Skip to main content
SpringerLink
Log in
Book cover

Molecular Theory of the Living Cell pp 297–390Cite as

Subcellular Systems

  • Chapter
  • First Online:

Abstract

The field of protein folding appears to have gone through a paradigm shift around 1995, largely due to the work of Wolynes and his group (Wolynes et al. 1995; Dill and Chan 1997; Harrison and Durbin 1985). The paradigm shift involves replacing the idea of folding pathways with the so-called folding funnel (see Fig. 11.1). In other words, the earlier notion of a denatured protein folding to its final native conformation through a series of distinct intermediate conformational states has been replaced by a new view, according to which an ensemble of conformational isomers (often called “conformers,” not to be confused with “conformons”; a conformer can carry many conformons in it; see Sect. 11.3.2) of a denatured protein undergoes a transition to a final native conformation through a series of “ensembles” of conformational intermediates, each intermediate following a unique folding path to the final common native structure. In short, the paradigm shift is from individual intermediate conformational isomers of a protein to an ensemble of the conformational isomers, on the one hand, and from a single folding pathway to an ensemble of folding pathways (down the folding funnel), on the other.

This is a preview of subscription content, log in via an institution.

Chapter
USD   29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   169.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD   219.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD   219.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Learn about institutional subscriptions

References

  • Abbott, D., Davies, P.C., Pati, A.K.: Quantum Aspects of Life, pp. 349–380. Imperial College Press, London (2009)

    Google Scholar 

  • Aksimentiev, A., Balabin, I.A., Fillingame, R.H., Schulten, K.: Insights into the molecular mechanism of rotation in the F0 sector of ATP synthase. Biophys. J. 86, 1332–1344 (2004)

    Article  ADS  Google Scholar 

  • Anderson, P.W.: Suggested model of prebiotic evolution: the use of Chaos. Proc. Natl. Acad. Sci. U. S. A. 80, 386–3390 (1983)

    Google Scholar 

  • Anderson, P.W.: Computer modeling of prebiotic evolution: general theoretical ideas on the origin of biological information. Comments Mol. Cell. Biophys. 4(2), 99–108 (1987)

    Google Scholar 

  • Ashe, M.P., De Long, S.K., Sachs, A.B.: Glucose depletion rapidly inhibits translation initiation in yeast. Mol. Biol. Cell 11, 833–848 (2000)

    Google Scholar 

  • Astumian, D.: The role of thermal activation in motion and force generation by molecular motors. Philos. Trans. R. Soc. Lond. B 355, 511–22 (2000)

    Article  Google Scholar 

  • Astumian, D.: Making molecules into motors. Sci. Am. 285(1), 57–64 (2001)

    Article  Google Scholar 

  • Axelrod, D.: Total internal reflectance fluorescence microscopy. Methods Cell Biol. 30, 245–270 (1989)

    Article  Google Scholar 

  • Babloyantz, A.: Molecules, Dynamics & Life: An Introduction to Self- Organization of Matter. Wiley-Interscience, New York (1986)

    Google Scholar 

  • Barabasi, A.L.: Linked: The New Science of Networks. Perseus Publishing, Cambridge (2002)

    Google Scholar 

  • Barbieri, M.: The Organic Codes: An Introduction to Semantic Biology. Cambridge University Press, Cmbridge (2003)

    Google Scholar 

  • Barbieri, M.: Introduction to Biosemiotics: The New Biological Synthesis. Springer, New York (2008a)

    Google Scholar 

  • Barbieri, M.: The code model of semiosis: the first steps towards a scientific biosemiotics. Am. J. Semiotics 24(1–3), 23–37 (2008b)

    Google Scholar 

  • Barbieri, M.: Biosemiotics: a new understanding of life. Naturwissenschaften (2008c). doi:10.1007/s00114-008-0368-x

  • Batey, R.T.: Structures of regulatory elements in mRNAs. Curr. Opin. Struct. Biol. 16(3), 299–306 (2006). doi:10.1016/j.sbi.2006.05.001 DOI:dx.doi.org. PMID 16707260

