Thesis (Ph. D.)--University of Washington. / Bibliography: l. 186-196.

The purpose of this study was to evaluate the influence of horizontal moisture fluxes from Atmospheric Rivers (ARs) on extreme precipitation (EP) events in the continental United States (CONUS). Climatological results for both EP, objectively defined using a peaks-over-threshold and block maxima approach, and ARs were processed and analyzed for co-occurrence. EP analyses produced a positive linear trend in magnitude, determined through the block maxima approach, in the Central US and a positive linear trend in frequency, determined by the peaks-over-threshold approach, predominantly for the Northern half of the CONUS. AR results show over 70 AR days throughout the country, and a linear trend of 10 less days per decade in the Central US. Results of the co-occurrence analysis suggest an increasing trend of about one instance of co-occurrence per decade throughout much of the Eastern Coast, Midwest and Pacific Northwest, with a corresponding negative linear trend of about one instance of co-occurrence per decade for much of the Southwest US to Louisiana. Throughout the world, the study of EP, and the careful analysis of its behavior, and possible amplification sources such as ARs, at the national and regional scale is imperative to obtain a comprehensive understanding of hydrometeorological impacts.

Cone snails are venomous marine gastropods that produce venom rich in neuroactive peptides, called conopeptides. The majority of published work on conopeptides has been from fish-hunting and mollusk-hunting cone snails. The work in this dissertation focuses on the discovery and characterization of novel conopeptides from the venom of worm-hunting cone snails. Eleven novel conopeptides have been isolated and biochemically characterized from the venom of C. nux using high performance liquid chromatography for the isolation and purification, and mass spectrometry and nuclear magnetic resonance (NMR) spectroscopy were used for the biochemical characterization of the conopeptides. Nano-NMR spectroscopy was used as a tool to elucidate the three-dimensional structures of four conotoxins using native quantities of peptide isolated from the venom of C. nux, C. villepinii, and C. regius. In addition, the sequence-specific assignments and molecular model of a conotoxin from the venom of C. flo ridanus was also completed. The first chapter reviews the known conotoxin three-dimensional structures and cystine-constrained frameworks. The second chapter presents the mini-M conotoxins isolated from the venom of C. nux. The third chapter presents the three-dimensional NMR solution structure of a mini-M conotoxin from the venom of C. regius. The fourth chapter presents the cysteine-free conopeptides isolated from the venom of C. nux; conorfamide-nux1, a RFamide-related peptide, and nux770, a short pentapeptide. The fifth chapter presents the T-superfamily conotoxins isolated from the venom of C. nux, as well as the three-dimensional solution structure of one of the T-superfamily conotoxins. The sixth chapter presents the NMR solution structure of the first conotoxin with a cysteine-stabilized helix-loop-helix fold. / Finally, the seventh chapter presents the O-superfamily conotoxins isolated from the venom of C. nux, as well as the three-dimensional solution structure of one of the O- superfamily conotoxins with an unusually knotted fold. This work shows the vast structural diversity of peptides that cone snails continue to engineer. / by Sanaz Dovell. / Thesis (Ph.D.)--Florida Atlantic University, 2010. / Includes bibliography. / Electronic reproduction. Boca Raton, Fla., 2010. Mode of access: World Wide Web.

by Fred. C. Pflueger. / Thesis (Ph.D.)--Florida Atlantic University, 2008. / Includes bibliographical references at end of each chapter. / Cone snails are predatory marine gastropods that use venom for means of predation and defense. This venom is a complex mixture of conopeptides that selectivity binds to ion channels and receptors, giving them a wide range of potential pharmaceutical applications. Conus brunneus is a wide spread Eastern Pacific cone snail species that preys upon worms (vermivorous). Vermivorous cone snails have developed very specific biochemical strategies for the immobilization of their prey and their venom has not been extensively studied to date. The main objective of this dissertation is the characterization of novel conopeptides isolated from Conus brunneus. Chapter 1 is an introduction and background on cone snails and conopeptides. Chapter 2 details the isolation and characterization of a novel P-superfamily conotoxin. Chapter 3 presents the 3D solution structure of the novel P-superfamily conotoxin. Chapter 4 details the isolation and characterization of two novel M-superfamily conotoxins. Chapter 5 covers the use of nano-NMR to characterize a novel P-superfamily conotoxin using nanomole quantities of sample. Chapter 6 is a reprint of a paper published in the Journal of the American Chemical Society in which we combined and implemented techniques developed in the previous chapters to report the presence of D-(Sd(B-Hydroxyvaline in a polypeptide chain. This dissertation contains the first reported work of a P-superfamily structure obtained directly from the crude venom therefore accurately representing native post-translational modifications. In this paper, crude cone snail venom was characterized by: high performance liquid chromatography, nuclear magnetic resonance spectroscopy, nanonuclear magnetic resonance spectroscopy, mass spectrometry, amino acid analysis, Edman degradation sequencing, and preliminary bioassays.

