RSS feeds
РусскийEnglish
Issue 12, 2024
Volume year page
Issues Authors PACS Subscription For authors

Issues

 / 

2002

 / 

November

←  →

Reviews of topical problems


Dynamical properties and energy landscape of simple globular proteins

,
Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, ul. Kosygina, 4, Moscow, 119991, Russian Federation

Analysis of dynamic properties of a simple globular protein, myoglobin, has demonstrated that it possesses a hierarchically organized energy landscape. It shows two types of specific protein motions, besides vibrations: 1) individual motions of small atomic groups — transitions between conformational substates (CS) of the lower tier 2, and 2) cooperative motions of secondary structure elements ( α-helices) — transitions between CS of the upper tier 1. The profile of macromolecule dynamic properties is highly heterogeneous. Only vibrations occur near the active center. The number of CS grows towards the periphery where specific type 1 and 2 motions become predominant. Such a picture is consistent with the concept of a protein as ’a random copolymer slightly edited in the vicinity of the active center’.

Fulltext pdf (615 KB)
Fulltext is also available at DOI: 10.1070/PU2002v045n11ABEH001145
PACS: 87.10.+e, 87.15.By, 87.15.He, 87.80.−y (all)
DOI: 10.1070/PU2002v045n11ABEH001145
URL: https://ufn.ru/en/articles/2002/11/b/
000181345500002
Citation: Krupyanskii Yu F, Gol’danskii V I "Dynamical properties and energy landscape of simple globular proteins" Phys. Usp. 45 1131–1151 (2002)
BibTexBibNote ® (generic)BibNote ® (RIS)MedlineRefWorks

Оригинал: Крупянский Ю Ф, Гольданский В И «Динамические свойства и энергетичесий ландшафт простых глобулярных белков» УФН 172 1247–1269 (2002); DOI: 10.3367/UFNr.0172.200211b.1247

References (141) ↓ Cited by (23) Similar articles (20)

