Yeast oligosaccharyltransferase subunit Ost4p

Proceedings of the National Academy of Sciences of the United States of America
Structural basis for the function of a minimembrane protein subunit of yeast oligosaccharyltransferase.

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.
J Biomol NMR. 1995 Nov;6(3):277-93

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

B. A. Johnson, R. A. Blevins
J. Biomol. NMR 1994 4, 603-614

The new program DYANA (DYnamics Algorithm for Nmr Applications) for efficient
calculation of three-dimensional protein and nucleic acid structures from
distance constraints and torsion angle constraints collected by nuclear
magnetic resonance (NMR) experiments performs simulated annealing by molecular
dynamics in torsion angle space and uses a fast recursive algorithm to
integrate the equations of motions. Torsion angle dynamics can be more
efficient than molecular dynamics in Cartesian coordinate space because of the
reduced number of degrees of freedom and the concomitant absence of
high-frequency bond and angle vibrations, which allows for the use of longer
time-steps and/or higher temperatures in the structure calculation. It also
represents a significant advance over the variable target function method in
torsion angle space with the REDAC strategy used by the predecessor program
DIANA. DYANA computation times per accepted conformer in the "bundle" used to
represent the NMR structure compare favorably with those of other presently
available structure calculation algorithms, and are of the order of 160 seconds
for a protein of 165 amino acid residues when using a DEC Alpha 8400 5/300
computer. Test calculations starting from conformers with random torsion angle
values further showed that DYANA is capable of efficient calculation of
high-quality protein structures with up to 400 amino acid residues, and of
nucleic acid structures.

Guntert P, Mumenthaler C, Wuthrich K.
J Mol Biol. 1997 Oct 17;273(1):283-98.

Torsion angle dynamics for NMR structure calculation with the new program DYANA.

MOTIVATION: In the light of several ongoing structural genomics projects, faster
and more reliable methods for structure calculation from NMR data are in great
demand. The major bottleneck in the determination of solution NMR structures is
the assignment of NOE peaks (nuclear Overhauser effect). Due to the high
complexity of the assignment problem, most NOEs cannot be directly converted
into unambiguous inter-proton distance restraints. RESULTS: We present version
1.2 of our program ARIA (Ambiguous Restraints for Iterative Assignment) for
automated assignment of NOE data and NMR structure calculation. We summarize
recent progress in correcting for spin diffusion with a relaxation matrix
approach, representing non-bonded interactions in the force field and refining
final structures in explicit solvent. We also discuss book-keeping, data
exchange with spectra assignment programs and deposition of the analysed
experimental data to the databases. AVAILABILITY: ARIA 1.2 is available from:
http://www.pasteur.fr/recherche/unites/Binfs/aria/. SUPPLEMENTARY INFORMATION:
XML DTDs (for chemical shifts and NOE crosspeaks), Python scripts for the
conversion of various NMR data formats and the results of example calculations
using data from the S. cerevisiae HRDC domain are available from:
http://www.pasteur.fr/recherche/unites/Binfs/aria/

Linge JP, Habeck M, Rieping W, Nilges M.
Bioinformatics. 2003 Jan 22;19(2):315-6.

ARIA: automated NOE assignment and NMR structure calculation.

Nmr Structure Of Yeast Oligosaccharyltransferase Subunit Ost4p

K7_Ost4p [Saccharomyces cerevisiae Kyokai no. 7]

oligosaccharyltransferase [Saccharomyces cerevisiae YJM789]

3.6 kDa protein [Saccharomyces cerevisiae RM11-1a]

RecName: Full=Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit OST4; Short=Oligosaccharyl transferase sub

TPA: Ost4p [Saccharomyces cerevisiae S288c]

torsion angle dynamics, simulated annealing