Issues

 / 

2012

 / 

December

  

Reviews of topical problems


Proteins as specific polar media for charge transfer processes


Institute of Physical Chemistry and Electro Chemistry, Russian Academy of Sciences, Leninskii prosp. 31, Moscow, 119991, Russian Federation

A great many of biological processes involve the transfer of charged particles: electrons and protons. The electrostatic interaction of a moving charge with its surroundings, primarily with protein, is the major factor determining the thermodynamics and kinetics involved. This paper treats protein as a pre-organized highly-polar low-dielectric medium that possesses a pre-existent intraprotein electric field, a low reorganization energy, and a wide range of dielectric relaxation times. These specific protein features are the factors controlling the catalytic acceleration of biochemical reactions. Methods for quantitatively calculating the energetics of a number of typical processes are considered, and examples of their application are given.

Fulltext pdf (1.2 MB)
Fulltext is also available at DOI: 10.3367/UFNe.0182.201212b.1275
PACS: 87.10.−e, 87.14.E−, 87.15.−v (all)
DOI: 10.3367/UFNe.0182.201212b.1275
URL: https://ufn.ru/en/articles/2012/12/b/
000315989900002
2012PhyU...55.1192K
Citation: Krishtalik L I "Proteins as specific polar media for charge transfer processes" Phys. Usp. 55 1192–1213 (2012)
BibTexBibNote ® (generic)BibNote ® (RIS)MedlineRefWorks

Received: 13th, December 2011, revised: 1st, February 2012, 7th, February 2012

Оригинал: Кришталик Л И «Белки как специфическая полярная среда процессов переноса заряда» УФН 182 1275–1300 (2012); DOI: 10.3367/UFNr.0182.201212b.1275

References (196) ↓ Cited by (4) Similar articles (20)

