You are lost without a map: Navigating the sea of protein structures

Biochimica et Biophysica Acta - Proteins and Proteomics

Volumn 1854, Issue 4, 2015, Pages 258-268

  Lamb, Audrey L ^a   Kappock, T Joseph ^b   Silvaggi, Nicholas R ^c  

^a UNIVERSITY OF KANSAS   (United States)

^b PURDUE UNIVERSITY   (United States)

^c UNIVERSITY OF WISCONSIN MILWAUKEE   (United States)

Author keywords

Atomic coordinate files; Atomic displacement parameters; Electron density maps; Molecular models; Protein structure; X ray crystallography

Indexed keywords

BUFFER; LIGAND; SOLVENT; MACROMOLECULE; PROTEIN;

CRYSTAL STRUCTURE; DENSITY; ELECTRON; MACROMOLECULE; OBSERVATIONAL STUDY; PRIORITY JOURNAL; PROTEIN DATA BANK; PROTEIN STRUCTURE; REVIEW; X RAY CRYSTALLOGRAPHY; CHEMICAL STRUCTURE; CHEMISTRY; HUMAN; METABOLISM; PROTEIN CONFORMATION; PROTEIN DATABASE; PROTEIN PROTEIN INTERACTION;

CRYSTALLOGRAPHY, X-RAY; DATABASES, PROTEIN; ELECTRONS; HUMANS; LIGANDS; MACROMOLECULAR SUBSTANCES; MODELS, MOLECULAR; PROTEIN CONFORMATION; PROTEIN INTERACTION MAPS; PROTEINS;

EID: 84921044740     PISSN: 15709639     EISSN: 18781454     Source Type: Journal    
DOI: 10.1016/j.bbapap.2014.12.021     Document Type: Review

References (56)