    Article  Google Scholar 

  • Benham, C.J.: Sites of predicted stress-induced DNA duplex destabilization occur preferentially at regulatory sites. Proc. Natl. Acad. Sci. U. S. A. 90, 2999–3003 (1992)

    Article  ADS  Google Scholar 

  • Benham, C.J.: Duplex destabilization in supercoiled DNA is predicted to occur at specific transcriptional regulatory regions. J. Mol. Biol. 255, 425–434 (1996a)

    Article  Google Scholar 

  • Benham, C.J.: Computation of DNA structural variability – a new predictor of DNA regulatory regions. Comput. Appl. Biosci. 12(5), 375–381 (1996b)

    Google Scholar 

  • Brooks, C.A., Onuchic, J.N., Wales, D.J.: Statistical Thermodynamics: taking a walk on a landscape. http://www.biology-online.org/articles/statistical _thermodynamics_taking_walk.html (2009)

  • Bryngelson, J.D., Wolynes, P.G.: Spin glasses and the statistical mechanics of protein folding. Proc. Natl. Acad. Sci. U. S. A. 84, 7524–7528 (1987)

    Article  ADS  Google Scholar 

  • Buchler, J.: Philosophical Writings of Peirce. Dover Publications, New York (1955)

    Google Scholar 

  • Cozzarelli, N.R.: DNA gyrase and the supercoiling of DNA. Science 207, 953–960 (1980)

    Article  ADS  Google Scholar 

  • Crick, F.H., Barnett, L., Brenner, S., Watts-Tobin, R.J.: General nature of the genetic code for proteins. Nature 192(4809), 1227–32 (1961)

    Article  ADS  Google Scholar 

  • Deniz, A.A., Mukhopadhyay, S., Lemke, E.A.: Single- molecule biophysics: at the interface of biology, physics and chemistry. J. R. Soc. Interface 5, 15–45 (2008)

    Article  Google Scholar 

  • DeRisi, J.L., Iyer, V.R., Brown, P.O.: Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 278, 680–686 (1997)

    Article  ADS  Google Scholar 

  • Dill, K.A., Chan U. S., U.S.: From Leventhal to pathways to funnels. Nat. Struct. Biol. 4(1), 10–19 (1997)

    Article  Google Scholar 

  • Domb, C.: The Critical Point: A Historical Introduction to the Modern Theory of Critical Phenomena. Taylor & Francis, London (1996)

    Google Scholar 

  • Douglas, K.: Think like a muscle. NewScientist. 18 Nov (1995)

    Google Scholar 

  • Eisenmesser, E.Z., Bosco, D.A., Akke, M., Kern, D.: Enzyme dynamics during catalysis. Science 295, 1520–1523 (2002)

    Article  ADS  Google Scholar 

  • ENCODE Proejct Consortium: Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447, 799–816 (2007)

    Article  ADS  Google Scholar 

  • Fink, T.M.A., Zinovyev, A., Ahnert, S.E.: How much non-coding DNA do eukaryotes require? http://arxiv.org/abs/q-bio.GN/0611047 (2007)

  • Frauenfelder, H.: Function and dynamics of myoglobin. N. Y. Acad. Sci. 504, 151–167 (1987)

    Article  ADS  Google Scholar 

  • Frauenfelder, H., McMahon, B.H., Austin, R.H., Chu, K., Groves, J.T.: The role of tructure, energy landscape, dynamics, and allostery in the enzymatic function of myoglobin. Proc. Natl. Acad. Sci. U. S. A. 98(5), 2370–74 (2001)

    Article  ADS  Google Scholar 

  • Frost, A.A., Pearson, R.G.: Kinetics and Mechanism: A Study of Homogeneous Chemical Reactions, 2nd edn. Wiley, New York (1965)

    Google Scholar 

  • Garcia-Martinez, J., Aranda, A., Perez-Ortin, J.E.: Genomic run-on evaluates transcription rates for all yeast genes and identifies gene regulatory mechanisms. Mol. Cell 15, 303–313 (2004)

