Free energy and information contents of Conformons in proteins and DNA

BioSystems

Volumn 54, Issue 3, 2000, Pages 107-130

  Ji, Sungchul ^a  

^a RUTGERS UNIVERSITY   (United States)

Author keywords

Conformational strains; DNA topoisomerases; Frank Condon principle; Free energy; Information; Stress induced duplex destabilization

Indexed keywords

BIOPOLYMER; CIRCULAR DNA; DNA TOPOISOMERASE (ATP HYDROLYSING); DOUBLE STRANDED DNA;

CELL ENERGY; CELL FUNCTION; CELL TRANSPORT; CONFORMATION; CONFORMON; DNA STRUCTURE; ENERGY TRANSFER; ENTROPY; GENETIC CODE; GENETIC TRANSCRIPTION; OXIDATIVE PHOSPHORYLATION; PROTEIN CONFORMATION; PROTEIN DNA INTERACTION; PROTEIN PHOSPHORYLATION; REVIEW;

EID: 0033956213     PISSN: 03032647     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0303-2647(99)00073-8     Document Type: Article

References (145)

1. Aczél J., Daróczy Z. On Measures of Information and their Characterizations. 1975;Academic Press, New York.
2. Anderson P.W. Suggested model for prebiotic evolution: the use of chaos. Proc. Natl. Acad. Sci. USA. 80:1983;3386-3390.
3. Anderson P.W. Computer modeling of prebiotic evolution: general theoretical ideas on the origin of biological information. Comm. Mol. Cell. Biophys. 4:1987;99-108.
4. Banerjee A., Sobell H.M. Presence of nonlinear excitations in DNA structure and their relationship to DNA premelting and drug intercalation. J. Biomol. Struct. Dyn. 1:1983;253-262.
5. Bauer W., Vinograd J. Interaction of closed circular DNA with intercalative dyes II. The free energy of superhelix formation in SV40 DNA. J. Mol. Biol. 47:1970;419-435.
6. Baverstock K.F., Cundall R.B. Solitons and energy transfer in DNA. Nature. 332:1988;312-313.
7. Beerman T.A., Lebowitz J. Further analysis of the altered secondary structure of superhelical DNA. Sensitivity to methyl mercuric hydroxide as chemical probe for unpaired bases. J. Mol. Biol. 79:1973;451.
8. Benham C.J. Theoretical analysis of heteropolymeric transitions in superhelical DNA molecules of specified sequences. J. Chem. Phys. 92:1990;6294-6305.
9. Benham C.J. Energetics of the strand separation transition in superhelical DNA. J. Mol. Biol. 225:1992;835-847.
10. Benham C.J. Sites of predicted stress-induced DNA duplex destabilization occur preferentially at regulatory sites. Proc. Natl. Acad. Sci. USA. 90:1993;2999-3003.
11. Benham C.J. Duplex destabilization in superhelical DNA is predicted to occur at specific transcriptional regulatory regions. J. Mol. Biol. 255:1996;425-434.
12. Benham C.J. Computation of DNA structural variabilitya new predictor of DNA regulatory regions. CABIOS. 12(5):1996;375-381.
13. Bennett C.H. Thermodynamics of computationa review. Int. J. Theor. Phys. 21(12):1982;905-940.
14. Berger J.M., Wang J.C. Recent developments in DNA topoisomerases II structure and mechanism. Curr. Opin. Struct. Biol. 6(1):1996;84-90.
15. Bohm D. Quantum Theory. 1979;Dover, New York.
16. Borman, S., 1994. High-resolution structure obtained for ATP synthesis enzyme. C and E News, September, pp. 31-32.
17. Boyer P.D. The binding change mechanism for ATP synthetaseSome probabilities and possibilities. Biochim. Biophys. Acta. 1140:1993;215-250.
