NMR paper Two- and three-dimensional proton NMR studies of apo-neocarzinostatin.

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[NMR paper] Two- and three-dimensional proton NMR studies of apo-neocarzinostatin.

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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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08-21-2010, 11:12 PM

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Two- and three-dimensional proton NMR studies of apo-neocarzinostatin.

Two- and three-dimensional proton NMR studies of apo-neocarzinostatin.

Related Articles Two- and three-dimensional proton NMR studies of apo-neocarzinostatin.

Biochemistry. 1991 Aug 6;30(31):7730-9

Authors: Gao XL, Burkhart W

Neocarzinostatin (NCS) is an antitumor protein from Streptomyces carzinostaticus that is identical in apo-protein sequence with mitomalcin (MMC) from Streptomyces malayensis. We describe the use of apo-NCS as a model system for applying combined two- and three-dimensional (2D and 3D) proton NMR spectroscopy to the structure determination of proteins (Mr greater than 10K) without isotope labeling. Strategies aimed at accurately assigning overlapped 2D cross-peaks by using semiautomated combined 2D and 3D data analysis are developed. Using this approach, we have assigned 99% of the protons, including those of the side chains, and identified about 1270 intra- and interresidue proton-proton interactions (fixed distances are not included) in apo-NCS. Comparing our results with those reported recently on 2D NMR studies of apo-NCS [Adjadj, E., Mispelter, J., Quiniou, E., Dimicoli, J.-L., Favadon, V., & Lhoste, J.-M. (1990) Eur. J. Biochem. 190, 263-271; Remerowski M. L., Glaser, S. J., Sieker, L., Samy, T. S. A., & Drobny, G. P. (1990) Biochemistry 29, 8401-8409] demonstrated advantages of proton 3D NMR spectroscopy in protein spectral assignments. We are able to obtain more complete proton resonance and secondary structural assignments and find several misassignments in the earlier report. Strategies utilized in this work should be useful for developing automation procedures for spectral assignments.

PMID: 1831044 [PubMed - indexed for MEDLINE]

Source: PubMed

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