    Article  Google Scholar 

  • Gerstein, M.B., Bruce, C., Rozowsky, J.S., Zheng, D., Du Jiang, J., Korbel, J.O., Emanuelsson, O., Zhang, Z.D., Weissman, S., Snyder, M.: What is a gene, post-ENCODE? History and updated definition. Genome Res. 17, 669–681 (2007)

    Article  Google Scholar 

  • Green, D.E., Ji, S.: The electromechanochemical model of mitochondrial strucutre and funciton. In: Schulz, J., Cameron, B.F. (eds.) Molecular Basis of Electron Transport, pp. 1–44. Academic Press, New York (1972a)

    Google Scholar 

  • Green, D.E., Ji, S.: Electromechanochemical model of mitochondrial structure and function. Proc. Natl. Acad. Sci. U. S. A. 69, 726–729 (1972b)

    Article  ADS  Google Scholar 

  • Harrison, S.C., Durbin, R.: Is there a single pathway for the folding of a polypeptide chain? Proc. Natl. Acad. Sci. U. S. A. 82, 4028–4030 (1985)

    Article  ADS  Google Scholar 

  • Herbert, N.: Quantum Reality: Beyond the New Physics, An Excursion into Metaphysics, p. 64. Anchor Books, Garden City (1987)

    Google Scholar 

  • Houser, N.J.R., Eller, J.R.A.C., Lewis, A.C.A., De Tienne, A.C.L., Clark, C.L., Davis, D.B.: The Essential Peirce: Selected Philosophical Writings, Volume 2 (1893–1913), p. 13. Indiana University Press, Bloomington (1998)

    Google Scholar 

  • Huxley, A.F., Hanson, J.: In: Bourne, G.H. (ed.) The Structure and Function of Muscle, vol. I, pp. 183–227. (1960)

    Google Scholar 

  • Ingber, D.: The architecture of life. Sci. Am. 278(1), 48–57 (1998)

    Article  ADS  Google Scholar 

  • Ishijima, A., Kojima, H., Higuchi, H., Harada, Y., Funatsu, T., Yanagida, T.: Simultaneous measurement of chemical and mechanical reaction. Cell 70, 161–171 (1998)

    Article  Google Scholar 

  • Ishii, Y., Yangida, T.: Single molecule detection in life science. Single Mol. 1(1), 5–16 (2000)

    Article  ADS  Google Scholar 

  • Ishii, Y., Yanagida, T.: How single molecule detection measures th dynamics of life. HFSP J. 1(1), 15–29 (2007)

    Article  Google Scholar 

  • Jencks, W.: Binding energy, specificity, and enzymic catalysis: the circe effect. Adv. Enzymol. 43, 219–410 (1975)

    Google Scholar 

  • Ji, S.: Energy and negentropy in enzymic catalysis. Ann. N. Y. Acad. Sci. 227, 419–437 (1974a)

    Article  ADS  Google Scholar 

  • Ji, S.: A general theory of ATP synthesis and utilization. Ann. N. Y. Acad. Sci. 227, 211–226 (1974b)

    Article  ADS  Google Scholar 

  • Ji, S.: A model of oxidative phosphorylation that accommodates the chemical intermediate, chemiosmotic, localized proton and conformational hypotheses. J. Theor. Biol. 59, 319–330 (1976)

    Article  Google Scholar 

  • Ji, S.: A possible molecular mechanism of free energy transfer in oxidative phosphorylation. J. Theor. Biol. 68, 607–612 (1977)

    Article  Google Scholar 

  • Ji, S.: The principles of ligand-protein interactions and their application to the mechanism of oxidative phosphorylation. In: Yagi, K. (ed.) Structure and Function of Biomembranes, pp. 25–37. Japan Scientific Societies Press, Tokyo (1979)

    Google Scholar 

  • Ji, S.: The bhopalator – a molecular model of the living cell based on the concepts of conformons and dissipative structures. J. Theor. Biol. 116, 399–426 (1985a)

