Crystallization of proteins from crude bovine rod outer segments

Methods in Enzymology

Volumn 557, Issue , 2015, Pages 439-458

  Baker, Bo Y ^a   Gulati, Sahil ^a   Shi, Wuxian ^a   Wang, Benlian ^a   Stewart, Phoebe L ^a   Palczewski, Krzysztof ^a  

^a CASE WESTERN RESERVE UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EYE PROTEIN; MEMBRANE PROTEIN;

ANIMAL; BOVINE; CHEMISTRY; CRYSTALLIZATION; MOLECULAR MODEL; PROCEDURES; PROTEIN CONFORMATION; RETINAL ROD OUTER SEGMENT; X RAY CRYSTALLOGRAPHY;

ANIMALS; CATTLE; CRYSTALLIZATION; CRYSTALLOGRAPHY, X-RAY; EYE PROTEINS; MEMBRANE PROTEINS; MODELS, MOLECULAR; PROTEIN CONFORMATION; ROD CELL OUTER SEGMENT;

EID: 84939966278     PISSN: 00766879     EISSN: 15577988     Source Type: Book Series    
DOI: 10.1016/bs.mie.2014.11.045     Document Type: Chapter

References (34)

1. R. Ahmad, and A.U. Hasnain Ontogenetic changes and developmental adjustments in lactate dehydrogenase isozymes of an obligate air-breathing fish Channa punctatus during deprivation of air access Comparative Biochemistry and Physiology. Part B, Biochemistry & Molecular Biology 140 2 2005 271 278 10.1016/j.cbpc.2004.10.012
2. B.Y. Baker, and K. Palczewski Detergents stabilize the conformation of phosphodiesterase 6 Biochemistry 50 44 2011 9520 9531 10.1021/bi2014695
3. B.Y. Baker, W. Shi, B. Wang, and K. Palczewski High-resolution crystal structures of the photoreceptor glyceraldehyde 3-phosphate dehydrogenase (GAPDH) with three and four-bound NAD molecules Protein Science 23 11 2014 1629 1639 10.1002/pro.2543 Epub 2014 Sep 25
4. --creatine transition-state analogue complex FEBS Letters 582 28 2008 3959 3965 10.1016/j.febslet.2008.10.039
5. J. Buczylko, and K. Palczewski Purification of arrestin from bovine retinas Methods in Neurosciences 15 1993 226 236
6. S.W. Cowan-Jacob, M. Kaufmann, A.N. Anselmo, W. Stark, and M.G. Grutter Structure of rabbit-muscle glyceraldehyde-3-phosphate dehydrogenase Acta Crystallographica. Section D, Biological Crystallography 59 Pt. 12 2003 2218 2227
7. A. Dong, X. Xu, A.M. Edwards, Midwest Center for Structural Genomics, Structural Genomics Consortium, and C. Chang In situ proteolysis for protein crystallization and structure determination Nature Methods 4 12 2007 1019 1021 10.1038/nmeth1118
8. P. Emsley, B. Lohkamp, W.G. Scott, and K. Cowtan Features and development of Coot Acta Crystallographica. Section D, Biological Crystallography 66 Pt. 4 2010 486 501 10.1107/S0907444910007493
9. E.H. Fischer, and E.G. Krebs The isolation and crystallization of rabbit skeletal muscle phosphorylase b The Journal of Biological Chemistry 231 1 1958 65 71
10. A. Goc, T.E. Angel, B. Jastrzebska, B. Wang, P.L. Wintrode, and K. Palczewski Different properties of the native and reconstituted heterotrimeric G protein transducin Biochemistry 47 47 2008 12409 12419 10.1021/bi8015444
11. T.D. Goddard, C.C. Huang, and T.E. Ferrin Visualizing density maps with UCSF Chimera Journal of Structural Biology 157 1 2007 281 287 10.1016/j.jsb.2006.06.010
12. J.L. Jenkins, and J.J. Tanner High-resolution structure of human D-glyceraldehyde-3-phosphate dehydrogenase Acta Crystallographica. Section D, Biological Crystallography 62 Pt. 3 2006 290 301 10.1107/S0907444905042289
13. R.A. Judge, E.L. Forsythe, and M.L. Pusey The effect of protein impurities on lysozyme crystal growth Biotechnology and Bioengineering 59 6 1998 776 785
14. W. Kabsch Integration, scaling, space-group assignment and post-refinement Acta Crystallographica. Section D, Biological Crystallography 66 Pt. 2 2010 133 144 10.1107/S0907444909047374
15. W. Kabsch XDS Acta Crystallographica. Section D, Biological Crystallography 66 Pt. 2 2010 125 132 10.1107/S0907444909047337
16. Y.J. Kim, K.P. Hofmann, O.P. Ernst, P. Scheerer, H.W. Choe, and M.E. Sommer Crystal structure of pre-activated arrestin p44 Nature 497 7447 2013 142 146 10.1038/nature12133
