Effects of macromolecular crowding on the structure of a protein complex: A small-angle scattering study of superoxide dismutase

Biophysical Journal

Volumn 108, Issue 4, 2015, Pages 967-974

  Rajapaksha, Ajith ^a   Stanley, Christopher B ^b   Todd, Brian A ^a  

^a PURDUE UNIVERSITY   (United States)

^b OAK RIDGE NATIONAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MACROGOL DERIVATIVE; PROTEIN BINDING; SUPEROXIDE DISMUTASE;

CHEMISTRY; NEUTRON DIFFRACTION; PROTEIN CONFORMATION; SMALL ANGLE SCATTERING;

NEUTRON DIFFRACTION; POLYETHYLENE GLYCOLS; PROTEIN BINDING; PROTEIN CONFORMATION; SCATTERING, SMALL ANGLE; SUPEROXIDE DISMUTASE;

EID: 84923248033     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2014.12.046     Document Type: Article

References (41)

1. R.J. Ellis Macromolecular crowding: obvious but underappreciated Trends Biochem. Sci. 26 2001 597 604
2. R.J. Ellis, and A.P. Minton Protein aggregation in crowded environments Biol. Chem. 387 2006 485 497
3. A.P. Minton Implications of macromolecular crowding for protein assembly Curr. Opin. Struct. Biol. 10 2000 34 39
4. V.A. Parsegian, R.P. Rand, and D.C. Rau Osmotic stress, crowding, preferential hydration, and binding: a comparison of perspectives Proc. Natl. Acad. Sci. USA 97 2000 3987 3992
5. T.O. Street, and K.A. Krukenberg D.A. Agard Osmolyte-induced conformational changes in the Hsp90 molecular chaperone Protein Sci. 19 2010 57 65
6. D.K. Eggers, and J.S. Valentine Molecular confinement influences protein structure and enhances thermal protein stability Protein Sci. 10 2001 250 261
7. K. Sasahara, P. McPhie, and A.P. Minton Effect of dextran on protein stability and conformation attributed to macromolecular crowding J. Mol. Biol. 326 2003 1227 1237
8. C. Stanley, and S. Krueger D.C. Rau Protein structure and hydration probed by SANS and osmotic stress Biophys. J. 94 2008 2777 2789
9. P.V. Konarev, and V.V. Volkov D.I. Svergun PRIMUS: a windows PC-based system for small-angle scattering data analysis J. Appl. Cryst. 36 2003 1277 1282
10. D.A. Jacques, and J. Trewhella Small-angle scattering for structural biology - expanding the frontier while avoiding the pitfalls Protein Sci. 19 2010 642 657
11. S.N. Timasheff Protein hydration, thermodynamic binding, and preferential hydration Biochemistry 41 2002 13473 13482
12. D.I. Svergun, and S. Richard G. Zaccai Protein hydration in solution: experimental observation by x-ray and neutron scattering Proc. Natl. Acad. Sci. USA 95 1998 2267 2272
13. N.S. Murthy, and J.R. Knox Hydration of proteins: SAXS study of native and methoxy polyethyleneglycol (mPEG)-modified L-asparaginase and bovine serum albumin in mPEG solutions Biopolymers 74 2004 457 466
14. F. Rodier, and R.P. Bahadur J. Janin Hydration of protein-protein interfaces Proteins 60 2005 36 45
15. F.J. Yost Jr., and I. Fridovich An iron-containing superoxide dismutase from Escherichia coli J. Biol. Chem. 248 1973 4905 4908
16. A.F. Miller Superoxide dismutase: ancient enzymes and new insights FEBS Lett 586 2012 585 595
17. C. Beauchamp, and I. Fridovich Superoxide dismutase: improved assays and an assay applicable to acrylamide gels Anal. Biochem. 44 1971 276 287
18. J.M. McCord, and I. Fridovich Superoxide dismutase. An enzymic function for erythrocuprein (hemocuprein) J. Biol. Chem. 244 1969 6049 6055
