Recommendations for the presentation of NMR structures of proteins and nucleic acids

Journal of Molecular Biology

Volumn 280, Issue 5, 1998, Pages 933-952

  Markley, John L ^a   Bax, Ad ^b   Arata, Yoji ^c   Hilbers, C W ^g   Kaptein, Robert ^g   Sykes, Brian D ^d   Wright, Peter E ^e   Wüthrich, Kurt ^f  

^a UNIVERSITY OF WISCONSIN MADISON   (United States)

^b NATIONAL INSTITUTE OF DIABETES AND DIGESTIVE AND KIDNEY DISEASES   (United States)

^c WATER RESEARCH INSTITUTE   (Japan)

^d UNIVERSITY OF ALBERTA   (Canada)

^e SCRIPPS RESEARCH INSTITUTE   (United States)

^f ETH ZURICH   (Switzerland)

^g NONE

Author keywords

Atom naming; Biomolecular NMR; Chemical shift referencing; Database; Deposition; Nomenclature

Indexed keywords

NUCLEIC ACID; PROTEIN;

ARTICLE; DATA BASE; INFORMATION SERVICE; NOMENCLATURE; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; NUCLEIC ACID STRUCTURE; PRIORITY JOURNAL; PROTEIN STRUCTURE;

EID: 0032584781     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1998.1852     Document Type: Article

References (72)