18. Bramhill D., Kornberg A. Duplex opening by dnaA protein at novel sequences in initiation of replication at the origin of the E. coli chromosome. Cell. 52:1988;743-755.
19. Breslauer K.J., Frank R., Blöcker H., Marky L.A. Predicting DNA duplex stability from the base sequence. Proc. Natl. Acad. Sci. USA. 83:1986;3746-3750.
20. Brillouin L. Science and Information Theory. 2nd edn:1962;Academic Press, New York.
21. Callen H.B. Thermodynamics: An Introduction to the Physical Theories of Equilibrium Thermostatics and Irreversible Thermodynamics. 1962;90-106 Wiley, New York.
22. Careri G., Wyman J. Soliton-assisted unidirectional circulation in a biochemical cycle. Proc. Natl. Acad. Sci. 81:1984;4386-4388.
23. Careri G., Wyman J. Unidirectional circulation in a prebiotic photochemical cycle. Proc. Natl. Acad. Sci. 82:1985;4115-4116.
24. Ciblis P., Cosic I. The possibility of soliton/exciton transfer in proteins. J. Theor. Biol. 184:1997;331-338.
25. Clark B.F.C. The Genetic Code. 1977;6 The Camelot Press, Southampton.
26. Collier J. Causation is the transfer of information. Sankey H. Causation, Natural Laws and Explanation. 1999;Kluwer, Dordrecht.
27. Culler J. Ferdinand de Saussure. Revised edn:1986;Cornell University Press, Ithaca, NY.
28. Davydov A.S. The theory of contraction of proteins under their excitation. J. Theor. Biol. 38:1973;559-569.
29. Davydov A.S. Excitons and solitons in molecular systems. Int. Rev. Cytol. 106:1987;183-225.
30. Dean W.W., Lebowitz J. Partial alteration of secondary structure in native superhelical DNA. Nat. New Biol. 231:1971;5-8.
31. Depew R.E., Wang J.C. Conformational fluctuations of DNA helix. Proc. Natl. Acad. Sci. USA. 72:1975;4275-4279.
32. Drlica K. Biology of bacterial deoxyribonucleic acid topoisomerases. Microbiol. Rev. 48(4):1984;273-289.
33. Drolet M., Wu H.-Y., Liu L.F. Roles of DNA topoisomerases in transcription. Adv. Pharmacol. 29A:1994;135-146.
34. Englander S.W., Kallenbach N.R., Heeger A.J., Krumhansl J.A., Litwin S. Nature of the open state in long polynucleotide double helices: Possibility of soliton excitation. Proc. Natl. Acad. Sci. USA. 77(12):1980;7222-7226.
35. Fersht A. Enzyme Structure and Mechanisms. 2nd edn:1985;W.H. Freeman, San Francisco, CA.
36. Frauenfelder H. Function and dynamics of myoglobin. Ann. N.Y. Acad. Sci. 504:1987;151-167.
37. Freund J.A. Information, long-range correlations and extended memory of symbol sequences. Kornwachs K., Jacoby K. Information: New Questions to a Multidisciplinary Concept. 1996;41-62 Akademie-Verlag, Berlin.
38. Frost A.A., Pearson R.G. Kinetics and Mechanism. 2nd edn:1961;211-213 Wiley, New York.
39. Gedda L., Brenci G. Chronogenetics: The Inheritance of Biological Time. 1978;Thomas, Springfield, IL.
40. Gellert M. DNA topoisomerases. Annu. Rev. Biochem. 50:1981;879-910.
41. Gellert M., Mizuuchi K., O'Dea M.H., Nash H. DNA gyrase: an enzyme that introduces superhelical turns into DNA. Proc. Natl. Acad. Sci. USA. 73:1976;3872-3876.
42. Gernert D. Pragmatic information as a unifying concept. Kornwachs K., Jacoby K. Information: New Questions to a Multidisciplinary Concept. 1996;147-162 Akademie-Verlag, Berlin.
43. Green D.E. General discussion. Ann. N.Y. Acad. Sci. 227:1974;108-110.
