Publication date: Available online 7 April 2016 Source:Journal of Magnetic Resonance
Author(s): Abhinav Dubey, Somnath Mondal, Kousik Chandra, Hanudatta S. Atreya
We present a simple approach to rapidly identify amino acid types in proteins from a 2D spectrum. The method is based on the fact that 13C? chemical shifts of different amino acid types fall in distinct spectral regions. By evolving the 13C chemical shifts in the conventional HNCACB or HN(CO)CACB type experiment for a single specified delay period, the phase of the cross peaks of different amino acid residues are modulated depending on their 13C? shift values. Following this specified evolution period, the 2D HN projections of these experiments are acquired. The 13C evolution period can be chosen such that all residues belonging to a given set of amino acid types have the same phase pattern (positive or negative) facilitating their identification. This approach does not require the preparation of any additional samples, involves the analysis of 2D [15N-1H] HSQC-type spectra obtained from the routinely used triple resonance experiments with minor modifications, and is applicable to deuterated proteins. The method will be useful for quick assignment of signals that shift during ligand binding or in combination with selective labeling/unlabeling approaches for identification of amino acid types to aid the sequential assignment process. Graphical abstract
Amino acid recognition for automatic resonance assignment of intrinsically disordered proteins
Amino acid recognition for automatic resonance assignment of intrinsically disordered proteins
Abstract
Resonance assignment is a prerequisite for almost any NMR-based study of proteins. It can be very challenging in some cases, however, due to the nature of the protein under investigation. This is the case with intrinsically disordered proteins, for example, whose NMR spectra suffer from low chemical shifts dispersion and generally low resolution. For these systems, sequence specific assignment is highly time-consuming, so the prospect of using...
nmrlearner
Journal club
0
02-19-2016 08:39 AM
Paramagnetic relaxation enhancement of membrane proteins by incorporation of the metal-chelating unnatural amino acid 2-amino-3-(8-hydroxyquinolin-3-yl)propanoic acid (HQA)
Paramagnetic relaxation enhancement of membrane proteins by incorporation of the metal-chelating unnatural amino acid 2-amino-3-(8-hydroxyquinolin-3-yl)propanoic acid (HQA)
Abstract
The use of paramagnetic constraints in protein NMR is an active area of research because of the benefits of long-range distance measurements (>10Â*Ã?). One of the main issues in successful execution is the incorporation of a paramagnetic metal ion into diamagnetic proteins. The most common metal ion tags are relatively long aliphatic chains attached to the side chain of a...
nmrlearner
Journal club
0
11-28-2014 11:37 AM
Movements of proteins can be predicted from their amino acid sequence - HealthCanal.com
Movements of proteins can be predicted from their amino acid sequence - HealthCanal.com
<img alt="" height="1" width="1" />
Movements of proteins can be predicted from their amino acid sequence
HealthCanal.com
Researchers of the VIB department of Structural Biology, in a collaboration within the 'Interuniversity Institute of Bioinformatics in Brussels (IB2)', have developed a method to predict how much the backbone chain of a protein moves based on only its ...
Read here
nmrlearner
Online News
0
11-26-2013 01:19 AM
New amino acid residue type identification experiments valid for protonated and deuterated proteins
New amino acid residue type identification experiments valid for protonated and deuterated proteins
Abstract Two experiments are presented that yield amino acid type identification of individual residues in a protein by editing the 1Hâ??15N correlations into four different 2D subspectra, each corresponding to a different amino acid type class, and that can be applied to deuterated proteins. One experiment provides information on the amino acid type of the residue preceding the detected amide 1Hâ??15N correlation, while the other gives information on the type of its own residue. Versions...
nmrlearner
Journal club
0
09-06-2012 05:03 PM
Amino acid selective unlabeling for sequence specific resonance assignments in proteins
Amino acid selective unlabeling for sequence specific resonance assignments in proteins
Abstract Sequence specific resonance assignment constitutes an important step towards high-resolution structure determination of proteins by NMR and is aided by selective identification and assignment of amino acid types. The traditional approach to selective labeling yields only the chemical shifts of the particular amino acid being selected and does not help in establishing a link between adjacent residues along the polypeptide chain, which is important for sequential assignments. An alternative...
nmrlearner
Journal club
1
03-20-2012 12:42 AM
[NMRpipe Yahoo group] processing phase-modulated Bruker QF data
processing phase-modulated Bruker QF data
Hi, Is there a way to process Bruker 2D spectra acquired with QF in t1 and end up with a phase-sensitive spectrum instead of a magnitude spectrum? I am trying
More...
NMRpipe Yahoo group news
News from other NMR forums
0
12-14-2011 06:42 AM
Broadband homonuclear TOCSY with amplitude and phase-modulated RF mixing schemes
Broadband homonuclear TOCSY with amplitude and phase-modulated RF mixing schemes
Anika Kirschstein, Christian Herbst, Kerstin Riedel, Michela Carella, Jörg Leppert, Oliver Ohlenschläger, Matthias Görlach and Ramadurai Ramachandran
Journal of Biomolecular NMR; 2008; 40(4); pp 227-237
Abstract:
We have explored the design of broadband scalar coupling mediated 13C–13C and cross-relaxation suppressed 1H–1H TOCSY sequences employing phase/amplitude modulated inversion pulses. Considering a variety of supercycles, pulsewidths and a RF field strength of 10 kHz, the Fourier coefficients...