Rapid Analysis of Protein Backbone Resonance Assignments Using Cryogenic Probes, a Distributed Linux-based Computing Architecture, and an Integrated Set of Spectral Analysis Tools

Overview

Journal J Struct Funct Genomics

Specialty Genetics

Date 2003 Jul 3

PMID 12836666

Citations 17

Authors

Daniel Monleon

Kimberly Colson

Hunter N B Moseley

Clemens Anklin

Robert Oswald

Thomas Szyperski

Gaetano T Montelione

Affiliations

Soon will be listed here.

Abstract

Rapid data collection, spectral referencing, processing by time domain deconvolution, peak picking and editing, and assignment of NMR spectra are necessary components of any efficient integrated system for protein NMR structure analysis. We have developed a set of software tools designated AutoProc, AutoPeak, and AutoAssign, which function together with the data processing and peak-picking programs NMRPipe and Sparky, to provide an integrated software system for rapid analysis of protein backbone resonance assignments. In this paper we demonstrate that these tools, together with high-sensitivity triple resonance NMR cryoprobes for data collection and a Linux-based computer cluster architecture, can be combined to provide nearly complete backbone resonance assignments and secondary structures (based on chemical shift data) for a 59-residue protein in less than 30 hours of data collection and processing time. In this optimum case of a small protein providing excellent spectra, extensive backbone resonance assignments could also be obtained using less than 6 hours of data collection and processing time. These results demonstrate the feasibility of high throughput triple resonance NMR for determining resonance assignments and secondary structures of small proteins, and the potential for applying NMR in large scale structural proteomics projects.

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References

Zimmerman D, Kulikowski C, Wang L, Lyons B, Montelione G . Automated sequencing of amino acid spin systems in proteins using multidimensional HCC(CO)NH-TOCSY spectroscopy and constraint propagation methods from artificial intelligence. J Biomol NMR. 1994; 4(2):241-56. DOI: 10.1007/BF00175251. View

Delaglio F, Grzesiek S, Vuister G, Zhu G, Pfeifer J, Bax A . NMRPipe: a multidimensional spectral processing system based on UNIX pipes. J Biomol NMR. 1995; 6(3):277-93. DOI: 10.1007/BF00197809. View

Leutner M, Gschwind R, Liermann J, Schwarz C, Gemmecker G, Kessler H . Automated backbone assignment of labeled proteins using the threshold accepting algorithm. J Biomol NMR. 1998; 11(1):31-43. DOI: 10.1023/a:1008298226961. View

Zimmerman D, Kulikowski C, Huang Y, Feng W, Tashiro M, Shimotakahara S . Automated analysis of protein NMR assignments using methods from artificial intelligence. J Mol Biol. 1997; 269(4):592-610. DOI: 10.1006/jmbi.1997.1052. View

Clore G, Gronenborn A . Structures of larger proteins in solution: three- and four-dimensional heteronuclear NMR spectroscopy. Science. 1991; 252(5011):1390-9. DOI: 10.1126/science.2047852. View

Szyperski T, Luginbuhl P, Otting G, Guntert P, Wuthrich K . Protein dynamics studied by rotating frame 15N spin relaxation times. J Biomol NMR. 1993; 3(2):151-64. DOI: 10.1007/BF00178259. View

Moseley H, Montelione G . Automated analysis of NMR assignments and structures for proteins. Curr Opin Struct Biol. 1999; 9(5):635-42. DOI: 10.1016/s0959-440x(99)00019-6. View

Ikura M, Kay L, Bax A . A novel approach for sequential assignment of 1H, 13C, and 15N spectra of proteins: heteronuclear triple-resonance three-dimensional NMR spectroscopy. Application to calmodulin. Biochemistry. 1990; 29(19):4659-67. DOI: 10.1021/bi00471a022. View

Wuthrich K . NMR - this other method for protein and nucleic acid structure determination. Acta Crystallogr D Biol Crystallogr. 1995; 51(Pt 3):249-70. DOI: 10.1107/S0907444994010188. View

10.

Rios C, Feng W, Tashiro M, Shang Z, Montelione G . Phase labeling of C-H and C-C spin-system topologies: application in constant-time PFG-CBCA(CO)NH experiments for discriminating amino acid spin-system types. J Biomol NMR. 1996; 8(3):345-50. DOI: 10.1007/BF00410332. View

11.

Grzesiek S, Bax A . Amino acid type determination in the sequential assignment procedure of uniformly 13C/15N-enriched proteins. J Biomol NMR. 1993; 3(2):185-204. DOI: 10.1007/BF00178261. View

12.

Wishart D, Sykes B . The 13C chemical-shift index: a simple method for the identification of protein secondary structure using 13C chemical-shift data. J Biomol NMR. 1994; 4(2):171-80. DOI: 10.1007/BF00175245. View

13.

Montelione G, Zheng D, Huang Y, Gunsalus K, Szyperski T . Protein NMR spectroscopy in structural genomics. Nat Struct Biol. 2000; 7 Suppl:982-5. DOI: 10.1038/80768. View

14.

Moseley H, Monleon D, Montelione G . Automatic determination of protein backbone resonance assignments from triple resonance nuclear magnetic resonance data. Methods Enzymol. 2001; 339:91-108. DOI: 10.1016/s0076-6879(01)39311-4. View

15.

Jansson M, Li Y, Jendeberg L, Anderson S, Montelione G, Nilsson B . High-level production of uniformly ¹⁵N- and ¹³C-enriched fusion proteins in Escherichia coli. J Biomol NMR. 1996; 7(2):131-41. DOI: 10.1007/BF00203823. View

16.

Kay L . Pulsed field gradient multi-dimensional NMR methods for the study of protein structure and dynamics in solution. Prog Biophys Mol Biol. 1995; 63(3):277-99. DOI: 10.1016/0079-6107(95)00007-0. View

17.

Guntert P, Salzmann M, Braun D, Wuthrich K . Sequence-specific NMR assignment of proteins by global fragment mapping with the program MAPPER. J Biomol NMR. 2000; 18(2):129-37. DOI: 10.1023/a:1008318805889. View

18.

Otting G, Liepinsh E, Wuthrich K . Disulfide bond isomerization in BPTI and BPTI(G36S): an NMR study of correlated mobility in proteins. Biochemistry. 1993; 32(14):3571-82. DOI: 10.1021/bi00065a008. View