  1. Schrödinger E What is Life? The Physical Aspect of the Living Cell (Cambridge: University Press, 1948) [Translated into Russian (Moscow: Atomizdat, 1972)]
  2. Blyumenfel’d L A Problemy Biologicheskoî Fiziki 2nd ed. (Problems of Biological Physics, Moscow: Nauka, 1977) [Translated into English (Berlin: Springer-Verlag, 1981)]
  3. Vol’kenshtein M V Biofizika (Biophysics, Moscow: Nauka, 1988)
  4. Rubin A B Biofizika (Biophysics, Moscow: Izd. Mosk. Univ., 1999)
  5. Chernavskiî D S, Chernavskaya N M Belok-Mashina: Biologicheskie Makromolekulyarnye Konstruktsii (Protein-Machine: Biological Macromolecular Structures, Moscow: Izd. Mosk. Univ., 1999)
  6. Shaîtan K V Biofizika 39 949 (1994) [Biophysics 39 993 (1994)]
  7. Frauenfelder H, Wolynes P G Phys. Today 47 (2) 58 (1994)
  8. Frauenfelder H, Wolynes P G, Austin R H Rev. Mod. Phys. 71 S419 (1999)
  9. White A et al. Principles of Biochemistry 6th ed. (New York: McGraw-Hill, 1978) [Translated into Russian (Moscow: Mir, 1981)]
  10. Ptitsyn O B, Finkelstein A V Quart. Rev. Biophys. 13 339 (1980)
  11. Finkel’shteîn A V et al. Biofizika 44 980 (1999) [Biophysics 44 946 (1999)]
  12. Finkelstein A V, in Protein Folding, Evolution, and Design (Proc. of the Intern. School of Physics `Enrico Fermi’, Course 165, Eds R A Broglia, E I Shakhnovich, G Tiana, Amsterdam: IOS Press, 2001) p. 249
  13. Huber R Nature 280 565 (1979)
  14. Richards F M Annu. Rev. Biophys. Bioeng. 6 151 (1977)
  15. Privalov P L Biofizika 32 742 (1987)
  16. Morozov V N, Morozova T Ya Mol. Biologiya 17 577 (1983)
  17. Abaturov L A, Lebedev Yu A, Nosova N T Mol. Biologiya 17 543 (1983)
  18. Doster W, Cusack S, Petry W Nature 337 754 (1989)
  19. Parak F, Frolov E N, Moessbauer R L, Goldanskii V I J. Mol. Biol. 145 825 (1981)
  20. Shaîtan K V, Rubin A B Biofizika 30 517 (1985)
  21. Parak F, Heidemeier J, Knapp W, in Biological and Artificial Intelligence Systems (Eds E Clementi, S Chin, Leiden: ESCOM, 1988) p. 23
  22. Krupyanskiî Yu F et al. Biofizika 32 761 (1987)
  23. Krupyanskii Yu F et al. Z. Naturforsch. C 37 57 (1982)
  24. Goldanskii V I, Krupyanskii Y F, Fleurov V N Phys. Scripta 33 527 (1986)
  25. Goldanskii V I, Krupyanskii Yu F Quart. Rev. Biophys. 22 39 (1989)
  26. Krupyanskii Yu F et al. Hyperfine Interact. 53 59 (1990)
  27. Anfinsen C Science 181 223 (1973)
  28. Levinthal C J. Chim. Phys. 65 44 (1968)
  29. Shulz G E, Schirmer R H Principles of Protein Structure (New York: Springer-Verlag, 1979)] [Translated into Russian (Moscow: Mir, 1982) p. 181]
  30. Govindarajan S, Goldstein R A Proc. Natl. Acad. Sci. USA 95 5545 (1998)
  31. Cooper A Proc. Natl. Acad. Sci. USA 73 2740 (1976)
  32. II S’ezd Biofizikov Rossii, 23-27 Aug. 1999, Moscow. Tezisy Dokladov (II Congress of Russian Biophysicists. Abstracts, Ed. A B Rubin, Pushchino: ONTI PNTs RAN, 1999)
  33. Proc. of the 3rd European Biophysics Congress, Munich, Germany, Sept. 9-13, 2000; Eur. Biophys. J. 29 239 (2000)
  34. 4th Intern. Conf. on Biological Physics, ICBP-2001, Kyoto, Japan, July 30-Aug. 3, 2001, Abstracts (2001)
  35. Alberts B et al. Molecular Biology of the Cell (New York: Garland Publ., 1983) [Translated into Russian: Vol. 1 [Moscow: Mir, 1987)]
  36. Khurgin Yu I, Chernavskiî D S, Shnol’ S E Biofizika 32 775 (1987)
  37. Kastler H Vozniknovenie Biologicheskoî Organizatsii (Origin of Biological Organization, Moscow: Mir, 1967)
  38. Vol’kenshtein M V Entropiya i Informatsiya (Entropy and Information, Moscow: Nauka, 1986)
  39. Gol’danskiî V I, Krupyanskiî Yu F, Flerov V N Dokl. Akad. Nauk SSSR 272 978 (1983)
  40. Austin R H et al. Biochemistry 14 5355 (1975)
  41. Frauenfelder H, Petsko G A, Tsernoglou D Nature 280 558 (1979)
  42. Gol’danskiî V I, Krupyanskiî Yu F, Flerov V N Mol. Biologiya 17 532 (1983)