  1. Schaefer M, van Vlijmen H W T, Karplus M Adv. Protein Chem. 51 1 (1998)
  2. Simonson T Curr. Opin. Struct. Biol. 11 243 (2001)
  3. Shurki A, Warshel A Adv. Protein Chem. 66 249 (2003)
  4. Simonson T Rep. Prog. Phys. 66 737 (2003)
  5. Olsson M H M, Parson W W, Warshel A Chem. Rev. 106 1737 (2006)
  6. Gunner M R et al. Biochim. Biophys. Acta (BBA) Bioenerg. 1757 942 (2006)
  7. Koehl P Curr. Opin. Struct. Biol. 16 142 (2006)
  8. Simonson T Photosynthesis Res. 97 21 (2008)
  9. Ullmann G M et al. Photosynthesis Res. 97 33 (2008)
  10. Kamerlin S C L, Haranczyk M, Warshel A J. Phys. Chem. B 113 1253 (2009)
  11. Marcus R A Annu. Rev. Phys. Chem. 15 155 (1964)
  12. Dogonadze R R, Kuznetsov A M Kinetika Khimicheskikh Reaktsii v Polyarnykh Rastvoritelyakh (Itogi nauki i tekhniki. Ser. Fizicheskaya khimiya. Kinetika) Vol. 2 (M.: VINITI, 1973) p. 5
  13. Dogonadze R R, Kuznetsov A M Prog. Surf. Sci. 6 1 (1975)
  14. Krishtalik L I Elektrodnye Reaktsii. Mekhanizm Elementarnogo Akta (M.: Nauka, 1979)
  15. Ulstrup J Charge Transfer Processes In Condensed Media (Lecture Notes in Chemistry) Vol. 10 (Berlin: Springer-Verlag, 1979)
  16. Dogonadze R R, Kuznetsov A M Kinetics And Mechanisms Of Electrode Processes (Comprehensive Treatise of Electrochemistry) Vol. 7 (Eds B E Conway et al.) (New York: Plenum Press, 1983) p. 1
  17. Newton M D, Sutin N Annu. Rev. Phys. Chem. 35 437 (1984)
  18. Marcus R A, Sutin N Biochim. Biophys. Acta (BBA) Rev. Bioenerg. 811 265 (1985)
  19. Krishtalik L I Charge Transfer Reactions In Electrochemical And Chemical Processes (New York: Consultants Bureau, 1986)
  20. Kuznetsov A M Charge Transfer In Physics, Chemistry, And Biology. Physical Mechanisms Of Elementary Processes And An Introduction To The Theory (Luxembourg: Gordon and Breach Publ., 1995)
  21. Marcus R A Protein Electron Transfer (Ed. D S Bendall) (Oxford: BIOS Sci.Publ., 1996) p. 249
  22. Kuznetsov A M, Ulstrup J Electron Transfer In Chemistry And Biology. An Introduction To The Theory (New York: Wiley, 1999)
  23. Kuznetsov A M Stochastic And Dynamic Views Of Chemical Reaction Kinetics In Solutions (Lausanne: Presses Polytechniques et Univ. Romandes, 1999)
  24. Krishtalik L I Biochim. Biophys. Acta (BBA) Bioenerg. 1458 6 (2000)
  25. Krishtalik L I Biochim. Biophys. Acta (BBA) Bioenerg. 849 162 (1986)
  26. Perutz M F Proc. R. Soc. Lond. B 167 448 (1967)
  27. Minkin V I, Osipov O A, Zhdanov Yu A Dipol’nye Momenty v Organicheskoi Khimii (L.: Khimiya, 1968); Minkin V I, Osipov O A, Zhdanov Yu A Dipole Moments In Organic Chemistry (New York: Plenum Press, 1970)
  28. Wada A Polyamino Acids, Polypeptides, and Proteins. Proc. of an Intern. Symp., 1961 (Ed. M A Stahmann) (Madison: Univ. of Wisconsin Press, 1962) p. 131
  29. Applequist J, Mahr T G J. Am. Chem. Soc. 88 5419 (1966)
  30. van Duijnen P T, Thole B T Biopolymers 21 1749 (1982)
  31. Krishtalik L I Molekulyarnaya Biologiya 8 91 (1974)
  32. Bayley S T Trans. Faraday Soc. 47 509 (1951)
  33. Marićić S, Pifat G, Pravdić V Biochim. Biophys. Acta (BBA) Special. Sect. Biophys. Subjects 79 293 (1964)
