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 â?? 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.
Content Type Journal Article
DOI 10.1007/s10858-010-9458-0
Authors
Alexander Lemak, Ontario Cancer Institute and The Campbell Family Cancer Research Institute, Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, ON M5G 1L7, Canada
Aleksandras Gutmanas, Ontario Cancer Institute and The Campbell Family Cancer Research Institute, Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, ON M5G 1L7, Canada
Seth Chitayat, Ontario Cancer Institute and The Campbell Family Cancer Research Institute, Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, ON M5G 1L7, Canada
Murthy Karra, Ontario Cancer Institute and The Campbell Family Cancer Research Institute, Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, ON M5G 1L7, Canada
Christophe Farès, Ontario Cancer Institute and The Campbell Family Cancer Research Institute, Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, ON M5G 1L7, Canada
Maria Sunnerhagen, Division of Molecular Biotechnology, Department of Physics, Chemistry and Biology, Linköping University, 58183 Linköping, Sweden
Cheryl H. Arrowsmith, Ontario Cancer Institute and The Campbell Family Cancer Research Institute, Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, ON M5G 1L7, Canada
A novel strategy for NMR resonance assignment and protein structure determination.
A novel strategy for NMR resonance assignment and protein structure determination.
A novel strategy for NMR resonance assignment and protein structure determination.
J Biomol NMR. 2010 Dec 14;
Authors: Lemak A, Gutmanas A, Chitayat S, Karra M, Farès C, Sunnerhagen M, Arrowsmith CH
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...
nmrlearner
Journal club
0
12-17-2010 11:23 AM
[NMR paper] Simultaneous assignment and structure determination of protein backbones by using NMR
Simultaneous assignment and structure determination of protein backbones by using NMR dipolar couplings.
Related Articles Simultaneous assignment and structure determination of protein backbones by using NMR dipolar couplings.
Angew Chem Int Ed Engl. 2004 Jun 28;43(26):3479-81
Authors: Jung YS, Sharma M, Zweckstetter M
nmrlearner
Journal club
0
11-24-2010 09:51 PM
[NMR paper] Automated protein fold determination using a minimal NMR constraint strategy.
Automated protein fold determination using a minimal NMR constraint strategy.
Related Articles Automated protein fold determination using a minimal NMR constraint strategy.
Protein Sci. 2003 Jun;12(6):1232-46
Authors: Zheng D, Huang YJ, Moseley HN, Xiao R, Aramini J, Swapna GV, Montelione GT
Determination of precise and accurate protein structures by NMR generally requires weeks or even months to acquire and interpret all the necessary NMR data. However, even medium-accuracy fold information can often provide key clues about protein evolution...
nmrlearner
Journal club
0
11-24-2010 09:01 PM
[NMR paper] Simultaneous assignment and structure determination of a membrane protein from NMR or
Simultaneous assignment and structure determination of a membrane protein from NMR orientational restraints.
Simultaneous assignment and structure determination of a membrane protein from NMR orientational restraints.
Protein Sci. 2003 Mar;12(3):403-11
Authors: Marassi FM, Opella SJ
A solid-state NMR approach for simultaneous resonance assignment and three-dimensional structure determination of a membrane protein in lipid bilayers is described. The approach is based on the scattering, hence the descriptor "shotgun," of (15)N-labeled amino...
nmrlearner
Journal club
0
11-24-2010 09:01 PM
[NMR paper] Protein NMR structure determination with automated NOE assignment using the new softw
Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA.
Related Articles Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA.
J Mol Biol. 2002 May 24;319(1):209-27
Authors: Herrmann T, Güntert P, Wüthrich K
Combined automated NOE assignment and structure determination module (CANDID) is a new software for efficient NMR structure determination of proteins by automated...
nmrlearner
Journal club
0
11-24-2010 08:49 PM
[NMR paper] A calculation strategy for the structure determination of symmetric dimers by 1H NMR.
A calculation strategy for the structure determination of symmetric dimers by 1H NMR.
Related Articles A calculation strategy for the structure determination of symmetric dimers by 1H NMR.
Proteins. 1993 Nov;17(3):297-309
Authors: Nilges M
The structure determination of symmetric dimers by NMR is impeded by the ambiguity of inter- and intramonomer NOE crosspeaks. In this paper, a calculation strategy is presented that allows the calculation of dimer structures without resolving the ambiguity by additional experiments (like asymmetric...
nmrlearner
Journal club
0
08-22-2010 03:01 AM
[NMR paper] Sequential NMR resonance assignment and structure determination of the Kunitz-type in
Sequential NMR resonance assignment and structure determination of the Kunitz-type inhibitor domain of the Alzheimer's beta-amyloid precursor protein.
Related Articles Sequential NMR resonance assignment and structure determination of the Kunitz-type inhibitor domain of the Alzheimer's beta-amyloid precursor protein.
Biochemistry. 1991 Oct 29;30(43):10467-78
Authors: Heald SL, Tilton RF, Hammond LJ, Lee A, Bayney RM, Kamarck ME, Ramabhadran TV, Dreyer RN, Davis G, Unterbeck A
Certain precursor proteins (APP751 and APP770) of the amyloid...
nmrlearner
Journal club
0
08-21-2010 11:12 PM
[NMR paper] Sequential NMR resonance assignment and structure determination of the Kunitz-type in
Sequential NMR resonance assignment and structure determination of the Kunitz-type inhibitor domain of the Alzheimer's beta-amyloid precursor protein.
Related Articles Sequential NMR resonance assignment and structure determination of the Kunitz-type inhibitor domain of the Alzheimer's beta-amyloid precursor protein.
Biochemistry. 1991 Oct 29;30(43):10467-78
Authors: Heald SL, Tilton RF, Hammond LJ, Lee A, Bayney RM, Kamarck ME, Ramabhadran TV, Dreyer RN, Davis G, Unterbeck A
Certain precursor proteins (APP751 and APP770) of the amyloid...