Structural Determination of an Elastin-Mimetic Model Peptide, (Val-Pro-Gly-Val-Gly)6, Studied by13C CP/MAS NMR Chemical Shifts, Two-Dimensional off Magic Angle Spinning Spin-Diffusion NMR, Rotational Echo Double Resonance, and Statistical Distribution of Torsion Angles from Protein Data Bank

2005 ◽  
Vol 38 (14) ◽  
pp. 6038-6047 ◽  
Author(s):  
Kosuke Ohgo ◽  
Jun Ashida ◽  
Kristin K. Kumashiro ◽  
Tetsuo Asakura
Keyword(s):  
Spin Diffusion ◽  
Chemical Shifts ◽  
Double Resonance ◽  
Data Bank ◽  
Magic Angle Spinning ◽  
Magic Angle ◽  
Diffusion Nmr ◽  
Rotational Echo Double Resonance ◽  
Angle Spinning

Recoupling of Heteronuclear Dipolar Interactions with Rotational-Echo Double-Resonance at High Magic-Angle Spinning Frequencies

2000 ◽  
Vol 146 (1) ◽  
pp. 132-139 ◽  
Author(s):  
Christopher P Jaroniec ◽  
Brett A Tounge ◽  
Chad M Rienstra ◽  
Judith Herzfeld ◽  
Robert G Griffin
Keyword(s):  
Double Resonance ◽  
Magic Angle Spinning ◽  
Magic Angle ◽  
Dipolar Interactions ◽  
Rotational Echo Double Resonance ◽  
Angle Spinning

scholarly journals Accelerating Prediction of Chemical Shift of Protein Structures on GPUs

2020 ◽  
Author(s):  
Eric Wright ◽  
Mauricio Ferrato ◽  
Alex Bryer ◽  
Robert Searles ◽  
Juan Perilla ◽  
...  
Keyword(s):  
Programming Model ◽  
Chemical Shifts ◽  
Protein Structures ◽  
Magic Angle Spinning ◽  
Magic Angle ◽  
Code Refactoring ◽  
Nuclear Magnetic Resonance Spectra ◽  
Level Information ◽  
Angle Spinning

AbstractExperimental chemical shifts (CS) from solution and solid state magic-angle-spinning nuclear magnetic resonance spectra provide atomic level information for each amino acid within a protein or protein complex. However, structure determination of large complexes and assemblies based on NMR data alone remains challenging due the complexity of the calculations. Here, we present a hardware accelerated strategy for the estimation of NMR chemical-shifts of large macromolecular complexes based on the previously published PPM_One software. The original code was not viable for computing large complexes, with our largest dataset taking approximately 14 hours to complete. Our results show that the code refactoring and acceleration brought down the time taken of the software running on an NVIDIA V100 GPU to 46.71 seconds for our largest dataset of 11.3M atoms. We use OpenACC, a directive-based programming model for porting the application to a heterogeneous system consisting of x86 processors and NVIDIA GPUs. Finally, we demonstrate the feasibility of our approach in systems of increasing complexity ranging from 100K to 11.3M atoms.Author summary

scholarly journals Determination of Histidine Protonation States in Proteins by Fast Magic Angle Spinning NMR

2021 ◽  
Vol 8 ◽  
Author(s):  
Roman Zadorozhnyi ◽  
Sucharita Sarkar ◽  
Caitlin M. Quinn ◽  
Kaneil K. Zadrozny ◽  
Barbie K. Ganser-Pornillos ◽  
...  
Keyword(s):  
Metal Binding ◽  
Double Resonance ◽  
Imidazole Ring ◽  
Magic Angle Spinning ◽  
Proton Channel ◽  
Magic Angle ◽  
Ionization State ◽  
Angle Spinning ◽  
Fast Magic Angle Spinning

Histidine residues play important structural and functional roles in proteins, such as serving as metal-binding ligands, mediating enzyme catalysis, and modulating proton channel activity. Many of these activities are modulated by the ionization state of the imidazole ring. Here we present a fast MAS NMR approach for the determination of protonation and tautomeric states of His at frequencies of 40–62 kHz. The experiments combine 1H detection with selective magnetization inversion techniques and transferred echo double resonance (TEDOR)–based filters, in 2D heteronuclear correlation experiments. We illustrate this approach using microcrystalline assemblies of HIV-1 CACTD-SP1 protein.

scholarly journals Efficient polynomial analysis of magic-angle spinning sidebands and application to order parameter determination in anisotropic samples

2021 ◽  
Vol 2 (2) ◽  
pp. 589-606
Author(s):  
Günter Hempel ◽  
Paul Sotta ◽  
Didier R. Long ◽  
Kay Saalwächter
Keyword(s):  
Chemical Shift ◽  
Magic Angle Spinning ◽  
Parameter Determination ◽  
Magic Angle ◽  
Chemical Shift Tensors ◽  
Line Shapes ◽  
Fitting Procedure ◽  
The Common ◽  
Angle Spinning

Abstract. Chemical shift tensors in 13C solid-state NMR provide valuable localized information on the chemical bonding environment in organic matter, and deviations from isotropic static-limit powder line shapes sensitively encode dynamic-averaging or orientation effects. Studies in 13C natural abundance require magic-angle spinning (MAS), where the analysis must thus focus on spinning sidebands. We propose an alternative fitting procedure for spinning sidebands based upon a polynomial expansion that is more efficient than the common numerical solution of the powder average. The approach plays out its advantages in the determination of CST (chemical-shift tensor) principal values from spinning-sideband intensities and order parameters in non-isotropic samples, which is here illustrated with the example of stretched glassy polycarbonate.

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