Self-organization versus watchmaker: Ambiguity of molecular recognition and design charts of cellular circuitry

Journal of Molecular Recognition

Volumn 20, Issue 4, 2007, Pages 205-214

  Kurakin, Alexei ^a  

^a BUCK INSTITUTE FOR RESEARCH ON AGING   (United States)

Author keywords

Adaptive plasticity; Bounded stochasticity; Evolutionary memory; Molecular recognition; Self organization

Indexed keywords

ENZYME; PROTEIN;

ADAPTATION; ANIMAL; BIOLOGICAL MODEL; CHEMICAL STRUCTURE; GENETIC SELECTION; HUMAN; METABOLISM; MOLECULAR EVOLUTION; NUCLEOTIDE SEQUENCE; PHYSIOLOGY; REVIEW; SIGNAL TRANSDUCTION;

ADAPTATION, BIOLOGICAL; ANIMALS; CONSERVED SEQUENCE; ENZYMES; EVOLUTION, MOLECULAR; HUMANS; METABOLIC NETWORKS AND PATHWAYS; MODELS, BIOLOGICAL; MODELS, MOLECULAR; PROTEINS; SELECTION (GENETICS); SIGNAL TRANSDUCTION;

EID: 34948901982     PISSN: 09523499     EISSN: 10991352     Source Type: Journal    
DOI: 10.1002/jmr.839     Document Type: Review

References (75)