1. H. Berman, K. Henrick, and H. Nakamura Announcing the worldwide Protein Data Bank Nat. Struct. Biol. 10 2003 980-980
2. Z. Dauter, A. Wlodawer, W. Minor, M. Jaskolski, and B. Rupp Avoidable errors in deposited macromolecular structures: an impediment to efficient data mining IUCrJ 1 2014 179 193
3. A. Wlodawer, W. Minor, Z. Dauter, and M. Jaskolski Protein crystallography for non-crystallographers, or how to get the best (but not more) from published macromolecular structures FEBS J. 275 2008 1 21
4. V.B. Chen, W.B. Arendall 3rd, J.J. Headd, D.A. Keedy, R.M. Immormino, G.J. Kapral, L.W. Murray, J.S. Richardson, and D.C. Richardson MolProbity: all-atom structure validation for macromolecular crystallography Acta Crystallogr. Sect. D: Biol. Crystallogr. 66 2010 12 21
5. G.J. Kleywegt Validation of protein crystal structures Acta Crystallogr. D Biol. Crystallogr. 56 2000 249 265
6. R.J. Read, P.D. Adams, W.B. Arendall 3rd, A.T. Brunger, P. Emsley, R.P. Joosten, G.J. Kleywegt, E.B. Krissinel, T. Lutteke, Z. Otwinowski, A. Perrakis, J.S. Richardson, W.H. Sheffler, J.L. Smith, I.J. Tickle, G. Vriend, and P.H. Zwart A new generation of crystallographic validation tools for the protein data bank Structure 19 2011 1395 1412
7. I.J. Tickle Statistical quality indicators for electron-density maps Acta Crystallogr. D Biol. Crystallogr. 68 2012 454 467
8. P. Emsley, and K. Cowtan Coot: model-building tools for molecular graphics Acta Crystallogr. Sect. D: Biol. Crystallogr. 60 2004 2126 2132
9. P. Emsley, B. Lohkamp, W.G. Scott, and K. Cowtan Features and development of Coot Acta Crystallogr. D Biol. Crystallogr. 66 2010 486 501
10. A.M. Davis, S.J. Teague, and G.J. Kleywegt Application and limitations of X-ray crystallographic data in structure-based ligand and drug design Angew. Chem. 42 2003 2718 2736
11. E.F. Pettersen, T.D. Goddard, C.C. Huang, G.S. Couch, D.M. Greenblatt, E.C. Meng, and T.E. Ferrin UCSF Chimera - a visualization system for exploratory research and analysis J. Comput. Chem. 25 2004 1605 1612
12. A. Herraez Biomolecules in the computer: Jmol to the rescue Biochem. Mol. Biol. Educ. 34 2006 255 261
13. D. Ringe, and G.A. Petsko Study of protein dynamics by X-ray diffraction Methods Enzymol. 131 1986 389 433
14. M.D. Winn, M.N. Isupov, and G.N. Murshudov Use of TLS parameters to model anisotropic displacements in macromolecular refinement Acta Crystallogr. D Biol. Crystallogr. 57 2001 122 133
15. J. Painter, and E.A. Merritt A molecular viewer for the analysis of TLS rigid-body motion in macromolecules Acta Crystallogr. D Biol. Crystallogr. 61 2005 465 471
16. P.B. Moore On the relationship between diffraction patterns and motions in macromolecular crystals Structure 17 2009 1307 1315
17. G.J. Kleywegt, M.R. Harris, J.Y. Zou, T.C. Taylor, A. Wahlby, and T.A. Jones The Uppsala Electron-Density Server Acta Crystallogr. D Biol. Crystallogr. 60 2004 2240 2249
18. T.C. Terwilliger, R.W. Grosse-Kunstleve, P.V. Afonine, N.W. Moriarty, P.D. Adams, R.J. Read, P.H. Zwart, and L.W. Hung Iterative-build OMIT maps: map improvement by iterative model building and refinement without model bias Acta Crystallogr. D 64 2008 515 524
19. A. Hodel, S.H. Kim, and A.T. Brunger Model bias in macromolecular crystal-structures Acta Crystallogr. A 48 1992 851 858
20. N. Collaborative Computational Project The CCP4 suite: programs for protein crystallography Acta Crystallogr. Sect. D: Biol. Crystallogr. 50 1994 760 763
21. C.X. Weichenberger, E. Pozharski, and B. Rupp Visualizing ligand molecules in Twilight electron density Acta Crystallogr. Sect. F: Struct. Biol. Cryst. Commun. 69 2013 195 200
22. P.D. Adams, P.V. Afonine, G. Bunkoczi, V.B. Chen, I.W. Davis, N. Echols, J.J. Headd, L.W. Hung, G.J. Kapral, R.W. Grosse-Kunstleve, A.J. McCoy, N.W. Moriarty, R. Oeffner, R.J. Read, D.C. Richardson, J.S. Richardson, T.C. Terwilliger, and P.H. Zwart PHENIX: a comprehensive Python-based system for macromolecular structure solution Acta Crystallogr. Sect. D: Biol. Crystallogr. 66 2010 213 221
23. R.E. Franklin, and R.G. Gosling Molecular configuration in sodium thymonucleate. 1953 Nature 421 2003 400 401 (discussion 396)
24. J.D. Watson, and F.H. Crick A structure for deoxyribose nucleic acid. 1953 Nature 421 2003 397 398 (discussion 396)
25. M.H. Wilkins, A.R. Stokes, and H.R. Wilson Molecular structure of deoxypentose nucleic acids Nature 171 1953 738 740
26. D.A. Doyle, J. Morais Cabral, R.A. Pfuetzner, A. Kuo, J.M. Gulbis, S.L. Cohen, B.T. Chait, and R. MacKinnon The structure of the potassium channel: molecular basis of K + conduction and selectivity Science 280 1998 69 77
27. A.M. Burroughs, R.W. Hoppe, N.C. Goebel, B.H. Sayyed, T.J. Voegtline, A.W. Schwabacher, T.M. Zabriskie, and N.R. Silvaggi Structural and functional characterization of MppR, an enduracididine biosynthetic enzyme from streptomyces hygroscopicus: functional diversity in the acetoacetate decarboxylase-like superfamily Biochemistry 52 2013 4492 4506
28. M.A. DePristo, P.I. de Bakker, and T.L. Blundell Heterogeneity and inaccuracy in protein structures solved by X-ray crystallography Structure 12 2004 831 838
29. R.B. Best, K. Lindorff-Larsen, M.A. DePristo, and M. Vendruscolo Relation between native ensembles and experimental structures of proteins Proc. Natl. Acad. Sci. U. S. A. 103 2006 10901 10906
