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

		BioNMR > Educational resources > Journal club
[NMR paper] 1H NMR assignment and global fold of napin BnIb, a representative 2S albumin seed pro

Webservers

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:

Thread Tools

Search this Thread

Rate Thread

Display Modes

08-22-2010, 02:20 PM

nmrlearner

Senior Member

Join Date: Jan 2005

Posts: 23,734

Points: 193,617, Level: 100

Level up: 0%, 0 Points needed

Activity: 50.7%

Last Achievements

Award-Showcase

NMR Credits: 0

NMR Points: 193,617

Downloads: 0

Uploads: 0

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

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
High-resolution protein structure determination starting with a global fold calculated from exact solutions to the RDC equations High-resolution protein structure determination starting with a global fold calculated from exact solutions to the RDC equations Abstract We present a novel structure determination approach that exploits the global orientational restraints from RDCs to resolve ambiguous NOE assignments. Unlike traditional approaches that bootstrap the initial fold from ambiguous NOE assignments, we start by using RDCs to compute accurate secondary structure element (SSE) backbones at the beginning of structure calculation. Our structure determination package, called rdc-Panda (RDC-based SSE PAcking with...	nmrlearner	Journal club	0	01-09-2011 12:46 PM
[NMR paper] NMR assignments, secondary structure, and global fold of calerythrin, an EF-hand calc NMR assignments, secondary structure, and global fold of calerythrin, an EF-hand calcium-binding protein from Saccharopolyspora erythraea. Related Articles NMR assignments, secondary structure, and global fold of calerythrin, an EF-hand calcium-binding protein from Saccharopolyspora erythraea. Protein Sci. 1999 Dec;8(12):2580-8 Authors: Aitio H, Annila A, Heikkinen S, Thulin E, Drakenberg T, Kilpeläinen I Calerythrin is a 20 kDa calcium-binding protein isolated from gram-positive bacterium Saccharopolyspora erythraea. Based on amino acid...	nmrlearner	Journal club	0	11-18-2010 08:31 PM
CABS-NMR-De novo tool for rapid global fold determination from chemical shifts, resid CABS-NMR-De novo tool for rapid global fold determination from chemical shifts, residual dipolar couplings and sparse methyl-methyl noes. CABS-NMR-De novo tool for rapid global fold determination from chemical shifts, residual dipolar couplings and sparse methyl-methyl noes. J Comput Chem. 2010 Aug 30; Authors: Latek D, Kolinski A Recent development of nuclear magnetic resonance (NMR) techniques provided new types of structural restraints that can be successfully used in fast and low-cost global protein fold determination. Here, we present...	nmrlearner	Journal club	0	09-02-2010 03:58 PM
[NMR paper] An approach to global fold determination using limited NMR data from larger proteins An approach to global fold determination using limited NMR data from larger proteins selectively protonated at specific residue types. An approach to global fold determination using limited NMR data from larger proteins selectively protonated at specific residue types. J Biomol NMR. 1996 Oct;8(3):360-8 Authors: Smith BO, Ito Y, Raine A, Teichmann S, Ben-Tovim L, Nietlispach D, Broadhurst RW, Terada T, Kelly M, Oschkinat H, Shibata T, Yokoyama S, Laue ED A combination of calculation and experiment is used to demonstrate that the global fold of...	nmrlearner	Journal club	0	08-22-2010 02:20 PM
[NMR paper] 1H and 15N assignment of NMR spectrum, secondary structure and global folding of the 1H and 15N assignment of NMR spectrum, secondary structure and global folding of the immunophilin-like domain of the 59-kDa FK506-binding protein. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www3.interscience.wiley.com-aboutus-images-wiley_interscience_pubmed_logo_FREE_120x27.gif Related Articles 1H and 15N assignment of NMR spectrum, secondary structure and global folding of the immunophilin-like domain of the 59-kDa FK506-binding protein. Eur J Biochem. 1995 Aug 1;231(3):761-72 Authors: RouviÃ¨re-Fourmy N, Craescu CT, Mispelter J, Lebeau MC,...	nmrlearner	Journal club	0	08-22-2010 03:50 AM
[NMR paper] Assignments, secondary structure, global fold, and dynamics of chemotaxis Y protein u Assignments, secondary structure, global fold, and dynamics of chemotaxis Y protein using three- and four-dimensional heteronuclear (13C,15N) NMR spectroscopy. Related Articles Assignments, secondary structure, global fold, and dynamics of chemotaxis Y protein using three- and four-dimensional heteronuclear (13C,15N) NMR spectroscopy. Biochemistry. 1994 Sep 6;33(35):10731-42 Authors: Moy FJ, Lowry DF, Matsumura P, Dahlquist FW, Krywko JE, Domaille PJ NMR spectroscopy has been used to study recombinant Escherichia coli CheY, a 128-residue...	nmrlearner	Journal club	0	08-22-2010 03:29 AM
[NMR paper] 1H-NMR resonance assignments, secondary structure, and global fold of the TR1C fragme 1H-NMR resonance assignments, secondary structure, and global fold of the TR1C fragment of turkey skeletal troponin C in the calcium-free state. Related Articles 1H-NMR resonance assignments, secondary structure, and global fold of the TR1C fragment of turkey skeletal troponin C in the calcium-free state. Biochemistry. 1993 Apr 6;32(13):3461-7 Authors: Findlay WA, Sykes BD The TR1C fragment of turkey skeletal muscle TnC (residues 12-87) comprises the two regulatory calcium binding sites of the protein. Complete assignments of the 1H-NMR...	nmrlearner	Journal club	0	08-21-2010 11:53 PM
[NMR paper] 1H NMR resonance assignments, secondary structure, and global fold of Apo bovine calb 1H NMR resonance assignments, secondary structure, and global fold of Apo bovine calbindin D9k. Related Articles 1H NMR resonance assignments, secondary structure, and global fold of Apo bovine calbindin D9k. Biochemistry. 1990 Jun 19;29(24):5752-61 Authors: Skelton NJ, ForsÃ©n S, Chazin WJ The solution structure and dynamics of apo bovine calbindin D9k have been studied by a wide range of two-dimensional 1H nuclear magnetic resonance experiments. Due to the presence of conformational heterogeneity in the wild-type protein, the sequential...	nmrlearner	Journal club	0	08-21-2010 10:48 PM

« Previous Thread | Next Thread »

Posting Rules
You may not post new threads You may not post replies You may not post attachments You may not edit your posts BB code is On Smilies are On [IMG] code is On HTML code is On Trackbacks are Off Pingbacks are Off Refbacks are Off