1. Almaas E, Kovacs B, Vicsek T, Oltvai ZN, Barabasi AL. 2004. Global organization of metabolic fluxes in the bacterium Escherichia coli. Nature 427: 839-843.
2. Babady NE, Pang YP, Elpeleg O, Isaya G. 2007. Cryptic proteolytic activity of dihydrolipoamide dehydrogenase. Proc. Natl Acad. Sci. USA 104: 6158-6163.
3. Bai C, Wang C, Xie XS, Wolynes PG. 1999. Single molecule physics and chemistry. Proc. Natl Acad. Sci. USA 96: 11075-11076.
4. Berezovsky IN, Shakhnovich EI. 2005. Physics and evolution of thermophilic adaptation. Proc. Natl Acad. Sci. USA 102: 12742-12747.
5. Bezprozvanny I, Maximov A. 2001. Classification of PDZ domains. FEBS Lett. 509: 457-462.
6. Bradbury J. 2005. Molecular insights into human brain evolution. PLoS Biol. 3: e50.
7. Castagnoli L, Costantini A, Dall'Armi C, Gonfloni S, Montecchi-Palazzi L, Panni S, Paoluzi S, Santonico E, Cesareni G. 2004. Selectivity and promiscuity in the interaction network mediated by protein recognition modules. FEBS Lett. 567: 74-79.
8. Clegg JS, Wheatley DN. 1991. Intracellular organization: evolutionary origins and possible consequences to metabolic rate control in vertebrates. Am. Zool. 31: 504-513.
9. Copley SD. 2003. Enzymes with extra talents: moonlighting functions and catalytic promiscuity. Curr. Opin. Chem. Biol. 7: 265-272.
10. Das S, Smith TF. 2000. Identifying nature's protein Lego set. Adv. Protein Chem. 54: 159-183.
11. Dev KK. 2004. Making protein interactions druggable: targeting PDZ domains. Nat. Rev. Drug Discov. 3: 1047-1056.
12. Dobzhansky T. 1973. Nothing in biology makes sense except in the light of evolution. Am. Biol. Teach. 35: 125-129.
13. Emmerling M, Dauner M, Ponti A, Fiaux J, Hochuli M, Szyperski T, Wuthrich K, Bailey JE, Sauer U. 2002. Metabolic flux responses to pyruvate kinase knockout in Escherichia coli. J. Bacteriol. 184: 152-164.
14. Farkas I, Jeong H, Vicsek T, Barabasi A, Oltvai Z. 2003. The topology of the transcription regulatory network in the yeast, Saccharomyces cerevisiae. Physica A 318: 601-612.
15. Fenimore PW, Frauenfelder H, McMahon BH, Parak FG. 2002. Slaving: solvent fluctuations dominate protein dynamics and functions. Proc. Natl Acad. Sci. USA 99: 16047-16051.
16. Fewell JH. 2003. Social insect networks. Science 301: 1867-1870.
17. Frauenfelder H. 2002. Proteins: paradigms of complexity. Proc. Natl Acad. Sci. USA 99 (Suppl 1): 2479-2480.
18. Fujita A, Kurachi Y. 2000. SAP family proteins. Biochem. Biophys. Pes. Commun. 269: 1-6.
19. Harris BZ, Lim WA. 2001. Mechanism and role of PDZ domains in signaling complex assembly. J. Cell. Sci. 114: 3219-3231.
20. Hartman H. 1975. Speculations on the origin and evolution of metabolism. J. Mol. Evol. 4: 359-370.
21. Herndon LA, Schmeissner PJ, Dudaronek JM, Brown PA, Listner KM, Sakano Y, Paupard MC, Hall DH, Driscoll M. 2002. Stochastic and genetic factors influence tissue-specific decline in ageing C. elegans. Nature 419: 808-814.
22. Hochachka PW. 1999. The metabolic implications of intracellular circulation. Proc. Natl Acad. Sci. USA 96: 12233-12239.
23. Horowitz NH. 1945. On the evolution of biochemical syntheses. Proc. Natl Acad. Sci. USA 31: 153-157.
24. Hu H, Columbus J, Zhang Y, Wu D, Lian L, Yang S, Goodwin J, Luczak C, Carter M, Chen L, James M, Davis R, Sudol M, Rodwell J, Herrero JJ. 2004. A map of WW domain family interactions. Proteomics 4: 643-655.
25. Hume DA. 2000. Probability in transcriptional regulation and its implications for leukocyte differentiation and inducible gene expression. Blood 96: 2323-2328.
26. Hung AY, Sheng M. 2002. PDZ domains: structural modules for protein complex assembly. J. Biol. Chem. 277: 5699-5702.
27. James LC, Tawfik DS. 2001. Catalytic and binding poly-reactivities shared by two unrelated proteins: the potential role of promiscuity in enzyme evolution. Protein Sci. 10: 2600-2607.
28. Jensen RA. 1976. Enzyme recruitment in evolution of new function. Annu. Rev. Microbiol. 30: 409-425.
29. Jeong H, Tombor B, Albert R, Oltvai ZN, Barabasi AL. 2000. The large-scale organization of metabolic networks. Nature 407: 651-654.
30. Kay BK, Kasanov J, Knight S, Kurakin A. 2000. Convergent evolution with combinatorial peptides. FEBS Lett. 480: 55-62.
31. Keskin O, Nussinov R. 2007. Similar binding sites and different partners: implications to shared proteins in cellular pathways. Structure 15: 341-354.
32. Kim E, Sheng M. 2004. PDZ domain proteins of synapses. Nat. Rev. Neurosci. 5: 771-781.
33. Kipp RA, Case MA, Wist AD, Cresson CM, Carrell M, Griner E, Wiita A, Albiniak PA, Chai J, Shi Y, Semmelhack MF, McLendon GL. 2002. Molecular targeting of inhibitor of apoptosis proteins based on small molecule mimics of natural binding partners. Biochemistry 41: 7344-7349.
34. Kuhn T. 1996. The Structure of Scientific Revolutions. The University of Chicago Press: Chicago and London.
35. Kurakin A. 2004. Self-organization versus watchmaker: stochasticity and determinism in molecular and cell biology. http://www.alexeikurakin.org/text/ ak030304.pdf
36. Kurakin A. 2005a. Self-organization versus watchmaker: stochastic dynamics of cellular organization. Biol. Chem. 386: 247-254.
37. Kurakin A. 2005b. Self-organization vs watchmaker: stochastic gene expression and cell differentiation. Dev. Genes Evol. 215: 46-52.
38. Kurakin A. 2005c. Stochastic cell. IUBMB Life 57: 59-63.
39. Kurakin A. 2006. Self-organization versus watchmaker: molecular motors and protein translocation. Biosystems 84: 15-23.