  34. Takashima S, Schwan H P J. Phys. Chem. 69 4176 (1965)
  35. Tanaka A, Ishida Y J. Polymer Sci. Phys. Ed. 11 1117 (1973)
  36. Pethig R Dielectric And Electronic Properties Of Biological Materials (Chichester: Wiley, 1979)
  37. Gilson M K, Honig B H Biopolymers 25 2097 (1986)
  38. Nakamura H, Sakamoto T, Wada A Protein Eng. 2 177 (1988)
  39. Simonson T, Perahia D, Bricogne G J. Mol. Biol. 218 859 (1991)
  40. Simonson T, Perahia D, Brünger A T Biophys. J. 59 670 (1991)
  41. King G, Lee F S, Warshel A J. Chem. Phys. 95 4366 (1991)
  42. Smith P E et al. J. Phys. Chem. 97 2009 (1993)
  43. Simonson T, Perahia D J. Am. Chem. Soc. 117 7987 (1995)
  44. Akhadov Ya Yu Dielektricheskie Parametry Chistykh Zhidkostei (M.: Izd-vo MAI, 1999)
  45. Johannin G, Kellersohn N Biochem. Biophys. Res. Commun. 49 321 (1972)
  46. Warshel A, Levitt M J. Mol. Biol. 103 227 (1976)
  47. Krishtalik L I IFIAS Workshop (1975) on Physico-Chemical Aspects of Electron Transfer Processes in Enzyme Systems (Ed. C G Hedén) (Stockholm: IFIAS, 1977) p. 76
  48. Krishtalik L I, Topolev V V Molek. Biologiya 17 1034 (1983); Krishtalik L I, Topolev VV Mol. Biol. 17 843 (1983)
  49. Topolev V V, Krishtalik L I Molek. Biologiya 17 1177 (1983); Krishtalik L I, Topolev VV Mol. Biol. 17 963 (1983)
  50. Krishtalik L I J. Theor. Biol. 139 143 (1989)
  51. Tanford C, Kirkwood J G J. Am. Chem. Soc. 79 5333 (1957)
  52. Warwicker J, Watson H C J. Mol. Biol. 157 671 (1982)
  53. Nicholls A, Honig B J. Comput. Chem. 12 435 (1991)
  54. Bashford D, Karplus M Biochemistry 29 10219 (1990)
  55. Karplus M, McCammon J A CRC Crit. Rev. Biochem. 9 293 (1991)
  56. Frauenfelder H, Sligar S G, Wolynes P G Science 254 1598 (1991)
  57. Brooks C L (III), Karplus M, Pettitt B M Proteins. A Theoretical Perspective Of Dynamics, Structure, And Thermodynamics (New York: J. Wiley, 1988)
  58. Krishtalik L I Biochim. Biophys. Acta (BBA) Bioenerg. 1228 58 (1995)
  59. Krishtalik L I Biochim. Biophys. Acta (BBA) Bioenerg. 1273 139 (1996)
  60. Gilson M K et al. J. Mol. Biol. 184 503 (1985)
  61. Sham Y Y, Chu Z T, Warshel A J. Phys. Chem. B 101 4458 (1997)
  62. Schutz C N, Warshel A Proteins Struct. Funct. Genet. 44 400 (2001)
  63. Warshel A, Åqvist J Annu. Rev. Biophys. Biophys. Chem. 20 267 (1991)
  64. Krishtalik L I, Kuznetsov A M, Mertz E L Proteins Struct. Funct. Genet. 28 174 (1997)
  65. Mertz E L, Krishtalik L I Bioelectrochem. Bioenerg. 48 397 (1999)
  66. Simonson T, Archontis G, Karplus M J. Phys. Chem. B 103 6142 (1999)
  67. Krishtalik L I, Topolev V V Molek. Biologiya 18 712 (1984); Krishtalik L I, Topolev V V Mol. Biol. 18 581 (1984)
  68. Krishtalik L I, Topolev V V Molek. Biologiya 18 892 (1984); Krishtalik L I, Topolev V V Mol. Biol. 18 721 (1984)
  69. Sharp K A, Honig B Annu. Rev. Biophys. Biophys. Chem. 19 301 (1990)
  70. Bashford D Current Opin. Struct. Biol. 1 175 (1991)
  71. Honig B, Nicholls A Science 268 1144 (1995)
  72. Gunner M R et al. Biophys. J. 78 1126 (2000)
  73. Voigt P, Knapp E-W J. Biol. Chem. 278 51993 (2003)
  74. Papazyan A, Warshel A J. Phys. Chem. B 101 11254 (1997)