44. Green D.E., Ji S. The electromechanochemical model of mitochondrial structure and function. Schultz J., Cameron B.F. Molecular Basis of Electron Transport. 1972;1-44 Academic Press, New York.
45. Hockett C.F. The origin of speech. Sci. Am. 203(3):1960;89-96.
46. Hsieh T., Wang J.C. Thermodynamic properties of superhelical DNAs. Biochemistry. 14(3):1975;527-535.
47. Huang R.-Y., Kowalski D. A DNA unwinding element and an ARS consensus comprise a replication origin within a yeast chromosome. EMBO J. 12(12):1993;4521-4531.
48. Huang R.-Y., Kowalski D. Multiple DNA elements in ARS305 determine replication origin activity in a yeast chromosome. Nucleic Acids Res. 24(5):1996;816-823.
49. Jencks W.P. Binding energy, specificity, and enzymic catalysis: The Circe Effect. Adv. Enzymol. 43:1975;219-410.
50. Jencks W.P. Reaction mechanisms, catalysis, and movement. Protein Sci. 3:1994;2459-2464.
51. Ji S. A general theory of ATP synthesis and utilization. Ann. N.Y. Acad. Sci. 227:1974;211-226.
52. Ji S. Energy and negentropy in enzymic catalysis. Ann. N.Y. Acad. Sci. 227:1974;419-437.
53. Ji S. A model of oxidative phosphorylation that accommodates the chemical intermediate, chemiosmotic, localized proton and conformational hypotheses. J. Theor. Biol. 59:1976;319-330.
54. Ji S. A possible molecular mechanisms of free energy transfer in oxidative phosphorylation. J. Theor. Biol. 68:1977;607-612.
55. Ji S. The principles of ligand-protein interactions and their application to the mechanism of oxidative phosphorylation. Yagi K. Structure and Function of Biomembranes. 1979;25-37 Japan Scientific Societies Press, Tokyo.
56. Ji S. Conformons and solitons: new concepts in bioenergetics. Mishra R.K. The Living StateII. 1985;563-574 World Scientific Publishing Company, Singapore.
57. Ji S. The Bhopalator: a molecular model of the living cell. Asian J. Exp. Sci. 1:1985;1-33.
58. Ji S. The Bhopalatora molecular model of the living cell based on the concepts of conformons and dissipative structures. J. Theor. Biol. 116:1985;399-426.
59. Ji S. Watson-Crick and Prigoginian forms of genetic information. J. Theor. Biol. 130:1988;239-245.
60. Ji S. The BhopalatorA molecular model of the living cell: new developments. Mishra R.K. Molecular and Biological Physics of Living Systems. 1990;187-214 Kluwer, Dordrecht.
61. Ji S. Biocybernetics: A machine theory of biology. Ji S. Molecular Theories of Cell Life and Death. 1991;1-237 The Rutgers University Press, New Brunswick.
62. Ji S. A cell linguistic analysis of apoptosis. Comm. Toxicol. 5(6):1997;571-585.
63. Ji S. Isomorphism between cell and human languages: molecular biological, bioinformatic and linguistic implications. BioSystems. 44:1997;17-39.
64. Ji S. The linguistics of DNA: Words, sentences, grammar, phonetics and semantics. Ann. N.Y. Acad. Sci. 870:1999;411-417.
65. Ji S. The cell as the smallest DNA-based molecular computer. BioSystems. 52:1999b;122-123.
66. Ji S., Finette S. Codons, conformons and dissipative structures: A molecular theory of the living state. Mishra R.K. The Living StateII. 1985;546-562 World Scientific Publishing, Singapore.
67. Kauzmann W. Quantum Chemistry: An Introduction. 1957;Academic Press, New York.
