Interactions of protein side chains with RNA defined with REDOR solid state NMR.

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Interactions of protein side chains with RNA defined with REDOR solid state NMR.

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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

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Structure from chemical shifts:

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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

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NOEs, other restraints:

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Backbone S2

Methyl S2

B-factor

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Shiftx2

Sparta+

Camshift

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ArShift- Aromatic

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Proshift

PPM

CheShift-2- Cα

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Shifty

Camcoil

Poulsen_rc_CS

Disordered proteins:

MAXOCC

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CCPN

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Protein disorder:

DisMeta

Protein solubility:

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09-30-2011, 06:00 AM

nmrlearner

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Interactions of protein side chains with RNA defined with REDOR solid state NMR.

Interactions of protein side chains with RNA defined with REDOR solid state NMR.

Interactions of protein side chains with RNA defined with REDOR solid state NMR.

J Biomol NMR. 2011 Sep 25;

Authors: Huang W, Varani G, Drobny GP

Abstract
Formation of the complex between human immunodeficiency virus type-1 Tat protein and the transactivation response region (TAR) RNA is vital for transcriptional elongation, yet the structure of the Tat-TAR complex remains to be established. The NMR structures of free TAR, and TAR bound to Tat-derived peptides have been obtained by solution NMR, but only a small number of intermolecular NOEs could be identified unambiguously, preventing the determination of a complete structure. Here we show that a combination of multiple solid state NMR REDOR experiments can be used to obtain multiple distance constraints from (15)N to (13)C spins within the backbone and side chain guanidinium groups of arginine in a Tat-derived peptide, using (19)F spins incorporated into the base of U23 in TAR and (31)P spins in the P22 and P23 phosphate groups. Distances between the side chain of Arg52 and the base and phosphodiester backbone near U23 measured by REDOR NMR are comparable to distances observed in solution NMR-derived structural models, indicating that interactions of TAR RNA with key amino acid side chains in Tat are the same in the amorphous solid state as in solution. This method is generally applicable to other protein-RNA complexes where crystallization or solution NMR has failed to provide high resolution structural information.

PMID: 21947838 [PubMed - as supplied by publisher]

Source: PubMed

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