  75. Vorotyntsev M A, Kornyshev A A Elektrostatika Sred s Prostranstvennoi Dispersiei (M.: Nauka, 1993)
  76. Bopp P A, Kornyshev A A, Sutmann G J. Chem. Phys. 109 1939 (1998)
  77. Medvedev I G Electrochim. Acta 49 207 (2004)
  78. Alpatova N M i dr. Elektrokhimiya 25 1341 (1989); Alpatova N M et al. Sov. Electrochem. 25 1195 (1989)
  79. Krishtalik L I, Alpatova N M, Ovsyannikova E V Elektrokhimiya 26 429 (1990); Krishtalik L I, Alpatova N M, Ovsyannikova E V Sov. Electrochem. 26 383 (1990)
  80. Krishtalik L I, Alpatova N M, Ovsyannikova E V Elektrokhimiya 26 436 (1990); Krishtalik L I, Alpatova N M, Ovsyannikova E V Sov. Electrochem. 26 390 (1990)
  81. Krishtalik L I i dr. Elektrokhimiya 27 154 (1991); Krishtalik L I et al. Sov. Electrochem. 27 137 (1991)
  82. Krishtalik L I, Alpatova N M, Ovsyannikova E V Electrochim. Acta 36 435 (1991)
  83. Krishtalik L I, Alpatova N M, Ovsyannikova E V Elektrokhimiya 31 871 (1995); Krishtalik L I, Alpatova N M, Ovsyannikova E V Sov. Electrochem. 31 802 (1995)
  84. Bunakova L V i dr. Elektrokhimiya 40 913 (2004); Bunakova L V et al. Russ. J. Electrochem. 40 794 (2004)
  85. Bunakova L V, Khanova L A, Krishtalik L I Elektrokhimiya 41 325 (2005); Bunakova LV, Khanova L A, Krishtalik L I Russ. J. Electrochem. 41 287 (2005)
  86. Ovsyannikova E V i dr. Elektrokhimiya 25 1348 (1989); Ovsyannikova E V et al. Sov. Electrochem. 25 1201 (1989)
  87. Alpatova N M, Ovsyannikova E V, Krishtalik L I Elektrokhimiya 27 931 (1991); Alpatova N M, Ovsyannikova E V, Krishtalik L I Sov. Electrochem. 27 823 (1991)
  88. Mertz E L, Krishtalik L I Proc. Natl. Acad. Sci. USA 97 2081 (2000)
  89. Khanova L A, Topolev V V, Krishtalik L I Chem. Phys. 326 33 (2006)
  90. Pratt L R, Hummer G, Gars<>ta A E Biophys. Chem. 51 147 (1994)
  91. Hummer G, Pratt L R, Garsía A E J. Phys. Chem. 100 1206 (1996)
  92. Ashbaugh H S, Wood R H J. Chem. Phys. 106 8135 (1997)
  93. Hummer G et al. J. Phys. Chem. B 101 3017 (1997)
  94. Garde S, Hummer G, Paulaitis M E J. Chem. Phys. 108 1552 (1998)
  95. Ashbaugh H S J. Phys. Chem. B 104 7235 (2000)
  96. Grossfield A J. Chem. Phys. 122 024506 (2005)
  97. Krishtalik L I Electrochim. Acta 53 3722 (2008); Krishtalik L I "Corrigendum" Electrochim. Acta 54 4741 (2009)
  98. Ptushenko V V et al. Photosynthesis Res. 97 55 (2008)
  99. Dracheva S M et al. Eur. J. Biochem. 174 253 (1988)
  100. Semenov A Yu, Mamedov M D, Chamorovsky S K FEBS Lett. 553 223 (2003)
  101. Semenov A Yu, Mamedov M D, Chamorovsky S K Photosystem I: The Light-Driven, Plastocyanin: Ferredoxin Oxidoreductase (Ed. J H Golbeck) (Dordrecht: Springer, 2006) p. 319
  102. Ishikita H, Knapp E-W J. Biol. Chem. 278 52002 (2003)
  103. Ishikita H et al. Proc. Natl. Acad. Sci. USA 103 9855 (2006)
  104. Holzwarth A R et al. Biophys. J. 90 552 (2006)
  105. Shelaev I V et al. J. Photochem. Photobiol. B Biol. 104 44 (2011)
  106. Kuznetsov A M et al. Biochim. Biophys. Acta (BBA) Bioenerg. 1797 347 (2010)
  107. Reiss H, Heller A J. Phys. Chem. 89 4207 (1985)
  108. Pleskov Yu V J. Phys. Chem. 91 1691 (1987)
