Assessment of the DNA partial specific volume and hydration layer properties from CHARMM Drude polarizable and additive MD simulations

DNA-based assay for calorimetric determination of protein concentrations in pure or mixed solutions

It was recently reported that values of the transition heat capacities, as measured by differential scanning calorimetry, for two globular proteins and a short DNA hairpin in NaCl buffer are essentially equivalent, at equal concentrations (mg/mL). To validate the broad applicability of this phenomenon, additional evidence for this equivalence is presented that reveals it does not depend on DNA sequence, buffer salt, or transition temperature (Tm). Based on the equivalence of transition heat capacities, a calorimetric method was devised to determine protein concentrations in pure and complex solutions. The scheme uses direct comparisons between the thermodynamic stability of a short DNA hairpin standard of known concentration, and thermodynamic stability of protein solutions of unknown concentrations. Sequences of two DNA hairpins were designed to confer a near 20°C difference in their Tm values. In all cases, evaluated protein concentrations determined from the DNA standard curves agreed with the UV-Vis concentration for monomeric proteins. For multimeric proteins evaluated concentrations were greater than determined by UV-Vis suggesting the calorimetric approach can also be an indicator of molecular stoichiometry.

Molecular Dynamics Simulations of Protein RNA Complexes by Using an Advanced Electrostatic Model

Protein-RNA interactions are integral to the biological functions of RNA. It is well recognized that molecular dynamics (MD) simulations of protein-RNA complexes are more challenging than those of each component. The difficulty arises from the strong electrostatic interactions and the delicate balance between various types of physical forces at the interface. Previously, MD simulations of protein-RNA complexes have predominantly employed fixed-charge force fields. Although force field modifications have been developed to address problems identified in the simulations, some protein-RNA structures are still hard to reproduce by simulations. Here, we present MD simulations of two representative protein-RNA complexes using the AMOEBA polarizable force field. The van der Waals parameters were refined to reproduce accurate quantum-mechanical data of base-base and base-amino acid interactions. It was found that the refined parameters produced a more stable hydrogen-bond network in the interface. One of the complexes remained stable during the short simulations, whereas it could quickly break down in previous simulations using fixed-charge force fields. There was reversible breaking and formation of hydrogen bonds that are observed in the crystal structure, which may indicate the difference in solution and crystal structures. While further improvement and validation of the force fields are still needed, this work demonstrates that polarizable force fields are promising for the study of protein-RNA complexes.

Markov state models elucidate the stability of DNA influenced by the chiral 5S-Tg base

The static and dynamic structures of DNA duplexes affected by 5S-Tg (Tg, Thymine glycol) epimers were studied using MD simulations and Markov State Models (MSMs) analysis. The results show that the 5S,6S-Tg base caused little perturbation to the helix, and the base-flipping barrier was determined to be 4.4 kcal mol-1 through the use of enhanced sampling meta-eABF calculations, comparable to 5.4 kcal mol-1 of the corresponding thymine flipping. Two conformations with the different hydrogen bond structures between 5S,6R-Tg and A19 were identified in several independent MD trajectories. The 5S,6R-Tg:O6HO6•••N1:A19 hydrogen bond is present in the high-energy conformation displaying a clear helical distortion, and near barrier-free Tg base flipping. The low-energy conformation always maintains Watson-Crick base pairing between 5S,6R-Tg and A19, and 5S-Tg base flipping is accompanied by a small barrier of ca. 2.0 KBT (T = 298 K). The same conformations are observed in the MSMs analysis. Moreover, the transition path and metastable structures of the damaged base flipping are for the first time verified through MSMs analysis. The data clearly show that the epimers have completely different influence on the stability of the DNA duplex, thus implying different enzymatic mechanisms for DNA repair.