[NMR paper] Resonance assignment for a particularly challenging protein based on systematic unlabeling of amino acids to complement incomplete NMR data sets.
Abstract
NMR-based structure determination of a protein requires the assignment of resonances as indispensable first step. Even though heteronuclear through-bond correlation methods are available for that purpose, challenging situations arise in cases where the protein in question only yields samples of limited concentration and/or stability. Here we present a strategy based upon specific individual unlabeling of all 20 standard amino acids to complement standard NMR experiments and to achieve unambiguous backbone assignments for the fast precipitating 23*kDa catalytic domain of human aprataxin of which only incomplete standard NMR data sets could be obtained. Together with the validation of this approach utilizing the protein GB1 as a model, a comprehensive insight into metabolic interconversion ("scrambling") of NH and CO groups in a standard Escherichia coli expression host is provided.
PMID: 23943084 [PubMed - as supplied by publisher]
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
Protein side-chain resonance assignment and NOE assignment using RDC-defined backbones without TOCSY data
Protein side-chain resonance assignment and NOE assignment using RDC-defined backbones without TOCSY data
Abstract One bottleneck in NMR structure determination lies in the laborious and time-consuming process of side-chain resonance and NOE assignments. Compared to the well-studied backbone resonance assignment problem, automated side-chain resonance and NOE assignments are relatively less explored. Most NOE assignment algorithms require nearly complete side-chain resonance assignments from a series of through-bond experiments such as HCCH-TOCSY or HCCCONH. Unfortunately, these TOCSY...
nmrlearner
Journal club
0
06-27-2011 04:30 AM
Systematic comparison of crystal and NMR protein structures deposited in the protein data bank.
Systematic comparison of crystal and NMR protein structures deposited in the protein data bank.
Systematic comparison of crystal and NMR protein structures deposited in the protein data bank.
Open Biochem J. 2010;4:83-95
Authors: Sikic K, Tomic S, Carugo O
Nearly all the macromolecular three-dimensional structures deposited in Protein Data Bank were determined by either crystallographic (X-ray) or Nuclear Magnetic Resonance (NMR) spectroscopic methods. This paper reports a systematic comparison of the crystallographic and NMR results deposited in...
nmrlearner
Journal club
0
02-05-2011 05:28 PM
[NMR paper] 14N NMR relaxation times of several protein amino acids in aqueous solution--comparis
14N NMR relaxation times of several protein amino acids in aqueous solution--comparison with 17O NMR data and estimation of the relative hydration numbers in the cationic and zwitterionic forms.
Related Articles 14N NMR relaxation times of several protein amino acids in aqueous solution--comparison with 17O NMR data and estimation of the relative hydration numbers in the cationic and zwitterionic forms.
J Magn Reson. 2003 Oct;164(2):294-303
Authors: Troganis AN, Tsanaktsidis C, Gerothanassis IP
The 14N nuclear magnetic resonance (NMR)...
nmrlearner
Journal club
0
11-24-2010 09:16 PM
[NMR paper] Selective 'unlabeling' of amino acids in fractionally 13C labeled proteins: an approa
Selective 'unlabeling' of amino acids in fractionally 13C labeled proteins: an approach for stereospecific NMR assignments of CH3 groups in Val and Leu residues.
Related Articles Selective 'unlabeling' of amino acids in fractionally 13C labeled proteins: an approach for stereospecific NMR assignments of CH3 groups in Val and Leu residues.
J Biomol NMR. 2001 Mar;19(3):267-72
Authors: Atreya HS, Chary KV
A novel methodology for stereospecific NMR assignments of methyl (CH3) groups of Val and Leu residues in fractionally 13C-labeled proteins is...
nmrlearner
Journal club
0
11-19-2010 08:32 PM
[NMR paper] Comparison between the phi distribution of the amino acids in the protein database an
Comparison between the phi distribution of the amino acids in the protein database and NMR data indicates that amino acids have various phi propensities in the random coil conformation.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Comparison between the phi distribution of the amino acids in the protein database and NMR data indicates that amino acids have various phi propensities in the random coil conformation.
J Mol Biol. 1995 Nov 24;254(2):322-33
Authors: Serrano L
...
Resonance assignment for a particularly challenging protein based on systematic unlabeling of amino acids to complement incomplete NMR data sets.
Linear Mode
