A chemical approach for site-specific identification of NMR signals from protein side-chain NH 3 + groups forming intermolecular ion pairs in proteinâ??nucleic acid complexes

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A chemical approach for site-specific identification of NMR signals from protein side-chain NH 3 + groups forming intermolecular ion pairs in proteinâ??nucleic acid complexes

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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

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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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02-18-2015, 06:15 PM

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A chemical approach for site-specific identification of NMR signals from protein side-chain NH 3 + groups forming intermolecular ion pairs in proteinâ??nucleic acid complexes

A chemical approach for site-specific identification of NMR signals from protein side-chain NH 3 + groups forming intermolecular ion pairs in proteinâ??nucleic acid complexes

Abstract

Proteinâ??nucleic acid interactions involve intermolecular ion pairs of protein side-chain and DNA or RNA phosphate groups. Using three proteinâ??DNA complexes, we demonstrate that site-specific oxygen-to-sulfur substitution in phosphate groups allows for identification of NMR signals from the protein side-chain NH3 + groups forming the intermolecular ion pairs. A characteristic change in their 1H and 15N resonances upon this modification (i.e., substitution of phosphate to phosphorodithioate) can represent a signature of an intermolecular ion pair. Hydrogen-bond scalar coupling between protein side-chain 15N and DNA phosphorodithiaote 31P nuclei provides direct confirmation of the intermolecular ion pair. The same approach is likely applicable to proteinâ??RNA complexes as well.

Source: Journal of Biomolecular NMR

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