The venom of marine gastropods belonging to the genus Conus has yielded numerous structurally and functionally diverse peptidic components. The increase variety of bioactive peptides identified in cone snail venoms is the product of the variety of molecular adaptations taken by Conus species in evolving neuroactive molecules to suit their diverse biological purposes. Toxins from cone snails are classified into two major groups. One group consists of disulfide-rich peptides commonly termed conotoxins; the second group comprises peptides with only one disulfide bond or none. In this work, we present the discovery and characterization from the marine snails C. planorbis and C. ferrugineus. Both species are commonly found in the Indo-Pacific region and are very similar and is not distinguishable by size and shape of the shell. Novel P and T-Supefamiles were found in both species along with small linear peptides with have a high frequency of tyrosine residues. Each chapter contains a detailed look at the discovery process for the isolation and characterization of C. planorbis and C. ferrugineus. At discussion part, we also compared the peptides isolated in this work with other peptides from the literature. / Includes bibliography. / Thesis (M.S.)--Florida Atlantic University, 2014. / FAU Electronic Theses and Dissertations Collection

Thesis (Ph.D.) - University of Queensland, 2006. / Includes bibliography.

The numerous toxic peptides, called conotoxins (Olivera et al 1990, 1991), that marine cone snails produce and use for capturing prey, deterring predators and presumably for other biotic interactions, are known to target several classes of mammalian voltage and ligand gated receptors with excellent specificity and good receptor-subtype discrimination (Terlau and Olivera 2004). This fine specificity has placed upon the conotoxins a great deal of scientific and medical interest, and cone snail venom is currently considered a vast natural resource of peptides that have the potential of eventually benefiting the prognosis of many human afflictions, either directly as therapeutics or indirectly as research tools. In this regard, the characterization of conotoxins and the identification of the specific receptors they target remains an actively pursued area of study in several countries. There has been an active effort to characterize peptides from Indian populations of cone snails that has resulted in several reports describing novel peptides from them. This thesis is part of these ongoing efforts and largely relates to the isolation and identification of cDNA sequences of precursor conotoxins from cone snails prospected in India. One final section of the thesis is concerned with the assessment of secondary structure predictions of conotoxin genes and discusses how such formations may determine the regions where variations and conservations are taking place among the conotoxins. Structure and Outline of the thesis Chapter 1 is an overview of the cone snails and the conotoxins that they produce. There is some emphasis on the variability and diversity that are found among conotoxins since these are some of the aspects that are discussed in subsequent chapters. Chapter 2 describes the identification of new cDNA sequences isolated from the relatively rare Indian population of the piscivorous cone snail, Conus achatinus. This species was chosen for the study since it is one of the few piscivorous cone species that have been reported from the coastlines of India. However, the limited availability of specimens belonging to this species precluded a direct study of individual venom peptides from it. To overcome this bottleneck of specimen availability, a molecular biological route to obtain cDNA sequences of superfamily specific conotoxins was considered. The steps of PCR mediated amplification and cloning that are incorporated within the procedures of preparing cDNA for sequencing, to some extent overcome the limitations of large sample requirements and in this respect have been used to investigate conotoxin sequences from this species. Using the cDNA route and comparative sequence analysis, it has been possible to identify 5 novel O-superfamily conotoxin sequences from C.achatinus. The precursor sequences have been classified as delta, omega and omega-like conotoxins that potentially target voltage gated sodium and calcium channels. A parallel study trying to detect the specific cDNA related conotoxins using mass spectrometry (MALDI-MS) as a screening tool is also discussed. In this search it has been possible to detect 3 of the 5 cDNA related peptides using small amounts of unpurified venom. The cDNA and mass spectrometric results show that precursor sequences of conotoxins from a relatively rare population of Conus species can be successfully identified and the existence of the peptides that they specify verified through the combined approach of obtaining cDNA sequences and MALDI-MS screening of total unpurified venom. Chapter 3 similarly relates to the isolation of cDNA sequences from a single specimen of the vermivorous cone snail, Conus monile. Three precursor sequences, Mo3.1, Mo15.1 and Mo16.1, of M-superfamily conotoxins have been isolated from this species out of which two precursors (Mo15.1 and Mo16.1) show unexpected cysteine distribution patterns within their putative mature toxin regions. In addition, several other features of these precursors do not fit into the description of known M-superfamily conotoxins. The sequence analyses and the deviations that have been noted among these sequences are described. Chapter 4 describes the efforts that have gone in towards detecting one of these deviant conotoxins (Mo16.1) in the venom of Conus monile using MALD-MS as a means for screening the venom. A peptide having the Mo16.1 predicted mass (1512 Da) has been detected as a minor component of the venom. The chapter describes additional mass-spectrometric experiments that strongly support the assignment of this detected peak being the specific Mo16.1 peptide. A speculative discussion on the role of minor peptide deviants such as the Mo16.1 peptide concludes the chapter. Chapter 5 is concerned with the assessment of secondary structure predictions of conotoxin genes and discusses how such formations may determine the regions where variations and conservations are taking place among the conotoxins. The comparative analysis of DNA sequences corresponding to the variable mature conotoxins reveal that it is possible to differentiate mature conotoxin sequences into variable and conserved regions. Using the prediction program mFold (Markham and Zuker 2005) it has been noted that regions of the DNA encompassing the conserved codons (including the highly conserved cysteine codons) correspond to predicted secondary structures of higher stabilities. In contrast the regions of the conotoxin that have a higher degree of variation correlate to regions of lower stability. These correlations have been observed quite consistently across several classes of conotoxins that show different patterns of variability and conservation in their sequence and representing different categories of conotoxins i.e intra species, inter species, and hyperconserved conotoxins. The observation on these co-relations allows for a simple model of inaccessibility of a mutator to these relatively structured regions of the conotoxin gene (including the cysteine codons) allowing them a relative degree of resistance towards change. Chapter 6 summarizes the findings of the thesis, briefly recapitulating the discussion of the individual chapters from a broader perspective.