17. P.D. Kiser, M. Golczak, D.T. Lodowski, M.R. Chance, and K. Palczewski Crystal structure of native RPE65, the retinoid isomerase of the visual cycle Proceedings of the National Academy of Sciences of the United States of America 106 41 2009 17325 17330 10.1073/pnas.0906600106 0906600106 [pii]
18. C.A. Kors, E. Wallace, D.R. Davies, L. Li, P.D. Laible, and P. Nollert Effects of impurities on membrane-protein crystallization in different systems Acta Crystallographica. Section D, Biological Crystallography 65 Pt. 10 2009 1062 1073 10.1107/S0907444909029163 S0907444909029163 [pii]
19. M.C. Kwok, J.M. Holopainen, L.L. Molday, L.J. Foster, and R.S. Molday Proteomics of photoreceptor outer segments identifies a subset of SNARE and Rab proteins implicated in membrane vesicle trafficking and fusion Molecular & Cellular Proteomics 7 6 2008 1053 1066 10.1074/mcp.M700571-MCP200
20. A. Mcpherson A brief-history of protein crystal-growth Journal of Crystal Growth 110 1-2 1991 1 10 10.1016/0022-0248(91)90859-4
21. D.J. Muller, N. Wu, and K. Palczewski Vertebrate membrane proteins: Structure, function, and insights from biophysical approaches Pharmacological Reviews 60 1 2008 43 78 10.1124/pr.107.07111 pr.107.07111 [pii]
22. Z. Otwinowski, and W. Minor Processing of X-ray diffraction data collected in oscillation mode Macromolecular Crystallography, Part A 276 1997 307 326 10.1016/S0076-6879(97)76066-X
23. K. Palczewski G protein-coupled receptor rhodopsin Annual Review of Biochemistry 75 2006 743 767 10.1146/annurev.biochem.75.103004.142743
24. K. Palczewski Chemistry and biology of vision The Journal of Biological Chemistry 287 3 2012 1612 1619 10.1074/jbc.R111.301150
25. J.H. Park, P. Scheerer, K.P. Hofmann, H.W. Choe, and O.P. Ernst Crystal structure of the ligand-free G-protein-coupled receptor opsin Nature 454 7201 2008 183 187 10.1038/nature07063 nature07063 [pii]
26. E.F. Pettersen, T.D. Goddard, C.C. Huang, G.S. Couch, D.M. Greenblatt, and E.C. Meng UCSF Chimera-a visualization system for exploratory research and analysis Journal of Computational Chemistry 25 13 2004 1605 1612 10.1002/jcc.20084
27. G.W. Pettigrew, R.G. Bartsch, T.E. Meyer, and M.D. Kamen Redox potentials of photosynthetic bacterial cytochromes-C2 and structural bases for variability Biochimica et Biophysica Acta 503 3 1978 509 523 10.1016/0005-2728(78)90150-0
28. K. Sachs, D. Maretzki, and K.P. Hofmann Assays for activation of opsin by all-trans-retinal Methods in Enzymology 315 2000 238 251
29. P. Scheerer, J.H. Park, P.W. Hildebrand, Y.J. Kim, N. Krauss, and H.W. Choe Crystal structure of opsin in its G-protein-interacting conformation Nature 455 7212 2008 497 502 10.1038/nature07330 nature07330 [pii]
30. N.P. Skiba, W.J. Spencer, R.Y. Salinas, E.C. Lieu, J.W. Thompson, and V.Y. Arshavsky Proteomic identification of unique photoreceptor disc components reveals the presence of PRCD, a protein linked to retinal degeneration Journal of Proteome Research 12 6 2013 3010 3018 10.1021/pr4003678
31. D. Tisi, B. Bax, and A. Loew The three-dimensional structure of cytosolic bovine retinal creatine kinase Acta Crystallographica. Section D, Biological Crystallography 57 Pt. 2 2001 187 193
32. M. Totir, N. Echols, M. Nanao, C.L. Gee, A. Moskaleva, and S. Gradia Macro-to-micro structural proteomics: Native source proteins for high-throughput crystallization PLoS One 7 2 2012 e32498 10.1371/journal.pone.0032498
33. A.A. Vagin, R.A. Steiner, A.A. Lebedev, L. Potterton, S. McNicholas, and F. Long REFMAC5 dictionary: Organization of prior chemical knowledge and guidelines for its use Acta Crystallographica. Section D, Biological Crystallography 60 Pt. 12 Pt. 1 2004 2184 2195 10.1107/S0907444904023510
34. M.D. Winn, C.C. Ballard, K.D. Cowtan, E.J. Dodson, P. Emsley, and P.R. Evans Overview of the CCP4 suite and current developments Acta Crystallographica. Section D, Biological Crystallography 67 Pt. 4 2011 235 242 10.1107/S0907444910045749