![](/images/ico/ico_close.png)
![](/images/ico/ico5.png)
Author: Fritzsching K.
Publisher: Springer Publishing Company
ISSN: 0925-2738
Source: Journal of Biomolecular NMR, Vol.56, Iss.2, 2013-06, pp. : 155-167
Disclaimer: Any content in publications that violate the sovereignty, the constitution or regulations of the PRC is not accepted or approved by CNPIEC.
Abstract
We introduce a Python-based program that utilizes the large database of 13C and 15N chemical shifts in the Biological Magnetic Resonance Bank to rapidly predict the amino acid type and secondary structure from correlated chemical shifts. The program, called PACSYlite Unified Query (PLUQ), is designed to help assign peaks obtained from 2D 13C-13C, 15N-13C, or 3D 15N-13C-13C magic-angle-spinning correlation spectra. We show secondary-structure specific 2D 13C-13C correlation maps of all twenty amino acids, constructed from a chemical shift database of 262,209 residues. The maps reveal interesting conformation-dependent chemical shift distributions and facilitate searching of correlation peaks during amino-acid type assignment. Based on these correlations, PLUQ outputs the most likely amino acid types and the associated secondary structures from inputs of experimental chemical shifts. We test the assignment accuracy using four high-quality protein structures. Based on only the Cα and Cβ chemical shifts, the highest-ranked PLUQ assignments were 40-60 % correct in both the amino-acid type and the secondary structure. For three input chemical shifts (CO-Cα-Cβ or N-Cα-Cβ), the first-ranked assignments were correct for 60 % of the residues, while within the top three predictions, the correct assignments were found for 80 % of the residues. PLUQ and the chemical shift maps are expected to be useful at the first stage of sequential assignment, for combination with automated sequential assignment programs, and for highly disordered proteins for which secondary structure analysis is the main goal of structure determination.
Related content
![](/images/ico/ico_close.png)
![](/images/ico/ico5.png)
By Brothers Michael Nesbitt Anna Hallock Michael Rupasinghe Sanjeewa Tang Ming Harris Jason Baudry Jerome Schuler Mary Rienstra Chad
Journal of Biomolecular NMR, Vol. 52, Iss. 1, 2012-01 ,pp. :
![](/images/ico/ico_close.png)
![](/images/ico/ico5.png)
By Miao Yimin Cross Timothy Fu Riqiang
Journal of Biomolecular NMR, Vol. 56, Iss. 3, 2013-07 ,pp. :
![](/images/ico/ico_close.png)
![](/images/ico/ico5.png)
By Wang Ching-Cheng Chen Jui-Hung Lai Wen-Chung Chuang Woei-Jer
Journal of Biomolecular NMR, Vol. 38, Iss. 1, 2007-05 ,pp. :
![](/images/ico/ico_close.png)
![](/images/ico/ico5.png)
By Bobay Benjamin Thompson Richele Milton Debra Cavanagh John
Biomolecular NMR Assignments, Vol. 8, Iss. 1, 2014-04 ,pp. :