40. Kurakin A, Swistowski A, Wu SC, Bredesen DE. 2007. The PDZ domain as a complex adaptive system (in press).
41. Kuriyan J, Cowburn D. 1997. Modular peptide recognition domains in eukaryotic signaling. Annu. Rev. Biophys. Biomol. Struct. 26: 259-288.
42. Ladbury JE, Arold S. 2000. Searching for specificity in SH domains. Chem. Biol. 7: R3-R8.
43. Landgraf C, Panni S, Montecchi-Palazzi L, Castagnoli L, Schneider-Mergener J, Volkmer-Engert R, Cesareni G. 2004. Protein interaction networks by proteome peptide scanning. PLoS Biol. 2: E14.
44. Lee WC, Huang H, Feng G, Sanes JR, Brown EN, So PT, Nedivi E. 2006. Dynamic remodeling of dendritic arbors in GABAergic interneurons of adult visual cortex. PLoS Biol. 4: e29.
45. Lim IA, Hall DD, Hell JW. 2002. Selectivity and promiscuity of the first and second PDZ domains of PSD-95 and synapse-associated protein 102. J. Biol. Chem. 277: 21697-21711.
46. Lindorff-Larsen K, Best RB, Depristo MA, Dobson CM, Vendruscolo M. 2005. Simultaneous determination of protein structure and dynamics. Nature 433: 128-132.
47. Ma B, Shatsky M, Wolfson HJ, Nussinov R. 2002. Multiple diverse ligands binding at a single protein site: a matter of pre-existing populations. Protein Sci. 11: 184-197.
48. Macchiarulo A, Nobeli I, Thornton JM. 2004. Ligand selectivity and competition between enzymes in silico. Nat. Biotechnol. 22: 1039-1045.
49. Major H, Castro-Perez J, Nicholson JK, Wilson ID. 2003. Characterisation of putative pentose-containing conjugates as minor metabolites of 4-bromoaniline present in the urine of rats following intraperitoneal administration. Rapid Commun. Mass Spectrom. 17: 76-80.
50. Masters C. 1991. Cellular differentiation and the microcompartmentation of glycolysis. Mech. Ageing Dev. 61: 11-22.
51. Mayer BJ. 2001. SH3 domains: complexity in moderation. J. Cell. Sci. 114: 1253-1263.
52. Misteli T. 2001. The concept of self-organization in cellular architecture. J. Cell. Biol. 155: 181-185.
53. Moriya H, Shimizu-Yoshida Y, Kitano H. 2006. In vivo robustness analysis of cell division cycle genes in Saccharomyces cerevisiae. PLoS Genet. 2: e111.
54. Nicholson JK, Wilson ID. 2003. Opinion: understanding 'global' systems biology: metabonomics and the continuum of metabolism. Nat. Rev. Drug Discov. 2: 668-676.
55. Nobe Y, Kawaguchi S, Ura H, Nakai T, Hirotsu K, Kato R, Kuramitsu S. 1998. The novel substrate recognition mechanism utilized by aspartate aminotransferase of the extreme thermophile Thermus thermophilus HB8. J. Biol. Chem. 273: 29554-29564.
56. O'Brien PJ, Herschlag D. 1999. Catalytic promiscuity and the evolution of new enzymatic activities. Chem. Biol. 6: R91-R105.
57. Ovadi J, Orosz F, Hollan S. 2004. Functional aspects of cellular microcompartmentation in the development of neurodegeneration: mutation induced aberrant protein-protein associations. Mol. Cell. Biochem. 256-257: 83-93.
58. Pawson T. 2007. Dynamic control of signaling by modular adaptor proteins. Curr. Opin. Cell Biol. 19: 112-116.
59. Porter KR. 1984. The cytomatrix: a short history of its study. J. Cell Biol. 99: 3s-12s.
60. Schacter D. 2001. The Seven Sins of Memory: How the Mind Forgets and Remembers. Houghton Mifflin: New York.
61. Song S, Sjostrom PJ, Reigl M, Nelson S, Chklovskii DB. 2005. Highly nonrandom features of synaptic connectivity in local cortical circuits. PLoS Biol. 3: e68.
62. Sudol M. 1998. From Src Homology domains to other signaling modules: proposal of the 'protein recognition code'. Oncogene 17: 1469-1474.
63. Theise ND. 2005. Now you see it, now you don't. Nature 435: 1165.
64. Theise ND, Harris R. 2006. Postmodern biology: (adult)(stem) cells are plastic, stochastic complex, and uncertain. Handb Exp Pharmacol 174: 389-408.
65. Tompa P, Szasz C, Buday L. 2005. Structural disorder throws new light on moonlighting. Trends Biochem. Sci. 30: 484-489.
66. Tong AH, Drees B, Nardelli G, Bader GD, Brannetti B, Castagnoli L, Evangelista M, Ferracuti S, Nelson B, Paoluzi S, Quondam M, Zucconi A, Hogue CW, Fields S, Boone C, Cesareni G. 2002. A combined experimental and computational strategy to define protein interaction networks for peptide recognition modules. Science 295: 321-324.
67. Uversky VN. 2002. What does it mean to be natively unfolded? Eur. J. Biochem. 269: 2-12.
68. Uversky VN, Oldfield CJ, Dunker AK. 2005. Showing your ID: intrinsic disorder as an ID for recognition, regulation and cell signaling. J. Mol. Recognit. 18: 343-384.
69. Vaccaro P, Dente L. 2002. PDZ domains: troubles in classification. FEBS Lett. 512: 345-349.
70. Van Regenmortel MHV. 2002. A paradigm shift is needed in proteomics: 'structure determines function' should be replaced by 'binding determines function'. J. Mol. Recognit. 15: 349-351.
71. Van Regenmortel MHV. 2007. The rational design of biological complexity: a deceptive metaphor. Proteomics 7: 965-975.
72. Welch GR, Clegg JS (eds). 1987. Organization of Cell Metabolism. Plenum Press: New York.
73. Wu D, Daugherty SC, Van Aken SE, Pai GH, Watkins KL, Khouri H, Tallon LJ, Zaborsky JM, Dunbar HE, Tran PL, Moran NA, Eisen JA. 2006. Metabolic complementarity and genomics of the dual bacterial symbiosis of sharpshooters. PLoS Biol. 4: e188.
74. Xie XS, Lu HP. 1999. Single-molecule enzymology. J. Biol. Chem. 274: 15967-15970.
75. Yang H, Luo G, Kamchanaphanurach P, Louie TM, Rech I, Cova S, Xun L, Xie XS. 2003. Protein conformational dynamics probed by single-molecule electron transfer. Science 302: 262-266.