A rate distortion approach to protein symmetry

BioSystems

Volumn 101, Issue 2, 2010, Pages 97-108

  Wallace, Rodrick ^a  

^a NEW YORK STATE PSYCHIATRIC INSTITUTE   (United States)

Author keywords

Development; Groupoid; Information theory; Phase transition; Protein folding disorders; Rate distortion; Spontaneous symmetry breaking

Indexed keywords

BIOCHEMISTRY; CONVERGENT EVOLUTION; DISEASE CONTROL; DISEASE TREATMENT; ETIOLOGY; EVOLUTIONARY BIOLOGY; GENOME; METABOLISM; NATURAL SELECTION; NUMERICAL MODEL; PROTEIN; SYMMETRY;

ARTICLE; CATALYSIS; DEVELOPMENTAL GENE; ECOSYSTEM; ENERGY; EVOLUTION; GENETIC CODE; MEASUREMENT; PROTEIN AGGREGATION; PROTEIN FOLDING; PROTEIN STRUCTURE; RATE DISTORTION; CHEMICAL MODEL; CODON; GENETICS; INFORMATION SCIENCE; MOLECULAR EVOLUTION; PROTEIN CONFORMATION; PROTEIN SYNTHESIS;

CODON;

CODON; EVOLUTION, MOLECULAR; INFORMATION THEORY; MODELS, CHEMICAL; PROTEIN BIOSYNTHESIS; PROTEIN CONFORMATION; PROTEIN FOLDING;

EID: 77954540255     PISSN: 03032647     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.biosystems.2010.05.002     Document Type: Article

References (48)

