The metaphysical features of the mechanism for the integration of the information underlying protein folding were studied by applying principles of system logic theory. We conclude that it is not possible to predict all protein three-dimensional structures from protein sequences by one program only. This conclusion is validated in structural genomics in that we also cannot predict protein function from three-dimensional structure by one program only. Our theory also demonstrates that bioinformation flow from gene to biological function is an integration process, rather than an expression (translation) process. A system relationship between a gene and its biological function is also proposed. This electronic document is a “live” template.
KeywordsSystemLogicReductionismFolding
Anfinsen, C.B. (1973) Principles that govern the folding of protein chains. Science, 181, 223-230. http://dx.doi.org/10.1126/science.181.4096.223
Watson, J.D., Laskowski, R.A., Thornton, J.M. (2005) Predicting protein function from sequence and structural data. Curr Opin Struct Biol, 15, 275-284. http://dx.doi.org/10.1016/j.sbi.2005.04.003
Jones, D.J., Sternberg, M.J.E., Thornton, J.M. (2006) Bioinformatics: from molecules to systems. Philosophical Transactions of the Royal Society B: Biological Sciences, 361, 389-391. http://dx.doi.org/10.1098/rstb.2005.1811
Onuchic, J.N., Luthey-Schulten, Z., Wolynes, P.G. (1997) Theory of protein folding: the energy landscape perspective. Annu Rev Phys Chem, 48, 545-600. http://dx.doi.org/10.1146/annurev.physchem.48.1.545
Zhao, Q. (2001) Irreversible thermodynamics theory for protein folding and protein thermodynamics structure. Progress in Biochemistry and Biophysics, 28, 429-435. http://www.pibb.ac.cn/cn/ch/common/view_abstract.aspx?file_no=20010336&flag=1
Lorenz, E.N. (1993) The essence of Chaos. University of Washington Press, Washington.
Ricard, J. (1999) Biological complexity and the dynamics of the life processes. Elsevier, Amsterdam.
Sole, R., Goodwin, B. (2001) Signs of life: How complex pervades biology. Basic Books, New York.
Ideker, T., Galitski, T., Hood, L. (2001) A new approach to decoding life: Systems Biology. Annu Rev Genom Hum Genet, 2, 343-372. http://dx.doi.org/10.1146/annurev.genom.2.1.343
Kondepudi, D., Prigogine, I. (1998) Modern Thermodynamics: from heat engine to dissipative structure. John Wiley Press, New York
Prigogine, I., Stengers, I. (1997) The end of certainty: time, chaos, and the new law of nature. Free Press, New York.
Schieve, W.C., Allen, P.M. (1982) Self-organisation and dissipative structure: application in the physical and social science. University of Texas Press, Austin.
Macy, J. (1991) Mutual Causality in Buddhism and General Systems Theory: The Dharma of Natural Systems. University of New York Press, New York.
Cooper, M.B., Loose, M., Brookfield, J.F.Y. (2008) Evolutionary modelling of feed forward loops in gene regulatory networks. Biosystem, 91, 231-244. http://dx.doi.org/10.1016/j.biosystems.2007.09.004
McCollun, G. (1999) Mutual Causality and the Generation of Biological Control Systems. International Journal of Theoretical Physics, 38, 3253-3267. http://dx.doi.org/10.1023/A:1026690417582
Ferrell, J.E. (2002) Self-perpetuating state in signal transduction: positive feedback, double-negative feedback and bistability. Current opinion in chemical Biology, 6, 140-148.
Dent, E.B. (2003) The Interactional Model: An Alternative to the Direct Cause and Effect Construct for Mutually Causal Organizational Phenomena. Foundations of Science, 8, 295-314. http://dx.doi.org/10.1023/A:1025006302568
Wiene, N (1948) Cybernetics. John Wiley & Sons Inc, New York.
Campbell, D.T. (1974): Downward causation in hierarchically organised biological systems. In: Studies in the Philosophy of Biology, edited by Ayala, F.J. and Dobzhansky, T., Macmillan, London. 139-163.
Crick, F. (1970) Central Dogma of Molecular Biology. Nature, 227, 561-563. http://dx.doi.org/10.1038/227561a0
Baker, D., Sali, A. (2001) Protein Structure Prediction and Structural Genomics. Science, 294, 93-96. http://dx.doi.org/10.1126/science.1065659
Werner, E. (2005) Genome Semantics, in Silico Multicellular Systems and the Central Dogma. FEBS Letters 579, 1779-1782. http://dx.doi.org/10.1016/j.febslet.2005.02.011
Barrow, J.D. (1998) Impossibility: the limits of science and the science of limit. Oxford university Press, London.
Paul, T. (1999) Logic. Routledge New York.
Chew, G.F. (1974) Impasse for the elementary particle concept. The Great ideas today. William Benton, Chicago.
Kline, M. (1980) Mathematics: The loss of certainty. Oxford University Press. London.
Dobbins, S.E., Lesk, V.I., Sternberg, M.J.E. (2008) Insight into protein flexibility: The relationship between normal modes and conformational change upon protein- protein docking. Proc Natl Acad Sci USA 105, 10390- 10395. http://dx.doi.org/10.1073/pnas.0802496105
Cuthbertson, R., Holcombe, M., Paton, R. (1996) Computation in Cellular and Molecular Biological Systems. World Scientific, Singapore.
Thomas, R., Thieffry, D., Kaufman, M. (1995) Dynamical Behaviour of Biological Regulatory Networks. I. Biological Role of Feedback Loops and Practical Use of the Concept of the Loop-Characteristic State. Bull Math Biol. 57, 247-276.
