"KlenTaq polymerase replicates unnatural base pairs by inducing a Watson-Crick geometry "

Betz, K., Malyshev, D.A., Lavergne, T., Welte, W., Diederichs, K., Dwyer, T.J., Ordoukhanian, P., Romesberg, F.E. and Marx, A.

Nature Chemical Biology Vol. 7(8), pp. 612-4 (2012)

Unnatural base pair formation induces conformational transitions of KlenTaq and the formation of a natural-like ternary complex.

"Linking crystallographic model and data quality"

Karplus, P.A. and Diederichs, K.

Science Vol. 336, pp. 1030-3 (2012)

Explanatory notes:

1. The split-half correlation of the data (CC1/2) proves the high significance of data discarded by current conventions and will simplify and improve high-resolution cutoff decisions;
2. the Spearman-Brown prophecy formula captures in CC* the expected correlation of the data with the underlying true values;
3. comparisons of CC* with the correlation of the observed data with values calculated from a refined model allows the discovery of overfitting or underfitting and the recognition of when data quality is limiting model improvement;
4. analyses of test cases proves that when data quality limits model improvement, the values calculated from the model may be substantially closer to the true values than are the experimental data.

"Transport of drugs by the multidrug transporter AcrB involves an access and a deep binding pocket that are separated by a switch-loop "

Eicher, T., Cha, H., Seeger, M., Brandstätter, L. El-Delik, J., Bohnert, J.A., Kern, W.V., Verrey, F., Grütter, M.G., Diederichs, K. and Pos, K.M.

PNAS Vol. 109, pp. 5687-92 (2012)

Explanatory notes:

Stepwise AcrB-catalyzed drug transport mediated by cycling between the Loose (blue), Tight (yellow), and Open (red) conformation within an AcrB trimer.

1. Initial drug uptake via the access pocket in the L monomer.
2. Transfer of the drug from the low-affinity access pocket to the high- affinity deep binding pocket during the L to T transition.
3. Directional drug transport during the T to O transition. Subdomains PC1 and PC2 close the lateral access and prevent backsliding of the drug, which is extruded through the tunnel.
4. Resetting the monomer by the O to L transition to reinitialize drug uptake via the access pocket.