PMID- 16041479
OWN - NLM
STAT- MEDLINE
DCOM- 20051108
LR  - 20181113
IS  - 0925-2738 (Print)
IS  - 0925-2738 (Linking)
VI  - 32
IP  - 1
DP  - 2005 May
TI  - Linear analysis of carbon-13 chemical shift differences and its application to 
      the detection and correction of errors in referencing and spin system 
      identifications.
PG  - 13-22
AB  - Statistical analysis reveals that the set of differences between the secondary 
      shifts of the alpha- and beta-carbons for residues i of a protein 
      (Deltadelta13C(alpha)i - Deltadelta13C(beta)i) provides the means to detect and 
      correct referencing errors for 1H and 13C nuclei within a given dataset. In a 
      correctly referenced protein dataset, linear regression plots of 
      Deltadelta13C(alpha)i, Deltadelta13C(beta)i, or Deltadelta1H(alpha)i vs. 
      (Deltadelta13C(alpha)i - Deltadelta13C(beta)i) pass through the origin from two 
      directions, the helix-to-coil and strand-to-coil directions. Thus, linear 
      analysis of chemical shifts (LACS) can be used to detect referencing errors and 
      to recalibrate the 1H and 13C chemical shift scales if needed. The analysis 
      requires only that the signals be identified with distinct residue types 
      (intra-residue spin systems). LACS allows errors in calibration to be detected 
      and corrected in advance of sequence-specific assignments and secondary structure 
      determinations. Signals that do not fit the linear model (outliers) deserve 
      scrutiny since they could represent errors in identifying signals with a 
      particular residue, or interesting features such as a cis-peptide bond. LACS 
      provides the basis for the automated detection of such features and for testing 
      reassignment hypotheses. Early detection and correction of errors in referencing 
      and spin system identifications can improve the speed and accuracy of chemical 
      shift assignments and secondary structure determinations. We have used LACS to 
      create a database of offset-corrected chemical shifts corresponding to nearly 
      1800 BMRB entries: 300 with and 1500 without corresponding three-dimensional (3D) 
      structures. This database can serve as a resource for future analysis of the 
      effects of amino acid sequence and protein secondary and tertiary structure on 
      NMR chemical shifts.
FAU - Wang, Liya
AU  - Wang L
AD  - National Magnetic Resonance Facility at Madison, Biochemistry Department, 433 
      Babcock Drive, Madison, WI 53706, USA.
FAU - Eghbalnia, Hamid R
AU  - Eghbalnia HR
FAU - Bahrami, Arash
AU  - Bahrami A
FAU - Markley, John L
AU  - Markley JL
LA  - eng
GR  - 1P50 GM64598/GM/NIGMS NIH HHS/United States
GR  - 5T15LM005359/LM/NLM NIH HHS/United States
GR  - P41 RR02301/RR/NCRR NIH HHS/United States
PT  - Journal Article
PT  - Research Support, N.I.H., Extramural
PT  - Research Support, U.S. Gov't, P.H.S.
PL  - Netherlands
TA  - J Biomol NMR
JT  - Journal of biomolecular NMR
JID - 9110829
RN  - 0 (Carbon Isotopes)
RN  - 0 (Proteins)
SB  - IM
MH  - Amino Acid Sequence
MH  - Carbon Isotopes/*chemistry
MH  - Nuclear Magnetic Resonance, Biomolecular/*methods
MH  - Protein Conformation
MH  - Proteins/*chemistry
MH  - Regression Analysis
MH  - Statistics as Topic
EDAT- 2005/07/26 09:00
MHDA- 2005/11/09 09:00
CRDT- 2005/07/26 09:00
PHST- 2004/12/02 00:00 [received]
PHST- 2005/01/24 00:00 [accepted]
PHST- 2005/07/26 09:00 [pubmed]
PHST- 2005/11/09 09:00 [medline]
PHST- 2005/07/26 09:00 [entrez]
AID - 10.1007/s10858-005-1717-0 [doi]
PST - ppublish
SO  - J Biomol NMR. 2005 May;32(1):13-22. doi: 10.1007/s10858-005-1717-0.