C4â?²/H4â?² selective, non-uniformly sampled 4D HC(P)CH experiment for sequential assignments of 13C-labeled RNAs

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C4â?²/H4â?² selective, non-uniformly sampled 4D HC(P)CH experiment for sequential assignments of 13C-labeled RNAs

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NMR processing:

MDD

NMR assignment:

Backbone:

Side-chains:

NOEs:

Structure from NMR restraints:

Ab initio:

Fragment-based:

Rosetta-NMR (Robetta)

Template-based:

GeNMR

I-TASSER

Refinement:

Amber

Structure from chemical shifts:

Fragment-based:

Homology-based:

Torsion angles from chemical shifts:

Preditor

TALOS

Promega- Proline

Secondary structure from chemical shifts:

CSI (via RCI server)

TALOS

MICS caps, β-turns

d2D

PECAN

Flexibility from chemical shifts:

RCI

Interactions from chemical shifts:

HADDOCK

Chemical shifts re-referencing:

NMR model quality:

NOEs, other restraints:

Chemical shifts:

RDCs:

Pseudocontact shifts:

Protein geomtery:

SAVES2 or SAVES4

Quality Control Check

NMR spectrum prediction:

FANDAS

MestReS

V-NMR

Flexibility from structure:

Backbone S2

Methyl S2

B-factor

Molecular dynamics:

Gromacs

Amber

Antechamber

Chemical shifts prediction:

From structure:

Shiftx2

Sparta+

Camshift

CH3shift- Methyl

ArShift- Aromatic

ShiftS

Proshift

PPM

CheShift-2- Cα

From sequence:

Shifty

Camcoil

Poulsen_rc_CS

Disordered proteins:

MAXOCC

Format conversion & validation:

CCPN

From NMR-STAR 3.1

Validate NMR-STAR 3.1

NMR sample preparation:

Protein disorder:

DisMeta

Protein solubility:

Isotope labeling:

Solid-state NMR:

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09-11-2014, 12:06 AM

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C4â?²/H4â?² selective, non-uniformly sampled 4D HC(P)CH experiment for sequential assignments of 13C-labeled RNAs

C4â?²/H4â?² selective, non-uniformly sampled 4D HC(P)CH experiment for sequential assignments of 13C-labeled RNAs

Abstract

A through bond, C4â?²/H4â?² selective, â??out and stayâ?? type 4D HC(P)CH experiment is introduced which provides sequential connectivity via H4â?²(i)â??C4â?²(i)â??C4â?²(iâ??1)â??H4â?²(iâ??1) correlations. The 31P dimension (used in the conventional 3D HCP experiment) is replaced with evolution of better dispersed C4â?² dimension. The experiment fully utilizes 13C-labeling of RNA by inclusion of two C4â?² evolution periods. An additional evolution of H4â?² is included to further enhance peak resolution. Band selective 13C inversion pulses are used to achieve selectivity and prevent signal dephasing due to the of C4â?²â??C3â?² and C4â?²â??C5â?² homonuclear couplings. For reasonable resolution, non-uniform sampling is employed in all indirect dimensions. To reduce sensitivity losses, multiple quantum coherences are preserved during shared-time evolution and coherence transfer delays. In the experiment the intra-nucleotide peaks are suppressed whereas inter-nucleotide peaks are enhanced to reduce the ambiguities. The performance of the experiment is verified on a fully 13C, 15N-labeled 34-nt hairpin RNA comprising typical structure elements.

Source: Journal of Biomolecular NMR

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