Multi-scale modelling of macromolecular conformational changes

Modelling protein flexibility and plasticity is computationally challenging but important for understanding the function of biological systems. Furthermore, it has great implications for the prediction of (macro) molecular complex formation. Recently, coarse-grained normal mode approaches have emerged as efficient alternatives for investigating large-scale conformational changes for which more accurate methods like MD simulation are limited due to their computational burden. We have developed a Normal Mode based Simulation (NMSim) approach for efficient conformation generation of macromolecules. Combinations of low energy normal modes are used to guide a simulation pathway, whereas an efficient constraints correction approach is applied to generate stereochemically allowed conformations. Non-covalent bonds like hydrogen bonds and hydrophobic tethers and phi-psi favourable regions are also modelled as constraints. Conformations from our approach were compared with a 10 ns MD trajectory of lysozyme. A 2-D RMSD plot shows a good overlap of conformational space, and rms fluctuations of residues show a correlation coefficient of 0.78 between the two sets of conformations. Furthermore, a comparison of NMSim simulations starting from apo structures of different proteins show that ligand-bound conformations can be sampled for those cases where conformational changes are mainly correlated, e.g., domain-like motion in adenylate kinase. Efforts are currently being made to also model localized but functionally important motions for protein binding pockets and protein-protein interfaces using relevant normal mode selection criteria and implicit rotamer basin creation

Aromatic N versus aromatic F: bioisosterism discovered in RNA base pairing interactions leads to a novel class of universal base analogs

The thermodynamics of base pairing is of fundamental importance. Fluorinated base analogs are valuable tools for investigating pairing interactions. To understand the influence of direct base–base interactions in relation to the role of water, pairing free energies between natural nucleobases and fluorinated analogs are estimated by potential of mean force calculations. Compared to pairing of AU and GC, pairing involving fluorinated analogs is unfavorable by 0.5–1.0 kcal mol−1. Decomposing the pairing free energies into enthalpic and entropic contributions reveals fundamental differences for Watson–Crick pairs compared to pairs involving fluorinated analogs. These differences originate from direct base–base interactions and contributions of water. Pairing free energies of fluorinated base analogs with natural bases are less unfavorable by 0.5–1.0 kcal mol−1 compared to non-fluorinated analogs. This is attributed to stabilizing C–F…H–N dipolar interactions and stronger N…H–C hydrogen bonds, demonstrating direct and indirect influences of fluorine. 7-methyl-7H-purine and its 9-deaza analog (Z) have been suggested as members of a new class of non-fluorinated base analogs. Z is found to be the least destabilizing universal base in the context of RNA known to date. This is the first experimental evidence for nitrogen-containing heterocylces as bioisosteres of aromatic rings bearing fluorine atoms

Starting Structure Dependence of NMR Order Parameters Derived from MD Simulations: Implications for Judging Force-Field Quality

Comparing experimental generalized N-H S2 order parameters to those calculated from molecular dynamics trajectories is increasingly used to judge force-field quality and completeness of sampling. Herein we demonstrate for the well-investigated system hen egg white lysozyme that different experimental starting structures can lead to significant differences in molecular-dynamics-derived S2 parameters that can be even larger than S2 parameter deviations due to different force fields. Caution should thus be taken in general when simulated S2 parameters are compared to experimental data with the aim of judging force-field quality. We show that adequately sampling flexible regions (∼100 ns) and only calculating S2 parameters averaged over short time windows proved necessary to obtain consistent results irrespective of the starting structure