Theoretical prediction of the binding free energy for mutants of replication protein A

Abstract

The replication protein A (RPA) is a heterotrimeric (70, 32, and 14 kDa subunits), single stranded DNA (ssDNA) binding protein required for pivotal functions in the cell metabolism, such as chromosomal replication, prevention of hairpin formation, DNA repair and recombination, and signaling after DNA damage. Studies based on deletions and mutations have identified the high affinity ssDNA binding domains in the 70 kDa subunit of RPA, regions A and B. Individually, the domain A and B have a low affinity for ssDNA, while tandems composed of AA, AB, BB, and BA sequences bind the ssDNA with moderate to high affinity. Single and double point mutations on polar residues in the binding domains leads to a reduction in affinity of RPA for ssDNA, in particular when two hydrophilic residues are involved. In view of these results, we performed a study based on molecular dynamics simulation aimed to reproduce the experimental change in binding free energy, ΔΔG, of RPA70 mutants to further elucidate the nature of the protein-ssDNA interaction. The MM-PB(GB)SA methods implemented in Amber10 and the code FoldX were used to estimate the binding free energy. The theoretical and experimental ΔΔG values correlate better when the results are obtained by MM-PBSA calculated on individual trajectories for each mutant. In these conditions, the correlation coefficient between experimental and theoretical ΔΔG reaches a value of 0.95 despite the overestimation of the energy change by one order of magnitude. The decomposition of the MM-GBSA energy per residue allows us to correlate the change of the affinity with the residue polarity and energy contribution to the binding. The method revealed reliable predictions of the change in the affinity in function of mutations, and can be used to identify new mutants with distinct binding properties.

Locating a Plausible Binding Site for an Open-Channel Blocker, GlyH-101, in the Pore of the Cystic Fibrosis Transmembrane Conductance Regulator

“…The voltage dependence of the EC 50 was analyzed by using a modified version of the Woodhull model (Woodhull, 1973;Tikhonov and Magazanik, 1998) (Guimarã es and Cardozo, 2008). Similar MM-GB/SA techniques were used to investigate the effects of protein mutations on ligand binding affinity (Carra et al, 2012). In the current study, the Embrace function of MacroModel 9.8 (Schrödinger) was used for the MM-GB/SA calculations.…”

Accuracy Comparison of Generalized Born Models in the Calculation of Electrostatic Binding Free Energies

“…Our findings demonstrate that different GB models lead to very different binding affinity predictions, with R 2 correlations varying largely among different complex sets, as well as among different GB models. An assessment of the literature reveals a similar behavior of R 2 correlations for other biomolecular complexes with varying energy range and spacing (e.g., refs − ). Future studies comparing the GB-predicted solvation free energies directly to experiment will need to evaluate to what extent performance of the promising GB models holds in realistic problems where binding free energies differ by only a few kcal/mol.…”

Molecular Simulation of Nicotine-Related Alkaloids Interaction with Human DNA

“…It was found, for example, nornicotine reacts with some human proteins and can lead to the appearance of certain types of cancer. [12][13][14][15] …”