Journal of Biomolecular NMR

, Volume 7, Issue 3, pp 207–213 | Cite as

Automated sequence-specific NMR assignment of homologous proteins using the program GARANT

  • Christian Bartels
  • Martin Billeter
  • Peter Güntert
  • Kurt Wüthrich
Research Papers

Summary

The program GARANT (General Algorithm for Resonance AssignmeNT) for automated sequence-specific NMR assignment of proteins is based on the mapping of peaks predicted from the amino acid sequence onto the peaks observed in multidimensional spectra [C. Bartels, P. Güntert, M. Billeter and K. Wüthrich (1996) J. Comput. Chem., manuscript submitted for publication]. In this paper we demonstrate the potential of GARANT for the assignment of homologous proteins when either the three-dimensional structure or the chemical shifts of the parent protein are known. In these applications, GARANT utilizes supplementary information either in the form of interatomic distances derived from the three-dimensional structure, in order to add nuclear Overhauser effects reflecting the tertiary structure to the list of expected peaks, or in the form of the chemical shifts of the parent protein, in order to obtain a better estimate of the positions of the expected peaks. The procedure is illustrated with three different proteins: (i) a mutant form of Tendamistat (74 residues), using homonuclear 2D 1H NMR spectra and either the three-dimensional structure or the chemical shifts of the wild-type protein; (ii) the mutant Antp(C39S, W56S) homeodomain (68 residues), using homonuclear 2D 1H NMR spectra and the three-dimensional structure of the Antp(C39S) homeodomain; and (iii) free cyclophilin A (165 residues), using heteronuclear 3D NMR spectra and the three-dimensional structure of a cyclophilin A-cyclosporin A complex. In these three systems nearly complete assignment of the polypeptide backbone resonances and assignment of over 80% of the amino acid side-chain resonances was obtained without manual intervention.

Keywords

NMR structure determination Automated sequence-specific resonance assignment Homologous proteins 

Abbreviations

1D, 2D, 3D

one-, two-, three-dimensional

NOE

nuclear Overhauser enhancement

NOESY

nuclear Overhauser enhancement spectroscopy

TOCSY

total correlation spectroscopy

COSY

correlation spectroscopy

Antp(C39S, W56S)

mutant Antennapedia homeodomain with the residues Cys39 and Trp56 replaced by serine

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Copyright information

© ESCOM Science Publishers B.V 1996

Authors and Affiliations

  • Christian Bartels
    • 1
  • Martin Billeter
    • 1
  • Peter Güntert
    • 1
  • Kurt Wüthrich
    • 1
  1. 1.Institut für Molekularbiologie und BiophysikEidgenössische Technische Hochschule-HönggerbergZürichSwitzerland

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