Investigation on two human defensin dimers: structure prediction and refinement using a combined simulation strategy

<p>Defensins are cationic cysteine-rich small molecules belonging to the innate immune system. Most defensins form dimers that can enhance their function. Thus, predicting their dimer structures, if unavailable, is important. In this project, a combined simulation strategy is applied to predict dimer structures of two defensins, human defensin type 2 (hBD-2) and human defensin type 5 (HD5), which includes predicting the initial dimer structure running implicit solvent replica-exchange (REX) simulations with a GBSW module, then running microsecond-long all-atom simulations with the CHARMM36 forcefield to refine the prediction. The combined simulations predicted the dimer structures in good agreement with crystal structures within simulation uncertainty. Microsecond-long refinement on the crystal structures of hBD-2 and HD5 dimers shows that CHARMM36 forcefield could contribute a structural deviation of 1.0–3.0 Å  from their crystal structures. Comparing the RMSD, RMSF, radius of gyration, accessible surface area (ASA), number of hydrogen bonds (H-bonds) and residue distance map for simulations starting from the REX initiated structure and the crystal structure, consistent agreements were reached for both dimers. However, hBD-2 dimer has a larger hydrophobic ASA, while HD5 has a larger hydrophilic ASA; HD5 forms 45 H-bonds on the binding interface while 12 for hBD-2 dimer.</p

Molecular Dynamics Simulations Reveal Isoform Specific Contact Dynamics between the Plexin Rho GTPase Binding Domain (RBD) and Small Rho GTPases Rac1 and Rnd1

The Plexin family of transmembrane receptors are unique in that their intracellular region interacts directly with small GTPases of the Rho family. The Rho GTPase binding domain of plexin (RBD)which is responsible for these interactionscan bind with Rac1 as well as Rnd1 GTPases. GTPase complexes have been crystallized with the RBDs of plexinA1, -A2, and -B1. The protein association is thought to elicit different functional responses in a GTPase and plexin isoform specific manner, but the origin of this is unknown. In this project, we investigated complexes between several RBD and Rac1/Rnd1 GTPases using multimicrosecond length all atom molecular dynamics simulations, also with reference to the free forms of the RBDs and GTPases. In accord with the crystallographic data, the RBDs experience more structural changes than Rho-GTPases upon complex formation. Changes in protein dynamics and networks of correlated motions are revealed by analyzing dihedral angle fluctuations in the proteins. The extent of these changes differs between the different RBDs and also between the Rac1 and Rnd1 GTPases. While the RBDs in the free and bound states have similarif not decreasedcorrelations, correlations within the GTPases are increased upon binding. Mapping highly correlated residues to the structures, it is found that the plexinA1, -B1, and -A2 RBDs all have similar communication pathways within the ubiquitin fold, but that different residues are involved. Dynamic network analyses indicate that plexinA1 and -B1 RBDs interact with small GTPases in a similar manner, whereas complexes with the plexinA2 RBD display different features. Importantly complexes with Rnd1 have a considerable number of dynamic correlations and network connections between the proteins, whereas such features are missing in the RBD–Rac1 complexes. Overall, the simulations suggest mechanisms that are consistent with the experimental data on plexinB1 and indicate RBD and GTPase isoform specific changes in protein dynamics upon complex formation

Comparison of RBD DSSP with available literature data.

Comparison of RBD DSSP with available literature data.</p

Effects of Polymer Modification on Properties and Microstructure of Model Asphalt Systems

Physical properties and microstructures of computational model asphalts were investigated using molecular dynamics simulations in an all-atom framework. A new model asphalt is proposed that is targeted toward core asphalt AAA-1 of the Strategic Highway Research Program (SHRP) based on elemental composition and speciation. Individual compounds were chosen from the literature to represent asphaltene, polar aromatic, naphthene aromatic, and saturate, with interactions ranked using Hansen solubility parameters. The density and thermal expansion coefficient agreed better with experimental data than had predictions using earlier model asphalts. In addition, one polystyrene molecule with 50 repeat units was added into a ternary model asphalt from earlier work and the new six-component AAA-1 model system to analyze polymer modification effects. The expansion coefficient, isothermal compressibility, and their temperature dependence decreased with one polymer chain present, while density increased. Self-diffusion coefficients of each component in both model asphalts decreased upon including the polymer. To assess microstructure, radial distribution functions <i>g</i>(<i>r</i>) of asphaltene and simplified resin molecules were calculated at different temperatures. Asphaltene results changed with temperature and upon including one polymer; artifacts of initial configuration were found at lower temperatures. Radial distribution functions for pairs of resin-like molecules (dimethylnaphthalene, benzoquinoline, and ethylbenzothiophene) and for asphaltene−resin pairs retained similar shapes and first peak positions at different temperatures and when including the polymer. Results for unlike molecules indicated a depletion of resin [<i>g</i>(<i>r</i>) <1] immediately surrounding an asphaltene molecule, rather than the enrichment expected from standard “colloid model” descriptions, in which resins solubilize asphaltenes. Intermolecular orientations between closest asphaltene pairs in original and polymer modified systems were strongly peaked toward parallel packing and remained similar at several high temperatures. Orientations between asphaltenes and resins and among resins were weighted toward parallel, compared to random packing, both with and without a polymer and over a range of temperatures

S14 Fig -

Community networks formed in the RBD-P479S(Left), in RBD-S477N (middle) and RBD-T478I (Right) based on MD simulation and dynamical network analysis. The RBD network structures are oriented in the same direction as the RBD shown in Fig 1. (TIF)</p

Fig 5 -

Hydrogen bonds formed on the ACE2&RBD interface for the wildtype (a) and tri-mutant (b) generated from ligplot program. Residues formed hydrogen bonds are connected using dashed green lines. Residues on RBD are labelled in light green with bonds shown in magenta, while residues on ACE2 are labelled in blue with bonds shown in orange.</p

Schematic illustrating that structures with like-topology can be connected via straight segments, while unlike structures require some bending, either of irregular or of helical structures.

<p>Schematic illustrating that structures with like-topology can be connected via straight segments, while unlike structures require some bending, either of irregular or of helical structures.</p

The distance maps of RBD-K417N, RBD-N501Y, RBD-trimutant variants bound with ACE2.

The binding region (RES455 to 505) on RBD are highlighted in light green. The color bars are shown on the right side of the distance maps, with a residue pair distance being no larger than 4 Å shown in red, while a residue pair distance larger or equal to 14 Å shown in white. (TIF)</p

ΔΔG predicted from FEP in comparison with available literature data.

ΔΔG predicted from FEP in comparison with available literature data.</p

S10 Fig -

Comparison of the averaged mixed dihedral angle covariance matrix for RBD-K417N (upper-left triangle above the diagonal line) and RBD in wildtype (lower-right triangle) in bound state. The result from RBD in wildtype is shown in the lower-right triangle below the diagonal line. (TIF)</p