  109. Kanevskii E A Zhurn. Fiz. Khimii 26 633 (1952)
  110. Kuznetsov An M, Maslii A N, Krishtalik L I Elektrokhimiya 44 39 (2008); Kuznetsov An M, Maslii A N, Krishtalik L I Russ. J. Electrochem. 44 34 (2008)
  111. Trasatti S J. Electroanal. Chem. Interfac. Electrochem. 52 313 (1974)
  112. Frumkin A N Potentsialy Nulevogo Zaryada (M.: Nauka, 1982)
  113. Ullmann G M, Noodleman L, Case D A J. Biol. Inorg. Chem. 7 632 (2002)
  114. Krishtalik L I Chem. Phys. 319 316 (2005)
  115. Antosiewicz J, McCammon J A, Gilson M K J. Mol. Biol. 238 415 (1994)
  116. Kuznetsov A M, Ulstrup J, Vorotyntsev M A The Chemical Physics Of Solvation Pt. C (Eds R R Dogonadze et al.) (Amsterdam: Elsevier, 1988) p. 163
  117. Krishtalik L I Molek. Biologiya 13 577 (1979)
  118. Krishtalik L I J. Theor. Biol. 86 757 (1980)
  119. Krishtalik L I, Kharkats Yu I Biofizika 29 19 (1984)
  120. Kharkats Yu I, Krishtalik L I J. Theor. Biol. 112 221 (1985)
  121. Zhou H-X J. Am. Chem. Soc. 116 10362 (1994)
  122. Krishtalik L I, Topolev V V Biochim. Biophys. Acta (BBA) Bioenerg. 1459 88 (2000)
  123. Churg A K et al. J. Phys. Chem. 87 1683 (1983)
  124. Warshel A, Chu Z T, Parson W W Science 246 112 (1989)
  125. Schulten K, Tesch M Chem. Phys. 158 421 (1991)
  126. Treutlein M et al. Proc. Natl. Acad. Sci. USA 89 75 (1992)
  127. Parson W W, Chu Z-T, Warshel A Biochim. Biophys. Acta (BBA) Bioenerg. 1017 251 (1990)
  128. Zheng C, McCammon J A, Wolynes P G Chem. Phys. 158 261 (1991)
  129. Yadav A et al. J. Am. Chem. Soc. 113 4800 (1991)
  130. Marchi M et al. J. Am. Chem. Soc. 115 4178 (1993)
  131. Åqvist J, Fothergill M, Warshel A J. Am. Chem. Soc. 115 631 (1993)
  132. Muegge I et al. J. Phys. Chem. B 101 825 (1997)
  133. Simonson T Proc. Natl. Acad. Sci. USA 99 6544 (2002)
  134. Tipmanee V et al. J. Am. Chem. Soc. 132 17032 (2010)
  135. Kaila V R I et al. Proc. Natl. Acad. Sci. USA 107 21470 (2010)
  136. Krishtalik L I Molek. Biologiya 15 290 (1981); Krishtalik L I Mol. Biol. 15 229 (1981)
  137. Krishtalik L I J. Theor. Biol. 112 251 (1985)
  138. Krishtalik L I J. Mol. Catalysis 47 211 (1988)
  139. Cech T R et al. J. Biol. Chem. 267 17479 (1992)
  140. Cate J H et al. Science 273 1678 (1996)
  141. Krishtalik L I Biochim. Biophys. Acta (BBA) Bioenerg. 1807 1444 (2011)
  142. Marcus R A J. Chem. Phys. 24 966 (1956)
  143. Marcus R A J. Phys. Chem. 98 7170 (1994)
  144. Mertz E L, German E D, Kuznetsov A M Chem. Phys. 215 355 (1997)
  145. Terrettaz S et al. J. Am. Chem. Soc. 118 7857 (1996)
  146. Blankman J I et al. Biochemistry 39 14799 (2000)
  147. Liu Y-P, Newton M D J. Phys. Chem. 98 7162 (1994)
  148. Sigfridsson E, Olsson M H M, Ryde U J. Phys. Chem. B 105 5546 (2001)
  149. Berghuis A M, Brayer G D J. Mol. Biol. 223 959 (1992)
  150. Berghuis A M et al. J. Mol. Biol. 236 786 (1994)
  151. Qi P X, Beckman R A, Wand A J Biochemistry 35 12275 (1996)
  152. Bertini I et al. FEBS Lett. 415 45 (1997)
  153. Bertini I et al. J. Magn. Reson. 147 1 (2000)
  154. Gray H B, Winkler J R Annu. Rev. Biochem. 65 537 (1996)
  155. Gray H B, Winkler J R Quart. Rev. Biophys. 36 341 (2003)
