Physical Sciences and Mathematics Commons^™

Investigating The Structural Complexity Of The Uch Knot Protein Using Trapped Ion Mobility Spectrometry – Mass Spectrometry, Shirley Hernandez

Undergraduate Research at FIU (URFIU) Conference

Knot proteins are rare proteins whose backbones adopt knotted configurations with a wide range of topologically interesting features [Lim, 2015]. They were regarded as structural impossibilities, until they were observed embedded in naturally-occurring proteins in the early 2000s [Taylor, 2000; Lim, 2003]. Ubiquitin carboxyl-terminal hydrolase, or UCH, is one of the most complex knot proteins studied to-date. UCH contains a knot structure composed of 5 crossings around the polypeptide chain (52 knot). Humans have four UCHs: UCH-L1, UCH-L3, UCH-L5 and BAP1. The UCH-L1 in particular is found in abundance in the nerve cells of the brain and is thought to …

Accessibility Of The Heme-Pocket In Hexa-Coordinate Globins, Maria Jose Santiago

Undergraduate Research at FIU (URFIU) Conference

Studies of fluorescence analogues of neuroglobin and cytoglobin to characterize conformational changes upon ligand binding Neuroglobin (Ngb) and cytoglobin (Cygb) are newly discovered hexacoordinate members of the globin family. Ngb is expressed in nerve cells and the retina and its main role is to protect cells under hypoxic–ischemic conditions. Cygb is expressed almost in all tissues in our body and it have tumor suppression role. Here we report a preparation of fluorescent analogues of Ngb and Cygb by replacing the non-fluorescent Fe protoporphyrin IX with a fluorescent probe, Zn protoporphyrin IX (ZnPPIX). The accessibility of the heme binding pocket in …

Novel Synthesis Of The Homologs Of Natural Nucleosides, Erika Lozano

Undergraduate Research at FIU (URFIU) Conference

Homologated nucleoside analogs are frequently studied for their antiviral activity. They are effective for the treatment of infectious species like the herpes virus, varicella-zoster viruses and retroviruses like HIV (Human Immunodeficiency Virus). Successful synthesis of these organic compounds has been achieved in the past through the transformation of the alcohol functionality into a carbonyl, often followed by Wittig reaction or Ardnt-Eistert homologation. Additionally, others have generated the homologated sugar moiety and then proceeded with the coupling to nucleobases. Researchers from Palacky University recently developed novel methodology for the homologation of primary and secondary alcohols. They generated the homologated esters of …

Synthesis Of (E)-2- Chlorhomovinyl Ribose To Examine The Mechanism Of 6-Chlorhomovinyl Adenosine, Mattew Pasteris

Undergraduate Research at FIU (URFIU) Conference

Nucleosides function as important agents in fundamental human metabolism and provide a broad range of activity in resulting modification of these nucleosides as functional prodrugs. Various modified nucleosides exhibit inhibitory activity towards enzymes and carry the possibility of containing anti-viral and anti-cancer properties. These properties are often exhibited by modifying the nucleobase moiety or the sugar moiety as synthesized novel nucleosides. In understanding my project aim, the sugar moiety of 6-chlorohomovinyl adenosine will be synthesized as the novel nucleoside (E)-2-chlorovinylribose to examine the nucleoside as the active component of 6-chlorohomovinyl adenosine. 6-chlorohomovinyl adenosine 1 demonstrates an active component …

Synthesis, Structure And Properties Of Two Symmetrical Oxorhenium(V) Dimers Derived From 4-Chloro Pyrazole, Juliana Cazzaniga

Undergraduate Research at FIU (URFIU) Conference

Oxorhenium(V) complexes are of considerable interest due to their multifaceted applications in the field of catalysis and in radiopharmaceuticals. The properties of these oxo-complexes can be “finetuned” through appropriate ligand choices. Our lab has been engaged in the development of coordination chemistry with pyrazoles due to their versatile binding modes. Pyrazole can bind a metal center in either monodentate or bridging bidentate fashion. Moreover, the 3, 4, and 5- positions on pyrazole ring offer the opportunity for suitable functionalization for desired applications. Although there has been a plethora of research work on transition metal coordination complexes involving pyrazole(s), there is …

The Application Of Ion Mobility Spectrometry And Ultrahigh Resolution Spectrometry For Analysis Of Anti- Microbial Peptides From Frog Skin Secretions, Benjamin Bokor

Undergraduate Research at FIU (URFIU) Conference

Frog skin secretions of antimicrobial peptides (AMPs) are of increasing interest due to the protection they impart against microbes. Such peptides offer the prospect of new and efficient sources of bacterial, fungal, and viral treatments. Recently, an epizootic of chytridiomycosis from the fungal pathogen Batrachochytrium dendrobatidis (Bd) caused the death of many amphibian species in the Andes. However, certain species of frogs such as Hypsiboas gladiator were able to survive. It is speculated that the survival of Hypsiboas gladiator is due to AMPs secreted from their skin.

