Preferred supramolecular organization and dimer interfaces of opioid receptors from simulated self-association.

Substantial evidence in support of the formation of opioid receptor (OR) di-/oligomers suggests previously unknown mechanisms used by these proteins to exert their biological functions. In an attempt to guide experimental assessment of the identity of the minimal signaling unit for ORs, we conducted extensive coarse-grained (CG) molecular dynamics (MD) simulations of different combinations of the three major OR subtypes, i.e., µ-OR, δ-OR, and κ-OR, in an explicit lipid bilayer. Specifically, we ran multiple, independent MD simulations of each homomeric µ-OR/µ-OR, δ-OR/δ-OR, and κ-OR/κ-OR complex, as well as two of the most studied heteromeric complexes, i.e., δ-OR/µ-OR and δ-OR/κ-OR, to derive the preferred supramolecular organization and dimer interfaces of ORs in a cell membrane model. These simulations yielded over 250 microseconds of accumulated data, which correspond to approximately 1 millisecond of effective simulated dynamics according to established scaling factors of the CG model we employed. Analysis of these data indicates similar preferred supramolecular organization and dimer interfaces of ORs across the different receptor subtypes, but also important differences in the kinetics of receptor association at specific dimer interfaces. We also investigated the kinetic properties of interfacial lipids, and explored their possible role in modulating the rate of receptor association and in promoting the formation of filiform aggregates, thus supporting a distinctive role of the membrane in OR oligomerization and, possibly, signaling.

Computational approaches to modeling viral structure and assembly.

The structures of biological macromolecules and macromolecular assemblies can be experimentally determined by X-ray crystallography, nuclear magnetic resonance (NMR), and cryo-electron microscopy (cryo-EM). The refinement of such structures is a difficult task, because of the size of the experimental data sets, and because of the very large number of degrees of freedom. Molecular modeling tools-particularly those based on the principles of molecular mechanics-have long been employed to assist in the refinement of macromolecular structures. Molecular mechanics methods are also used to generate de novo models when there are only limited experimental data available. Ideally, such models provide information on structure-function relationships, and on the thermodynamic and kinetic properties of the system of interest. Here, we summarize some of the molecular mechanics methods used to investigate questions of viral structure and assembly, including both all-atom and coarse-grained approaches.

Structural and electrostatic characterization of pariacoto virus: implications for viral assembly.

We present the first all-atom model for the structure of a T = 3 virus, pariacoto virus (PaV), which is a nonenveloped, icosahedral RNA virus and a member of the Nodaviridae family. The model is an extension of the crystal structure, which reveals about 88% of the protein structure but only about 35% of the RNA structure. New modeling methods, combining coarse-grained and all-atom approaches, were required for developing the model. Evaluation of alternative models confirms our earlier observation that the polycationic N- and C-terminal tails of the capsid proteins must penetrate deeply into the core of the virus, where they stabilize the structure by neutralizing a substantial fraction of the RNA charge. This leads us to propose a model for the assembly of small icosahedral RNA viruses: nonspecific binding of the protein tails to the RNA leads to a collapse of the complex, in a fashion reminiscent of DNA condensation. The globular protein domains are excluded from the condensed phase but are tethered to it, so they accumulate in a shell around the condensed phase, where their concentration is high enough to trigger oligomerization and formation of the mature virus.

Viral assembly: a molecular modeling perspective.

Icosahedral viruses are among the smallest and simplest of biological systems. The investigation of their structures represented the first step toward the establishment of molecular biophysics, over half a century ago. Many research groups are now pursuing investigations of viral assembly, a process that could offer new opportunities for the design of antiviral drugs and novel nanoparticles. A variety of experimental, theoretical and computational methods have been brought to bear on the study of virus structure and assembly. In this Perspective we review the contributions of theoretical and computational approaches to our understanding of the structure, energetics, thermodynamics and assembly of DNA bacteriophage and single-stranded icosahedral RNA viruses.

The conformation of double-stranded DNA inside bacteriophages depends on capsid size and shape.

The packaging of double-stranded DNA into bacteriophages leads to the arrangement of the genetic material into highly-packed and ordered structures. Although modern experimental techniques reveal the most probable location of DNA inside viral capsids, the individual conformations of DNA are yet to be determined. In the current study we present the results of molecular dynamics simulations of the DNA packaging into several bacteriophages performed within the framework of a coarse-grained model. The final DNA conformations depend on the size and shape of the capsid, as well as the size of the protein portal, if any. In particular, isometric capsids with small or absent portals tend to form concentric spools, whereas the presence of a large portal favors coaxial spooling; slightly and highly elongated capsids result in folded and twisted toroidal conformations, respectively. The results of the simulations also suggest that the predominant factor in defining the global DNA arrangement inside bacteriophages is the minimization of the bending stress upon packaging.