  43. Anderson P W, Halperin B I, Varma C M Philos. Mag. 25 1 (1972)
  44. Phillips W A J. Low Temp. Phys. 7 351 (1972)
  45. Grosberg A Yu, Khokhlov A R Statisticheskaya Fizika Makromolekul (Statistical Physics of Macromolecules, Moscow: Nauka, 1989) [Translated into English (New York: AIP Press, 1994)]
  46. Ptitsyn O B, Volkenstein M V J. Biomol. Struct. Dyn. 4 137 (1986)
  47. Klinger M I Comments Cond. Matter Phys. 16 137 (1992)
  48. Fizicheskiî Entsiklopedicheskiî Slovar’ (Physical Encyclopedic Dictionary, Ed.-in-Chief B A Vvedenskiî, Moscow: Sovetskaya Entsiklopediya, 1960)
  49. Vollmayr K, Kob W, Binder K J. Chem. Phys. 105 4714 (1996)
  50. Böttcher C J F, Bordewijk P Theory of Electric Polarization Vol. 2, 2nd ed. (Amsterdam: Elsevier Sci. Publ. Co., 1978)
  51. Bässler H Phys. Rev. Lett. 58 767 (1987)
  52. Davidson D W, Cole R H J. Chem. Phys. 18 1417 (1950)
  53. Nienhaus G U, Parak F Hyperfine Interact. 90 243 (1994)
  54. Dobson C M, Ptitsyn O B Curr. Opin. Struct. Biol. 7 1 (1997)
  55. Ptitsyn O B J. Protein Chem. 6 273 (1987)
  56. Dobson C M, Karplus M Curr. Opin. Struct. Biol. 9 92 (1999)
  57. Fersht A R Curr. Opin. Struct. Biol. 7 3 (1997)
  58. Shakhnovich E I Curr. Opin. Struct. Biol. 7 29 (1997)
  59. Brooks C L III et al. Proc. Natl. Acad. Sci. USA 95 11037 (1998)
  60. Onuchic J N, Luthey-Schulten Z, Wolynes P G Annu. Rev. Phys. Chem. 48 545 (1997)
  61. Brockwell D J, Smith D A, Radford S E Curr. Opin. Struct. Biol. 10 16 (2000)
  62. Grosberg A Yu Usp. Fiz. Nauk 167 129 (1997) [Phys. Usp. 40 125 (1997)]
  63. Finkel’shteîn A V, Badretdinov A Ya Mol. Biologiya 31 469 (1997) [Mol. Biol. 31 391 (1997)]
  64. Kim P S, Baldwin R L Annu. Rev. Biochem. 51 459 (1982)
  65. Bryngelson J D, Wolynes P G Proc. Natl. Acad. Sci. USA 84 7524 (1987)
  66. Go N, Abe H Biopolymers 20 991 (1981)
  67. Shakhnovich E I, Gutin A M Biophys. Chem. 34 187 (1989)
  68. Abkevich V I, Gutin A M, Shakhnovich E I Biochemistry 33 10026 (1994)
  69. Karplus M, Shakhnovich E, in Protein Folding (Ed. T E Greighton, New York: W.H. Freeman and Co., 1992) p. 127
  70. Landau L D, Lifshitz E M Statisticheskaya Fizika (Statistical Physics, Moscow: Nauka, 1964) [Translated into English (Oxford: Pergamon Press, 1969)]
  71. Ellis R J, Hartl F U Curr. Opin. Struct. Biol. 9 102 (1999)
  72. Feldman D E, Frydman J Curr. Opin. Struct. Biol. 10 26 (2000)
  73. Spirin A S, in II S’ezd Biofizikov Rossii, 23-27 Aug. 1999, Moscow. Tezisy Dokladov (II Congress of Russian Biophysicists. Abstracts, Ed. A B Rubin) Vol. 1 (Pushchino: ONTI PNTs RAN, 1999) p. 5
  74. Hardesty B, Tsalkova T, Kramer G Curr. Opin. Struct. Biol. 9 111 (1999)
  75. Frauenfelder H, Sligar S G, Wolynes P G Science 254 1598 (1991)
  76. Frauenfelder H et al. Proc. Natl. Acad. Sci. USA 98 2370 (2001)
  77. Frauenfelder H et al. J. Phys. Chem. 94 1024 (1990)
  78. Beece D et al. Biochemistry 19 5147 (1980)
  79. Rupley J A, Careri G Adv. Protein Chem. 41 37 (1991)
  80. Krupyanskiî Yu F et al. Mol. Biologiya 20 1356 (1986)
  81. DeVault D, Chance B Biophys. J. 6 825 (1966)
  82. Murzin A G, Finkelstein A V J. Mol. Biol. 204 749 (1988)
  83. Kendrew J C et al. Nature 181 662 (1958)
  84. Privalov P L et al. J. Mol. Biol. 190 487 (1986)
  85. Strambini G B, Gabellieri E Biophys. J. 70 971 (1996)
  86. Singh G et al. Z. Phys. B 55 23 (1984)
  87. Verkin B I et al. Fiz. Nizk. Temp. 10 1225 (1984)
  88. Yang I-S, Anderson A C, Preprint Univ. of Illinois, IL -(CM)-87-02 (1987)
  89. Yang I-S, Anderson A C Phys. Rev. B 34 2942 (1986)
  90. Friedrich J Methods Enzymol. 246 226 (1995)
  91. Iben I E T et al. Phys. Rev. Lett. 62 1916 (1989)
  92. Barkalov I M, Bolshakov A I, Goldanskii V I, Krupyanskii Yu F Chem. Phys. Lett. 208 1 (1993)
  93. Sartor G et al. J. Phys. Chem. 96 5133 (1992)
