Low-frequency collective motion in proteins and DNA

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Low-frequency collective motion in proteins and DNA refers to the application of statistical thermodynamics to understand low-frequency vibrations in biomolecules.

The concept of low-frequency phonons (or internal motion) in proteins was originally proposed by Professor Kuo-Chen Chou and Professor Nian-Yi Chen in order to solve a perplexing “free-energy deficit” problem in protein binding. In studying the binding interaction between proteins such as insulin and insulin receptor, it was noted that enumerating the known explanations for the free energy change, such as translational and rotational entropy, hydrogen bonds, van der Waals interactions, and hydrophobic interactions, did not fully account for the observed free energy change for the reaction. It was inferred that the deficit could be explained by the creation of extra vibrational modes with very low wave numbers in the range of 10–100 cm−1, corresponding to the range of terahertz frequency (3×1011 to 3×1012 Hz).[1][2][3]

Subsequently, the aforementioned low-frequency modes have been indeed observed by Raman spectroscopy for a number of protein molecules[4] and different types of DNA.[5][6] These observed results have also been further confirmed by neutron scattering experiments.[7]

Quasi-continuum model [edit]

The quasi-continuum model is one model developed to identify and analyze this kind of low-frequency motions in protein and DNA molecules. This model operates on an intermediate level of complexity between the elastic global model, which treats the biomolecule as a continuous elastic sphere, and atomistic normal mode methods[8]. It treats the biomolecule's backbone as a continuous mass distribution, with discrete interactions representing hydrogen bonds modeling the effects of internal conformation. This has the advantage of being simpler than explicit-atom methods, and providing a much more intuitive physical picture of the dynamics involved.[3]

It has been successfully used to simulate various low-frequency collective motions in protein and DNA molecules, such as accordion-like motion, pulsation or breathing motion, as reflected by the fact that the low-frequency wave numbers thus derived were quite close to the experimental observations.[9][10][11][12]

Application to biological functions and medical treatments [edit]

Many biological functions and their profound dynamic mechanisms can be revealed through the low-frequency collective motion or resonance in protein and DNA molecules, such as cooperative effects,[13][14] allosteric transition,[15] and intercalation of drugs into DNA.[16] In this regard, some phenomenological theories[17] were established. Meanwhile, the solitary wave motion was also used to address the internal motion during microtubule growth.[18] The relationship between solitons—a self-reinforcing solitary wave (a wave packet or pulse) that maintains its shape while it travels at constant speed—and the low-frequency phonons in proteins have been discussed in a recent paper.[19]

This kind of low-frequency collective motion has also been observed in calmodulin by NMR,[20] and applied in medical treatments.[21][22][23]

References [edit]

