Crowders perturb the entropy of RNA energy landscapes to favor folding

Journal of the American Chemical Society

Volumn 135, Issue 27, 2013, Pages 10055-10063

  Kilburn, Duncan ^a   Roh, Joon Ho ^a,b,c   Behrouzi, Reza ^a   Briber, Robert M ^b   Woodson, Sarah A ^a  

^a JOHNS HOPKINS UNIVERSITY   (United States)

^b UNIVERSITY OF MARYLAND   (United States)

^c NATIONAL INSTITUTE OF STANDARDS AND TECHNOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL MACROMOLECULE; CONFIGURATIONAL ENTROPY; ENTROPIC STABILIZATION; MOLECULAR CROWDING; MONO- AND DIVALENT ION; RNA ENERGY LANDSCAPES; SCATTERING FUNCTIONS; SCATTERING LENGTH;

ENTROPY; RNA; SCATTERING; STABILIZATION;

IONIC STRENGTH;

ION; MAGNESIUM CHLORIDE; RIBOZYME; RNA; SODIUM CHLORITE;

ARTICLE; AZOARCUS; ENERGY; ENTROPY; IONIC STRENGTH; LIMIT OF QUANTITATION; MOLECULAR WEIGHT; NONHUMAN; RNA FOLDING; RNA STRUCTURE; STATIC ELECTRICITY;

ENTROPY; NUCLEIC ACID CONFORMATION; POLYETHYLENE GLYCOLS; RNA; RNA, CATALYTIC; SCATTERING, SMALL ANGLE; SODIUM CHLORIDE; X-RAY DIFFRACTION;

EID: 84880029470     PISSN: 00027863     EISSN: 15205126     Source Type: Journal    
DOI: 10.1021/ja4030098     Document Type: Article

References (52)

