Assignment of protein NMR spectra based on projections, multi-way decomposition and a fast correlation approach.
We present an approach for the assignment of protein NMR resonances that combines established and new concepts: (a) Based on published reduced dimensionality methods, two 5-dimensional experiments are proposed. (b) Multi-way decomposition (PRODECOMP) applied simultaneously to all acquired NMR spectra provides the assignment of resonance frequencies under conditions of very low signal-to-noise. (c) Each resulting component characterizes all spin (1/2) nuclei in a (doubly-labeled) CbetaH(n)-CalphaH-C'-NH-CalphaH-CbetaH(n) fragment in an unambiguous manner, such that sequentially neighboring components have about four atoms in common. (d) A new routine (SHABBA) determines correlations for all component pairs based on the common nuclei; high correlation values yield sequential chains of a dozen or more components. (e) The potentially error-prone peak picking is delayed to the last step, where it helps to place the component chains within the protein sequence, and thus to achieve the final backbone assignment. The approach was validated by achieving complete backbone resonance assignments for ubiquitin.
Staykova
Doroteya K
DK
Biophysics Group, Department of Chemistry, University of Gothenburg, Gothenburg, Sweden.
Fredriksson
Jonas
J
Bermel
Wolfgang
W
Billeter
Martin
M
D000465:Algorithms; D000595:Amino Acid Sequence; D008969:Molecular Sequence Data; D019906:Nuclear Magnetic Resonance, Biomolecular / Q000379:methods*; D025801:Ubiquitin / Q000737:chemistry / Q000235:genetics
D025801:Ubiquitin
J Biomol NMR. 1993 Mar;3(2):185-204
8477186
J Am Chem Soc. 2005 Oct 5;127(39):13486-7
16190698
J Am Chem Soc. 2007 Sep 5;129(35):10823-8
17691781
J Biomol NMR. 2003 Oct;27(2):101-13
12962120
J Biomol NMR. 1991 Sep;1(3):217-36
1841696
Proc Natl Acad Sci U S A. 2004 Jun 29;101(26):9642-7
15210958
J Am Chem Soc. 2003 Feb 5;125(5):1385-93
12553842
Magn Reson Chem. 2006 Jul;44 Spec No:S51-60
16826541
J Magn Reson. 2005 Jun;174(2):188-99
15862234
Proc Natl Acad Sci U S A. 2002 Jun 11;99(12):8009-14
12060747
Proc Natl Acad Sci U S A. 2005 Aug 2;102(31):10876-81
16043707
Magn Reson Chem. 2006 Jul;44 Spec No:S185-95
16823902
J Magn Reson. 2004 Oct;170(2):263-77
15388090
J Am Chem Soc. 2005 Sep 14;127(36):12528-36
16144400
J Am Chem Soc. 2006 May 10;128(18):6020-1
16669655
J Biomol NMR. 2001 May;20(1):49-60
11430755
J Biomol NMR. 1993 Mar;3(2):225-31
8477187
Magn Reson Chem. 2006 Mar;44(3):197-209
16566032
J Am Chem Soc. 2004 Oct 20;126(41):13180-1
15479045