68. Kemeny G., Goklany I.M. Polarons and conformons. J. Theor. Biol. 40:1973;107-123.
69. Kemeny G., Goklany I.M. Quantum mechanical model for conformons. J. Theor. Biol. 48:1974;23-38.
70. Klonowski W., Klonowska M.T. Biophysical time on macromolecular level. Biomathematics. 80:1982;28-33.
71. Kornwachs K., Jacoby K. Information: New Questions to a Multidisciplinary Concept. 1996;Akademie-Verlag, Berlin.
72. Kowalski D., Eddy M.J. The DNA unwinding element: a novel, cis-acting component that facilitates opening of the Escherichia coli replication origin. EMBO J. 8(13):1989;4335-4344.
73. Kowalski D., Natale D.A., Eddy M.J. Stable DNA unwinding, not `breathing,' accounts for single-strand-specific nuclease hypersensitivity of specific A+T-rich sequences. Proc. Natl. Acad. Sci. USA. 85:1988;9464-9468.
74. Kroemer G., Zamzami N., Susin S.A. Mitochondrial control of apoptosis. Immunol. Today. 18(1):1997;44-51.
75. Küppers B.-O. The context-dependence of biological information. Kornwachs K., Jacoby K. Information: New Questions to a Multidisciplinary Concept. 1996;137-145 Akademie-Verlag, Berlin.
76. Lauffer M.A. The significance of entropy-driven processes in biological systems. Comm. Mol. Cell. Biophys. 2(2):1983;99-109.
77. Lin S., Kowalski D. DNA helical instability facilitates initiation at the SV40 replication origin. J. Mol. Biol. 235:1994;496-507.
78. Lindsley J.E., Wang J.C. Study of allosteric communication between protomers by immunotagging. Nature. 361:1993;749-750.
79. Liszka J.J. A General Introduction to the Semeiotic of Charles Sanders Peirce. 1996;Indiana University Press, Bloomington, IN.
80. Liu L.F. Preface. Adv. Pharmacol. 29a:1994;xv.
81. Liu L.F., Wang J.C. Micrococcus luteus DNA gyrase: Active components and a model for its supercoiling of DNA. Proc. Natl. Acad. Sci. USA. 75(5):1978;2098-2102.
82. Liu L.F., Wang J.C. Supercoiling of the DNA template during transcription. Proc. Natl. Acad. Sci. USA. 84:1987;7024-7027.
83. Lomdahl P.S., Kerr W.C. Do Davydov solitons exist at 300 K? Phys. Rev. Lett. 55(11):1985;1235-1238.
84. Lomdahl P.S., Layne S.P., Bigio I.J. Solitons in biology. Los Alamos Sci. 10:1984;2-22.
85. Lumry R. Conformational mechanisms for free energy transduction in protein systems: Old ideas and new facts. Ann. N. Y. Acad. Sci. 227:1974;46-73.
86. Lumry, R., Gregory, R.B., 1986. Free-energy management in protein reactions: concepts, complications, and compensation. In: Welch, G.R. (Ed.) The Fluctuating Enzyme, John Wiley & Sons, New York, pp. 1-190.
87. Mahler G. Quantum information. Kornwachs K., Jacoby K. Information: New Questions to a Multidisciplinary Concept. 1996;103-118 Akademie-Verlag, Berlin.
88. Maxwell A., Gellert M. Mechanistic aspects of DNA topoisomerases. Adv. Protein Chem. 38:1986;69-107.
89. McClare C.W.F. Chemical machines, Maxwell's demon and living organisms. J. Theor. Biol. 30:1971;1-34.
90. McClare C.W.F. Resonance in bioenergetics. Ann. N.Y. Acad. Sci. 227:1974;74-97.
91. Miller C.A., Kowalski D. cis-acting components in the replication origin from ribosomal DNA of Saccharomyces cerevisiae. Mol. Cell. Biol. 13(9):1993;5360-5369.
92. Moore W.J. Physical Chemistry. 3rd edn:1963;597 Prentice-Hall, Englewood Cliffs, NJ.