1. Doudna, J. A.; Cech, T. R. Nature 2002, 418, 222
2. Ellis, R. J. Trends Biochem. Sci. 2001, 26, 597
3. Zhou, H.-X.; Rivas, G.; Minton, A. P. Ann. Rev. Biophys. 2008, 37, 375
4. Manning, G. S. Q. Rev. Biophys. 1978, 11, 179
5. Misra, V. K.; Draper, D. E. J. Mol. Biol. 2000, 299, 813
6. Draper, D. E.; Grilley, D.; Soto, A. M. Annu. Rev. Biomol. Struct. 2005, 34, 221
7. Cheatham, T. E. Curr. Opin. Struct. Biol. 2004, 14, 360
8. Thirumalai, D.; Klimov, D. K.; Lorimer, G. H. Proc. Natl. Acad. Sci. 2003, 100, 11195
9. Minton, A. P. Biopolymers 1981, 20, 2093
10. Minton, A. P. Methods Enzym. 1998, 295, 127
11. Minton, A. P. Curr. Opin. Struc. Biol. 2000, 10, 34
12. Minton, A. P. Biophys. J. 2000, 78, 101
13. Zhou, H.-X.; Qin, S. Phys. Rev. E 2010, 81, 031919
14. Rubinstein, M.; Colby, R. H. Polymer Physics; Oxford University Press: Oxford, 2003.
15. Nashimoto, M. Eur. J. Biochem. 2000, 267, 2738
16. Nakano, S.; Karimata, H. T.; Kitagawa, Y.; Sugimoto, N. J. Am. Chem. Soc. 2009, 131, 16881
17. Nakano, S.-I.; Kitigawa, Y.; Karimata, H. T.; Sugimoto, N. Nucleic Acids Symp. 2008, 52, 519
18. Denesyuk, N. A.; Thirumalai, D. J. Am. Chem. Soc. 2011, 133, 11858
19. Tan, Z.-J.; Chen, S.-J. Biophys. J. 2012, 103, 827
20. Hong, J.; Gierasch, L. M. J. Am. Chem. Soc. 2010, 132, 10445
21. Lambert, D.; Draper, D. E. J. Mol. Biol. 2007, 370, 993
22. Miklos, A. C.; Sarkar, M.; Wang, Y.; Pielak, G. J. J. Am. Chem. Soc. 2011, 133, 7116
23. Ignatova, Z.; Krishnan, B.; Bombardier, J. P.; Marcelino, A. M. C.; Hong, J.; Gierasch, L. M. Peptide Sci. 2007, 88, 157
24. Kilburn, D.; Roh, J. H.; Guo, L.; Briber, R. M.; Woodson, S. A. J. Am. Chem. Soc. 2010, 132, 8690
25. Chauhan, S.; Caliskan, G.; Briber, R. M.; Perez-Salas, U. A.; Rangan, P.; Thirumalai, D.; Woodson, S. A. J. Mol. Biol. 2005, 353, 1199
26. Rangan, P.; Masquida, B.; Westhof, E.; Woodson, S. A. Proc. Natl. Acad. Sci. 2003, 100, 1574
27. Silverman, S. K.; Cech, T. R. Biochemistry 1999, 38, 8691
28. Baird, N. J.; Westhof, E.; Qin, H.; Pan, T.; Sosnick, T. R. J. Mol. Biol. 2005, 352, 712
29. Fang, X.; Pan, T.; Sosnick, T. R. Biochemistry 1999, 38, 16840
30. Kuznetsov, S. V.; Shen, Y.; Benight, A. S.; Ansari, A. Biophys. J. 2001, 81, 2864
31. Ma, H.; Proctor, D.; Bevilacqua, P.; Gruebele, M. J. Am. Chem. Soc. 2006, 128, 1523
32. Chauhan, S.; Woodson, S. A. J. Am. Chem. Soc. 2008, 130, 1296
33. Moghaddam, S.; Caliskan, G.; Chauhan, S.; Hyeon, C.; Briber, R. M.; Thirumalai, D.; Woodson, S. A. J. Mol. Biol. 2009, 393, 753
34. Draper, D. E. Biophys. J. 2008, 95, 5489
35. Record, M. T., Jr.; Anderson, C. F.; Lohman, T. M. Q. Rev. Biophys. 1978, 11, 103
36. Tan, Z.-J.; Chen, S.-J. Biophys. J. 2006, 90, 1175
37. Leipply, D.; Draper, D. E. Biochemistry 2010, 49, 1843
38. Cohen, J. A.; Podgornik, P. R.; Hansen, P. L.; Parsegian, V. A. J. Phys. Chem. B 2009, 113, 3709
39. Briber, R. M.; Liu, X.; Bauer, B. J. Science 1995, 268, 395
40. Nakano, S.; Karimata, H.; Ohmichi, T.; Kawakami, J.; Sugimoto, N. J. Am. Chem. Soc. 2004, 126, 14330
41. Miyoshi, D.; Karimata, H.; Sugimoto, N. J. Am. Chem. Soc. 2006, 128, 7957
42. Muhuri, S.; Mimura, K.; Miyoshi, D.; Sugimoto, N. J. Am. Chem. Soc. 2009, 131, 9268
43. Roh, J. H.; Guo, L.; Kilburn, J. D.; Briber, R. M.; Irving, T.; Woodson, S. A. J. Am. Chem. Soc. 2010, 132, 10148
44. Knowles, D. B.; LaCroix, A. S; Deines, N. F.; Shkel, I.; Record, M. T., Jr. Proc. Natl. Acad. Sci. 2011, 108 (31) 12699
45. Svergun, D. J. Appl. Crystallogr. 1992, 25, 495
46. Porod, G. General Theory. In Small Angle X-ray Scattering; Glatter, O.; Kratky, O., Eds.; Academic Press: London, 1982; pp 18-51.
47. Bonifacio, G. F.; Brown, T.; Conn, G. L.; Lane, A. N. Biophys. J. 1997, 73, 1532
48. Fiore, J. L.; Hodak, J. H.; Piestert, O.; Downey, C. D.; Nesbitt, D. J. Biophys. J. 2008, 95, 3892
49. Caliskan, G.; Hyeon, C.; Perez-Salas, U.; Briber, R. M.; Woodson, S. A.; Thirumalai, D. Phys. Rev. Lett. 2005, 95, 268303
50. Bai, Y.; Chu, V. B.; Lipfert, J.; Pande, V. S.; Herschlag, D.; Doniach, S. J. Am. Chem. Soc. 2008, 130, 12334
51. Chen, H.; Meisburger, S. P.; Pabit, S. A.; Sutton, J. L.; Webb, W. W.; Pollack, L. Proc. Natl. Acad. Sci. 2012, 109, 799
52. Rangan, P.; Woodson, S. A. J. Mol. Biol. 2003, 329, 229