Structure from NMR and molecular dynamics: Distance restraining inhibits motion in the essential subspace.
We address the question how well proteins can be modelled on the basis of NMR data, when these data are incorporated into the protein model using distance restraints in a molecular dynamics simulation. We found, using HPr as a model protein, that distance restraining freezes the essential motion of proteins, as defined by Amadei et al. [Amadei, A., Linssen, A.B.M. and Berendsen, H.J.C. (1993) Protein Struct. Funct. Genet., 17, 412-425]. We discuss how modelling protocols can be improved in order to solve this problem.
BIOSON Research Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands.
R M
RM
Scheek
N A
NA
van Nuland
B L
BL
de Groot
A
A
Amadei