93. Morrison A., Cozzarelli N.R. Contacts between DNA gyrase and its binding site on DNA: Features of symmetry and asymmetry revealed by protection from nucleases. Proc. Natl. Acad. Sci. USA. 78:1981;1416-1420.
94. Natale D.A., Schubert A.E., Kowalski D. DNA helical stability accounts for mutational defects in a yeast replication origin. Proc. Natl. Acad. Sci. USA. 89:1992;2654-2658.
95. Nicholls D.G. Bioenergetics: An Introduction to the Chemiosmotic Theory. 1982;Academic Press, New York.
96. 1-ATPase. Nature. 386:1997;299-302.
97. Pierce J.R. An Introduction to Information Theory: Symbols, Signals and Noise. 2nd edn:1980;Dover, New York.
98. Pilar F.L. Elementary Quantum Chemistry. 1968;McGraw-Hill, New York.
99. Polozov R.V., Yakushevich L.V. Nonlinear waves in DNA and regulation of transcription. J. Theor. Biol. 130:1988;423-430.
100. Prigogine I. Dissipative structures and biological order. Adv. Biol. Med. Phys. 16:1977;99-113.
101. Prigogine I. From Being to Becoming: Time and Complexity in Physical Sciences. 1980;W.H. Freeman, San Francisco, CA.
102. Pulleyblank D.E., Shive M., Tang D., Vinograd J., Vosberg H.-P. Action of nicking-closing enzyme on supercoiled and nonsupercoiled closed circular DNA: Formation of a Boltzmann distribution of topological isomers. Proc. Natl. Acad. Sci. USA. 72:1975;4280-4284.
103. Rebbi C. Solitons. Sci. Am. 240(2):1979;92-116.
104. Reynolds W.L., Lumry R.W. Mechanisms of Electron Transfer. 1966;Ronald Press, New York.
105. Salthe S.N. Development and Evolution: Complexity and Change in Biology. 1996;MIT Press, Cambridge, MA.
106. Scott A.C. Solitons in biological molecules. Comm. Mol. Cell. Biophys. 3(1):1985;15-37.
107. Scott A.C., Chu F.Y.F., McLaughlin D.W. The soliton: A new concept in applied science. Proc. IEEE. 61(10):1973;1443-1483.
108. Schiff L.I. Quantum Mechanics. 3rd edn:1968;McGraw-Hill, New York.
109. Schrödinger E. What is Life? With Mind and Matter and Autobiographical Sketches. 1998;Cambridge University Press, Cambridge.
110. Service R.F. Chemists explore the power of one. Science. 276:1997;1027-1029.
111. Shaitan K.V., Rubin A.B. Equation of motion of conformon and primitive molecular machines for electron (ion) transport in biological systems. Mol. Biol. 16(5):1982;1004-1018.
112. Shannon C.E. A mathematical theory of communication. Bell Syst. Tech. J. 27:1948;5-18.
113. Shen L.L. Molecular mechanisms of DNA gyrase inhibition by quinolone antibacterials. Adv. Pharmacol. 29A:1994;285-304.
114. Shen Y.R. Solitons made simple. Science. 276:1997;1520-1541.
115. Slater E.C. The oxidative phosphorylation potential. Papa S., Tager J.M., Quagliariello E., Slater E.C. The Energy Level and Metabolic Control in Mitochondria. 1969;255-259 Adriatica Editrice, Bari.
116. Sobell H.M. Actinomycin and DNA transcription. Proc. Natl. Acad. Sci. USA. 82:1985;5328-5331.
117. Sobell H.M., Banerjee A., Lozansky E.D., Zhou G.-P., Chou K.-C. The role of low frequency (acoustic) phonons in determining the premelting and melting behaviours of DNA. Comm. J. Mol. Sci. (Wuhan, China). 2(4):1982;113-128.
118. Souid A.-K., Penefsky H.S. Energetics of ATP dissociation from the mitochondrial ATPase during oxidative phosphorylation. J. Biol. Chem. 270(16):1995;9074-9082.
