Summary
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.
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Scheek, R.M., van Nuland, N.A.J., de Groot, B.L. et al. Structure from NMR and molecular dynamics: Distance restraining inhibits motion in the essential subspace. J Biomol NMR 6, 106–111 (1995). https://doi.org/10.1007/BF00417496
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DOI: https://doi.org/10.1007/BF00417496