Two-dimensional protein crystallization via metal-ion coordination by naturally occurring surface histidines

A powerful and potentially general approach to the targeting and crystallization of proteins on lipid interfaces through coordination of surface histidine residues to lipid-chelated divalent metal ions is presented. This approach, which should be applicable to the crystallization of a wide range of naturally occurring or engineered proteins, is illustrated here by the crystallization of streptavidin on a monolayer of an iminodiacetate-Cu(II) lipid spread at the air-water interface. This method allows control of the protein orientation at interfaces, which is significant for the facile production of highly ordered protein arrays and for electron density mapping in structural analysis of two-dimensional crystals. Binding of native streptavidin to the iminodiacetate-Cu lipids occurs via His-87, located on the protein surface near the biotin binding pocket. The two-dimensional streptavidin crystals show a previously undescribed microscopic shape that differs from that of crystals formed beneath biotinylated lipids

On the linearization of the generalized Ermakov systems

A linearization procedure is proposed for Ermakov systems with frequency depending on dynamic variables. The procedure applies to a wide class of generalized Ermakov systems which are linearizable in a manner similar to that applicable to usual Ermakov systems. The Kepler--Ermakov systems belong into this category but others, more generic, systems are also included

Tzitz\'eica transformation is a dressing action

We classify the simplest rational elements in a twisted loop group, and prove that dressing actions of them on proper indefinite affine spheres give the classical Tzitz\'eica transformation and its dual. We also give the group point of view of the Permutability Theorem, construct complex Tzitz\'eica transformations, and discuss the group structure for these transformations

Generalizing the autonomous Kepler Ermakov system in a Riemannian space

We generalize the two dimensional autonomous Hamiltonian Kepler Ermakov dynamical system to three dimensions using the sl(2,R) invariance of Noether symmetries and determine all three dimensional autonomous Hamiltonian Kepler Ermakov dynamical systems which are Liouville integrable via Noether symmetries. Subsequently we generalize the autonomous Kepler Ermakov system in a Riemannian space which admits a gradient homothetic vector by the requirements (a) that it admits a first integral (the Riemannian Ermakov invariant) and (b) it has sl(2,R) invariance. We consider both the non-Hamiltonian and the Hamiltonian systems. In each case we compute the Riemannian Ermakov invariant and the equations defining the dynamical system. We apply the results in General Relativity and determine the autonomous Hamiltonian Riemannian Kepler Ermakov system in the spatially flat Friedman Robertson Walker spacetime. We consider a locally rotational symmetric (LRS) spacetime of class A and discuss two cosmological models. The first cosmological model consists of a scalar field with exponential potential and a perfect fluid with a stiff equation of state. The second cosmological model is the f(R) modified gravity model of {\Lambda}_{bc}CDM. It is shown that in both applications the gravitational field equations reduce to those of the generalized autonomous Riemannian Kepler Ermakov dynamical system which is Liouville integrable via Noether integrals.Comment: Reference [25] update, 21 page

Generalized Hamiltonian structures for Ermakov systems

We construct Poisson structures for Ermakov systems, using the Ermakov invariant as the Hamiltonian. Two classes of Poisson structures are obtained, one of them degenerate, in which case we derive the Casimir functions. In some situations, the existence of Casimir functions can give rise to superintegrable Ermakov systems. Finally, we characterize the cases where linearization of the equations of motion is possible

Computational analysis of anti-HIV-1 antibody neutralization panel data to identify potential functional epitope residues

Advances in single-cell antibody cloning methods have led to the identification of a variety of broadly neutralizing anti–HIV-1 antibodies. We developed a computational tool (Antibody Database) to help identify critical residues on the HIV-1 envelope protein whose natural variation affects antibody activity. Our simplifying assumption was that, for a given antibody, a significant portion of the dispersion of neutralization activity across a panel of HIV-1 strains is due to the amino acid identity or glycosylation state at a small number of specific sites, each acting independently. A model of an antibody’s neutralization IC_(50) was developed in which each site contributes a term to the logarithm of the modeled IC_(50). The analysis program attempts to determine the set of rules that minimizes the sum of the residuals between observed and modeled IC_(50) values. The predictive quality of the identified rules may be assessed in part by whether there is support for rules within individual viral clades. As a test case, we analyzed antibody 8ANC195, an anti-glycoprotein gp120 antibody of unknown specificity. The model for this antibody indicated that several glycosylation sites were critical for neutralization. We evaluated this prediction by measuring neutralization potencies of 8ANC195 against HIV-1 in vitro and in an antibody therapy experiment in humanized mice. These experiments confirmed that 8ANC195 represents a distinct class of glycan-dependent anti–HIV-1 antibody and validated the utility of computational analysis of neutralization panel data

On a direct approach to quasideterminant solutions of a noncommutative KP equation

A noncommutative version of the KP equation and two families of its solutions expressed as quasideterminants are discussed. The origin of these solutions is explained by means of Darboux and binary Darboux transformations. Additionally, it is shown that these solutions may also be verified directly. This approach is reminiscent of the wronskian technique used for the Hirota bilinear form of the regular, commutative KP equation but, in the noncommutative case, no bilinearising transformation is available.Comment: 11 page

Darboux transformations for a 6-point scheme

We introduce (binary) Darboux transformation for general differential equation of the second order in two independent variables. We present a discrete version of the transformation for a 6-point difference scheme. The scheme is appropriate to solving a hyperbolic type initial-boundary value problem. We discuss several reductions and specifications of the transformations as well as construction of other Darboux covariant schemes by means of existing ones. In particular we introduce a 10-point scheme which can be regarded as the discretization of self-adjoint hyperbolic equation