1. Bernstein, F. C., Koetzle, T. F., Williams, G. J. B., Meyer, E. F., Jr, Brice, M. D., Rogers, J. R., Kennard, O., Shimanouchi, T. & Tasumi, M. (1977). The Protein Data Bank: a computer-based archival file for macromolecular structures. J. Mol. Biol. 112, 535-542. The Protein Data Bank can be accessed on the Internet at http://www.pdb.bnl.gov/
2. Seavey, B. R., Farr, E. A., Westler, W. M. & Markley, J. L (1991) A relational database for sequence-specific protein NMR data. J. Biomol. NMR, 1, 217-230; Markley, J. L., Farr, E. A. & Seavey, B. R. (1991) Appendix: Check list for protein NMR data to be submitted for publication or for database inclusion. J. Biomol. NMR, 1, 231-236. The Biomolecular NMR Data Bank (BioMagResBank or BMRB) can be reached on the Internet at http// www.bmrb.wisc.edu/
3. Seavey, B. R., Farr, E. A., Westler, W. M. & Markley, J. L (1991) A relational database for sequence- specific protein NMR data. J. Biomol. NMR, 1, 217- 230; Markley, J. L., Farr, E. A. & Seavey, B. R. (1991) Appendix: Check list for protein NMR data to be submitted for publication or for database inclusion. J. Biomol. NMR, 1, 231-236. The Biomolecular NMR Data Bank (BioMagResBank or BMRB) can be reached on the Internet at http// www.bmrb.wisc.edu/
4. Berman, H. M., Olson, W. K., Beveridge, D. L., Westbrook, J., Gelbin, A., Demeny, T., Hsieh, S.-H., Srinivasan, A. R. & Schneider, B. (1992). The Nucleic Acid Database: A comprehensive relational database of three-dimensional structures of nucleic acids. Biophys. J. 63, 751-759. The Nucleic Acid Data Bank can be reached on the Internet at http// www.ndvserver.rutgers.edu:80/
5. Hendrickson, W. A. & Wüthrich, K. (1991). Macromolecular Structures, Current Biology, London, UK.
6. Nomenclature Committee of IUBMB (NC-IUBMB) IUPAC-IUBMB Joint Commission on Biochemical Nomenclature (JCBN) (1992). Newsletter 1992. Biochem. Int. 26, 567-575.
7. Commission on Molecular Structure Spectroscopy (1972). Recommendations for presentation of NMR data for publication in chemical journals. Pure Appl. Chem. 29, 627-628.
8. Commission on Molecular Structure Spectroscopy (1976). Presentation of NMR data for publication in chemical journals, B. Conventions relating to spectra from nuclei other than protons (Recommendations 1975). Pure Appl. Chem. 45, 219.
9. Harris, R. K., Kowalewski, J. & Cabral de Menezes, S. (1996) Parameters and symbols for use in Nuclear magnetic resonance, Pure App. Chem. 69, 2489-2495.
10. Liébecq, C., (ed.) (1992). Biochemical Nomenclature and Related Documents - A Compendium, 2nd edit., Portland Press on behalf of IUBMB, London.
11. Bonnett, R. (1978). The Porphyrins, vol. 1, part A (Dolphin, D., ed.), Academic Press, New York.
12. IUPAC-IUB Commission on Biochemical Nomenclature (CBN) (1975). Nomenclature of iron-sulfur proteins. Recommendations 1973. Eur. J. Biochem. 35, 1-2.
13. IUPAC-IUB Commission on Biochemical Nomenclature (1975). The nomenclature of peptide hormones. Recommendations 1974. Biochemistry, 14, 2559-2560; reprinted in the Compendium (ref. 9).
14. IUPAC-IUB Commission on Biochemical Nomenclature (1972). Abbreviated nomenclature of synthetic polypeptides (polymerized amino acids). Revised recommendations 1971. Biochemistry, 11, 942-944; reprinted in the Compendium (ref. 9).
15. Nomenclature Committee of the International Union of Biochemistry (NC-IUB) (1985). Nomenclature for Incompletely Specified Bases in Nucleic Acids. Eur. J. Biochem. 150, 1-5; reprinted in the Compendium (ref. 9).
16. Access to various databases (e.g. GenBank, DDBJ, EBI (EMBL), EC Enzyme Data Bank, PIR SWISS-PROT, PRF, PDB, NDB, BMRB) is provided over the Internet. Useful compilations of Internet addresses are found, for example, on the home pages of the Protein Data Bank (http:// www.pdb.bnl.gov/), BioMagResBank (http:// www/bmrb.wisc.edu), and the NCSA Biology Workbench (http://biology.ncsa.uiuc.edu)
17. Protein Identification Resource, Georgetown University, Washington, D.C., USA. The Protein Identification Resource can be searched with tools located at: http://www.gdb.org/Dan/proteins/pir.html
18. SWISS-PROT Annotated Protein Sequence Database (http://www.expasy.hcuge.ch/sprot/sprot-top. html)
19. International Union of Biochemistry Molecular Biology (1992). Enzyme Nomenclature. Recommendations 1992, Academic Press, Orlando, Florida.
20. Chemical Abstracts Service, Columbus, OH, USA (http://info.cas.org/).
21. IUPAC-IUB Commission on Biochemical Nomenclature (CBN) (1970). Abbreviations and symbols for the description of the conformation of polypeptide chains. Tentative rules 1969. Biochemistry, 9, 3471-3479; reprinted in the Compendium (ref. 9).
22. IUPAC-IUB Joint Commission on Biochemical Nomenclature (JCBN) (1984). Nomenclature and symbolism for amino acids and peptides. Recommendations 1983. Eur. J. Biochem. 138, 9-37; reprinted in the Compendium (ref. 9).
