A standard set of three APSY-NMR experiments has been used in daily practice to obtain polypeptide backbone NMR assignments in globular proteins with sizes up to about 150 residues, which had been identified as targets for structure determination by the Joint Center for Structural Genomics (JCSG) under the auspices of the Protein Structure Initiative (PSI). In a representative sample of 30 proteins, initial fully automated data analysis with the software UNIO-MATCH-2014 yielded complete or partial assignments for over 90Â*% of the residues. For most proteins the APSY data acquisition was completed in less than 30Â*h. The results of the automated procedure provided a basis for efficient interactive validation and extension to near-completion of the assignments by reference to the same 3D heteronuclear-resolved [1H,1H]-NOESY spectra that were subsequently used for the collection of conformational constraints. High-quality structures were obtained for all 30 proteins, using the J-UNIO protocol, which includes extensive automation of NMR structure determination.
A six-dimensional alpha proton detection-based APSY experiment for backbone assignment of intrinsically disordered proteins
A six-dimensional alpha proton detection-based APSY experiment for backbone assignment of intrinsically disordered proteins
Abstract
Sequence specific resonance assignment is the prerequisite for the NMR-based analysis of the conformational ensembles and their underlying dynamics of intrinsically disordered proteins. However, rapid solvent exchange in intrinsically disordered proteins often complicates assignment strategies based on HN-detection. Here we present a six-dimensional alpha proton detection-based automated projection spectroscopy (APSY)...
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11-04-2014 01:02 AM
[NMR paper] Reduced dimensionality (3,2)D NMR experiments and their automated analysis: implications to high-throughput structural studies on proteins.
Reduced dimensionality (3,2)D NMR experiments and their automated analysis: implications to high-throughput structural studies on proteins.
Related Articles Reduced dimensionality (3,2)D NMR experiments and their automated analysis: implications to high-throughput structural studies on proteins.
Magn Reson Chem. 2014 Sep 1;
Authors: Reddy JG, Kumar D, Hosur RV
Abstract
Protein NMR spectroscopy has expanded dramatically over the last decade into a powerful tool for the study of their structure, dynamics, and interactions. The...
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09-03-2014 11:44 AM
Automated NMR resonance assignment strategy for RNA via the phosphodiester backbone based on high-dimensional through-bond APSY experiments
Automated NMR resonance assignment strategy for RNA via the phosphodiester backbone based on high-dimensional through-bond APSY experiments
Abstract
A fast, robust and reliable strategy for automated sequential resonance assignment for uniformly -labeled RNA via its phosphodiester backbone is presented. It is based on a series of high-dimensional through-bond APSY experiments: a 5D HCP-CCH COSY, a 4D H1â?²C1â?²CH TOCSY for ribose resonances, a 5D HCNCH for ribose-to-base connection, a 4D H6C6C5H5 TOCSY for pyrimidine resonances, and a 4D...
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06-19-2014 10:21 PM
High dimensional and high resolution pulse sequences for backbone resonance assignment of intrinsically disordered proteins
High dimensional and high resolution pulse sequences for backbone resonance assignment of intrinsically disordered proteins
Abstract Four novel 5D (HACA(N)CONH, HNCOCACB, (HACA)CON(CA)CONH, (H)NCO(NCA)CONH), and one 6D ((H)NCO(N)CACONH) NMR pulse sequences are proposed. The new experiments employ non-uniform sampling that enables achieving high resolution in indirectly detected dimensions. The experiments facilitate resonance assignment of intrinsically disordered proteins. The novel pulse sequences were successfully tested using δ subunit (20 kDa) of Bacillus subtilis RNA polymerase...
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02-21-2012 03:40 AM
Sugar-to-base correlation in nucleic acids with a 5D APSY-HCNCH or two 3D APSY-HCN experiments
Sugar-to-base correlation in nucleic acids with a 5D APSY-HCNCH or two 3D APSY-HCN experiments
Abstract A five-dimensional (5D) APSY (automated projection spectroscopy) HCNCH experiment is presented, which allows unambiguous correlation of sugar to base nuclei in nucleic acids. The pulse sequence uses multiple quantum (MQ) evolution which enables long constant-time evolution periods in all dimensions, an improvement that can also benefit non-APSY applications. Applied with an RNA with 23 nucleotides the 5D APSY-HCNCH experiment produced a complete and highly precise 5D chemical shift...
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12-07-2011 10:22 PM
[NMR paper] High-throughput 3D structural homology detection via NMR resonance assignment.
High-throughput 3D structural homology detection via NMR resonance assignment.
Related Articles High-throughput 3D structural homology detection via NMR resonance assignment.
Proc IEEE Comput Syst Bioinform Conf. 2004;:278-89
Authors: Langmead CJ, Donald BR
One goal of the structural genomics initiative is the identification of new protein folds. Sequence-based structural homology prediction methods are an important means for prioritizing unknown proteins for structure determination. However, an important challenge remains: two highly...
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11-24-2010 09:25 PM
[NMR paper] High-throughput screening of structural proteomics targets using NMR.
High-throughput screening of structural proteomics targets using NMR.
Related Articles High-throughput screening of structural proteomics targets using NMR.
FEBS Lett. 2003 Sep 25;552(2-3):207-13
Authors: Galvão-Botton LM, Katsuyama AM, Guzzo CR, Almeida FC, Farah CS, Valente AP
We applied a high-throughput strategy for the screening of targets for structural proteomics of Xanthomonas axonopodis pv citri. This strategy is based on the rapid (1)H-(15)N HSQC NMR analysis of bacterial lysates containing selectively (15)N-labelled heterologous...
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11-24-2010 09:16 PM
[NMR paper] An efficient high-throughput resonance assignment procedure for structural genomics a
An efficient high-throughput resonance assignment procedure for structural genomics and protein folding research by NMR.
Related Articles An efficient high-throughput resonance assignment procedure for structural genomics and protein folding research by NMR.
Biochemistry. 2001 Dec 11;40(49):14727-35
Authors: Bhavesh NS, Panchal SC, Hosur RV
Sequence specific resonance assignment is the primary requirement for all investigations of proteins by NMR methods. In the present postgenomic era where structural genomics and protein folding have...
APSY-NMR for protein backbone assignment in high-throughput structural biology
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