    Article  Google Scholar 

  • Ji, S.: The Bhopalator: a molecular model of the living cell. Asian J. Exp. Sci 1, 1–33 (1985b)

    Google Scholar 

  • Ji, S.: Watson-crick and prigoginian forms of genetic information. J. Theor. Biol. 130, 239–245 (1988)

    Article  Google Scholar 

  • Ji, S.: The bhopalator – a molecular model of the living cell; New developments. In: Mishra, R.K. (ed.) Molecular and Biological Physics of Living Systems, pp. 187–214. Kluwer Academic Publishers, Dordrecht (1990)

    Chapter  Google Scholar 

  • Ji, S.: Biocybernetics: a machine theory of biology. In: Ji, S. (ed.) Molecular Theories of Cell Life and Death, pp. 1–237. Rutgers University Press, New Brunswick (1991)

    Google Scholar 

  • Ji, S.: Isomorphism between cell and human languages: molecular biological, bioinformatics and linguistic implications. Biosystems 44, 17–39 (1997a)

    Article  Google Scholar 

  • Ji, S.: A cell-linguistic analysis of apoptosis. Comment Toxicol. 5(6), 571–85 (1997b)

    Google Scholar 

  • Ji, S.: The cell as the smallest DNA-based molecular computer. Biosystems 52, 123–133 (1999a)

    Article  Google Scholar 

  • Ji, S.: The linguistics of DNA: words, sentences, grammar, phonetics, and semantics. Ann. N. Y. Acad. Sci. 870, 411–417 (1999b)

    Article  ADS  Google Scholar 

  • Ji, S.: Free energy and information contents of Conformons in proteins and DNA. Biosystems 54, 107–130 (2000)

    Article  Google Scholar 

  • Ji, S.: Isomorphism between cell and human languages: micro- and macrosemiotics. In: Simpkins, S., Deely, J. (eds.) Semiotics 2000: “Sebeok’s Century”, pp. 357–374. Legas, Ottawa (2001)

    Google Scholar 

  • Ji, S.: Microsemiotics of DNA. Semiotica 138(1/4), 15–42 (2002a)

    Google Scholar 

  • Ji, S.: The Bhopalator: an information/energy dual model of the living cell (II). Fundam. Inform. 49(1–3), 147–165 (2002b)

    MATH  Google Scholar 

  • Ji, S.: Molecular information theory: solving the mysteries of DNA. In: Ciobanu, G., Rozenberg, G. (eds.) Modeling in Molecular Biology, Natural Computing Series, pp. 141–150. Springer, Berlin (2004a)

    Chapter  Google Scholar 

  • Ji, S.: Life an “Informed” critical phenomenon? 97th Statistical Mechanics Conference, Rutgers University, Piscataway, 6–8 May (2007a)

    Google Scholar 

  • Ji, S.: ‘Stochastic mechanics’ of molecular machines. In: Abstract of Short Talks, The 99th Statistical Mechanics Conference, Rutgers University, Piscataway, N.J, 11–13 May (2008a)

    Google Scholar 

  • Ji, S.: Modeling the single-molecule enzyme kinetics of cholesterol oxidase based on Planck's radiation formula and the principle of enthalpy-entropy compensation. In: Short Talk Abstracts The 100th Statistical Mechanics Conference, Rutgers University, Piscataway, N.J, 13–16 Dec (2008b)

    Google Scholar 

  • Ji, S., Ciobanu, G.: Conformon-driven biopolymer shape changes in cell modeling. Biosystems 70, 165–181 (2003)

    Article  Google Scholar 

  • Ji, S. and Zinovyev, A.: A dynamic second-order clustering method for classifying dissipative structures in living cells. In: The 29th Middle Atlantic Regional Meeting, American Chemical Society, Ursinus College, Collegeville, PA, 20–23 May (2007b)

    Google Scholar 

  • Ji, S., Chaovalitwongse, A., Fefferman, N., Yoo, W., Perez-Ortin, J.E.: Mechanism-based clustering of genome-wide mRNA levels: roles of transcription and transcript-degradation rates. In: Butenko, S., Chaovalitwongse, A., Pardalos, P. (eds.) Clustering Challenges in Biological Networks, pp. 237–255. World Scientific Publishing Co, Singapore (2009a)

