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SOLUTION STRUCTURE OF THE BACTERIOPHAGE PHI21 N PEPTIDE-BOXB RNA COMPLEX
SOLUTION NMR
NMR Spectrometer Information
Spectrometer
Manufacturer
Model
Field Strength
1
Varian
INOVA
600
2
Bruker
DRX
750
3
Bruker
AMX
600
NMR Refinement
Method
Details
Software
There were a total of 1016 distance restraints (including 48 hydrogen bond distance restraints) and 167 torsion restraints used to determine this structure. The molecular modeling of the phi21 N peptide-boxB RNA complex was done in three steps. First, a complete intramolecular restraint set was generated for each molecule, and then peptide and RNA structures were generated separately using ab initio simulated annealing (SA) starting from a random extended structure in CNSsolve. For both the peptide and the RNA, constrained (torsion) dynamics was used at 50000K. A total of 100 structures each of the peptide and RNA were generated.
In the second step, each of the 20 lowest energy peptide and 20 lowest energy RNA structures were combined in single PDB files, in all 400 possible combinations. The RNA was held at the origin and the peptide was randomly rotated and moved 100 angstroms away in a random direction from the origin. These 400 possible "complexes" were docked using CNSsolve. The objective of the docking was to bring the peptide and RNA together without dramatically perturbing their folded structures from the first round of SA, so the temperatures for the docking were set much lower than in the initial calculations (1000 vs. 50000K).
Finally, the 100 lowest energy docked structures were minimized by two rounds of low temperature annealing using Sander, a module of AMBER. As with the docking, the temperature was kept low (1000K). The 14 lowest energy structures were used for generating an average structure, which was energy minimized using a conjugate gradient.
NMRPipe
NMR Ensemble Information
Conformer Selection Criteria
structures with the lowest energy
Conformers Calculated Total Number
100
Conformers Submitted Total Number
15
Representative Model
1 (minimized average structure)
Additional NMR Experimental Information
Details
The structure was determined using 2D homonuclear and 3D heteronuclear NMR spectroscopy. The two most important samples
were uniformly labeled 15N,13C peptide or RNA in complex with its unlabeled counterpart.
Computation: NMR Software
#
Classification
Version
Software Name
Author
1
processing
NMRPipe
2.1
F. Delaglio, S. Grzesiek, G. Vuister, G. Zhu, J. Pfeifer, and A. Bax
2
data analysis
NMRView
4.1.3
Bruce A. Johnson
3
refinement
CNS
1.0
A.T. Brunger, P.D. Adams, G.M. Clore, W.L. Delano, P. Gros, R.W. Grosse-Kunstleve, J.S. Jiang, J. Kuszewski, M. Nilges, N.S. Pannu, R.J. Read, L.M. Rice, T. Simonson, G.L. Warren