30. P.V. Burra, Y. Zhang, A. Godzik, and B. Stec Global distribution of conformational states derived from redundant models in the PDB points to non-uniqueness of the protein structure Proc. Natl. Acad. Sci. U. S. A. 106 2009 10505 10510
31. D.A. Kondrashov, W. Zhang, R.T. Aranda, B. Stec, and G.N. Phillips Jr. Sampling of the native conformational ensemble of myoglobin via structures in different crystalline environments Proteins 70 2008 353 362
32. J.S. Fraser, M.W. Clarkson, S.C. Degnan, R. Erion, D. Kern, and T. Alber Hidden alternative structures of proline isomerase essential for catalysis Nature 462 2009 669 673
33. J.S. Fraser, H. van den Bedem, A.J. Samelson, P.T. Lang, J.M. Holton, N. Echols, and T. Alber Accessing protein conformational ensembles using room-temperature X-ray crystallography Proc. Natl. Acad. Sci. U. S. A. 108 2011 16247 16252
34. N. Furnham, T.L. Blundell, M.A. DePristo, and T.C. Terwilliger Is one solution good enough? Nat. Struct. Mol. Biol. 13 2006 184 185 (discussion 185)
35. R.B. Fenwick, H. van den Bedem, J.S. Fraser, and P.E. Wright Integrated description of protein dynamics from room-temperature X-ray crystallography and NMR Proc. Natl. Acad. Sci. U. S. A. 111 2014 E445 E454
36. A. Ramanathan, A. Savol, V. Burger, C.S. Chennubhotla, and P.K. Agarwal Protein conformational populations and functionally relevant substates Acc. Chem. Res. 47 2014 149 156
37. I.E. Iben, D. Braunstein, W. Doster, H. Frauenfelder, M.K. Hong, J.B. Johnson, S. Luck, P. Ormos, A. Schulte, P.J. Steinbach, A.H. Xie, and R.D. Young Glassy behavior of a protein Phys. Rev. Lett. 62 1989 1916 1919
38. Y. Miao, Z. Yi, D.C. Glass, L. Hong, M. Tyagi, J. Baudry, N. Jain, and J.C. Smith Temperature-dependent dynamical transitions of different classes of amino acid residue in a globular protein J. Am. Chem. Soc. 134 2012 19576 19579
39. B. Rupp Detection and analysis of unusual features in the structural model and structure-factor data of a birch pollen allergen Acta Crystallogr. Sect. F: Struct. Biol. Cryst. Commun. 68 2012 366 376
40. D.W.J. Cruickshank Protein precision re-examined: Luzzati plots do not estimate final errors E. Dodson, M. Moore, A. Ralph, S. Bailey, Proceedings of the CCP4 Study WeekendDaresbury Laboratory, UK 1996
41. N.D. Werbeck, J. Kirkpatrick, J. Reinstein, and D.F. Hansen Using N-ammonium to characterise and map potassium binding sites in proteins by NMR spectroscopy Chembiochem 15 4 2014 543 548
42. Y.J. Im, S. Raychaudhuri, W.A. Prinz, and J.H. Hurley Structural mechanism for sterol sensing and transport by OSBP-related proteins Nature 437 2005 154 158
43. A.M. Davis, S.A. St-Gallay, and G.J. Kleywegt Limitations and lessons in the use of X-ray structural information in drug design Drug Discov. Today 13 2008 831 841
44. E. Pozharski, C.X. Weichenberger, and B. Rupp Techniques, tools and best practices for ligand electron-density analysis and results from their application to deposited crystal structures Acta Crystallogr. D Biol. Crystallogr. 69 2013 150 167
45. C.-I. Branden, and T. Alwyn Jones Between objectivity and subjectivity Nature 343 1990 687 689
46. T.A. Jones, J.Y. Zou, S.W. Cowan, and M. Kjeldgaard Improved methods for building protein models in electron density maps and the location of errors in these models Acta Crystallogr. Sect. A: Found. Crystallogr. 47 Pt 2 1991 110 119
47. A. Cereto-Massague, M.J. Ojeda, R.P. Joosten, C. Valls, M. Mulero, M.J. Salvado, A. Arola-Arnal, L. Arola, S. Garcia-Vallve, and G. Pujadas The good, the bad and the dubious: VHELIBS, a validation helper for ligands and binding sites J. Cheminform. 5 2013 36
48. K. Cowtan The Buccaneer software for automated model building. 1. Tracing protein chains Acta Crystallogr. D Biol. Crystallogr. 62 2006 1002 1011
49. T.C. Terwilliger, R.W. Grosse-Kunstleve, P.V. Afonine, N.W. Moriarty, P.H. Zwart, L.W. Hung, R.J. Read, and P.D. Adams Iterative model building, structure refinement and density modification with the PHENIX AutoBuild wizard Acta Crystallogr. D Biol. Crystallogr. 64 2008 61 69
50. G. Langer, S.X. Cohen, V.S. Lamzin, and A. Perrakis Automated macromolecular model building for X-ray crystallography using ARP/wARP version 7 Nat. Protoc. 3 2008 1171 1179
51. L.L.C. Schrodinger The PyMOL Molecular Graphics System, Version 1.3r1 2010
52. M.J. Hartshorn AstexViewer: a visualisation aid for structure-based drug design J. Comput. Aided Mol. Des. 16 2002 871 881
53. C.C.G. Inc Molecular Operating Environment (MOE), 1010 Sherbooke St. West, Suite #910, Montreal, QC, Canada, H3A 2R7 2013
54. N.R. Silvaggi, D. Wilson, S. Tzipori, and K.N. Allen Catalytic features of the botulinum neurotoxin A light chain revealed by high resolution structure of an inhibitory peptide complex Biochemistry 47 2008 5736 5745
55. N.R. Silvaggi, G.E. Boldt, M.S. Hixon, J.P. Kennedy, S. Tzipori, K.D. Janda, and K.N. Allen Structures of Clostridium botulinum Neurotoxin Serotype A Light Chain complexed with small-molecule inhibitors highlight active-site flexibility Chem. Biol. 14 2007 533 542
56. S. Gu, S. Rumpel, J. Zhou, J. Strotmeier, H. Bigalke, K. Perry, C.B. Shoemaker, A. Rummel, and R. Jin Botulinum neurotoxin is shielded by NTNHA in an interlocked complex Science 335 2012 977 981