Agriculture Reference
In-Depth Information
PDB
The number of solved protein structures appearing in the protein data bank (PDB)
is fast growing, and has been one of the most popular resources for biomolecular
structural data; the PDB site has had a dramatically increased in available data de-
posited during the past decade (Kouranov et al. 2006 ).
CLC BIO
CLC has an integrated 3D molecular viewer for determining structures of proteins.
It has a fully navigational and integrated 3D viewer tool for use. It has file systems
and graphics that are compatible with publication of the 3D structures directly.
Cell-Free System (Wheat Germ Embryo)
Although methodological problems still exist in structural and analytical pro-
teomics, some new methods and computational advances have played important
roles in cellular protein determination and identification. One major bottleneck has
been the production of proteins as they may be present in living organism, in 3D
structure. Most researchers in structural proteomics have used Escherichia coli cells
for protein production in automated methods, as an approximation of the cell-based
3D protein structure. However Escherichia coli is a bacterium and prokaryote, and
doubts have been expressed as to the protein folds and structures assembled in a
prokaryote being relevant to eukaryotic organisms. Cell-free expression systems
have also been used mainly as a method to address several limitations of cell-based
methods, such as protein quality and quantity, and high throughput issues. The wheat
germ embryo cell-free system has been developed as a eukaryotic cell-free system
to overcome such problems, and has the advantage of producing multi-domain pro-
teins (Endo and Sawasaki 2003 , 2006 ). For example, a comparative study of protein
production from 96 Arabidopsis open reading frames (ORFs) demonstrated marked
differences in protein profiles between the wheat germ cell system and the cell free
system (Tyler et al. 2005 ).
NMR Methods Plus CP/MAS/DD
The technology and platform of NMR spectroscopy has played an important role in
structural proteomics. High-resolution multidimensional solid-state NMR methods
used in combination with cross polarization (CP), magic angle spinning (MAS)
and dipolar decoupling (DD) are now becoming the methods of choice for struc-
tural analysis in NMR equipment (Castellani et al. 2002 ; McDermott 2009 ). Recent
improvements in NMR include a cryoprobe for improved sensitivity, a micro-coil
probe for sample mitigation, and a flow-probe designed to shorten preparation time.
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