Nanohedra: Using symmetry to design self assembling protein cages, layers, crystals, and filaments

A general strategy is described for designing proteins that self assemble into large symmetrical nanomaterials, including molecular cages, filaments, layers, and porous materials. In this strategy, one molecule of protein A, which naturally forms a self-assembling oligomer, An, is fused rigidly to one molecule of protein B, which forms another self-assembling oligomer, Bm. The result is a fusion protein, A-B, which self assembles with other identical copies of itself into a designed nanohedral particle or material, (A-B)p. The strategy is demonstrated through the design, production, and characterization of two fusion proteins: a 49-kDa protein designed to assemble into a cage approximately 15 nm across, and a 44-kDa protein designed to assemble into long filaments approximately 4 nm wide. The strategy opens a way to create a wide variety of potentially useful protein-based materials, some of which share similar features with natural biological assemblies.

Inversion of the chordate body axis: Are there alternatives?

One major morphological difference between chordates and annelids or arthropods is the opposite orientation of the nerve cord and heart. A long-standing proposal is that the chordate axis evolved by inverting the body of an ancestor with the annelid/arthropod orientation. However, the data can also be explained by a common ancestor with diffuse dorsoventral organization, followed by oppositely directed condensation of the nerve cord and relocation of the heart in the two lines.

A brief survey of symmetry in mathematics

This paper presents a brief survey of the idea of symmetry in mathematics, as exemplified by some particular developments in algebra, differential equations, topology, and number theory.

Symmetry, stability, and dynamics of multidomain and multicomponent protein systems

Symmetry is commonly observed in many biological systems. Here we discuss representative examples of the role of symmetry in structural molecular biology. Point group symmetries are observed in many protein oligomers whose three-dimensional atomic structures have been elucidated by x-ray crystallography. Approximate symmetry also occurs in multidomain proteins. Symmetry often confers stability on the molecular system and results in economical usage of basic components to build the macromolecular structure. Symmetry is also associated with cooperativity. Mild perturbation from perfect symmetry may be essential in some systems for dynamic functions.

Symmetry and the energy landscapes of biomolecules

The role of symmetry in the folding of proteins is discussed using energy landscape theory. An analytical argument shows it is much easier to find sequences with funneled energy landscape capable of fast folding if the structure is symmetric. The analogy with phase transitions of small clusters with magic numbers is discussed.

The role of symmetry in fundamental physics

The role of symmetry in fundamental physics is reviewed.

Symmetry arguments in chemistry

The use (and misuse) of symmetry arguments in constructing molecular models and in the interpretation of experimental observations bearing on molecular structure (spectroscopy, diffraction, etc.) is discussed. Examples include the development of point groups and space groups for describing the external and internal symmetry of crystals, the derivation of molecular symmetry by counting isomers (the benzene structure), molecular chirality, the connection between macroscopic and molecular chirality, pseudorotation, the symmetry group of nonrigid molecules, and the use of orbital symmetry arguments in discussing aspects of chemical reactivity.

Five-fold symmetry in crystalline quasicrystal lattices

To demonstrate that crystallographic methods can be applied to index and interpret diffraction patterns from well-ordered quasicrystals that display non-crystallographic 5-fold symmetry, we have characterized the properties of a series of periodic two-dimensional lattices built from pentagons, called Fibonacci pentilings, which resemble aperiodic Penrose tilings. The computed diffraction patterns from periodic pentilings with moderate size unit cells show decagonal symmetry and are virtually indistinguishable from that of the infinite aperiodic pentiling. We identify the vertices and centers of the pentagons forming the pentiling with the positions of transition metal atoms projected on the plane perpendicular to the decagonal axis of quasicrystals whose structure is related to crystalline η phase alloys. The characteristic length scale of the pentiling lattices, evident from the Patterson (autocorrelation) function, is ∼τ2 times the pentagon edge length, where τ is the golden ratio. Within this distance there are a finite number of local atomic motifs whose structure can be crystallographically refined against the experimentally measured diffraction data.

From symmetry to asymmetry: Phylogenetic patterns of asymmetry variation in animals and their evolutionary significance

Phylogenetic analyses of asymmetry variation offer a powerful tool for exploring the interplay between ontogeny and evolution because (i) conspicuous asymmetries exist in many higher metazoans with widely varying modes of development, (ii) patterns of bilateral variation within species may identify genetically and environmentally triggered asymmetries, and (iii) asymmetries arising at different times during development may be more sensitive to internal cytoplasmic inhomogeneities compared to external environmental stimuli. Using four broadly comparable asymmetry states (symmetry, antisymmetry, dextral, and sinistral), and two stages at which asymmetry appears developmentally (larval and postlarval), I evaluated relations between ontogenetic and phylogenetic patterns of asymmetry variation. Among 140 inferred phylogenetic transitions between asymmetry states, recorded from 11 classes in five phyla, directional asymmetry (dextral or sinistral) evolved directly from symmetrical ancestors proportionally more frequently among larval asymmetries. In contrast, antisymmetry, either as an end state or as a transitional stage preceding directional asymmetry, was confined primarily to postlarval asymmetries. The ontogenetic origin of asymmetry thus significantly influences its subsequent evolution. Furthermore, because antisymmetry typically signals an environmentally triggered asymmetry, the phylogenetic transition from antisymmetry to directional asymmetry suggests that many cases of laterally fixed asymmetries evolved via genetic assimilation.