119. Stein W.D., Eilam Y., Lieb W.R. Active transport of cations across biological membranes. Ann. N.Y. Acad. Sci. 227:1974;328-336.
120. Stonier T. Information and the Internal Structure of the Universe. 1990;Springer, London.
121. Stonier T. Information as a basic property of the universe. BioSystems. 38:1996;135-140.
122. Sweeney H.L. Special topic: Molecular motors of eukaryotic cells. Annu. Rev. Physiol. 58:1996;670.
123. Tanford C. Mechanism of free energy coupling in active transport. Annu. Rev. Biochem. 52:1983;379-409.
124. van der Lubbe J.C.A. Information Theory. 1997;Cambridge University Press, Cambridge.
125. Volkenstein M.V. The Conformon. J. Theor. Biol. 34:1972;193-195.
126. Volkenstein M.V. Simple physical presentation of enzymic catalysis. J. Theor. Biol. 89:1981;45-51.
127. Volkenstein, M.V., 1986. Electronic-conformational interaction in biopolymers. In: Welch, G.R. (Ed.), The Fluctuating Enzyme, John Wiley & Sons, New York, pp. 403-419.
128. Volkenstein M.V., Dogonatze R.R., Madumarov A.K., Urushadze Z.D., Kharkatz Y.I. The theory of enzyme catalysis. Mol. Biol. 6(3):1972;431-439.
129. Wang J.C. Interaction between DNA and an Escherichia coli protein. J. Mol. Biol. 55:1971;523-533.
130. Wang J.C. DNA topoisomerases. Sci. Am. 247(1):1982;94-97.
131. Wang J.C. DNA topoisomerases. Annu. Rev. Biochem. 54:1985;665-697.
132. Wang J.C. DNA topoisomerases as targets of therapeutics: An overview. Adv. Pharmacol. 29A:1994;1-19.
133. Wang J.C. DNA topoisomerases. Annu. Rev. Biochem. 65:1996;635-692.
134. Weil R., Vinograd J. The cyclic helix and cyclic coil forms of polyoma viral DNA. Proc. Natl. Acad. Sci. USA. 50:1963;730-738.
135. Welch, G.R., Kell, D.B., 1986. Not just catalystsMolecular machines in bioenergetics. In: Welch, G.R. (Ed.), The Fluctuating Enzyme, John Wiley & Sons, New York, pp. 451-492.
136. White J.H. Self-linking and the Gauss integral in higher dimensions. Am. J. Math. 91:1969;693-728.
137. White J.H., Bauer W.R. Calculation of the twist and the writhe for representative models of DNA. J. Mol. Biol. 189:1986;329-341.
138. Whitty A., Fierke C.A., Jencks W.P. Role of binding energy with coenzyme A in catalysis by 3-oxoacid coenzyme A transferase. Biochemistry. 34:1995;11678-11689.
139. Wicken J.S. Entropy and information: suggestions for common language. Phil. Sci. 54:1987;176-193.
140. Wicken J.S. Evolution, Thermodynamics, and Information: Extending the Darwinian Program. 1987;Oxford University Press, New York.
141. Wiener N. Cybernetics: or Control and Communication in the Animal and the Machine. 2nd edn:1948;MIT Press, Cambridge, MA.
142. van Workum M., van Dooren S.J.M., Oldenburg N., Molenaar D., Jensen P.R., Snoep J.L., Westerhoff H.V. DNA supercoiling depends on the phosphorylation potential in Escherichia coli. Mol. Microbiol. 20(2):1996;351-360.
143. Yockey H.P. Information Theory and Molecular Biology. 1992;Cambridge University Press, Cambridge.
144. Zgierski M.Z. Mechanisms of conformon creation in α-helical structures. J. Theor. Biol. 55:1975;95-106.
145. Zurek W.H. Complexity, Entropy and the Physics of Information. 1990;Addison-Wesley, Reading, MA.