ABSTRACT
We introduce a mean-field theoretical framework for generalizing isotropic pair potentials to anisotropic shapes. This method is suitable for generating pair potentials that can be used in both Monte Carlo and molecular dynamics simulations. We demonstrate the application of this theory by deriving a Lennard-Jones (LJ)-like potential for arbitrary geometries along with a Weeks-Chandler-Anderson-like repulsive variant, showing that the resulting potentials behave very similarly to standard LJ potentials while also providing a nearly conformal mapping of the underlying shape. We then describe an implementation of this potential in the simulation engine HOOMD-blue and discuss the challenges that must be overcome to achieve a sufficiently robust and performant implementation. The resulting potential can be applied to smooth geometries like ellipsoids and to convex polytopes. We contextualize these applications with reference to the existing methods for simulating such particles. The pair potential is validated using standard criteria, and its performance is compared to existing methods for comparable simulations. Finally, we show the results of self-assembly simulations, demonstrating that this method can be used to study the assembly of anisotropic particles into crystal structures.
ABSTRACT
Symmetrical protein oligomers are ubiquitous in biological systems and perform key structural and regulatory functions. However, there are few methods for constructing such oligomers. Here we have engineered completely synthetic, symmetrical oligomers by combining pairs of oppositely supercharged variants of a normally monomeric model protein through a strategy we term 'supercharged protein assembly' (SuPrA). We show that supercharged variants of green fluorescent protein can assemble into a variety of architectures including a well-defined symmetrical 16-mer structure that we solved using cryo-electron microscopy at 3.47 Å resolution. The 16-mer is composed of two stacked rings of octamers, in which the octamers contain supercharged proteins of alternating charges, and interactions within and between the rings are mediated by a variety of specific electrostatic contacts. The ready assembly of this structure suggests that combining oppositely supercharged pairs of protein variants may provide broad opportunities for generating novel architectures via otherwise unprogrammed interactions.
Subject(s)
Protein Multimerization , Protein Subunits/metabolism , Recombinant Proteins/metabolism , Synthetic Biology/methods , Green Fluorescent Proteins/chemistry , Green Fluorescent Proteins/genetics , Green Fluorescent Proteins/metabolism , Models, Molecular , Protein Subunits/chemistry , Protein Subunits/genetics , Recombinant Proteins/chemistry , Recombinant Proteins/genetics , Static ElectricityABSTRACT
Restriction-modification systems protect bacteria from foreign DNA. Type I restriction-modification enzymes are multifunctional heteromeric complexes with DNA-cleavage and ATP-dependent DNA translocation activities located on endonuclease/motor subunit HsdR. The recent structure of the first intact motor subunit of the type I restriction enzyme from plasmid EcoR124I suggested a mechanism by which stalled translocation triggers DNA cleavage via a lysine residue on the endonuclease domain that contacts ATP bound between the two helicase domains. In the present work, molecular dynamics simulations are used to explore this proposal. Molecular dynamics simulations suggest that the Lys-ATP contact alternates with a contact with a nearby loop housing the conserved QxxxY motif that had been implicated in DNA cleavage. This model is tested here using in vivo and in vitro experiments. The results indicate how local interactions are transduced to domain motions within the endonuclease/motor subunit.