1. Adami C., Ofria C., Collier T. Evolution of biological complexity. Proceedings of the National Academy of Sciences of the United States of America 2000, 97:4463-4468.
2. Adami C., Cerf N. Physical complexity of symbolic sequences. Physica D 2000, 137:62-69.
3. Andre I., Strauss C., Kaplan D., Bradley P., Baker D. Emergence of symmetry in homooligomeric biological assemblies. Proceedings of the National Academy of Sciences of the United States of America 2008, 105:16148-16152.
4. Anfinsen C. Principles that govern the folding of protein chains. Science 1973, 181:223-230.
5. Ash R. Information Theory 1990, Dover, New York.
6. Atlan H., Cohen I. Immune information, self-organization, and meaning. International Immunology 1998, 10:711-717.
7. Beck C., Schlogl F. Thermydynamics of Chaotic Systems 1995, Cambridge University Press.
8. Bennett C. Logical depth and physical complexity. The Universal Turing Machine: A Half-Century Survey 1988, 227-257. Oxford University Press. R. Herkin (Ed.).
9. Bos, R., 2007. Continuous representations of groupoids. arXiv:math/0612639.
10. Buneci, M., 2003. Representare de Groupoizi, Editura Mirton, Timosoara, Romania.
11. Canfield D., Rosing M., Bjerrum C. Early anaerobic metabolisms. Philosophical Transactions of the Royal Society B 2006, 351:1819-1836.
12. Champagnat N., Ferriere R., Meleard S. Unifying evolutionary dynamics: from individual stochastic processes to macroscopic models. Theoretical Population Biology 2006, 69:297-321.
13. Cover T., Thomas H. Elements of Information Theory 1991, Wiley, New York.
14. Dembo A., Zeitouni O. Large Deviations and Applications 1998, Springer, New York. 2nd ed.
15. Diekmann U., Law R. The dynamical theory of coevolution: a derivation from stochastic ecological processes. Journal of Mathemaical Biology 1996, 34:579-612.
16. Dill K., Banu Ozkan S., Weikl T., Chodera J., Voelz V. The protein folding problem: when will it be solved?. Current Opinion in Structural Biology 2007, 17:342-346.
17. Ellis R. Entropy, Large Deviations, and Statistical Mechanics 1985, Springer, New York.
18. Feynman R. Lectures on Computation 2000, Westview, New York.
19. Goodsell D., Olson A. Structural symmetry and protein function. Annual Reviews of Biophysics and Biomolecular Structure 2000, 29:105-153.
20. Gunderson L. Ecological resilience in theory and application. Annual Reviews of Ecological Systematics 2000, 31:425-439.
21. Haataja L., Gurlo T., Huang C., Butler P. Islet amylod in type 2 diabetes, and the toxic oligomer hypothesis. Endocrine Reviews 2008, 29:303-316.
22. Holling C. Resilience and stability of ecological systems. Annual Reviews of Ecological Systematics 1973, 4:1-23.
23. Holling C. Cross-scale morphology, geometry, and dynamics of ecosystems. Ecological Monographs 1992, 41:1-50.
24. Khinchin A. Mathematical Foundations of Information Theory 1957, Dover, New York.
25. Landau L., Lifshitz E. Statistical Physics, Part I 2007, Elsevier, New York.
26. Lei, J., Huang, K., 2010. Protein folding: a perspective from statistical physics. arXiv:10025013v1.
27. Levin, S., 1989. Ecology in theory and application. In: Levin, S., Hallam, T., Gross, L. (Eds.), Applied Mathematical Ecology, Biomathematics Texts, vol. 18. Springer, NY.
28. Levinthal C. Are there pathways for protein folding?. Journal de Chimie Physique et de Physicochimie Biologique 1968, 65:44-45.
29. Levinthal, C., 1969. In: Debrunner, et al. (Eds.), Mossbauer Spectroscopy. University of Illinois Press, Urbana, pp. 22-24.
30. Ofria C., Adami C., Collier T. Selective pressures on genomes in molecular evolution. Journal of Theoretical Biology 2003, 222:477-483.
31. Onuchic J., Wolynes P. Theory of protein folding. Current Opinion in Structural Biology 2004, 14:70-75.
32. Pettini M. Geometry and Topology in Hamiltonian Dynamics 2007, Springer, New York.
33. Plaxco K., Simons K., Baker D. Contact order, transition state placement and the refolding rates of single domain proteins. Journal of Molecular Biology 1998, 277:985-994.
34. Protter P. Stochastic Integration and Differential Equations: A New approach 1990, Springer, New York.
35. Rockafellar R. Convex Analysis 1970, Princeton University Press, Princeton, NJ.
36. Scheuner D., Kaufman R. The unfolded protein response: a pathway that links insulin demand with β-cell failure and daibetes. Endocrine Reviews 2008, 29:317-333.
37. Sharma V., Kaila V., Annila A. Protein folding as an evolutionary process. Physica A 2009, 388:851-862.
38. Tlusty T. A model for the emergence of the genetic code as a transition in a noisy information channel. Journal of Theoretical Biology 2007, 249:331-342.
39. Wallace R., Wallace D. Punctuated equilibrium in statistical models of generalized coevolutionary resilience: how sudden ecosystem transitions can entrain both phenotype expression and Darwinian selection. Transactions on Computational Systems Biology IX 2008, LNBI 5121:23-85.
40. Wallace R., Wallace R.G., Wallace D. Farming Human Pathogens: Ecological Resilience and Evolutionary Process 2009, Springer, New York.
41. Wallace R., Wallace D. Code, context, and epigenetic catalysis in gene expression. Transactions on Computational Systems Biology XI 2009, LNBI 5750:283-334.
42. Wallace R. Consciousness: A Mathematical Treatment of the Global Neuronal Workspace Model 2005, Springer, New York.
43. Wallace R. Metabolic constraints on the eukaryotic transition. Origins of Life and Evolution of Biospheres 2009, 39:165-176.
44. Wallace, R., 2010. Metabolic constraints on the evolution of genetic codes: did multiple 'preaerobic' ecosystem transitions entrain richer dialects via Serial Endosymbiosis? http://precedings.nature.com/documents/4120/version/3.
45. Wallach, J., Rey, M., 2009. A socioeconomic analysis of obesity and diabetes in New York City. In: Public Health Research, Practice, and Policy. Centers for Disease Control and Prevention, http://www.cdc.gov/pcd/issues/2009/jul/08_0215.htm.
46. Weinstein A. Groupoids: unifying internal and external symmetry. Notices of the American Mathematical Association 1996, 43:744-752.
47. Wolynes P. Symmetry and the energy landscapes of biomolecules. Proceedings of the National Academy of Sciences of the United States of America 1996, 93:14249-14255.
48. Zhang, Q., Wang, Y., Huang, E., 2009. Changes in racial/ethnic disparities in the prevalence of type 2 diabetes by obesity level among US adults. Ethnicity and Health 14, 439-457.