    Chapter  Google Scholar 

  • Ji, S., Bianchini, J., Davidson, A., Kim, W.: Experimental evidence for a quasi-deterministic relation between structural and timing genes in the budding yeast Saccharomyces cerevisiae. In: Abstract, The 101st Statistical Mechanics Conference, Rutgers University, Piscataway, N.J, 10–12 May (2009b)

    Google Scholar 

  • Ji, S., Davidson, A., Bianchini, J.: Genes as molecular machines: microarray evidence that structural genes regulate their own transcripts, A poster presented at the 2009 Joint RECOMB Satellite Conference on Regualtory Genomics, Systems Biology and DREAM4, MIT/The Broad Institute, Cambridge, MA, p. 99 (2009c)

    Google Scholar 

  • Johnston, M.: Feasting, fasting and fermenting: glucose sensing in yeast and other cells. Trends Genet. 15(1), 29–33 (1999)

    Article  Google Scholar 

  • Jona, G., Choder, M., Gileadi, O.: Glucose starvation induces a drastic reduction in the rates of both transcription and degradation of mRNA in yeast. Biochim Biophys Acta Gene Struct. Expr. 1491, 37–48 (2000)

    Article  Google Scholar 

  • Junge, W., Lill, H., Engelbrecht, S.: ATP synthase: an electrochemical transducer with rotatory mechanics. Trends Biochem. Sci. 22, 420–423 (1997)

    Article  Google Scholar 

  • Junge, W., Müller, D.J.: Seeintg a molecular motor at work. Science 333, 704–705 (2011)

    Article  ADS  Google Scholar 

  • Klonowski, W., Klonowska, M.T.: Biophysical time on macromolecular level. Biomathematics 80, 28–33 (1982)

    Google Scholar 

  • Klir, G.J.: Developments in uncertainty-based information. Adv. Comput. 36, 255–332 (1993)

    Article  Google Scholar 

  • Kondepudi, D.: Introduction to Thermodynamics. Wiley, Chichester (2008)

    Google Scholar 

  • Kondepudi, D., Prigogine, I.: Modern Thermodynamics: From Heat Engine to Dissipative Structures. Wiley, Chichester (1998)

    Google Scholar 

  • Kragh, H.: Max Planck: the reluctant revolutionary. From Physics World Dec 2000. Available at http://www.physicsworldarchive.iop.org (2000)

  • Kruger, K., Grabowski, P.J., Zaug, A.J., Sands, J., Gottschling, D.E., Cech, T.R.: Self-splicing RNA: autoexcision and autocyclization of the ribosomal RNA intervening sequence of Tetrahymena. Cell 31(1), 147–57 (1982)

    Article  Google Scholar 

  • Kuhn, K.M., DeRisis, J.L., Brown, P.O., Sarnow, P.: Global and specific translational regulation in the genomic response of saccharomyces cerevisiae to nonfermental carnbon source. Mol. Cell. Biol. 21(3), 916–927 (2001)

    Article  Google Scholar 

  • Kurzynski, M.: Enzymatic catalysis as s process controlled by protein conformational relaxation. FEBS Lett. 328(3), 221–224 (1993)

    Article  Google Scholar 

  • Kurzynski, M.: Protein machine model of enzymatic reactions gated by enzymes internal dynamics. Biophys. Chem. 65, 1–28 (1997)

    Article  Google Scholar 

  • Kurzynski, M.: The Thermodynamic Machinery of Life. Springer, Berlin (2006)

    Google Scholar 

  • Leopold, P.E., Montal, M., Onuchic, J.N.: Protein folding funnels: a kinetic approach to the sequence-structure relationship. Proc. Nat. Acad. Sci. USA 89, 8721–8725 (1992)

    Article  ADS  Google Scholar 

  • Lockless, S.W., Ranganathan, R.: Evolutionarily conserved pathways of energetic connectivity in protein families. Science 286, 295–299 (1999)

