Evolutionary diversification of the multimeric states of proteins

Proceedings of the National Academy of Sciences of the United States of America

Volumn 110, Issue 30, 2013, Pages

  Lynch, Michael ^a  

^a INDIANA UNIVERSITY   (United States)

Author keywords

Complex adaptation; Oligomer; Quaternary structure

Indexed keywords

ARTICLE; DIRECTIONAL SELECTION; EVOLUTION; GENE STRUCTURE; GENETIC DRIFT; GENOME ANALYSIS; MOLECULAR EVOLUTION; MUTATION RATE; PRIORITY JOURNAL; PROTEIN ASSEMBLY; PROTEIN MULTIMERIZATION;

COMPLEX ADAPTATION; OLIGOMER; QUATERNARY STRUCTURE;

BIOPOLYMERS; EVOLUTION, MOLECULAR; PHYLOGENY; PROTEINS;

EID: 84880659609     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1310980110     Document Type: Article

References (46)

1. Monod J, Wyman J, Changeux JP (1965) On the nature of allosteric transitions: A plausible model. J Mol Biol 12:88-118.
2. Marianayagam NJ, Sunde M, Matthews JM (2004) The power of two: Protein dimerization in biology. Trends Biochem Sci 29(11):618-625.
3. Ali MH, Imperiali B (2005) Protein oligomerization: How and why. Bioorg Med Chem 13(17):5013-5020.
4. Hashimoto K, Nishi H, Bryant S, Panchenko AR (2011) Caught in self-interaction: Evolutionary and functional mechanisms of protein homooligomerization. Phys Biol 8(3):035007.
5. Griffin MD, Gerrard JA (2012) The relationship between oligomeric state and protein function. Adv Exp Med Biol 747:74-90.
6. Smoluchowski MV (1917) Attempt of a mathematical theory of Koagulationskinetik colloidal solutions. Z Phys Chem 92:129-168.
7. Phillips R, Kondev J, Theriot J, Garcia H (2013) Physical Biology of the Cell (Garland Science, New York), 2nd Ed.
8. Bershtein S, Mu W, Shakhnovich EI (2012) Soluble oligomerization provides a beneficial fitness effect on destabilizing mutations. Proc Natl Acad Sci USA 109(13): 4857-4862.
9. Lukes J, Archibald JM, Keeling PJ, Doolittle WF, Gray MW (2011) How a neutral evolutionary ratchet can build cellular complexity. IUBMB Life 63(7):528-537.
10. Lynch M (2012) The evolution of multimeric protein assemblages. Mol Biol Evol 29(5): 1353-1366.
11. Chiti F, Dobson CM (2009) Amyloid formation by globular proteins under native conditions. Nat Chem Biol 5(1):15-22.
12. Semple JI, Vavouri T, Lehner B (2008) A simple principle concerning the robustness of protein complex activity to changes in gene expression. BMC Syst Biol 2:1.
13. Vavouri T, Semple JI, Garcia-Verdugo R, Lehner B (2009) Intrinsic protein disorder and interaction promiscuity are widely associated with dosage sensitivity. Cell 138(1): 198-208.
14. Levy ED, Boeri Erba E, Robinson CV, Teichmann SA (2008) Assembly reflects evolution of protein complexes. Nature 453(7199):1262-1265.
15. Levy ED, Teichmann S (2013) Structural, evolutionary, and assembly principles of protein oligomerization. Prog Mol Biol Transl Sci 117:25-51.
16. Lynch M (2007) The Origins of Genome Architecture (Sinauer, Sunderland, MA).
17. Schomburg I, et al. (2013) BRENDA in 2013: Integrated reactions, kinetic data, enzyme function data, improved disease classification: New options and contents in BRENDA. Nucleic Acids Res 41(Database issue):D764-D772.
18. Krissinel E, Henrick K (2007) Inference of macromolecular assemblies from crystalline state. J Mol Biol 372(3):774-797.
19. Royer WE, Jr., Love WE, Fenderson FF (1985) Cooperative dimeric and tetrameric clam haemoglobins are novel assemblages of myoglobin folds. Nature 316(6025):277-280.
20. Kolatkar PR, Meador WE, Stanfield RL, Hackert ML (1988) Novel subunit structure observed for noncooperative hemoglobin from Urechis caupo. J Biol Chem 263(7): 3462-3465.
