NMR paper Amino Acid Selective Unlabeling in Protein NMR Spectroscopy.

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[NMR paper] Amino Acid Selective Unlabeling in Protein NMR Spectroscopy.

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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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11-19-2015, 05:22 PM

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Amino Acid Selective Unlabeling in Protein NMR Spectroscopy.

Amino Acid Selective Unlabeling in Protein NMR Spectroscopy.

Related Articles Amino Acid Selective Unlabeling in Protein NMR Spectroscopy.

Methods Enzymol. 2015;565:167-189

Authors: Prasanna C, Dubey A, Atreya HS

Abstract
Three-dimensional structure determination of proteins by NMR requires the acquisition of multidimensional spectra followed by assignment of chemical shifts to the respective nuclei. In order to speed up this process, resonances corresponding to individual amino acid types are often selectively identified and assigned. One of the ways of achieving this is by using the method of "selective unlabeling." In this method, resonances from one or more amino acid types are suppressed selectively in the NMR spectra, which can be achieved using both cell-based and cell-free methods. This helps not only in identifying them but also results in spectral simplification by reducing the number of peaks observed. Further, the assignments are not limited to amino acids that are specifically unlabeled. Using specially designed NMR experiments, assignments of amino acids in the neighborhood of those being selectively unlabeled can also be obtained. In this chapter, we discuss the theoretical and practical aspects of selective unlabeling focusing on how the sample is prepared, which amino acid or a combination of amino acids should be optimally chosen for unlabeling, and how this method can be used for sequential assignments of proteins.

PMID: 26577732 [PubMed - as supplied by publisher]

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