    Article  Google Scholar 

  • Lu, H.P., Xun, L., Xie, X.S.: Single-molecule enzymatic dynamics. Science 282, 1877–1882 (1998)

    Article  ADS  Google Scholar 

  • Lumry, R., Biltonen, R.: In: Timasheff, S.N., Fasman, G.D. (eds.) Structure and Stability of Biological Macromolecules, pp. 65–212. Marcel Dekker, New York (1969)

    Google Scholar 

  • Lumry, R.: Conformational mechanisms for free energy transduction in protein systems: old ideas and new facts. Ann. N. Y. Acad. Sci. 227, 46–73 (1974)

    Article  ADS  Google Scholar 

  • Lumry, R.: The Protein Primer, available at http://www.chem.umn.edu/groups/lumry/Volume_2_Protein_Primer/ (2009)

  • Lumry, R., Gregory, R.B.: Free-energy management in protein reactions: concepts, complications, and compensation. In: Welch, G.R. (ed.) The Fluctuating Enzymes, pp. 1–190. Wiley, New York (1986)

    Google Scholar 

  • Mattick, J.S.: Challenging the dogma: the hidden layer of non-protein-coding RNAs in complex organisms. Bioessays 25(10), 930–939 (2003)

    Article  Google Scholar 

  • Mattick, J.S.: RNA regulation: a new genetics? Nat. Rev. Genet. 5, 316–323 (2004)

    Article  Google Scholar 

  • McClare, C.W.F.: Chemical machines, maxwell's demon and living organisms. J. theoret. Biol. 30, 1–34 (1971)

    Article  Google Scholar 

  • McClare, C.W.F.: Resonance in bioenergetics. Ann. N. Y. Acad. Sci. 227, 74–97 (1974)

    Article  ADS  Google Scholar 

  • Mitchell, P.: Coupling of phosphorylation to electron and hydrogen transfer by a chemiosmotic type of mechanism. Nature 191, 144–148 (1961)

    Article  ADS  Google Scholar 

  • Mitchell, P.: Chemiosmotic Coupling and Energy Transduction. Glyn Research Ltd, Bodmin (1968)

    Google Scholar 

  • Morrison, M.A.: Understanding Quantum Physics: A User’s Manual, p. 169. Prentice Hall, Englewood (1990)

    Google Scholar 

  • Nahvi, A., Sudarsan, N., Ebert, M.S., Zou, X., Brown, K.L., Breaker, R.R.: Genetic control by a metabolite binding mRNA. Chem. Biol. 9(9), 1043–1049 (2002). doi:10.1016/S1074-5521(02)00224-7 DOI:dx.doi.org. PMID 12323379

    Article  Google Scholar 

  • Nave, R.: Blackbody radiation. http://hyperphysics.phys-astr.gsu.edu/ hbase/mod6.html (2009)

  • Newman, S.A., Bhat, R.: Genes and proteins: dogmas in decline. J. Biosci. 32(6), 1041–1043 (2007)

    Article  Google Scholar 

  • Nicholls, D.G.: Bioenergetgics: An Introduction to the Chemiosmotic Theory. Academic Press, London (1982)

    Google Scholar 

  • Northrup, S.H., Hynes, J.: The stable state picture of chemical reactions I Formulation for rate constants and initial condition effects. J. Chem. Phys. 73(6), 2700–2714 (1980)

    Article  MathSciNet  ADS  Google Scholar 

  • Nudler, E., Mironov, A.S.: The riboswitch control of bacterial metabolism. Trends Biochem. Sci. 29(1), 11–7 (2004). doi:10.1016/j.tibs.2003.11.004 DOI:dx.doi.org. PMID 14729327

    Article  Google Scholar 

  • Pattee, H.: The physics of symbols and the evolution of semiotic controls. In: Coombs M.,Sulcoski M.(eds) Proceedings of the 1996 International Workshop on Control Mechanisms for Complex Systems, Issues of Measurement & Semiotic Analysis (1996)

