Traversable Lorentzian wormhole on the Shtanov-Sahni braneworld with matter obeying the energy conditions

In this paper we have explored the possibility of constructing a traversable wormhole on the Shtanov-Sahni braneworld with a timelike extra dimension. We find that the Weyl curvature singularity at the throat of the wormhole can be removed with physical matter satisfying the NEC $\rho+p \geq 0$, even in the absence of any effective $\Lambda$-term or any type of charge source on the brane. (The NEC is however violated by the effective matter description on the brane arising due to effects of higher dimensional gravity.) Besides satisfying NEC the matter constituting the wormhole also satisfies the Strong Energy Condition (SEC), $\rho+3p \geq 0$, leading to the interesting possibility that normal matter on the brane may be harnessed into a wormhole. Incidentally, these conditions also need to be satisfied to realize a non-singular bounce and cyclic cosmology on the brane\cite{Sahni4} where both past and future singularities can be averted. Thus, such a cyclic universe on the brane, constituted of normal matter can naturally contain wormholes. The wormhole shape function on the brane with a time-like extra dimension represents the tubular structure of the wormhole spreading out at large radial distances much better than in wormholes constructed in a braneworld with a spacelike extra dimension and have considerably lower mass resulting in minimization of the amount of matter required to construct a wormhole. Wormholes in the Shtanov-Sahni (SS) braneworld also have sufficiently low tidal forces, facilitating traversability. Additionally they are found to be stable and exhibit a repulsive geometry. We are left with the intriguing possibilty that both types of curvature singularity can be resolved with the SS model, which we discuss at the end of the concluding section.Comment: 31 Pages, 16 Figure

Toward Computationally Designed Self-Reporting Biosensors Using Leave-One-Out Green Fluorescent Protein

Leave-one-out green fluorescent protein (LOO<i>n</i>-GFP) is a circularly permuted and truncated GFP lacking the <i>n</i>th β-strand element. LOO7-GFP derived from the wild-type sequence (LOO7-WT) folds and reconstitutes fluorescence upon addition of β-strand 7 (S7) as an exogenous peptide. Computational protein design may be used to modify the sequence of LOO7-GFP to fit a different peptide sequence, while retaining the reconstitution activity. Here we present a computationally designed leave-one-out GFP in which wild-type strand 7 has been replaced by a 12-residue peptide (HA) from the H5 antigenic region of the Thailand strain of H5N1 influenza virus hemagglutinin. The DEEdesign software was used to generate a sequence library with mutations at 13 positions around the peptide, coding for approximately 3 × 10⁵ sequence combinations. The library was coexpressed with the HA peptide in <i>E. coli</i> and colonies were screened for in vivo fluorescence. Glowing colonies were sequenced, and one (LOO7-HA4) with 7 mutations was purified and characterized. LOO7-HA4 folds, fluoresces in vivo and in vitro, and binds HA. However, binding results in a decrease in fluorescence instead of the expected increase, caused by the peptide-induced dissociation of a novel, glowing oligomeric complex instead of the reconstitution of the native structure. Efforts to improve binding and recover reconstitution using in vitro evolution produced colonies that glowed brighter and matured faster. Two of these were characterized. One lost all affinity for the HA peptide but glowed more brightly in the unbound oligomeric state. The other increased in affinity to the HA peptide but still did not reconstitute the fully folded state. Despite failing to fold completely, peptide binding by computational design was observed and was improved by directed evolution. The ratio of HA to S7 binding increased from 0.0 for the wild-type sequence (no binding) to 0.01 after computational design (weak binding) and to 0.48 (comparable binding) after in vitro evolution. The novel oligomeric state is composed of an open barrel

Mispacking and the Fitness Landscape of the Green Fluorescent Protein Chromophore Milieu

The autocatalytic maturation of the chromophore in green fluorescent protein (GFP) was thought to require the precise positioning of the side chains surrounding it in the core of the protein, many of which are strongly conserved among homologous fluorescent proteins. In this study, we screened for green fluorescence in an exhaustive set of point mutations of seven residues that make up the chromophore microenvironment, excluding R96 and E222 because mutations at these positions have been previously characterized. Contrary to expectations, nearly all amino acids were tolerated at all seven positions. Only four point mutations knocked out fluorescence entirely. However, chromophore maturation was found to be slower and/or fluorescence reduced in several cases. Selected combinations of mutations showed nonadditive effects, including cooperativity and rescue. The results provide guidelines for the computational engineering of GFPs