Major constituents of the venom of various animals are peptidogenic in nature. Marine snails belonging to the species Conus are venomous predators that use small, structurally constrained peptides present in their venom for prey capture and defense. It is known that ~500 Conus species are present in nature and the venom of each of these Conus species is a complex mixture of nearly 100 peptides accounting for > 50,000 peptides with little overlap among the different species. The peptides isolated from the venom of Conus species are commonly known as conotoxins or conopeptides. Some of the common targets of these peptides include the different ion channels like Na+, K+, and Ca2+, and receptor subtypes such as nicotinic acetylcholine and NMDA receptors. The ion channels and receptor subtypes were targeted by conopeptides with high degree of specificity and selectivity. The structural information on the peptides from cone snails can prove to be a valuable starting tool for the understanding of the function of different ion channels and hence in the design of neuropharmacologically active drugs. Conotoxins are disulfide-rich peptides and the number of disulfide generally ranges from two to five. Based on the arrangement of cysteines in their primary sequence, they are classified into different superfamilies. The signal sequences of the precursors belonging to a particular superfamily are highly conserved and hence the members within the same family have, in common, the unique disulfide arrangement and pharmacological activity. Conotoxins are classified into eleven superfamilies till date. In order to understand the underlying the principles involved in the action of these peptides on different ion channels, one needs to know the three-dimensional structures which, in potential, will help in the identification of the pharmacophores responsible for the observed pharmacological activity. With the aim of studying the structure-activity relationships found among the conotoxins, we have initiated a study on the peptides isolated from the marine snails found in the Indian coastal waters. This thesis is focused in the structural studies of the peptide toxins from marine cone snails and a terrestrial scorpion. The tool used for the structural studies of these peptide toxins is Nuclear Magnetic Resonance Spectroscopy. Chapter 1 provides an overview of the peptide toxins found among various animal species with more emphasis on conotoxins and scorpion toxins. In addition, the rationale behind the present study has also been explained. Chapter 2 describes the structure determination of two conopeptides isolated from Conus amadis, δ-Am2766 and Am2735, which are active on mammalian sodium channels. The structural aspects and comparison with other known conopeptides belonging to the same superfamily as that of these two peptides have also been described. Solution NMR studies of Ar1446 and Ar1248, two conopeptides isolated from the species Conus araneosus have also been studied using Homonuclear NMR methods. Ar1446 is a three disulfide-bonded peptide. Our studies have revealed that this peptide has a novel disulfide connectivity not previously observed in the M superfamily or any other superfamily of conotoxins. The structural features of Ar1446 will be described along with the NMR studies on two-disulfide bonded peptide, Ar1248, belonging to the A-superfamily of conotoxins. The main problem faced in the kind of study of peptides isolated from natural sources is the amount that can be isolated and purified to homogeneity. In order to obtain large quantities of peptides, we have successfully used Cytochrome b5 as fusion host to clone, over express and purify these peptides using recombinant methods. The use of recombinant methods has aided in the preparation of isotopically enriched peptides. The use of cyt b5 as fusion host for the large scale production of some of the peptides from Indian marine snails is described in Chapter 4. A novel pharmacologically active linear peptide, Mo1659 isolated from Conus monile, have been studied using Heteronuclear NMR methods. This peptide was cloned, over expressed and purified using Cytochrome b5 as a fusion host. Another linear peptide, Mo1692 (also from Conus monile), has been prepared using the same method and was studied using Homonuclear NMR methods. Both these peptides were liberated from the fusion host using cyanogen bromide cleavage and were subsequently purified using RP-HPLC. The results of the biosynthetic preparation and NMR studies of these two peptides have been described in Chapter 5. Chapter 6 describes the solution structure determination of a novel scorpion toxin characterized in the venom of the Indian red scorpion Buthus tamulus. The cloning, over expression, folding and purification of BTK-2 is described here. The structure and the function of this recombinantly produced BTK-2 will also be described.

