NMR paper 1H NMR assignment and global fold of napin BnIb, a representative 2S albumin seed pro

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[NMR paper] 1H NMR assignment and global fold of napin BnIb, a representative 2S albumin seed pro

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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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08-22-2010, 02:20 PM

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1H NMR assignment and global fold of napin BnIb, a representative 2S albumin seed pro

1H NMR assignment and global fold of napin BnIb, a representative 2S albumin seed protein.

Related Articles 1H NMR assignment and global fold of napin BnIb, a representative 2S albumin seed protein.

Biochemistry. 1996 Dec 10;35(49):15672-82

Authors: Rico M, Bruix M, GonzÃ¡lez C, Monsalve RI, RodrÃ*guez R

Napin BnIb is a representative member of the 2S albumin seed proteins, which consists of two polypeptide chains of 3.8 and 8.4 kDa linked by two disulfide bridges. In this work, a complete assignment of the 1H spectra of napin BnIb has been carried out by two-dimensional NMR sequence-specific methods and its secondary structure determined on the basis of spectral data. A calculation of the tertiary structure has been performed using approximately 500 distance constraints derived from unambiguously assigned NOE cross-correlations and distance geometry methods. The resulting global fold consists of five helices and a C-terminal loop arranged in a right-handed spiral. The folded protein is stabilized by two interchain disulfide bridges and two additional ones between cysteine residues in the large chain. The structure of napin BnIb represents a third example of a new and distinctive folding pattern first described for the hydrophobic protein from soybean and nonspecific lipid transfer proteins from wheat and maize. The presence of an internal cavity is not at all evident, which rules out in principle the napin BnIb as a carrier of lipids. The determined structure is compatible with activities attributed to these proteins such as phospholipid vesicle interaction, allergenicity, and calmodulin antagonism. Given the sequence homology of BnIb with other napins and napin-type 2S albumin seed proteins from different species, it is likely that all these proteins share a common architecture. The determined structure will be crucial to establish structure-function relationships and to explore the mechanisms of folding, processing, and deposition of these proteins. It will also provide a firm basis for a rational use of genetic engineering in order to develop improved transgenic plants.

PMID: 8961930 [PubMed - indexed for MEDLINE]

Source: PubMed

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