Adenylate Kinase Potential of Mean Force

Zipping and unzipping of adenylate kinase: Atomistic insights into the ensemble of open ? closed transitions . J. Mol. Biol., 394(1):160–176, 2009.

Data The file free_bw2_tol1e-05.dat contains the PMF data shown in Fig. 4a of the JMB paper 2 . The image shows the data plotted with cubic spline smoothing. File format free_bw2_tol1e-05.dat is the output from WHAM.

The important data columns are NMP-core angle (degrees) LID-core angle (degrees) free energy in kcal/mol (Other columns are output from wham and can be ignored.)

Methods

Conformations of E. coli AdK were umbrella-sampled in the space of the NMP-core and LID-core angles. 3 The protein was modelled in implicit solvent with the ACE2 electrostatics model. The resulting umbrella data were unbiased using Alan Grossfield’s wham code with bin size 2º tolerance of the self consistency procedure 1e-5 kT limits 34º < NMP < 80º and 94º < LID < 156º The first 2000 frames (200ps) of each window were discarded as equilibration and the remaining 3000 frames were used for the PMF.

For further details please see the paper. 2 References S. L. Seyler and O. Beckstein, O. Sampling large conformational transitions: adenylate kinase as a testing ground . Mol. Simul., 40(10–11): 855–877, 2014.

O. Beckstein, E. J. Denning, J. R. Perilla, and T. B. Woolf. Zipping and unzipping of adenylate kinase: Atomistic insights into the ensemble of open / closed transitions . J. Mol.

Biol., 394(1):160–176, 2009. See the 2009 paper 2 for the definitions and the MDAnalysis tutorial’s Exercise 4 for Python code to calculate the angles. M. Gur, J. D. Madura, and I. Bahar.

Global transitions of proteins explored by a multiscale hybrid methodology: Application to adenylate kinase Biophysical Journal, 105(7):1643 – 1652, 2013. A. Uyar, N. Kantarci-Carsibasi, T. Haliloglu, and P. Doruker. Features of large hinge-bending conformational transitions.

Prediction of closed structure from open state . Biophysical Journal, 106(12):2656 – 2666, 2014