21. Bourne Y, et al. (1996) Novel dimeric interface and electrostatic recognition in bacterial Cu,Zn superoxide dismutase. Proc Natl Acad Sci USA 93(23):12774-12779.
22. Vassylyev DG, et al. (2006) Crystal structure of the translocation ATPase SecA from Thermus thermophilus reveals a parallel, head-to-head dimer. J Mol Biol 364(3): 248-258.
23. Atkinson SC, et al. (2012) Crystal, solution and in silico structural studies of dihydrodipicolinate synthase from the common grapevine. PLoS ONE 7(6):e38318.
24. Dayhoff JE, Shoemaker BA, Bryant SH, Panchenko AR (2010) Evolution of protein binding modes in homooligomers. J Mol Biol 395(4):860-870.
25. Archibald JM, Blouin C, Doolittle WF (2001) Gene duplication and the evolution of group II chaperonins: Implications for structure and function. J Struct Biol 135(2): 157-169.
26. Hashimoto K, Madej T, Bryant SH, Panchenko AR (2010) Functional states of homooligomers: Insights from the evolution of glycosyltransferases. J Mol Biol 399(1): 196-206.
27. Hashimoto K, Panchenko AR (2010) Mechanisms of protein oligomerization, the critical role of insertions and deletions in maintaining different oligomeric states. Proc Natl Acad Sci USA 107(47):20352-20357.
28. Lukatsky DB, Shakhnovich BE, Mintseris J, Shakhnovich EI (2007) Structural similarity enhances interaction propensity of proteins. J Mol Biol 365(5):1596-1606.
29. André I, Strauss CE, Kaplan DB, Bradley P, Baker D (2008) Emergence of symmetry in homooligomeric biological assemblies. Proc Natl Acad Sci USA 105(42):16148-16152.
30. Kuriyan J, Eisenberg D (2007) The origin of protein interactions and allostery in colocalization. Nature 450(7172):983-990.
31. Dey S, Pal A, Chakrabarti P, Janin J (2010) The subunit interfaces of weakly associated homodimeric proteins. J Mol Biol 398(1):146-160.
32. Bogan AA, Thorn KS (1998) Anatomy of hot spots in protein interfaces. J Mol Biol 280(1):1-9.
33. Bennett MJ, Choe S, Eisenberg D (1994) Domain swapping: Entangling alliances between proteins. Proc Natl Acad Sci USA 91(8):3127-3131.
34. Grueninger D, et al. (2008) Designed protein-protein association. Science 319(5860): 206-209.
35. Zeldovich KB, Chen P, Shakhnovich EI (2007) Protein stability imposes limits on organism complexity and speed of molecular evolution. Proc Natl Acad Sci USA 104(41):16152-16157.
36. Kimura M (1962) On the probability of fixation of mutant genes in a population. Genetics 47:713-719.
37. Sella G, Hirsh AE (2005) The application of statistical physics to evolutionary biology. Proc Natl Acad Sci USA 102(27):9541-9546.
38. Lynch M (2012) Evolutionary layering and the limits to cellular perfection. Proc Natl Acad Sci USA 109(46):18851-18856.
39. Lynch M, et al. (1999) Spontaneous deleterious mutation. Evolution 53:645-663.
40. Eyre-Walker A, Keightley PD (2007) The distribution of fitness effects of new mutations. Nat Rev Genet 8(8):610-618.
41. Schneider A, Charlesworth B, Eyre-Walker A, Keightley PD (2011) A method for inferring the rate of occurrence and fitness effects of advantageous mutations. Genetics 189(4):1427-1437.
42. Weissman DB, Desai MM, Fisher DS, Feldman MW (2009) The rate at which asexual populations cross fitness valleys. Theor Popul Biol 75(4):286-300.
43. Lynch M, Abegg A (2010) The rate of establishment of complex adaptations. Mol Biol Evol 27(6):1404-1414.
44. Belle EM, Duret L, Galtier N, Eyre-Walker A (2004) The decline of isochores in mammals: An assessment of the GC content variation along the mammalian phylogeny. J Mol Evol 58(6):653-660.
45. Rho M, et al. (2009) Independent mammalian genome contractions following the KT boundary. Genome Biol Evol 1:2-12.
46. Iwasa Y, Michor F, Nowak MA (2004) Stochastic tunnels in evolutionary dynamics. Genetics 166(3):1571-1579.