 |
|
Title
|
|
"Ensemble" iterative relaxation matrix approach: a new NMR refinement protocol applied to the solution structure of crambin.
|
|
|
Authors
|
|
A.M.Bonvin,
J.A.Rullmann,
R.M.Lamerichs,
R.Boelens,
R.Kaptein.
|
|
|
Ref.
|
|
Proteins, 1993,
15,
385-400.
|
|
|
PubMed id
|
|
|
|
|
|
Abstract
|
|
|
The structure in solution of crambin, a small protein of 46 residues, has been
determined from 2D NMR data using an iterative relaxation matrix approach (IRMA)
together with distance geometry, distance bound driven dynamics, molecular
dynamics, and energy minimization. A new protocol based on an "ensemble"
approach is proposed and compared to the more standard initial rate analysis
approach and a "single structure" relaxation matrix approach. The effects of
fast local motions are included and R-factor calculations are performed on NOE
build-ups to describe the quality of agreement between theory and experiment. A
new method for stereospecific assignment of prochiral groups, based on a
comparison of theoretical and experimental NOE intensities, has been applied.
The solution structure of crambin could be determined with a precision (rmsd
from the average structure) of 0.7 A on backbone atoms and 1.1 A on all heavy
atoms and is largely similar to the crystal structure with a small difference
observed in the position of the side chain of Tyr-29 which is determined in
solution by both J-coupling and NOE data. Regions of higher structural
variability (suggesting higher mobility) are found in the solution structure, in
particular for the loop between the two helices (Gly-20 to Pro-22).
|
|
|
|