Solution Structure of the 30S ribosomal protein S28E from Pyrococcus horikoshii.
Northeast Structural Genomics Consortium target JR19

Protein science : a publication of the Protein Society
Solution NMR structure of the 30S ribosomal protein S28E from Pyrococcus horikoshii.

The complete sequence of the genome of a hyper-thermophilic archaebacterium,
Pyrococcus horikoshii OT3, has been determined by assembling the sequences of
the physical map-based contigs of fosmid clones and of long polymerase chain
reaction (PCR) products which were used for gap-filling. The entire length of
the genome was 1,738,505 bp. The authenticity of the entire genome sequence was
supported by restriction analysis of long PCR products, which were directly
amplified from the genomic DNA. As the potential protein-coding regions, a
total of 2061 open reading frames (ORFs) were assigned, and by similarity
search against public databases, 406 (19.7%) were related to genes with
putative function and 453 (22.0%) to the sequences registered but with unknown
function. The remaining 1202 ORFs (58.3%) did not show any significant
similarity to the sequences in the databases. Sequence comparison among the
assigned ORFs in the genome provided evidence that a considerable number of
ORFs were generated by sequence duplication. By similarity search, 11 ORFs were
assumed to contain the intein elements. The RNA genes identified were a single
16S-23S rRNA operon, two 5S rRNA genes and 46 tRNA genes including two with the
intron structure. All the assigned ORFs and RNA coding regions occupied 91.25%
of the whole genome. The data presented in this paper are available on the
internet at http:@www.nite.go.jp.

Kawarabayasi et al. (1998) DNA Res. 5, 55-76
DNA research : an international journal for rapid publication of reports on genes and genomes
Complete sequence and gene organization of the genome of a hyper-thermophilic archaebacterium, Pyrococcus horikoshii OT3.

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 G.W., Zhu G., Pfeifer J., Bax A.
J. Biomol. NMR. (1995) 6, 277-293.

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

T. D. Goddard and D. G. Kneller, SPARKY 3,
University of California, San Francisco.

An expert system for determining resonance assignments from NMR spectra of
proteins is described. Given the amino acid sequence, a two-dimensional 15N-1H
heteronuclear correlation spectrum and seven to eight three-dimensional
triple-resonance NMR spectra for seven proteins, AUTOASSIGN obtained an average
of 98% of sequence-specific spin-system assignments with an error rate of less
than 0.5%. Execution times on a Sparc 10 workstation varied from 16 seconds for
smaller proteins with simple spectra to one to nine minutes for medium size
proteins exhibiting numerous extra spin systems attributed to conformational
isomerization. AUTOASSIGN combines symbolic constraint satisfaction methods
with a domain-specific knowledge base to exploit the logical structure of the
sequential assignment problem, the specific features of the various NMR
experiments, and the expected chemical shift frequencies of different amino
acids. The current implementation specializes in the analysis of data derived
from the most sensitive of the currently available triple-resonance
experiments. Potential extensions of the system for analysis of additional
types of protein NMR data are also discussed.

Zimmerman D.E., Kulikowski C.A., Huang Y., Feng W., Tashiro M.,
Shimotakahara S., Chien C., Powers R., Montelione G.T.
J. Mol. Biol. (1997) 269, 592-610

Automated analysis of protein NMR assignments using methods from artificial intelligence.

Huang, Y.J. (2001). Automated determination of protein structures from
NMR data by iterative analysis of self-consistent contact patterns,
PhD thesis, Rutgers University, New Brunswick, NJ.

see: www-nmr.cabm.rutgers.edu/NMRsoftware/nmr_software.html

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. (1999)
J. Biomol. NMR 13, 289-302.

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

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. (1997)
J. Mol. Biol. 273, 283-98.

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

Northeast Structural Genomics Consortium

30S ribosomal protein S28e [Pyrococcus furiosus DSM 3638]

30S ribosomal protein S28e [Pyrococcus abyssi GE5]

30S ribosomal protein S28e [Pyrococcus horikoshii OT3]

rps28E SSU ribosomal protein S28E [Pyrococcus abyssi GE5]

SSU ribosomal protein S28E; (rps28E) [Pyrococcus furiosus DSM 3638]

Solution Structure Of The 30s Ribosomal Protein S28e From Pyrococcus Horikoshii. Northeast Structural Genomics Consortium Target Jr19

71aa long hypothetical 50S ribosomal protein S28 [Pyrococcus horikoshii OT3]

In-house developed software for automating the peak assignment process

In-house developed software for automating the NOESY assignment
and structure determination process.
Structure calculations were performed using DYANA.

In-house developed software for the determination of dihedral
angle restraints from NMR data.

Determination of torsion angle restraints based on chemical shift data
and sequence homology.

Structure refinement using torsion angle dynamics.

In-house software for the analysis and superposition of the PDB structures.

automated assignment of backbone 1H, 13C, 15N chemical shifts