19. P.J. Janknegt, and J.W. Rijstenbil A.G.J. Buma A comparison of quantitative and qualitative superoxide dismutase assays for application to low temperature microalgae J. Photochem. Photobiol. B 87 2007 218 226
20. O. Arnold, and J.C. Bilheux J. Zikovsky MANTID - data analysis and visualization package for neutron scattering and mu-SR experiments Nucl. Instrum. Methods Phys. Res. A A764 2014 156 166
21. D.I. Svergun Determination of the regularization parameter in indirect-transform methods using perceptual criteria J. Appl. Cryst. 25 1992 495 503
22. D.I. Svergun, and M.H.J. Koch R.P. May Small angle x-ray and neutron scattering from solutions of biological macromolecules IUCr Texts on Crystallography Vol. 19 2013 Oxford University Press New York
23. M.S. Lah, and M.M. Dixon M.L. Ludwig Structure-function in Escherichia coli iron superoxide dismutase: comparisons with the manganese enzyme from Thermus thermophilus Biochemistry 34 1995 1646 1660
24. D. Harries, and J. Rösgen A practical guide on how osmolytes modulate macromolecular properties Methods Cell Biol. 84 2008 679 735
25. N.P. Money Osmotic pressure of aqueous polyethylene glycols' relationship between molecular weight and vapor pressure deficit Plant Physiol. 91 1989 766 769
26. A. Guinier X-Ray Diffraction 1963 Freeman San Francisco, CA
27. O. Glatter, and O. Kratky Small Angle X-Ray Scattering 1982 Academic Press London, United Kingdom
28. D.I. Svergun, and M.H.J. Koch Small-angle scattering studies of biological macromolecules in solution Rep. Prog. Phys. 66 2003 1735 1782
29. M.J. Tait, and F. Franks Water in biological systems Nature 230 1971 91 94
30. I.D. Kuntz Jr., and W. Kauzmann Hydration of proteins and polypeptides Adv. Protein Chem. 28 1974 239 345
31. C.G. Windsor An introduction to small-angle neutron scattering J. Appl. Cryst. 21 1988 582 588
32. D.K. Eggers, and J.S. Valentine Crowding and hydration effects on protein conformation: a study with sol-gel encapsulated proteins J. Mol. Biol. 314 2001 911 922
33. B. van den Berg, R.J. Ellis, and C.M. Dobson Effects of macromolecular crowding on protein folding and aggregation EMBO J. 18 1999 6927 6933
34. D. Miyoshi, A. Nakao, and N. Sugimoto Molecular crowding regulates the structural switch of the DNA G-quadruplex Biochemistry 41 2002 15017 15024
35. B. van den Berg, and R. Wain R.J. Ellis Macromolecular crowding perturbs protein refolding kinetics: implications for folding inside the cell EMBO J. 19 2000 3870 3875
36. S. Schnell, and T.E. Turner Reaction kinetics in intracellular environments with macromolecular crowding: simulations and rate laws Prog. Biophys. Mol. Biol. 85 2004 235 260
37. H.-X. Zhou, G. Rivas, and A.P. Minton Macromolecular crowding and confinement: biochemical, biophysical, and potential physiological consequences Annu. Rev. Biophys 37 2008 375 397
38. I. Fridovich Superoxide dismutases Annu. Rev. Biochem. 44 1975 147 159
39. S. Leikin, D.C. Rau, and V.A. Parsegian Direct measurement of forces between self-assembled proteins: temperature-dependent exponential forces between collagen triple helices Proc. Natl. Acad. Sci. USA 91 1994 276 280
40. I. Markovic, and R.H. Ottewill J.F. Marsh Small angle neutron scattering studies on non-aqueous dispersions of calcium carbonate Colloid Polym. Sci. 262 1984 648 656
41. Munter, A. 2014. Scattering length density (SLD) calculator. http://www.ncnr.nist.gov/resources/sldcalc.html.