    Google Scholar 

  • Pattee, H.: The physics of symbols: bridging the epistemic cut. Biosystems 60, 5–12 (2001)

    Article  Google Scholar 

  • Pattee, H.: The nessecity of biosemiotics: matter-symbol complementarity. In: Barbieri, M. (ed.) Introduction to Biosemiotics, pp. 115–132. Cambridge University Press, Cambridge (2008)

    Google Scholar 

  • Pierce, J.R.: Introduction to Information Theory. Second, Revised Edition. Dover Publications, New York (1980)

    MATH  Google Scholar 

  • Poole, A.M., Ranganathan, R.: Knowledge-based potentials in protein design. Curr. Opin. Struct. Biol. 16, 508–513 (2006)

    Article  Google Scholar 

  • Prakash, M.K., Marcus, R.A.: An interpretation of fluctuations in enzyme catalysis, spectral diffusion, and radiative component of lifetimes in terms of electric field fluctuations. Proc. Nat. Acad. Sci. USA 104(41), 15982–15987 (2007)

    Article  ADS  Google Scholar 

  • Prigogine, I.: Dissipative structures and biological order. Adv. Biol. Med. Phys. 16, 99–113 (1977)

    MathSciNet  Google Scholar 

  • Prigogine, I.: From Being To Becoming: Time and complexity in Physical Sciences, pp. 19–26. W. H. Freeman and Company, San Francisco (1980)

    Google Scholar 

  • Qian, H., Xie, S.: Generalized haldane equation and fluctuation theorem in the steady-state cycle kinetics of single enzymes. Phys. Rev. E 74, 0100902(R) (2006)

    Article  ADS  Google Scholar 

  • Reece, R.J., Maxwell, A.: DNA gyrase: structure and function. Critical Rev. Biochem. Mol. Biol. 26(3/4), 335–375 (1991)

    Article  Google Scholar 

  • Reynolds, W.L., Lumry, R.: Mechanisms of Electron Transfer. The Ronald Press Company, New York (1966). Chapter 1

    Google Scholar 

  • Skulachev, V.P., Hinkle, P.C.: Chemiosmotic Proton Circuits in Biological Membranes. Addison-Wesley Publishing Company, London (1981)

    Google Scholar 

  • Smith, H.A., Welch, G.R.: Cytosociology: a field-theoretic view of cell metabolism. In: Ji, S. (ed.) Molecular Theories of Cell Life and Death, pp. 282–323. Rutgers University Press, New Brunswick (1991)

    Google Scholar 

  • Socolich, M., Lockless, S.W., Russ, W.P., Lee, H., Gardneer, K.H., Ranganathan, R.: Evolutionary information for specifying a protein fold. Nature 437, 512–518 (2005)

    Article  ADS  Google Scholar 

  • Storz, G.: An expanding universe of noncoding RNAs. Science 296, 1260–1263 (2002)

    Article  ADS  Google Scholar 

  • Süel, G.M., Lockless, S.W., Wall, M.A., Ranganathan, R.: Evolutionarily conserved networks of residues mediate allosteric communication in proteins. Nat. Struct. Biol. 10(1), 59–69 (2003)

    Article  Google Scholar 

  • Tanenbaum, A.S.: Structured Computer Organization, 4th edn. Prentice- Hall of India, New Delhi (2003). 5

    Google Scholar 

  • Tang, J., Breaker, R.R.: Structural diversity of self-cleaving ribozymes. Proc. Natl. Acad. Sci. U.S.A. 97(11), 5784–9 (2000)

    Article  ADS  Google Scholar 

  • Tjian, R.: Molecular machines that control genes. Sci. Am. 272(2), 54–61 (1995)

    Article  Google Scholar 

  • Tucker, B.J., Breaker, R.R.: Riboswitches as versatile gene control elements. Curr. Opin. Struct. Biol. 15(3), 342–8 (2005). doi:10.1016/j.sbi.2005.05.003 DOI:dx.doi.org. PMID 15919195