Aramli, L.A., Teschke, C.M. (1999) Single amino acid substitutions globally suppress the folding defects of temperature-sensitive folding mutants of phage P22 coat protein. J Biol Chem, 274, 22217-24. http://dx.doi.org/10.1074/jbc.274.32.22217
Doyle, S.M., Anderson, E., Parent, K.N., Teschke, C.M. (2004) A Concerted Mechanism for the Suppression of a Folding Defect through Interactions with Chaperones. J Biol Chem, 279, 17473-17482. http://dx.doi.org/10.1074/jbc.M400467200
Horovitz, A., Fersht, A.R. (1992) Cooperative interactions during protein folding. J Mol Biol, 224, 733-40. http://dx.doi.org/10.1016/0022-2836(92)90557-Z
Koshland, D.E., Hamadani, K. (2002) Proteomics and Models for Enzyme Cooperativity. J Biol Chem, 277, 46841-46844. http://dx.doi.org/10.1074/jbc.R200014200
Meiler, J., Baker, D. (2003) Coupled prediction of protein secondary and tertiary structure. Proc Natl Acad Sci USA, 100, 12105-12110. http://dx.doi.org/10.1073/pnas.1831973100
Jiang, Y., Lee, A., Chen, J., Ruta, V., Cadene, M., Chait, B.T., Mackinnon, R.(2003) X-ray structure of a voltage- dependent K+ Channel. Nature, 423, 33-41. http://dx.doi.org/10.1038/nature01580
Jiang, Y., Ruta, V., Chen, J., Lee, A., Mackinnon, R. (2003) The principle of gating charge movement in a voltage-dependent K+ channel. Nature, 423, 42-48. http://dx.doi.org/10.1073/pnas.0602350103
Yarov-Yarovoy, V., Baker, D., Catterall, W.A. (2006) Voltage sensor conformations in the open and closed states in ROSETTA structural models of K(+) channels. Proc Natl Acad Sci USA, 103, 7292-7.
Wallqvist, A., Smythers, G.W., Covell, D.G. (1997) Identification of cooperative folding units in a set of native proteins. Protein Sci, 6, 1627-1642. http://dx.doi.org/10.1002/pro.5560060804
Danner, M., Seckler, R. (1993) Mechanism of phage P22 tailspike protein folding mutations. Protein Sci. 2, 1869- 1881. http://dx.doi.org/10.1002/pro.5560021109
Barabási, A., Oltvai, Z.N. (2004) Network biology: understanding the cell’s functional organization. Nature Reviews genetics. 5, 101-113.
Portin, P. (2002) Historical development of the concept of the gene. J Med. Philos, 27, 257-86. http://dx.doi.org/10.1076/jmep.27.3.257.2980
Gerstein, M.B., Bruce, C., Rozowsky, J.S., Zheng, D., Du, J., Korbel, J.O., Emanuelsson, O., Zhang, Z.D., Weissman, S., Snyder, M (2007) What is a gene, post- ENCODE? History and updated definition. Genome Res, 17, 669-681. http://dx.doi.org/10.1101/gr.6339607
Simeonov, P.L. (2010) Integral biomathics: a post- Newtonian view into the logos of bios. Prog Biophys Mol Biol. 102, 85-121. http://dx.doi.org/10.1016/j.pbiomolbio.2010.01.005
Noble, D. (2008) Genes and causation. Philos Transact A Math Phys Eng Sci. 366, 3001-15. http://dx.doi.org/10.1098/rsta.2008.0086
Nicholls, A., Sharp, K.A., Honig, B. (1991) Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins, 11, 281-96. http://dx.doi.org/10.1002/prot.340110407
Sturtevant, J., Yu, M.H., Haase-Pettingell, C., King, J. (1989) Thermostability of temperature sensitive folding mutants of the P22 tailspike protein. J Biol Chem, 264, 10693-10698.
Ellis, R.J. (2006) Molecular chaperones: assisting assembly in addition to folding. Trends Biochem Sci, 31, 395-401. http://dx.doi.org/10.1016/j.tibs.2006.05.001
Collinge, J., Sidle, K.C., Meads, J., Ironside, J., Hill, A.F. (1996) Molecular analysis of prion strain variation and the aetiology of 'new variant' CJD. Nature, 383, 685-90. http://dx.doi.org/10.1038/383685a0
Gunasekaran, K., Tsai, C.J., Kumar, S., Zanuy, D., Nussinov, R. (2003) Extended disordered proteins: targeting function with less scaffold. Trends Biochem. Sci. 28, 81-85. http://dx.doi.org/10.1016/S0968-0004(03)00003-3
Dyson, H.J., Wright, P.E. (2005) Intrinsically unstructured proteins and their functions. Nat Rev Mol Cell Biol. 6, 197-208. http://dx.doi.org/10.1038/nrm1589
Tetreau, C., Lavalette, D. (2005) Dominant features of protein reaction dynamics: conformational relaxation and ligand migration. Biochim Biophys Acta, 1724, 411-24
Bode, C., Kovacs, I.A., Szalay, M.S., Palotai, R., Korcsmaros, T., Csermely, P. (2007) Network analysis of protein dynamics. FEBS Lett. 581, 2776-2782. http://dx.doi.org/10.1016/j.febslet.2007.05.021
Zhao, Q. (2011) Dynamic model of enzyme action. Protein Pept Lett. 18, 92-99. http://dx.doi.org/10.2174/09298661179432861