Structure of At3g01050.1, a ubiquitin-fold protein from Arabidopsis thaliana

Cell-free protein production and labeling protocol for NMR-based structural proteomics.

The NMRPipe system is a UNIX software environment of processing, graphics, and
analysis tools designed to meet current routine and research-oriented
multidimensional processing requirements, and to anticipate and accommodate
future demands and developments. The system is based on UNIX pipes, which allow
programs running simultaneously to exchange streams of data under user control.
In an NMRPipe processing scheme, a stream of spectral data flows through a
pipeline of processing programs, each of which performs one component of the
overall scheme, such as Fourier transformation or linear prediction. Complete
multidimensional processing schemes are constructed as simple UNIX shell
scripts. The processing modules themselves maintain and exploit accurate
records of data sizes, detection modes, and calibration information in all
dimensions, so that schemes can be constructed without the need to explicitly
define or anticipate data sizes or storage details of real and imaginary
channels during processing. The asynchronous pipeline scheme provides other
substantial advantages, including high flexibility, favorable processing
speeds, choice of both all-in-memory and disk-bound processing, easy adaptation
to different data formats, simpler software development and maintenance, and
the ability to distribute processing tasks on multi-CPU computers and computer
networks.

Delaglio F, Grzesiek S, Vuister GW, Zhu G, Pfeifer J, Bax A.
NMRPipe: a multidimensional spectral processing system based on UNIX pipes.
J Biomol NMR. 1995 Nov;6(3):277-93.

NMRPipe: a multidimensional spectral processing system based on UNIX pipes.

Bartels, C., Xia, T.-H., Billeter, M., Guntert, P. and Wuthrich, K. (1995)
J. Biomol. NMR, 6, 1-10.

Bartels, C., Guntert, P., Billeter, M. and Wuthrich, K. (1997)
GARANT-A general algorithm for resonance assignment of multidimensional nuclear
magnetic resonance spectra.
J. Comp. Chem. 18, 139-149.

Chemical shifts of backbone atoms in proteins are exquisitely sensitive to local
conformation, and homologous proteins show quite similar patterns of secondary
chemical shifts. The inverse of this relation is used to search a database for
triplets of adjacent residues with secondary chemical shifts and sequence
similarity which provide the best match to the query triplet of interest. The
database contains 13C alpha, 13C beta, 13C', 1H alpha and 15N chemical shifts
for 20 proteins for which a high resolution X-ray structure is available. The
computer program TALOS was developed to search this database for strings of
residues with chemical shift and residue type homology. The relative importance
of the weighting factors attached to the secondary chemical shifts of the five
types of resonances relative to that of sequence similarity was optimized
empirically. TALOS yields the 10 triplets which have the closest similarity in
secondary chemical shift and amino acid sequence to those of the query
sequence. If the central residues in these 10 triplets exhibit similar phi and
psi backbone angles, their averages can reliably be used as angular restraints
for the protein whose structure is being studied. Tests carried out for
proteins of known structure indicate that the root-mean-square difference
(rmsd) between the output of TALOS and the X-ray derived backbone angles is
about 15 degrees. Approximately 3% of the predictions made by TALOS are found
to be in error.

Cornilescu G, Delaglio F, Bax A.
Protein backbone angle restraints from searching a database for chemical shift
and sequence homology.
J Biomol NMR. 1999 Mar;13(3):289-302.

Protein backbone angle restraints from searching a database for chemical shift and sequence homology.

Combined automated NOE assignment and structure determination module (CANDID) is
a new software for efficient NMR structure determination of proteins by
automated assignment of the NOESY spectra. CANDID uses an iterative approach
with multiple cycles of NOE cross-peak assignment and protein structure
calculation using the fast DYANA torsion angle dynamics algorithm, so that the
result from each CANDID cycle consists of exhaustive, possibly ambiguous NOE
cross-peak assignments in all available spectra and a three-dimensional protein
structure represented by a bundle of conformers. The input for the first CANDID
cycle consists of the amino acid sequence, the chemical shift list from the
sequence-specific resonance assignment, and listings of the cross-peak
positions and volumes in one or several two, three or four-dimensional NOESY
spectra. The input for the second and subsequent CANDID cycles contains the
three-dimensional protein structure from the previous cycle, in addition to the
complete input used for the first cycle. CANDID includes two new elements that
make it robust with respect to the presence of artifacts in the input data,
i.e. network-anchoring and constraint-combination, which have a key role in de
novo protein structure determinations for the successful generation of the
correct polypeptide fold by the first CANDID cycle. Network-anchoring makes use
of the fact that any network of correct NOE cross-peak assignments forms a
self-consistent set; the initial, chemical shift-based assignments for each
individual NOE cross-peak are therefore weighted by the extent to which they
can be embedded into the network formed by all other NOE cross-peak
assignments. Constraint-combination reduces the deleterious impact of artifact
NOE upper distance constraints in the input for a protein structure calculation
by combining the assignments for two or several peaks into a single upper limit
distance constraint, which lowers the probability that the presence of an
artifact peak will influence the outcome of the structure calculation. CANDID
test calculations were performed with NMR data sets of four proteins for which
high-quality structures had previously been solved by interactive protocols,
and they yielded comparable results to these reference structure determinations
with regard to both the residual constraint violations, and the precision and
accuracy of the atomic coordinates. The CANDID approach has further been
validated by de novo NMR structure determinations of four additional proteins.
The experience gained in these calculations shows that once nearly complete
sequence-specific resonance assignments are available, the automated CANDID
approach results in greatly enhanced efficiency of the NOESY spectral analysis.
The fact that the correct fold is obtained in cycle 1 of a de novo structure
calculation is the single most important advance achieved with CANDID, when
compared with previously proposed automated NOESY assignment methods that do
not use network-anchoring and constraint-combination.

Herrmann T, Guntert P, Wuthrich K.
Protein NMR structure determination with automated NOE assignment using the new
software CANDID and the torsion angle dynamics algorithm DYANA.
J Mol Biol. 2002 May 24;319(1):209-27.

Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA.

We announce the availability of the Xplor-NIH software package for NMR
biomolecular structure determination. This package consists of the pre-existing
XPLOR program, along with many NMR-specific extensions developed at the NIH. In
addition to many features which have been developed over the last 20 years, the
Xplor-NIH package contains an interface with a new programmatic framework
written in C++. This interface currently supports the general purpose scripting
languages Python and TCL, enabling rapid development of new tools, such as new
potential energy terms and new optimization methods. Support for these
scripting languages also facilitates interaction with existing external
programs for structure analysis, structure manipulation, visualization, and
spectral analysis.

Schwieters CD, Kuszewski JJ, Tjandra N, Marius Clore G.
The Xplor-NIH NMR molecular structure determination package.
J Magn Reson. 2003 Jan;160(1):65-73.

Journal of magnetic resonance (San Diego, Calif. : 1997)
The Xplor-NIH NMR molecular structure determination package.

Center for Eukaryotic Structural Genomics

Structure Of At3g01050, A Ubiquitin-Fold Protein From Arabidopsis Thaliana

membrane-anchored ubiquitin-fold protein 1 precursor [Arabidopsis thaliana]

RecName: Full=Membrane-anchored ubiquitin-fold protein 1; Short=AtMUB1; Short=Membrane-anchored ub-fold protein 1; Flags: Precu

Wheat germ cell-free expression system using peU-(N)-His6 vector.

torsion angle dynamics followed by cartesian molecular dynamics in explicit solvent

CANDID module used for automated NOE crosspeak assignment