Question from NMRWiki Q&A forum What are the biggest differences in solving NMR structures of DNA or RNA vs. proteins?

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[Question from NMRWiki Q&A forum] What are the biggest differences in solving NMR structures of DNA or RNA vs. proteins?

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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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06-28-2016, 04:38 AM

nmrlearner

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What are the biggest differences in solving NMR structures of DNA or RNA vs. proteins?

What are the biggest differences in solving NMR structures of DNA or RNA vs. proteins?

I've only solved NMR structure of globular proteins (actually in a complex with a short stretch of DNA), but never a structure of nucleic acid alone.

What are (are there?) the major differences in the approaches when working on a structure of nucleic acid - in terms of choice of the NMR technique, maybe specific parameters and structure simulation?

Are distance restraints alone sufficient to obtain structure of DNA or RNA?

Thank you in advance!

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