Predatory shallow-water tropical marine snails within the genus Conus are estimated to consist of up to 700 species. These carnivorous mollusks have devised efficient venom harpoon-like radular teeth that allow them to predominantly incapacitate polychaete annelids (vermivores), in some cases fish (piscivores), or other mollusks (molluscivores) as an envenomation survival strategy for feeding, defense, and competitor deterrence. The venom of each Conus species contains a distinctive assortment of over 50 diversified disulfide-rich conotoxins with varied pharmacological specificities that selectively inhibit the function of ion channels (Ca2+, Na+, K+) or nicotinic acetylcholine receptors (nAChRs) involved in the animal neurotransmission. Across the genus Conus, the conotoxins represent an extensive array of ion channel blockers each showing an exquisite selectivity to distinguish between channels / receptors and even particular their subtypes. Novel conotoxins detected in the molecular neurobiological approach, providing chemists and pharmacologists a vast library (>50,000 individual toxins) of conotoxins have been further screened for their abilities to modify the responses of tissues to pain stimuli as a first step in describing their potential as lead compounds for novel drugs. In this article, we present the natural history of the Conus biology as well as the nomenclature, classification, structure, neurotoxicological mechanisms, post-translational modification, and pharmaceutical applications of conotoxins. In addition, we also set up the bioinformatic database and search engine about hitherto-identified name and distribution of Conus species and neuropharmacological mechanism, accession number, sequence, and 3D structure of conotoxins and provide researchers advantageous tools for further investigation.