Symmetry in chemistry from the hydrogen atom to proteins

The last 2 decades have seen discoveries in highly excited states of atoms and molecules of phenomena that are qualitatively different from the “planetary” model of the atom, and the near-rigid model of molecules, characteristic of these systems in their low-energy states. A unified view is emerging in terms of approximate dynamical symmetry principles. Highly excited states of two-electron atoms display “molecular” behavior of a nonrigid linear structure undergoing collective rotation and vibration. Highly excited states of molecules described in the “standard molecular model” display normal mode couplings, which induce bifurcations on the route to molecular chaos. New approaches such as rigid–nonrigid correlation, vibrons, and quantum groups suggest a unified view of collective electronic motion in atoms and nuclear motion in molecules.

Mirror symmetry breaking at the molecular level.

Reasoning from two basic principles of molecular physics, P invariance of electromagnetic interaction and the second law of thermodynamics, one would conclude that mirror symmetry retained in the world of chiral molecules. This inference is fully consistent with what is observed in inorganic nature. However, in the bioorganic world, the reverse is true. Mirror symmetry there is definitely broken. Is it possible to account for this phenomenon without going beyond conventional concepts of the kinetics of enantioselective processes? This study is an attempt to survey all existing hypotheses containing this phenomenon.

Independent determination of symmetry and polarity in the Drosophila eye.

In each facet of the Drosophila compound eye, a cluster of photoreceptor cells assumes an asymmetric trapezoidal pattern. These clusters have opposite orientations above and below an equator, showing global dorsoventral mirror symmetry. However, in the mutant spiny legs, the polarization of each cluster appears to be random, so that no equator is evident. The apparent lack of an equator suggests that spiny legs+ may be involved in the establishment of global dorsoventral identity that might be essential for proper polarization of the photoreceptor clusters. Alternatively, a global dorsoventral pattern could be present, but spiny legs+ may be required for local polarization of individual clusters. Using an enhancer trap strain in which white+ gene expression is restricted to the dorsal field, we show that white+ expression in spiny legs correctly respects dorsoventral position even in facets with inappropriate polarizations; the dorsoventral boundary is indeed present, whereas the mechanism for polarization is perturbed. It is suggested that the boundary is established before the action of spiny legs+ by an independent mechanism.

Thermodynamic glass transition in a spin glass without time-reversal symmetry

Spin glasses are a longstanding model for the sluggish dynamics that appear at the glass transition. However, spin glasses differ from structural glasses in a crucial feature: they enjoy a time reversal symmetry. This symmetry can be broken by applying an external magnetic field, but embarrassingly little is known about the critical behavior of a spin glass in a field. In this context, the space dimension is crucial. Simulations are easier to interpret in a large number of dimensions, but one must work below the upper critical dimension (i.e., in d < 6) in order for results to have relevance for experiments. Here we show conclusive evidence for the presence of a phase transition in a four-dimensional spin glass in a field. Two ingredients were crucial for this achievement: massive numerical simulations were carried out on the Janus special-purpose computer, and a new and powerful finite-size scaling method.

Interplay between sublattice and spin symmetry breaking in graphene

We study the effect of sublattice symmetry breaking on the electronic, magnetic, and transport properties of two-dimensional graphene as well as zigzag terminated one- and zero-dimensional graphene nanostructures. The systems are described with the Hubbard model within the collinear mean field approximation. We prove that for the noninteracting bipartite lattice with an unequal number of atoms in each sublattice, in-gap states still exist in the presence of a staggered on-site potential ±Δ/2. We compute the phase diagram of both 2D and 1D graphene with zigzag edges, at half filling, defined by the normalized interaction strength U/t and Δ/t, where t is the first neighbor hopping. In the case of 2D we find that the system is always insulating, and we find the Uc(Δ) curve above which the system goes antiferromagnetic. In 1D we find that the system undergoes a phase transition from nonmagnetic insulator for U

Stress Inversion Using LiDAR Tunnel Deformation Measurements

Far-field stresses are those present in a volume of rock prior to excavations being created. Estimates of the orientation and magnitude of far-field stresses, often used in mine design, are generally obtained by single-point measurements of stress, or large-scale, regional trends. Point measurements can be a poor representation of far-field stresses as a result of excavation-induced stresses and geological structures. For these reasons, far-field stress estimates can be associated with high levels of uncertainty. The purpose of this thesis is to investigate the practical feasibility, applications, and limitations of calibrating far-field stress estimates through tunnel deformation measurements captured using LiDAR imaging. A method that estimates the orientation and magnitude of excavation-induced principal stress changes through back-analysis of deformation measurements from LiDAR imaged tunnels was developed and tested using synthetic data. If excavation-induced stress change orientations and magnitudes can be accurately estimated, they can be used in the calibration of far-field stress input to numerical models. LiDAR point clouds have been proven to have a number of underground applications, thus it is desired to explore their use in numerical model calibration. The back-analysis method is founded on the superposition of stresses and requires a two-dimensional numerical model of the deforming tunnel. Principal stress changes of known orientation and magnitude are applied to the model to create calibration curves. Estimation can then be performed by minimizing squared differences between the measured tunnel and sets of calibration curve deformations. In addition to the back-analysis estimation method, a procedure consisting of previously existing techniques to measure tunnel deformation using LiDAR imaging was documented. Under ideal conditions, the back-analysis method estimated principal stress change orientations within ±5° and magnitudes within ±2 MPa. Results were comparable for four different tunnel profile shapes. Preliminary testing using plastic deformation, a rough tunnel profile, and profile occlusions suggests that the method can work under more realistic conditions. The results from this thesis set the groundwork for the continued development of a new, inexpensive, and efficient far-field stress estimate calibration method.