Deterministic design of peptide-membrane interactions

Antimicrobial peptides (AMPs) are present in virtually every multi-cellular organism and comprise an important component of the innate host defense system. Collectively, AMPs have broad spectrum and selective microbicidal effects. A general mechanism of AMP activity is destabilization of the physical integrity of cell plasma membranes leading to depolarization, leakage, and eventual cell death. This thesis provides a detailed molecular model how AMPs destabilize membranes specifically, based upon their fundamental structural motif: they are amphipathic and cationic. Generic electrostatic and hydrophobic interactions between a cationic, amphipathic AMP and a cell membrane lead to strong binding between the peptide and membrane and subsequent partial insertion of the peptide into the bilayer. The physical chemistry of AMPs leads to a whole taxonomy of local membrane distortions, specific combinations of which are topologically active and can lead to membrane destabilization. AMPs permeabilize model bacterial membranes but not model eukaryotic membranes by selectively generating topologically active saddle-splay ('negative Gaussian') curvature in membranes rich in negative curvature lipids and anionic lipids, compositions characteristic of bacterial cell membranes. A mechanism of action based on saddle-splay membrane curvature generation is broadly enabling, since it is a necessary condition for processes such as pore formation, blebbing, budding, vesicularization, all of which destabilize the barrier function of cell membranes. The topological requirement for saddle-splay curvature places constraints on the amino acid compositions of membrane disruptive peptides. In AMPs decreasing arginine content is offset by a simultaneous increase in lysine and hydrophobic content. This 'saddle-splay curvature design rule' is consistent with the amino acid compositions of 1,080 known cationic AMPs. Furthermore, good correspondence is observed between membrane curvature generation and the microbicidal profiles of prototypical AMPs, suggesting that curvature generation is an indicator of AMP activity. Finally, this thesis concludes with brief discussions on the possibility of other AMP design rules, as well as the presence of amphipathic domains in other curvature generating proteins which generate similar or distinct curvatures to AMPs depending on their structural motifs

Multiplicity one for LL-functions and applications

We give conditions for when two Euler products are the same given that they satisfy a functional equation and their coefficients satisfy a partial Ramanujan bound and do not differ by too much. Additionally, we prove a number of multiplicity one type results for the number-theoretic objects attached to $L$-functions. These results follow from our main result about $L$-functions

Characterizations of the Saito-Kurokawa lifting: a survey

There are a variety of characterizations of Saito-Kurokawa lifts from elliptic modular forms to Siegel modular forms of degree 2. In addition to giving a survey of known characterizations, we apply a recent result of Weissauer to provide a number of new and simpler characterizations of Saito-Kurokawa lifts

Hawking radiation - quasi-normal modes correspondence and effective states for nonextremal Reissner-Nordstr\"{o}m black holes

It is known that the nonstrictly thermal character of the Hawking radiation spectrum harmonizes Hawking radiation with black hole (BH) quasi-normal modes (QNM). This paramount issue has been recently analyzed in the framework of both Schwarzschild BHs (SBH) and Kerr BHs (KBH). In this assignment, we generalize the analysis to the framework of nonextremal Reissner-Nordstr\"{o}m BHs (RNBH). Such a generalization is important because in both SBHs and KBHs an absorbed (or emitted) particle has only mass. Instead, in RNBHs the particle has charge as well as mass. In doing so, we expose that for the RNBH, QNMs can be naturally interpreted in terms of quantum levels for both particle emission and absorption. Conjointly, we generalize some concepts concerning the RNBH's "effective states".Comment: 16 pages, accepted for publication in Advances in High Energy Physic

Further Investigation of a Novel Rhabditid Nematode

Nematodes are among the most numerous and widespread animals on earth. The nematode Caenorhabditis elegans is a well-established model organism used for a wide-variety of studies ranging from biomedical to behavioral to ecological, and more. While C. elegans is well characterized, there are thousands of different species of nematodes, many of which have not been studied. We are characterizing several Rhabditid nematodes isolated in association with millipedes from both Ohio and Florida. Sequence analysis of rDNA genes supports that one of the species of worms we isolated is Oscheius myriophila. Other worms we isolated are similar, but we believe may be a distinct species that for now we are calling Rhabditis sp.. We are using a combination of molecular, phenotypic and genetic approaches to characterize these worms and to establish if they represent a previously undescribed species. One of our primary approaches is to use scanning electron microscopy (SEM) to visualize key structural features. We developed a method for SEM and have gotten detailed images to compare C. elegans to O. myriophila to our Rhabditis sp. worms. We are also using light microscopy to capture images and do measurements critical for species identification. Finally, we are conducting crosses. Previous work in the lab has resulted in conflicting evidence about whether O. myriophila and Rhabditis sp. can produce normal offspring, so we are extending these studies. Together with examining embryonic development in these worms, we believe our studies will help us to better understand this diverse phylum of animals

SNAC-tag for sequence-specific chemical protein cleavage.

Site-specific protein cleavage is essential for many protein-production protocols and typically requires proteases. We report the development of a chemical protein-cleavage method that is achieved through the use of a sequence-specific nickel-assisted cleavage (SNAC)-tag. We demonstrate that the SNAC-tag can be inserted before both water-soluble and membrane proteins to achieve fusion protein cleavage under biocompatible conditions with efficiency comparable to that of enzymes, and that the method works even when enzymatic cleavages fail

Dynamics of confined water reconstructed from inelastic x-ray scattering measurements of bulk response functions

Nanoconfined water and surface-structured water impacts a broad range of fields. For water confined between hydrophilic surfaces, measurements and simulations have shown conflicting results ranging from “liquidlike” to “solidlike” behavior, from bulklike water viscosity to viscosity orders of magnitude higher. Here, we investigate how a homogeneous fluid behaves under nanoconfinement using its bulk response function: The Green's function of water extracted from a library of S(q,ω) inelastic x-ray scattering data is used to make femtosecond movies of nanoconfined water. Between two confining surfaces, the structure undergoes drastic changes as a function of surface separation. For surface separations of ≈9 Å, although the surface-associated hydration layers are highly deformed, they are separated by a layer of bulklike water. For separations of ≈6 Å, the two surface-associated hydration layers are forced to reconstruct into a single layer that modulates between localized “frozen’ and delocalized “melted” structures due to interference of density fields. These results potentially reconcile recent conflicting experiments. Importantly, we find a different delocalized wetting regime for nanoconfined water between surfaces with high spatial frequency charge densities, where water is organized into delocalized hydration layers instead of localized hydration shells, and are strongly resistant to `freezing' down to molecular distances (<6 Å)