Not all proteins are amenable to uniform isotopic labeling with ^(13)C and ^(15)N, something needed for the widely used, and largely deductive, triple resonance assignment process. Among them are proteins expressed in mammalian cell culture where native glycosylation can be maintained, and proper formation of disulfide bonds facilitated. Uniform labeling in mammalian cells is prohibitively expensive, but sparse labeling with one or a few isotopically enriched amino acid types is an option for...
[NMR paper] Simultaneous Assignment and Structure Determination of Proteins From Sparsely Labeled NMR Datasets
Simultaneous Assignment and Structure Determination of Proteins From Sparsely Labeled NMR Datasets
Sparsely labeled NMR samples provide opportunities to study larger biomolecular assemblies than is traditionally done by NMR. This requires new computational tools that can handle the sparsity and ambiguity in the NMR datasets. The MELD (modeling employing limited data) Bayesian approach was assessed to be the best performing in predicting structures from sparsely labeled NMR data in the 13th edition of the Critical Assessment of Structure Prediction (CASP) event-and limitations of the...
...
nmrlearner
Journal club
0
12-16-2021 10:50 PM
[NMR paper] NMR Resonance Assignment Methodology: Characterizing Large Sparsely Labeled Glycoproteins.
NMR Resonance Assignment Methodology: Characterizing Large Sparsely Labeled Glycoproteins.
Related Articles NMR Resonance Assignment Methodology: Characterizing Large Sparsely Labeled Glycoproteins.
J Mol Biol. 2019 Apr 26;:
Authors: Chalmers GR, Eletsky A, Morris LC, Yang JY, Tian F, Woods RJ, Moremen KW, Prestegard JH
Abstract
Characterization of proteins using NMR methods begins with assignment of resonances to specific residues. This is usually accomplished using sequential connectivities between nuclear pairs in proteins...
nmrlearner
Journal club
0
04-30-2019 03:58 PM
[NMR paper] NMR assignments of sparsely labeled proteins using a genetic algorithm.
NMR assignments of sparsely labeled proteins using a genetic algorithm.
Related Articles NMR assignments of sparsely labeled proteins using a genetic algorithm.
J Biomol NMR. 2017 Mar 13;:
Authors: Gao Q, Chalmers GR, Moremen KW, Prestegard JH
Abstract
Sparse isotopic labeling of proteins for NMR studies using single types of amino acid ((15)N or (13)C enriched) has several advantages. Resolution is enhanced by reducing numbers of resonances for large proteins, and isotopic labeling becomes economically feasible for glycoproteins...
nmrlearner
Journal club
0
03-16-2017 06:36 PM
NMR assignments of sparsely labeled proteins using a genetic algorithm
NMR assignments of sparsely labeled proteins using a genetic algorithm
Abstract
Sparse isotopic labeling of proteins for NMR studies using single types of amino acid (15N or 13C enriched) has several advantages. Resolution is enhanced by reducing numbers of resonances for large proteins, and isotopic labeling becomes economically feasible for glycoproteins that must be expressed in mammalian cells. However, without access to the traditional triple resonance strategies that require uniform isotopic labeling, NMR assignment of crosspeaks in...
nmrlearner
Journal club
0
03-14-2017 10:36 PM
[NMR paper] Exploiting image registration for automated resonance assignment in NMR.
Exploiting image registration for automated resonance assignment in NMR.
Exploiting image registration for automated resonance assignment in NMR.
J Biomol NMR. 2015 Apr 1;
Authors: Strickland M, Stephens T, Liu J, Tjandra N
Abstract
Analysis of protein NMR data involves the assignment of resonance peaks in a number of multidimensional data sets. To establish resonance assignment a three-dimensional search is used to match a pair of common variables, such as chemical shifts of the same spin system, in different NMR spectra. We...
nmrlearner
Journal club
0
04-02-2015 10:09 AM
Exploiting image registration for automated resonance assignment in NMR
Exploiting image registration for automated resonance assignment in NMR
Abstract
Analysis of protein NMR data involves the assignment of resonance peaks in a number of multidimensional data sets. To establish resonance assignment a three-dimensional search is used to match a pair of common variables, such as chemical shifts of the same spin system, in different NMR spectra. We show that by displaying the variables to be compared in two-dimensional plots the process can be simplified. Moreover, by utilizing a fast Fourier transform cross-correlation...
nmrlearner
Journal club
0
04-01-2015 08:27 AM
Sparsely-sampled High-resolution 4-D Experiments for Efficient Backbone Resonance Assignment of Disordered Proteins
Sparsely-sampled High-resolution 4-D Experiments for Efficient Backbone Resonance Assignment of Disordered Proteins
Publication year: 2011
Source: Journal of Magnetic Resonance, In Press, Accepted Manuscript, Available online 4 January 2011</br>
Jie, Wen , Jihui, Wu , Pei, Zhou</br>
Intrinsically disordered proteins (IDPs) play important roles in many critical cellular processes. Due to their limited chemical shift dispersion, IDPs often require four pairs of resonance connectivities (H?, C?, C? and CO) for establishing sequential backbone assignment. Because most conventional 4-D...
nmrlearner
Journal club
0
01-05-2011 11:03 AM
[NMR paper] Resonance assignment of 13C/15N labeled solid proteins by two- and three-dimensional
Resonance assignment of 13C/15N labeled solid proteins by two- and three-dimensional magic-angle-spinning NMR.
Related Articles Resonance assignment of 13C/15N labeled solid proteins by two- and three-dimensional magic-angle-spinning NMR.
J Biomol NMR. 1999 Sep;15(1):1-14
Authors: Hong M
The comprehensive structure determination of isotopically labeled proteins by solid-state NMR requires sequence-specific assignment of 13C and 15N spectra. We describe several 2D and 3D MAS correlation techniques for resonance assignment and apply them, at 7.0...
AssignSLP_GUI, a software tool exploiting AI for NMR resonance assignment of sparsely labeled proteins
Linear Mode