  156. Mines G A et al. J. Am. Chem. Soc. 118 1961 (1996)
  157. Farver O, Pecht I Biophys. Chem. 50 203 (1994)
  158. Olsson M H M, Ryde U, Roos B O Protein Sci. 7 2659 (1998)
  159. Gamelin D R et al. J. Am. Chem. Soc. 120 5246 (1998)
  160. Kümmerle R et al. J. Biol. Inorg. Chem. 6 446 (2001)
  161. Krishtalik L I Biochim. Biophys. Acta (BBA) Bioenerg. 977 200 (1989)
  162. Vos M H et al. Biochemistry 39 8353 (2000)
  163. Shuvalov V A, Yakovlev A G FEBS Lett. 540 26 (2003)
  164. Woodbury N W T, Parson W W Biochim. Biophys. Acta (BBA) Bioenerg. 767 345 (1984)
  165. Woodbury N W et al. Biochim. Biophys. Acta (BBA) Bioenerg. 851 6 (1986)
  166. Woodbury N W et al. Biochemistry 33 8101 (1994)
  167. Peloquin J M et al. Biochemistry 33 8089 (1994)
  168. Goldstein R A, Takif L, Boxer S G Biochim. Biophys. Acta (BBA) Bioenerg. 934 253 (1988)
  169. Shopes R J, Wraight C A Biochim. Biophys. Acta (BBA) Bioenerg. 893 409 (1987)
  170. Creighton S et al. Biochemistry 27 774 (1988)
  171. Cherepanov D A, Krishtalik L I, Mulkijanian A Y Biophys. J. 80 1033 (2001)
  172. Jia Y et al. J. Phys. Chem. 97 13180 (1993)
  173. Wang Z et al. Chem. Phys. 176 421 (1993)
  174. McMahon B H et al. Biophys. J. 74 2567 (1998)
  175. Jasaitis A et al. Proc. Natl. Acad. Sci. USA 102 10882 (2005)
  176. Ramirez B E et al. Proc. Natl. Acad. Sci. USA 92 11949 (1995)
  177. Brzezinski P Biochemistry 35 5611 (1996)
  178. Olsson M H M, Ryde U J. Am. Chem. Soc. 123 7866 (2001)
  179. McLendon G, Hake R Chem. Rev. 92 481 (1992)
  180. Takayama S J et al. J. Biol. Inorg. Chem. 14 821 (2009)
  181. Davidson V L Arch. Biochem. Biophys. 428 32 (2004)
  182. Marcus R A J. Chem. Phys. 38 1858 (1963)
  183. Hush N S Progress In Inorganic Chemistry Vol. 8 (Ed. F A Cotton) (Hoboken, NJ: John Wiley and Sons, 2007) p. 391
  184. Mertz E L Chem. Phys. Lett. 262 27 (1996)
  185. Mertz E L, Tikhomirov V A, Krishtalik L I J. Phys. Chem. A 101 3433 (1997)
  186. Mertts E L, Krishtalik L I Biofizika 41 320 (1996); Mertz E L, Krishtalik L I Biophysics 41 303 (1996)
  187. Pierce D W, Boxer S G J. Phys. Chem. 96 5560 (1992)
  188. Chernavskii D S, Khurgin Yu I, Shnol’ S E Molek. Biologiya 14 19 (1967)
  189. Blyumenfel’d L A Problemy Biologicheskoi Fiziki (M.: Nauka, 1977); Blumenfeld L A Problems Of Biological Physics (Berlin: Springer-Verlag, 1981)
  190. Crofts A R, Berry E A Curr. Opin. Struct. Biol. 8 501 (1998)
  191. Tikhonov A N Sorosovskii Obrazovatel’nyi Zhurn. (6) 17 (1999)
  192. Romanovskii Yu M, Tikhonov A N Usp. Fiz. Nauk 180 931 (2010); Romanovsky Yu M, Tikhonov A N Phys. Usp. 53 893 (2010)
  193. Moser C C, Dutton P L Protein Electron Transfer (Ed. D S Bendall) (Oxford: Bios Sci. Publ., 1996) p. 1
  194. Beratan D N, Onuchic J N Protein Electron Transfer (Ed. D S Bendall) (Oxford: Bios Sci. Publ., 1996) p. 23
  195. Niki K et al. J. Phys. Chem. B 107 9947 (2003)
  196. Khanova L A, Krishtalik L I Electrochim. Acta 50 1085 (2005)

© 1918–2024 Uspekhi Fizicheskikh Nauk
Email: ufn@ufn.ru Editorial office contacts About the journal Terms and conditions