Venomous animals have evolved a vast array of peptide toxins for prey capture and defense. Nature has evolved the venoms into a huge library of active molecules with high selectivity and affinity, which could be explored as therapeutics or serve as a template for drug design. The individual components of venom i.e. toxins are used in ion channel and receptor studies, drug discovery, and formulation of insecticides. ‘Venominformatics is a systematic bioinformatics approach in which classified, consolidated and cleaned venom data are stored into repositories and integrated with advanced bioinformatics tools and computational biology for the analysis of structure and function of toxins.’ Conus peptides (conopeptides), the main components of Conus venom, represent a unique arsenal of neuropharmacologically active molecules that have been evolutionarily tailored to afford unprecedented and exquisite selectivity for a wide variety of ion-channel subtypes and neuronal receptors. Ziconotide (ω-conotoxin MVIIa from Conus magus (Magician's cone snail)), is proven as an intrathecally administered N-type calcium channel antagonist for the treatment of chronic pain (U.S. Food and Drug Administration. Center for Drug Evaluation and Research) attesting to the pharmaceutical importance of Conus peptides. From the point of view of protein sequence and structure analysis, conopeptides can serve as attractive systems for the studies in sequence comparison, pattern extraction, structure–function correlations, protein–protein interactions and evolutionary analysis. Despite their importance and extensive experimental investigations on them, they have been hardly explored through in silico methods. The present thesis is perhaps the first attempt at deploying a multi-pronged bioinformatics approaches for studies in the burgeoning field of conopeptides. In the process of sequence-structure-function studies of conopeptides, we have created several sequence patterns of different conopeptide families and these have been accepted for inclusion in international databases such as PROSITE, the first pattern database to have been developed (http://www.expasy.org/prosite) and INTERPRO (http://www.ebi.ac.uk/interpro). More importantly, we have carried out extensive literature survey on the peptides for which we have defined the patterns to create PROSITE compatible documentation files (PDOC6004, PDOC60025 and PDOC60027). We have also created a series of sequence patterns and associated documentation filesof pharmaceutically promising peptides from plants and venomous animals (including O-conotoxin and P-conotoxin superfamily members) with knottin scaffold. Knottins provide appealing scaffolds for protein engineering and drug design due to their small size, high structural stability, strong sequence tolerance and easy access to chemical synthesis. The sequence patterns and associated documentation files created by us should be useful in protein family classification and functional annotation. Even though patterns might be useful at the family level, they may not always be adequate at the superfamily level due to hypervariability of mature toxins. In order to overcome this problem, we have demonstrated the applicationos of multi-class support vector machines (MC-SVMs) for the successful in silico classification of the mature conotoxins into their superfamilies. TheI- and J-conotoxin-superfamily members were analyzed in greater detail. On the basis of in silico analysis, we have divided the 28 entries previously grouped as I-conotoxin superfamily in UniProtKB/Swiss-Prot (release 49.0) into I1 and I2 superfamilies inview of their having two different types of signal peptides and exhibiting distinct functions. A comparative study of the theoretically modeled structure of ViTx from Conus virgo, a typical member of I2-conotoxin superfamily, reveals the crucial role of C-terminal region of ViTx in blocking therapeutically important voltage-gated potassium channels. Putative complexes created by us of very recently characterized J-superfamily conotoxin p11-4a with Kv1.6 suggest that the peptide interacts with negatively charged extracellular loops and pore-mouth of the potassium channel and blocks the channel by covering the pore as a lid, akin to previously proposed blocking mechanism of kM-conotoxin RIIIK from Conus radiatus to Tsha1 potassium channel. This finding provides a pointer to experimental work to validate the observations made here. Based on differences in the number and distribution of the positively charged residues in other conopeptides from the J-superfamily, we hypothesize different selectivity profile against subtypes of the potassium channels for these conopeptides. Furthermore, the present thesis reports the application of order-statistic filters and hydrophobicity profiles for predicting the location of membrane-spanning helices. The Proposed method is in particular effective for the class of helical membrane proteins, namely the therapeutically important voltage-gated ion channels, which are natural targets of several conotoxins. Our suggested ab initio approach is comparatively better than other spatial filters, confirming to the efficacy of including the concept of order or ranking information for prediction of TM helicdes. Such approaches should be of value for improved prediction performance including in large-scale applications. In addition, anlaysis has been carried out of the role of context in the relationship between form and function for the true PDB hits of some nonCys-rich PROSITE patterns. We have found specific examples of true hits of some PROSITE patterns displaying structural plasticity by assuming significantly different local conformation, depending upon the context. The work was carried out as a part of the research interest in our group in studying structural and other features of protein sequence patterns. The Contributions of the candidate to venominormatics include, creation of protein sequence patterns and information highlighting the importance of the patterns as gleaned from the lteratures for family classification: profile HMM and MC-SVMs for conotoxin superfamily classification; in silico characterization of I1 and I2 conotoxin superfamilies; studies of interaction with Kv1 channels of typical members of I2 and 3 conotoxin superfamilies and development of improved methods for detecting membrane-spanning helices. Chapter I starts with a brief account of venominformatics; bioinformatics for venoms and toxins. Chapter 2 presents a regular expression based classification of Conus peptides. Chapter 3 revisits the 28 entries previously grouped as I-conotoxin superfamily in UniProt Swiss-Prot knowledgebase (release 49.0) having four disulfide bonds with Cys arrangement C-C-CC-CC-C-C and they inhibit or modify ion channels of nerve cells. Chapter 4 describes pseudo-amino acid composition and MC-SVMs approach for conotoxin superfamily classification. Chapter 5 describes in silico detection of binding mode with Kv1.6 channel of J-superfamily conotoxin p114a from bermivorouos cone snail, Conus planorbis. Chapter 6 presents a comparative sequence-structure-function analysis of naturally occurring Cys-rich peptides having the Knottin or inhibitor cystine knot(ICK) scaffold, from different plants and venomous animals based on information available in the knottin database(http://knottin.cbs.cnrs.fr/). Chapter 7 describes the application of order-statistic filters and hydrophobicity profiles for detecting membrane-spanning helices. Chapter 8 describes the role of context in the relationship between form and function for the true PDB hits of some non Cys-rich PROSITE patterns. Chapter 9 summaries the important findings of the present studies on naturally occurring bioactive Cys-rich peptides with emphasis on Conus peptides and their interactions with respective target such as voltage-gated ion channels.