A novel strategy for NMR resonance assignment and protein structure determination |
| |
Authors: | Alexander Lemak Aleksandras Gutmanas Seth Chitayat Murthy Karra Christophe Farès Maria Sunnerhagen Cheryl H Arrowsmith |
| |
Institution: | 1.Ontario Cancer Institute and The Campbell Family Cancer Research Institute, Department of Medical Biophysics,University of Toronto,Toronto,Canada;2.Division of Molecular Biotechnology, Department of Physics, Chemistry and Biology,Link?ping University,Link?ping,Sweden;3.The Northeast Structural Genomics Consortium,University of Toronto,Toronto,Canada;4.Max-Planck-Institut f. Kohlenforschung,Mülheim an der Ruhr,Germany;5.Protein Data Bank Europe,European Bioinformatics Institute,Hinxton, Cambridge,UK |
| |
Abstract: | The quality of protein structures determined by nuclear magnetic resonance (NMR) spectroscopy is contingent on the number
and quality of experimentally-derived resonance assignments, distance and angular restraints. Two key features of protein
NMR data have posed challenges for the routine and automated structure determination of small to medium sized proteins; (1)
spectral resolution – especially of crowded nuclear Overhauser effect spectroscopy (NOESY) spectra, and (2) the reliance on
a continuous network of weak scalar couplings as part of most common assignment protocols. In order to facilitate NMR structure
determination, we developed a semi-automated strategy that utilizes non-uniform sampling (NUS) and multidimensional decomposition
(MDD) for optimal data collection and processing of selected, high resolution multidimensional NMR experiments, combined it
with an ABACUS protocol for sequential and side chain resonance assignments, and streamlined this procedure to execute structure
and refinement calculations in CYANA and CNS, respectively. Two graphical user interfaces (GUIs) were developed to facilitate
efficient analysis and compilation of the data and to guide automated structure determination. This integrated method was
implemented and refined on over 30 high quality structures of proteins ranging from 5.5 to 16.5 kDa in size. |
| |
Keywords: | |
本文献已被 PubMed SpringerLink 等数据库收录! |
|