bovine seminal ribonuclease monomer (N67D mutant)

(2S)-2-azanyl-5-[[(2R)-1-(2-hydroxy-2-oxoethylamino)-1-oxidanylidene-3-sulfanyl-propan-2-yl]amino]-5-oxidanylidene-pentanoic acid

Letter to the Editor: 1H and 15N sequential assignment and secondary structure
of the monomeric N67D mutant of bovine seminal ribonuclease

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.
NMRPipe: a multidimensional spectral processing system based on UNIX pipes.
J. Biomol. NMR (1995) 6, 277-93

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

Johnson, B.A., Blevins, R.A.
NMR View: a computer program for the visualization and analysis of NMR data.
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.
Torsion angle dynamics for NMR structure calculation with the new program DYANA.
J. Mol. Biol. (1997) 273, 283-98

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

Pearlman, D.A., Case, D.A., Caldwell, J.W., Ross, W.S., Cheatham III, T.E., DeBolt, S., Ferguson, D., Seibel, G & Kollman, P.A.
AMBER, a computer program for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to elucidate the structures and energies of molecules.
Comp. Phys. Commun. (1995) 91, 1-41

The N-terminal Met-0 is introduced by expression in E. coli.
The N67D mutation has been engeneered to prevent deamidation, which occurs spontaneously at the Asn-67 site.

Binding Of A Substrate Analogue To A Domain Swapping Protein In The Complex Of Bovine Seminal Ribonuclease With Uridylyl-2',5'-Adenosine

A Potential Allosteric Subsite Generated By Domain Swapping In Bovine Seminal Ribonuclease

Bovine Seminal Ribonuclease Structure At 1.9 Angstroms Resolution

Solution Structure Of The Monomeric N67d Mutant Of Bovine Seminal Ribonuclease

Crystal Structure Of The Dimeric Unswapped Form Of Bovine Seminal Ribonuclease

X-Ray Structure Of The Complex Of Bovine Seminal Ribonuclease Swapping Dimer With D(Cpa)

X-Ray Structure Of Bovine Seminal Ribonuclease Swapping Dimer From A New Crystal Form

Crystal Structure Of The P19aN67D VARIANT OF BOVINE Seminal Ribonuclease

Crystal Structure Of The Unswapped Form Of P19aL28QN67D Bs-Rnase

Crystal Structure Of The Swapped Form Of P19aL28QN67D BS- Rnase

bovine seminal ribonuclease; BS-RNase [synthetic construct]

Seminal ribonuclease precursor (Seminal RNase) (S-RNase) (Ribonuclease BS-1)

1H and 15N sequential assignment and secondary structure of the monomeric N67D
mutant of bovine seminal ribonuclease

TORSION ANGLE DYNAMICS, ENERGY MINIMIZATION