. P.63. 16. Sivozhelezov V.S. Interpretation of Ionic Strength Dependencies of the Electron Transfer in the Cytochrome cCytochrome b5 System for the Wild-type and Lysine-mutated Yeast Cytochrome c // Molecular Engineering. 1996. V.6. 4. .405414. 17. Dzhelyadin T.R., Sorokin A.A., Sivozhelezov V.S., Ivanova N.N., Polozov R.V., Kamzolova S.G. New approach in studying RNA polymerase-promoter recognition code // J. Biomol. Struct. Dyn. 2001. V.18. P.922923.

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THE APPLICATION OF CALCULATIONS OF THE ELECTROSTATIC FIELD OF PROTEINS IN THE CHOICE OF ENZYMES FOR MICROCAPSULATION Saburova E. A., Dybovskaya Yu. N., Avseenko N. V., and Sivozhelezov V. S.
(Russia, Puschino)

In the development of enzyme polyelectrolyte microreactors, some properties of enzymes, e. g., the isoelectric point of the protein pI, i. e., the value of its full charge Q, should be taken into account. However, of particular importance is exact knowledge of the distribution of the electrostatic potential on the surface of the protein. This paper is devoted to the calculation of the distribution of the electrostatic potential of some proteins with consideration of the local microenvironment for every charged amino acid residue and accordingly a change in the value. The distribution of the electrostatic potential of ribonuclease A and lysozyme was calculated at different values 4,5, 6, 7 and 8, using both standard values and values corrected for local microenvironment for every titrated amino acid residue of the protein. A comparison of these calculations showed that taking the microenvironment of amino acid residue into account changes the distribution of the electrostatic potential of enzymes in the limited range (35). The areas of regions with the corresponding distribution of the electrostatic potential on the protein surface that are capable of binding to the polyelectrolyte were calculated.The analysis of the distribution of the electrostatic potential in the range 58 of these proteins showed that the correction for the change in the values does not appreciably affect the distribution of the electrostatic potential and that it can be neglected when constructing permolecular complexes.

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