Related ArticlesAssignment of methyl NMR resonances of a 52*kDa protein with residue-specific 4D correlation maps.
J Biomol NMR. 2015 May 8;
Authors: Mishra SH, Frueh DP
Abstract
Methyl groups have become key probes for structural and functional studies by nuclear magnetic resonance. However, their NMR signals cluster in a small spectral region and assigning their resonances can be a tedious process. Here, we present a method that facilitates assignment of methyl resonances from assigned amide groups. Calculating the covariance between sensitive methyl and amide 3D spectra, each providing correlations to C(?) and C(?) separately, produces 4D correlation maps directly correlating methyl groups to amide groups. Optimal correlation maps are obtained by extracting residue-specific regions, applying derivative to the dimensions subject to covariance, and multiplying 4D maps stemming from different 3D spectra. The latter procedure rescues weak signals that may be missed in traditional assignment procedures. Using these covariance correlation maps, nearly all assigned isoleucine, leucine, and valine amide resonances of a 52*kDa nonribosomal peptide synthetase cyclization domain were paired with their corresponding methyl groups.
PMID: 25953312 [PubMed - as supplied by publisher]
Assignment of methyl NMR resonances of a 52Â*kDa protein with residue-specific 4D correlation maps
Assignment of methyl NMR resonances of a 52Â*kDa protein with residue-specific 4D correlation maps
Abstract
Methyl groups have become key probes for structural and functional studies by nuclear magnetic resonance. However, their NMR signals cluster in a small spectral region and assigning their resonances can be a tedious process. Here, we present a method that facilitates assignment of methyl resonances from assigned amide groups. Calculating the covariance between sensitive methyl and amide 3D spectra, each providing correlations to Cα and Cβ...
nmrlearner
Journal club
0
05-07-2015 03:04 PM
FLAMEnGO 2.0: An Enhanced Fuzzy Logic Algorithm for Structure-Based Assignment of Methyl Group Resonances
FLAMEnGO 2.0: An Enhanced Fuzzy Logic Algorithm for Structure-Based Assignment of Methyl Group Resonances
Publication date: Available online 2 May 2014
Source:Journal of Magnetic Resonance</br>
Author(s): Fa-An Chao , Jonggul Kim , Youlin Xia , Michael Milligan , Nancy Rowe , Gianluigi Veglia</br>
We present an enhanced version of the FLAMEnGO (Fuzzy Logic Assignment of Methyl Group) software, a structure-based method to assign methyl group resonances in large proteins. FLAMEnGO utilizes a fuzzy logic algorithm coupled with Monte Carlo sampling to obtain a...
nmrlearner
Journal club
0
05-02-2014 06:49 PM
[NMR paper] Identifying inter-residue resonances in crowded 2D (13)C- (13)C chemical shift correlation spectra of membrane proteins by solid-state MAS NMR difference spectroscopy.
Identifying inter-residue resonances in crowded 2D (13)C- (13)C chemical shift correlation spectra of membrane proteins by solid-state MAS NMR difference spectroscopy.
Identifying inter-residue resonances in crowded 2D (13)C- (13)C chemical shift correlation spectra of membrane proteins by solid-state MAS NMR difference spectroscopy.
J Biomol NMR. 2013 May 25;
Authors: Miao Y, Cross TA, Fu R
Abstract
The feasibility of using difference spectroscopy, i.e. subtraction of two correlation spectra at different mixing times, for substantially...
nmrlearner
Journal club
0
05-28-2013 06:36 PM
[NMR paper] Efficient resonance assignment of proteins in MAS NMR by simultaneous intra- and inter-residue 3D correlation spectroscopy.
Efficient resonance assignment of proteins in MAS NMR by simultaneous intra- and inter-residue 3D correlation spectroscopy.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--production.springer.de-OnlineResources-Logos-springerlink.gif Related Articles Efficient resonance assignment of proteins in MAS NMR by simultaneous intra- and inter-residue 3D correlation spectroscopy.
J Biomol NMR. 2013 Jan 19;
Authors: Daviso E, Eddy MT, Andreas LB, Griffin RG, Herzfeld J
Abstract
Resonance assignment is the first step in NMR structure...
nmrlearner
Journal club
0
02-03-2013 10:19 AM
Automated sequence- and stereo-specific assignment of methyl-labeled proteins by paramagnetic relaxation and methylâ??methyl nuclear overhauser enhancement spectroscopy
Automated sequence- and stereo-specific assignment of methyl-labeled proteins by paramagnetic relaxation and methylâ??methyl nuclear overhauser enhancement spectroscopy
Abstract Methyl-transverse relaxation optimized spectroscopy is rapidly becoming the preferred NMR technique for probing structure and dynamics of very large proteins up to ~1 MDa in molecular size. Data interpretation, however, necessitates assignment of methyl groups which still presents a very challenging and time-consuming process. Here we demonstrate that, in combination with a known 3D structure, paramagnetic...