    Article  Google Scholar 

  • Uchihashi, T., Iino, R., Ando, T., Noji, H.: High-speed atomic force microscopy reveals rotary catalysis of Rotorless F1-ATPase. Science 333, 755–758 (2011)

    Article  ADS  Google Scholar 

  • Vitreschak, A.G., Rodionov, D.A., Mironov, A.A., Gelfand, M.S.: Riboswitches: the oldest mechanism for the regulation of gene expression. Trends Genet. 20(1), 44–50 (2004). doi:10.1016/j.tig.2003.11.008 DOI:dx.doi.org. PMID 14698618

    Article  Google Scholar 

  • Volkenstein, M.V.: The conformon. J. Theoret. Biol. 34, 193–195 (1972)

    Article  Google Scholar 

  • Volkenstein, M.V.: Electronic-conformational interaction in biopolymers. In: Welch, G.R. (ed.) The Fluctuating Enzymes, pp. 403–419. Wiley, New York (1986)

    Google Scholar 

  • Wang, D., Gribskov, M.: Examining the architecture of cellular computing through a comparative study with a computer. J. Roy. Soc. Interface 2, 187–195 (2005)

    Article  Google Scholar 

  • Welch, G.R., Kell, D.B.: Not just catalysts—molecular machines in bioenergetics. In: Welch, G.R. (ed.) The Fluctuating Enzymes, pp. 451–492. Wiley, New York (1986)

    Google Scholar 

  • Widom, B.: Molecular transitions and chemical reactions rates. Science 148, 1555–15560 (1965)

    Article  ADS  Google Scholar 

  • Williams, R.J.P.: Electron transfer and energy conservation. Curr. Top. Bioenerg. 3, 79–158 (1969)

    Google Scholar 

  • Winkler, W.C., Nahvi, A., Roth, A., Collins, J.A., Breaker, R.R.: Control of gene expression by a natural metabolite-responsive ribozyme. Nature 428(6980), 281–286 (2004)

    Article  ADS  Google Scholar 

  • Wochner, A., Attwater, J., Coulson, A., Holliger, P.: Ribozyme-catalyzed transcription of an active ribozyme. Science 332(6026), 209–12 (2011)

    Article  ADS  Google Scholar 

  • Wolynes, P.G., Omuchic, J.N., Thirumalai, D.: Navigating the folding routes. Science 267, 1619–1620 (1995)

    Article  ADS  Google Scholar 

  • Xie, X.S., Lu, P.H.: Single-molecule enzymology. J. Biol. Chem. 274(23), 15967–15970 (1999)

    Article  Google Scholar 

  • Xie, X.S.: Single-molecule approach to enzymology. Single Mol. 2(4), 229–239 (2001)

    Article  ADS  Google Scholar 

  • Zamore, P.D.: Ancient pathways programmed by small RNAs. Science 296, 1265–1269 (2002)

    Article  ADS  Google Scholar 

  • Zwanzig, R.: Rate processes with dynamic disorder. Acc. Chem. Res. 23, 148–152 (1990)

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Dept. of Pharmacol. & Toxicol. Ernest Mario School of Pharmacy, Rutgers University, Piscataway, NJ, 08854, USA

    Sungchul Ji PhD

Authors
  1. Sungchul Ji PhD
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Sungchul Ji PhD .

Rights and permissions

Reprints and permissions

Copyright information

© 2012 Springer Science+Business Media, LLC

About this chapter

Cite this chapter

Ji, S. (2012). Subcellular Systems. In: Molecular Theory of the Living Cell. Springer, New York, NY. https://doi.org/10.1007/978-1-4614-2152-8_11

Download citation

  • DOI: https://doi.org/10.1007/978-1-4614-2152-8_11

  • Published:

  • Publisher Name: Springer, New York, NY

  • Print ISBN: 978-1-4614-2151-1

  • Online ISBN: 978-1-4614-2152-8

  • eBook Packages: Physics and AstronomyPhysics and Astronomy (R0)

Publish with us

Policies and ethics

Search

Navigation