  1. ^ Chou K-C, Chen N-Y (1977). "The biological functions of low-frequency phonons". Scientia Sinica 20: 447–457. 
  2. ^ Chothia C, Janin J (August 1975). "Principles of protein-protein recognition". Nature 256 (5520): 705–8. Bibcode:1975Natur.256..705C. doi:10.1038/256705a0. PMID 1153006. 
  3. ^ a b Sinkala Z (August 2006). "Soliton/exciton transport in proteins". J. Theor. Biol. 241 (4): 919–27. doi:10.1016/j.jtbi.2006.01.028. PMID 16516929. 
  4. ^ Painter PC, Mosher LE, Rhoads C (July 1982). "Low-frequency modes in the Raman spectra of proteins". Biopolymers 21 (7): 1469–72. doi:10.1002/bip.360210715. PMID 7115900. 
  5. ^ Painter PC, Mosher LE, Rhoads C (1981). "Low-frequency modes in the Raman spectrum of DNA.". Biopolymers 20: 243–247. doi:10.1002/bip.1981.360200119. 
  6. ^ Urabe H, Tominaga Y (December 1982). "Low-lying collective modes of DNA double helix by Raman spectroscopy". Biopolymers 21 (12): 2477–81. doi:10.1002/bip.360211212. PMID 7150706. 
  7. ^ Martel P (1992). "Biophysical aspects of neutron scattering from vibrational modes of proteins". Prog. Biophys. Mol. Biol. 57 (3): 129–79. doi:10.1016/0079-6107(92)90023-Y. PMID 1603938. 
  8. ^ Thirumuruganandham, Saravana and Urbassek, Herbert (2009). "Low-frequency vibrational modes and infrared absorbance of red, blue and green opsin". Journal of Molecular Modeling 15: 1545. 
  9. ^ Chou KC (December 1983). "Identification of low-frequency modes in protein molecules". Biochem. J. 215 (3): 465–9. PMC 1152424. PMID 6362659. 
  10. ^ Chou KC (July 1984). "Low-frequency vibrations of DNA molecules". Biochem. J. 221 (1): 27–31. PMC 1143999. PMID 6466317. 
  11. ^ Chou KC (August 1985). "Low-frequency motions in protein molecules. Beta-sheet and beta-barrel". Biophys. J. 48 (2): 289–97. Bibcode:1985BpJ....48..289C. doi:10.1016/S0006-3495(85)83782-6. PMC 1329320. PMID 4052563. 
  12. ^ Chou KC, Maggiora GM, Mao B (August 1989). "Quasi-continuum models of twist-like and accordion-like low-frequency motions in DNA". Biophys. J. 56 (2): 295–305. Bibcode:1989BpJ....56..295C. doi:10.1016/S0006-3495(89)82676-1. PMC 1280479. PMID 2775828. 
  13. ^ Chou K-C, Chen NY, Forsen S (1981). "The biological functions of lowfrequency phonons: 2. Cooperative effects". Chemica Scripta 18: 126–132. 
  14. ^ Chou KC (June 1989). "Low-frequency resonance and cooperativity of hemoglobin". Trends Biochem. Sci. 14 (6): 212–3. doi:10.1016/0968-0004(89)90026-1. PMID 2763333. 
  15. ^ Chou KC (August 1984). "The biological functions of low-frequency vibrations (phonons). 4. Resonance effects and allosteric transition". Biophys. Chem. 20 (1–2): 61–71. doi:10.1016/0301-4622(84)80005-8. PMID 6487745. 
  16. ^ Chou KC, Mao B (November 1988). "Collective motion in DNA and its role in drug intercalation". Biopolymers 27 (11): 1795–815. doi:10.1002/bip.360271109. PMID 3233332. 
  17. ^ Chou KC, Kiang YS (August 1985). "The biological functions of low-frequency vibrations (phonons) 5. A phenomenological theory". Biophys. Chem. 22 (3): 219–35. doi:10.1016/0301-4622(85)80045-4. PMID 4052576. 
  18. ^ Chou KC, Zhang CT, Maggiora GM (January 1994). "Solitary wave dynamics as a mechanism for explaining the internal motion during microtubule growth". Biopolymers 34 (1): 143–53. doi:10.1002/bip.360340114. PMID 8110966. 
  19. ^ Sinkala, Z. (2006). "Soliton/exciton transport in proteins". J Theor Biol 241 (4): 919–927. doi:10.1016/j.jtbi.2006.01.028. PMID 16516929. 
  20. ^ Chou JJ, Li S, Klee CB, Bax A (November 2001). "Solution structure of Ca(2+)-calmodulin reveals flexible hand-like properties of its domains". Nat. Struct. Biol. 8 (11): 990–7. doi:10.1038/nsb1101-990. PMID 11685248. 
  21. ^ Gordon GA (September 2007). "Designed electromagnetic pulsed therapy: clinical applications". J. Cell. Physiol. 212 (3): 579–82. doi:10.1002/jcp.21025. PMID 17577213. 
  22. ^ Gordon GA (2008). "Extrinsic electromagnetic fields, low frequency (phonon) vibrations, and control of cell function: a non-linear resonance system". Journal of Biomedical Science and Engineering 1 (3): 152–156. doi:10.4236/jbise.2008.13025. 
  23. ^ Madkan A, Blank M, Elson E, Chou K-C, Geddis MS, Goodman R (2009). "Steps to the clinic with ELF EMF". Natural Science 1 (3): 157–165. doi:10.4236/ns.2009.13020. 
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