Towards automatic protein backbone assignment using proton-detected 4D solid-state NMR data

Xiang, ShengQi; Chevelkov, Veniamin; Becker, Stefan; Lange, Adam

doi:10.1007/s10858-014-9859-6

Cited by 46 publications

(42 citation statements)

References 43 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The use of nonuniform sampling (NUS) for solid-state NMR is attracting attention [69, 73, 75, 90–92]. In solution, NUS is typically applied to speed up the data collection, and this mode has also been explored in the solids NMR experiments.…”

Section: Sample Preparation and Mas Nmr Methods For Structural Anamentioning

confidence: 99%

“…demonstrated that a set of four-dimensional experiments, (H)CACO(CA)NH and (H)COCA(CO)NH, could be used to collect data with appropriate sensitivity and resolution in a reasonable amount of time using NUS. With 20% nonuniform sampling coverage, the combined experiment time could be reduced from 55 days to 11 days [92]. Another study by Lin and Opella demonstrated that with NUS coverage of 25–33%, two- and three-dimensional datasets could be collected and reconstructed using compressed sensing processing, thus saving experiment time [90].…”

Section: Sample Preparation and Mas Nmr Methods For Structural Anamentioning

confidence: 99%

See 1 more Smart Citation

MAS NMR of HIV-1 protein assemblies

Suiter

Quinn

et al. 2015

Journal of Magnetic Resonance

View full text Add to dashboard Cite

The negative global impact of the AIDS pandemic is well known. In this perspective article, the utility of magic angle spinning (MAS) NMR spectroscopy to answer pressing questions related to the structure and dynamics of HIV-1 protein assemblies is examined. In the recent years, MAS NMR has undergone major technological developments enabling studies of large viral assemblies. We discuss some of these evolving methods and technologies and provide a perspective on the current state of MAS NMR as applied to the investigations into structure and dynamics of HIV-1 assemblies of CA capsid protein and of Gag maturation intermediates.

show abstract

Section: Sample Preparation and Mas Nmr Methods For Structural Anamentioning

confidence: 99%

Section: Sample Preparation and Mas Nmr Methods For Structural Anamentioning

confidence: 99%

MAS NMR of HIV-1 protein assemblies

Suiter

Quinn

et al. 2015

Journal of Magnetic Resonance

View full text Add to dashboard Cite

show abstract

“…Failure to assign spectra is often the bottleneck to structure determination. Under MAS, sequence-specific resonance assignment is accomplished primarily by interresidue matching with 13 C shifts, either using 13 C detection (Hong 1999;Rienstra et al 2000;Böckmann et al 2003) or more recently, 1 H detection (van Rossum et al 2003;Knight et al 2011;Linser et al 2011;Ward et al 2011;Marchetti et al 2012;Zhou et al 2012; Barbet-Massin et al 2014;Xiang et al 2014).…”

mentioning

confidence: 99%

Protein residue linking in a single spectrum for magic-angle spinning NMR assignment

et al. 2015

View full text Add to dashboard Cite

Here we introduce a new pulse sequence for resonance assignment that halves the number of data sets required for sequential linking by directly correlating sequential amide resonances in a single diagonal-free spectrum. The method is demonstrated with both microcrystalline and sedimented deuterated proteins spinning at 60 and 111 kHz, and a fully protonated microcrystalline protein spinning at 111 kHz, with as little as 0.5 mg protein sample. We find that amide signals have a low chance of ambiguous linkage, which is further improved by linking in both forward and backward directions. The spectra obtained are amenable to automated resonance assignment using general-purpose software such as UNIO-MATCH.

show abstract

“…Although only 15 N and 13 C chemical shifts are considered in the simulations described above, multidimensional solid state NMR spectra of proteins that include 1 H chemical shifts are also obtained in some experiments [46–48]. Simulations that include 1 H chemical shifts can be carried out with the mcassign2b program, without any modifications, and could be used to design assignment strategies for such experiments.…”

Section: Discussionmentioning

confidence: 99%

On the problem of resonance assignments in solid state NMR of uniformly 15N,13C-labeled proteins

Tycko

2015

Journal of Magnetic Resonance

View full text Add to dashboard Cite

Determination of accurate resonance assignments from multidimensional chemical shift correlation spectra is one of the major problems in biomolecular solid state NMR, particularly for relative large proteins with less-than-ideal NMR linewidths. This article investigates the difficulty of resonance assignment, using a computational Monte Carlo/simulated annealing (MCSA) algorithm to search for assignments from artificial three-dimensional spectra that are constructed from the reported isotropic 15N and 13C chemical shifts of two proteins whose structures have been determined by solution NMR methods. The results demonstrate how assignment simulations can provide new insights into factors that affect the assignment process, which can then help guide the design of experimental strategies. Specifically, simulations are performed for the catalytic domain of SrtC (147 residues, primarily β-sheet secondary structure) and the N-terminal domain of MLKL (166 residues, primarily α-helical secondary structure). Assuming unambiguous residue-type assignments and four ideal three-dimensional data sets (NCACX, NCOCX, CONCA, and CANCA), uncertainties in chemical shifts must be less than 0.4 ppm for all MCSA runs to yield fully correct assignments for SrtC, and less than 0.2 ppm for MLKL. Eliminating CANCA data has no significant effect, but additionally eliminating CONCA data leads to more stringent requirements for chemical shift precision. Introducing moderate ambiguities in residue-type assignments does not have a significant effect.

show abstract

Towards automatic protein backbone assignment using proton-detected 4D solid-state NMR data

Cited by 46 publications

References 43 publications

MAS NMR of HIV-1 protein assemblies

MAS NMR of HIV-1 protein assemblies

Protein residue linking in a single spectrum for magic-angle spinning NMR assignment

On the problem of resonance assignments in solid state NMR of uniformly 15N,13C-labeled proteins

Contact Info

Product

Resources

About