23. IUPAC-IUB Joint Commission on Biochemical Nomenclature (JCBN) (1983). Abbreviations and symbols for the description of conformations of polynucleotide chains. Recommendations 1982. Eur. J. Biochem. 131, 9-15; reprinted in the Compendium (ref. 9).
24. ghi. J. Am. Chem. Soc. 88, 2731-2742.
25. The 1983 recommendations (ref. 21) specified the use of numbers to designate atoms and the use of the R/S rules of Cahn, Ingold, & Prelog (refs 25, 26, see also refs 27-29) to define stereochemistry. According to the R/S rules, a tetrahedral carbon X with prochiral substituents A > B > C = C′ (where the priority is according to decreasing atomic mass and C and C′ have equivalent mass and are labeled arbitrarily) is labeled as follows: one sights down the A-X axis and assumes that C′ takes precedence over C (as it would if it were replaced, for example, with a heavier isotope). Then, if B, C′ and C (projecting away from the viewer) are clockwise, C′ is labeled as pro-R and C is labeled as pro-S; if they are counterclockwise, C′ is labeled as pro-S and C is labeled as pro-R.
26. Cahn, R. S., Ingold, C. K. & Prelog, V. (1966). Specification of molecular chirality. Agnew. Chem. Int. Ed. Engl. 5, 385-415; 511.
27. Prelog, V. & Helmchen, G. (1982). Basic principles of the CIP-system and proposals for a revision. Agnew. Chem. Int. Ed. Engl. 21, 567-583.
28. Blackwood, J. E., Gladys, C. L., Loening, K. L., Petrarca, A. E. & Rush, J. E. (1968). Unambiguous specification of stereoisomerism about a double bond. J. Am. Chem. 90, 509-510.
29. Blackwood, J. E., Gladys, C. L., Petrarca, A. E., Powell, W. H. & Rush, J. E. (1968). Unique and unambiguous specification of stereoisomerism about a double bond in nomenclature and other notation systems. J. Chem. Doc. 8, 30-32.
30. IUPAC Commission on Nomenclature of Organic Chemistry (CNOC) (1976). Nomenclature of organic chemistry, section E: Stereochemistry. Recommendations 1974. Pure Appl. Chem. 45, 11-30; reprinted in the Compendium (ref. 9).
31. Wüthrich, K., Billeter, M. & Braun, W. (1983). Pseudo-structures for the 20 common amino acids for use in studies of protein conformations by measurements of intramolecular proton-proton distance constraints with nuclear magnetic resonances. J. Mol. Biol. 169, 949-961.
32. Since the experimental NOEs involve distances to the individual protons rather than to the reference point of the pseudoatom, NOE distance constraints involving pseudoatoms must contain a correction factor. A conservative and straightforward approach is to set these corrections equal to the distance between the reference point of the pseudoatom and the protons that is replaces. Tables listing these corrections for the common amino acid residues have been published (refs 30, 33) as well as more refined corrections (for example, see refs 32, 34).
33. Koning, T. M. G., Boelens, R. & Kaptein, R. (1990). Calculations of the nuclear Overhauser effect and determination of proton-proton distances in the presence of internal motions. J. Magn. Reson. 90, 111-123.
34. Wüthrich, K. (1986). NMR Proteins and Nucleic Acids, Wiley Interscience, New York.
35. Güntert, P., Braun, W. & Wüthrich, K. (1991). Efficient computation of three-dimensional protein structures in solution from nuclear magnetic resonance data using the program DIANA and the supporting programs CALIBA, HABAS and GLOMSA. J. Mol. Biol. 217, 517-530.
36. Historical changes in the definition of these angles have contributed to confusion. Their use in numerous textbooks does not conform to the current IUPAC-IUBMB nomenclature: Clauwaert, J. & Xia, J.-Z. (1993). Straightening out of the dihedral angles. Trends Biochem. Sci, 18, 317-318; 464.
37. Wilmott, C. M. & Thornton, J. M. (1990). β-Turns and their distortions: a proposed new nomenclature. Protein Eng. 3, 479-493.
38. Richardson, J. S. (1981). The anatomy and taxonomy of protein structure. Advan. Protein Chem. 34, 167-339.
39. Milner-White, E. J., Bell, L. H. & Maccallum, P. H. (1992). Pyrolidine ring puckering in cis- and trans-proline residues in proteins and polypeptides. Different puckers are favoured in certain situations. J. Mol. Biol. 228, 725-734.
40. de Leeuw, H. P. M., Haasnoot, C. A. G. & Altona, C. (1980). Empirical correlations between conformational parameters in β-D-furanoside fragments derived from a statistical survey of crystal structures of nucleic acid constituents. Israel J. Chem. 20, 108-126.
41. Haasnoot, C. A. G., de Leeuw, F. A. A. M., de Leeuw, H. P. M. & Altona, C. (1981). The relationship between proton-proton NMR coupling constants and substituent electronegativities. Org. Magn. Reson. 15, 43-52.
42. Harris, R. K., Becker, E. D., Bremser, W., Cabral de Menezes, S., Goodfellow, R. & Granger, P., IUPAC Commission on Molecular Structure and Spectroscopy, I.5. Recommendations for NMR nomenclature. A. Nuclear spin properties and conventions for chemical shifts, in preparation.
43. 15N chemical shift referencing in biomolecular NMR. J. Biomol. NMR, 6, 135-140.
