Paper Citing NAMD - Abstract
Mikulska, Karolina; Strzelecki, Janusz; Nowak, Wieslaw
Nanomechanics of beta-rich proteins related to neuronal disorders studied by AFM, all-atom and coarse-grained MD methods
JOURNAL OF MOLECULAR MODELING, 20 Art. No. 2144, MAR 2014
Computer simulations of protein unfolding substantially help to interpret force-extension curves measured in single-molecule atomic force microscope (AFM) experiments. Standard all-atom (AA) molecular dynamics simulations (MD) give a good qualitative mechanical unfolding picture but predict values too large for the maximum AFM forces with the common pulling speeds adopted here. Fine tuned coarse-grain MD computations (CG MD) offer quantitative agreement with experimental forces. In this paper we address an important methodological aspect of MD modeling, namely the impact of numerical noise generated by random assignments of bead velocities on maximum forces (F-max) calculated within the CG MD approach. Distributions of CG forces from 2000 MD runs for several model proteins rich in structures and having folds with increasing complexity are presented. It is shown that F-max have nearly Gaussian distributions and that values of Fmax for each of those beta-structures may vary from 93.2+/- 28.9 pN (neurexin) to 198.3 +/- 25.2 pN (fibronectin). The CG unfolding spectra are compared with AA steered MD data and with results of our AFM experiments for modules present in contactin, fibronectin and neurexin. The stability of these proteins is critical for the proper functioning of neuronal synaptic clefts. Our results confirm that CG modeling of a single molecule unfolding is a good auxiliary tool in nanomechanics but large sets of data have to be collected before reliable comparisons of protein mechanical stabilities are made.
