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 and biochemical function(s). In this article we describe a largely automatic strategy for rapid determination of medium-accuracy protein backbone structures. Our strategy derives from ideas originally introduced by other groups for determining medium-accuracy NMR structures of large proteins using deuterated, (13)C-, (15)N-enriched protein samples with selective protonation of side-chain methyl groups ((13)CH(3)). Data collection includes acquiring NMR spectra for automatically determining assignments of backbone and side-chain (15)N, H(N) resonances, and side-chain (13)CH(3) methyl resonances. These assignments are determined automatically by the program AutoAssign using backbone triple resonance NMR data, together with Spin System Type Assignment Constraints (STACs) derived from side-chain triple-resonance experiments. The program AutoStructure then derives conformational constraints using these chemical shifts, amide (1)H/(2)H exchange, nuclear Overhauser effect spectroscopy (NOESY), and residual dipolar coupling data. The total time required for collecting such NMR data can potentially be as short as a few days. Here we demonstrate an integrated set of NMR software which can process these NMR spectra, carry out resonance assignments, interpret NOESY data, and generate medium-accuracy structures within a few days. The feasibility of this combined data collection and analysis strategy starting from raw NMR time domain data was illustrated by automatic analysis of a medium accuracy structure of the Z domain of Staphylococcal protein A.
Advances in automated NMR protein structure determination.
Advances in automated NMR protein structure determination.
Advances in automated NMR protein structure determination.
Q Rev Biophys. 2011 Mar 17;:1-53
Authors: Guerry P, Herrmann T
Around half of all protein structures solved nowadays using solution-state nuclear magnetic resonance (NMR) spectroscopy have been because of automated data analysis. The pervasiveness of computational approaches in general hides, however, a more nuanced view in which the full variety and richness of the field appears. This review is structured around a comparison of...
nmrlearner
Journal club
0
03-18-2011 06:00 PM
High-resolution protein structure determination starting with a global fold calculated from exact solutions to the RDC equations
High-resolution protein structure determination starting with a global fold calculated from exact solutions to the RDC equations
Abstract We present a novel structure determination approach that exploits the global orientational restraints from RDCs to resolve ambiguous NOE assignments. Unlike traditional approaches that bootstrap the initial fold from ambiguous NOE assignments, we start by using RDCs to compute accurate secondary structure element (SSE) backbones at the beginning of structure calculation. Our structure determination package, called rdc-Panda (RDC-based SSE PAcking with...
nmrlearner
Journal club
0
01-09-2011 12:46 PM
A novel strategy for NMR resonance assignment and protein structure determination
A novel strategy for NMR resonance assignment and protein structure determination
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...
nmrlearner
Journal club
0
12-18-2010 01:31 AM
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] Rapid protein fold determination using unassigned NMR data.
Rapid protein fold determination using unassigned NMR data.
Related Articles Rapid protein fold determination using unassigned NMR data.
Proc Natl Acad Sci U S A. 2003 Dec 23;100(26):15404-9
Authors: Meiler J, Baker D
Experimental structure determination by x-ray crystallography and NMR spectroscopy is slow and time-consuming compared with the rate at which new protein sequences are being identified. NMR spectroscopy has the advantage of rapidly providing the structurally relevant information in the form of unassigned chemical shifts (CSs),...
nmrlearner
Journal club
0
11-24-2010 09:16 PM
[NMR paper] Protein NMR structure determination with automated NOE-identification in the NOESY sp
Protein NMR structure determination with automated NOE-identification in the NOESY spectra using the new software ATNOS.
Related Articles Protein NMR structure determination with automated NOE-identification in the NOESY spectra using the new software ATNOS.
J Biomol NMR. 2002 Nov;24(3):171-89
Authors: Herrmann T, Güntert P, Wüthrich K
Novel algorithms are presented for automated NOESY peak picking and NOE signal identification in homonuclear 2D and heteronuclear-resolved 3D -NOESY spectra during de novo protein structure determination by NMR,...
nmrlearner
Journal club
0
11-24-2010 08:58 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
Automated protein NMR structure determination in solution.
Automated protein NMR structure determination in solution.
Automated protein NMR structure determination in solution.
Methods Mol Biol. 2010;673:95-127
Authors: Gronwald W, Kalbitzer HR
The main drawback of protein NMR spectroscopy today is still the extensive amount of time required for solving a single structure. The main bottleneck in this respect is the manual evaluation of the experimental spectra. A clear solution to this challenge is the development of automated methods for this purpose. At the current stage of development, this goal has...
Automated protein fold determination using a minimal NMR constraint strategy.
Linear Mode