44. DSS = 0.0246 ppm (i.e. to high frequency from that of DSS).
45. 15N NMR study of gramicidin D in water and organic solvents. J. Am. Chem. Soc. 106, 1939-1943.
46. 2H signals of a water sample at 298 K as measured by Frits Abildgaard and David M. LeMaster at the National Magnetic Resonance Facility at Madison. This value is a surrogate for the isotopomers of DSS, and its derivation assumes that there is no primary isotope effect on the ratio.
47. 2O solution containing 10% trimethylphosphate as the indirect reference and DSS as the direct reference.
48. HαHβ.
49. 1H NMR spectroscopy and distance geometry. J. Mol. Biol. 182, 295-315.
50. 13C chemical shifts. J. Biomol. NMR, 4, 455-458.
51. Eberstadt, M., Gemmecker, G., Mierke, D. F. & Kessler, H. (1995). Scalar coupling constants - Their analysis and their application for the elucidation of structures. Agnew. Chem. Int. Ed. Engl. 34, 1671-1695.
52. Ottiger, M., Szyperski, T., Luginbühl, L., Ortenzi, C., Luporini, P., Bradshaw, R. A. & Wüthrich, K. (1994). The NMR solution structure of the pheromone Er-2 from the ciliated protozoan Euplotes raikovi. Protein Sci. 3, 1515-1526.
53. Saenger, W. (1983). Principles of Nucleic Add Structure, pp. 123-124, Springer Verlag, New York.
54. Sutcliffe, M. J. (1993). Representing an ensemble of NMR-derived protein structures by a single structure. Protein Sci. 2, 936-944.
55. Fletcher, C. M., Jones, D. N. M., Diamond, R. & Neuhaus., D. (1996). Treatment of NOE constraints involving equivalent or nonstereoassigned protons in calculations of biomacromolecular structures. J. Biomol. NMR, 8, 292-310.
56. MacArthur, M. W. & Thornton, J. M. (1993). Conformational analysis of proteins structures derived from NMR data. Proteins: Struct. Funct. Genet. 17, 232-251.
57. Hyberts, S. G., Goldberg, M. S., Havel, T. F. & Wagner, G. (1992). The solution structure of eglin c based on measurements of many NOEs and coupling constants and its comparison with X-ray structures. Protein Sci. 1, 736-751.
58. Colovos, C. & Yeates, T. O. (1993). Verification of protein structures: Patterns of nonbonded atomic Interactions. Protein Sci. 2, 1511-1519.
59. Sippl, M. J. (1993). Recognition of errors in 3-dimensional structures of proteins. Proteins: Struct. Funct. Genet. 17, 355-362.
60. Vriend, G. & Sander, C. (1993). Quality control of proteins models: Directional atomic contact analysis. J. Appl. Crystallog. 26, 47-60.
61. MacArthur, M. W., Laskowski, R. A. & Thornton, J. M. (1994). Knowledge-based validation of protein-structure coordinates derived by X-ray crystallography and NMR spectroscopy. Curr. Opin. Struct. Biol. 4, 731-737.
62. Laskowski, R. A., Rullmann, J. A. C., MacArthur, M. W., Kaptein, R. & Thornton, J. M. (1996). AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR. J. Biomol. NMR, 8, 477-486.
63. Jardetzky, O. & Roberts, G. C. K. (1981). NMR in Molecular Biology, pp. 126-142, Academic Press, New York.
64. Watenpaugh, K. D., Berman, H. M., Bourne, P. E. & Fitzgerald, P. M. D. (1993). The macromolecular CIF dictionary. Acta Crystallog. sect. A, 49, (Supplement), IVI International Congress (IUCr), Abstract OCM-18.02.07.
65. Fitzgerald, P. M. D., Berman, H., Bourne, P. & Watenpaugh, K. (1993). The Macromolecular CIF Dictionary, Abstract no. D008, American Crystallographic Association Annual Meeting, Albuquerque, NM, May 23-28 (available from: http://ndbserver. rutgers.edu:80/mmcif/).
66. Hall, S. R. & Spadaccini, N. (1994). The STAR file: Detailed specifications. J. Chem. Inf. Comput. Sci. 34, 505-508.
67. Hall, S. R., Allen, F. H. & Brown, I. D. (International Union of Crystallography Commission on Crystallographic Data Commission on Journals Working Party on Crystallographic Information) (1991). The crystallographic information file (CIF): a new archive file for crystallography. Acta Crystallog. sect. A, 47, 655-685.
68. International Organization for Standardization (1987). Information Processing Systems - Open Systems Interconnection - Specification of Abstract Syntax Notation One (ASN.1). Technical report ISO8824.
69. International Organization for Standardization (1987). Information Processing Systems - Open Systems Interconnection - Specification of basic encoding rules for Abstract syntax notation one (ASN.1). Technical report ISO8825.
70. Ostell, J. (1990). GenInfo ASN.1 Syntax: Sequences. Technical reports 1 and 2, National Center for Biotechnology Information, National Library of Medicine.
71. Mockus, J. & Steckert, T. D. (1994). CXF Chemical eXchange Format Version 1.0, Chemical Abstracts Service, Columbus, OH, USA.
72. Ulrich, E. L. & Markley, J. L. (1994). A Data Dictionary and Information File for the Exchange and Archiving of NMR Experimental Results, 35th Experimental Nuclear Magnetic Resonance Conference, April 10-15, Asilomar, California, Abs. WP 112, p. 264. The BioMagResBank web pages (http://www.bmrb. wisc.edu/) contain complete information about this effort including user entry protocols and software.