Generating NMR Chemical Shift Assignments of Intrinsically Disordered Proteins Using Carbon-Detect NMR Methods

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Generating NMR Chemical Shift Assignments of Intrinsically Disordered Proteins Using Carbon-Detect NMR Methods

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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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12-10-2013, 04:48 AM

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Generating NMR Chemical Shift Assignments of Intrinsically Disordered Proteins Using Carbon-Detect NMR Methods

Generating NMR Chemical Shift Assignments of Intrinsically Disordered Proteins Using Carbon-Detect NMR Methods

Publication date: Available online 10 December 2013
Source:Analytical Biochemistry

Author(s): Debashish Sahu , Monique Bastidas , Scott Showalter

There is an extraordinary need to describe the structures of intrinsically disordered proteins (IDPs) due to their role in various biological processes involved in signaling and transcription. However, general study of IDPs by NMR spectroscopy is limited by the poor 1H-amide chemical shift dispersion typically observed in their spectra. Recently, 13C direct-detected NMR spectroscopy has been recognized as enabling broad structural study of IDPs. Most notably, multi-dimensional experiments based on the 15N,13C-CON spectrum make complete chemical shift assignment feasible. Here we document a collection of NMR based tools that efficiently lead to chemical shift assignment of IDPs, motivated by a case study of the C-terminal disordered region from the human pancreatic transcription factor Pdx1. Our strategy builds on the combination of two 3D experiments, (HN-flip)N(CA)CON and 3D (HN-flip)N(CA)NCO, that enable daisy-chain connections to be built along the IDP backbone, facilitated by acquisition of amino-acid specific 15N,13C-CON detected experiments. Assignments are completed through carbon-detected, TOCSY based side chain chemical shift measurement. Conducting our study required producing valuable modifications to many previously published pulse sequences, motivating us to announce the creation of a database of our pulse programs, which we make freely available through the web.

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