Atomic-scale modeling of compacted nucleic acids has the ability to reveal the inner workings of spectacular biomolecular machines such as ribosomes or virus particles. Yet, the outcome of such modeling efforts sensitively depends on the accuracy of the underlying computational models. Our molecular dynamics simulations of an array of 64 parallel duplex DNA revealed considerable artifacts in the standard parametrization of cation-DNA phosphate interactions: both the DNA arrangement and the internal pressure inside the DNA arrays were found in considerable disagreement with experiment. To improve the model, we fine-tuned the parametrization of van der Waals interactions of specific ion pairs to reproduce experimental osmotic pressure of binary electrolyte solutions. Our reparametrization applied to the combinations of four cations (lithium, sodium, potassium and magnesium) and three anions (chloride, acetate and dimethylphosphate), for both CHARMM and AMBER parameter sets. Repeating the DNA array simulation using our reparametrization of ion-phosphate interaction produced results consistent with experiment. Our improved parametrization can be directly applied to molecular dynamics simulations of various charged biomolecular systems, including nucleic acids, proteins rich in aspartate and glutamate side chains and lipid bilayer membranes.
In the biennial Winter Aspen Physics Conference on Single Molecule Biophysics organized by Steven Block of Stanford University and Thomas Perkins of JILA and University of Colorado, CPLC scientists Yann Chemla, Taekjip Ha and Paul Selvin presented their latest research to more than one hundred researchers from the US, Europe and Japan. Thomas Perkins is a member of the external advisory board of CPLC. As part of the tradition of Aspen Physics Conferences, CPLC co-director Taekjip Ha gave a public lecture at the Wheeler Opera House in Aspen, attended by Aspenites as well as biophysicists. You can watch the lecture online from the grassroots TV Aspen. Previous public lectures of the Single Molecule Biophysics Winter Conference were given by Steven Chu (2003), Yale Goldman (2005), W.E. Moerner (2007), James Spudich (2009) and Xiaowei Zhuang (2011). The public lecture was preceded by 'Physics Cafe' run by Olga Dudko of UC San Diego, Jeff Gelles of Brandeis University and David Rueda of Imperial College.