  94. Sartor G, Hallbrucker A, Mayer E Biophys. J. 69 2679 (1995)
  95. Miyazaki Y, Matsuo T, Suga H Chem. Phys. Lett. 213 303 (1993)
  96. Miyazaki Y, Matsuo T, Suga H J. Phys. Chem. B 104 8044 (2000)
  97. Doster W et al. Biophys J. 50 213 (1986)
  98. Sochava I V, Smirnova O I Food Hydrocolloids 6 513 (1993); Biofizika 36 725 (1991)
  99. Angell C A Science 267 1924 (1995)
  100. Leeson D T et al. J. Phys. Chem. B 101 6331 (1997)
  101. Van Hove L Phys. Rev. 95 249 (1954)
  102. Moessbauer R L Hyperfine Interact. 33 199 (1987)
  103. Krupyanskii Yu F, Goldanskii V I, in Protein Folding, Evolution, and Design (Proc. of the Intern. School of Physics "Enrico Fermi", Course 165, Eds R A Broglia, E I Shakhnovich, G Tiana, Amsterdam: IOS Press, 2001) p. 25
  104. Krupyanskii Yu F et al. J. Biol. Phys. 28 139 (2002)
  105. Krupyanskii Yu F et al. Khim. Fiz. 22 41 (2003)
  106. Dwiwedi A, Petersen T, Debrunner P G J. Phys. Colloq. (Paris) 40 C2-531 (1979)
  107. Wise H, Debrunner P, Wagner G, Preprint Univ. of Illinois, IL -(Ex)-84 (1984)
  108. Chang I et al. Chem. Phys. 212 221 (1996)
  109. Krupyanskii Yu et al. Eur. Biophys. J. 26 25 (1997)
  110. Chernavskii D S et al. Proc. Natl. Acad. Sci. USA 77 7218 (1980)
  111. Doster W, Cusack S, Petry W Phys. Rev. Lett. 65 1080 (1990)
  112. Réat V et al. Proc. Natl. Acad. Sci. USA 95 4970 (1998)
  113. Götze W, Sjogren L Rep. Prog. Phys. 55 241 (1992)
  114. Frauenfelder H, McMahon B Proc. Natl. Acad. Sci. USA 95 4795 (1998)
  115. Parak F et al. Eur. Biophys. J. 15 237 (1987)
  116. Parak F, Frauenfelder H Physica A 201 332 (1993)
  117. Bialek W, Goldstein R F Biophys. J. 48 1027 (1985)
  118. Goldstein R F, Bialek W Comm. Mol. Cell. Biophys. 3 407 (1986)
  119. Bialek W, Onuchic J N Proc. Natl. Acad. Sci. USA 85 5908 (1988)
  120. Case D A Curr. Opin. Struct. Biol. 4 285 (1994)
  121. Seno Y, Go N J. Mol. Biol. 216 111 (1990)
  122. Kidera A, Go N J. Mol. Biol. 225 457 (1992)
  123. Hayward S, Go N Annu. Rev. Phys. Chem. 46 223 (1995)
  124. Zach C et al. Hyperfine Interact. 126 83 (2000)
  125. Melchers B et al. Biophys. J. 70 2092 (1996)
  126. Kitao A, Hayward S, Go N Proteins 33 496 (1998)
  127. Krupyanskii Yu F et al. Biofizika 33 401 (1988) [Biophysics 33 430 (1988)]
  128. Frauenfelder H, McMahon B H Ann. Phys. (Leipzig) 9 655 (2000)
  129. Ansari A et al. Proc. Natl. Acad. Sci. USA 82 5000 (1985)
  130. Barlow A J, Lamb J, Matheson A J Proc. R. Soc. London Ser. A 292 322 (1966)
  131. Zallen R The Physics of Amorphous Solids (New York: Wiley, 1983)
  132. Fischer K H, Hertz J A Spin Glasses (Cambridge: Cambridge Univ. Press, 1991)
  133. Metzler R, Klafter J, Jortner J Proc. Natl. Acad. Sci. USA 96 11085 (1999)
  134. Jackson T A, Lim M, Anfinrud P A Chem. Phys. 180 131 (1994)
  135. Frauenfelder H Nature Struct. Biol. 2 821 (1995)
  136. Guerra F, Peliti L, Vulpiani A, in Measures of Complexity: Proc. of the Conf., Rome, Sept. 30-Oct. 2, 1987 (Lecture Notes in Physics, 314, Eds L Peliti, A Vulpiani, Berlin: Springer-Verlag, 1988)
  137. Parisi G, in Measures of Complexity: Proc. of the Conf., Rome, Sept. 30-Oct. 2, 1987 (Lecture Notes in Physics, 314, Eds L Peliti, A Vulpiani, Berlin: Springer-Verlag, 1988)
  138. Kolmogorov A N Problemy Peredachi Informatsii 1 (1) 3 (1965); in Novoe v Zhizni, Nauke, Tekhnike (Ser. Matematika, Kibernetika, Vyp. 1) [News in Life, Science, Technique (Ser. Mathematics, Cybernetics, Issue 1)] (Moscow: Znanie, 1991) p. 24
  139. Chaitin G J. Assoc. Comput. Mach. 13 547 (1966)
  140. Adami C, Ofria Ch, Collier T C Proc. Natl. Acad. Sci. USA 97 4463 (2000)
  141. Ptitsyn O B J. Mol. Biol. 278 655 (1998)
© 1918–2024 Uspekhi Fizicheskikh Nauk
Email: ufn@ufn.ru Editorial office contacts About the journal Terms and conditions