The identification and characterization of these peptides is necessary for understanding the antimicrobial …

The Bioaccessibility Of Methylmercury In Rice And Fish, Michael Angelo Ojeda

Undergraduate Research at FIU (URFIU) Conference

Traditionally, fish is considered as the major source for humans exposed to methylmercury (MeHg), which is a highly toxic contaminant,-however recent study has shown that consumption of rice could be another MeHg exposure pathway to human beings. To evaluate the potential health risk caused by consumption of rice and rice product contraining MeHg, not only amount but also the bioaccessibility of MeHg in rice and rice products are required, because the amounts of methylmercury in samples is an overestimate and does not provide the accurate fraction that is mobilized from the food source. An in vitro digestive method was used …

Crude Oil Characterization Using Sara Fractionation And Gc-Ms, Nicholas Hernandez

Undergraduate Research at FIU (URFIU) Conference

Crude oil is a naturally-occurring liquid mixture, composed of hydrocarbons as well as oxygen, nitrogen and sulfur-containing compounds. While previous research has been able to identify broad differences between classes of crude oil, the elucidating the structure of compounds within oils remains elusive, especially for heavier compounds. To determine the composition of Boscan, a heavy crude oil, SARA fractionation was performed to separate the sample into 4 different classes of chemical compounds: saturated hydrocarbons, aromatic compounds, resins, and asphaltenes. A sample of oil was chromatographically separated on activated alumina using solvents of increasing polarity. Each fraction was analyzed using gas …

Molecular Modeling Of Conformational Space Of The Knot Protein Yibk, Daniel Gimeno

Undergraduate Research at FIU (URFIU) Conference

Structurally, proteins follow entropy favorable layouts that have high stability while performing their function. Knots are typically not observed due the amount of energy needed to form this structure outweighed the stability of the protein. Despite this, there are several rare proteins whose polypeptide backbone form knotted configurations. YibK is one such protein with a trefoil knot (e.g., 3-1 knot) in its carboxy terminus. These proteins reveal interesting topographies with less entropy than if the protein were compressed. In the present work, we studied the main interactions involved in the folding pathway of YibK, based on molecular dynamics (MD) simulations …

Software Assisted Molecular Elucidation Based On Timsft- Icr Ms/Ms Analysis Of Complex Mixtures, Carlos Acosta

Undergraduate Research at FIU (URFIU) Conference

The determination of the chemical structure of a molecule within a complex mixture is a challenging analytical problem. In the present work, we describe a workflow based on the analytical characterization of complex mixtures using complementary Trapped Ion Mobility Separation and ultra-high resolution FT-ICR mass separation (TIMS-FT-ICR MS/MS) for the analysis of complex mixtures (e.g., crude oils and dissolved organic matter). In particular, we take advantage of the high mobility resolution and high mass accuracy of TIMS-FT-ICR MS/MS to generate candidate structures using a custom developed theoretical workflow for Software Assisted Molecular Elucidation (SAME) based on the ion-neutral collision cross …

Terpene Adsorption Analysis In Tedlar Air Sampling Bags, Jeremy B. Guedes, Alison G. Simon

Undergraduate Research at FIU (URFIU) Conference

Tedlar® air sampling bags, which are composed of a polyvinyl fluoride polymer, are the EPA recommended bags used in several whole-air sampling and analytical methods for determining the presence of volatiles. Recent studies suggest that compounds which exhibit hydrogen bonding, as well as those that have a low vapor pressure, will tend to adsorb to the Tedlar® bags at a high rate. Furthermore, alkenes seem to display significant adsorption rates. For example, terpenes are a type of volatile organic compound (VOC) which contain the alkene functional group, and are found in oils produced by plants and some insects. In the …

Molecular Modeling Of The Conformational Space Of The Knot Protein Dehl, Virgilio Velasco

Undergraduate Research at FIU (URFIU) Conference

Knot conformations in proteins are folding patterns in the amino acid chain that lead to the formation of a knot via pathways that are not yet understood. The bacteria Pseudomonas putida expresses a protein known as DehI, that serves as a halo acid dehalogenase. The tertiary conformation of DehI in the native state is a Stevedore 6-1 knot, making it one of the most complex of its kind. In the present work, we studied the influence of the charge state on the folding dynamics of the knot protein DehI. Briefly, the conformational space of DehI was sampled by coarse molecular …

Reduction Of Sugar Lactones To Lactols With Super-Hydride, Andersson Sanchez

Undergraduate Research at FIU (URFIU) Conference

Reduction reactions are an important area of study in organic synthesis and are used to synthesize a variety of compounds. In particular, the reduction of lactones to their respective lactols or hemiacetals is important for the synthesis of biologically active modified carbohydrates which are often used in drug design. The reduction of the sugar-based lactones to their respective lactols with lithium triethyl borohydride (LiEt3BH) will be the focus of this project. The efficiency of this reagent to reduce sugar lactones to sugar hemiacetals (lactols) will be studied under different reaction parameters to develop an efficient protocol for its uses. The …

Examining The Effects Of The Binding Of The Carcinogen 4-Nitroquinoline-1-Oxide To Dna Phix174 On Dna Structure Using Mung Bean Nuclease And Topoisomerase I Assays, Elizabeth Tinoco

Undergraduate Research at FIU (URFIU) Conference

Optical titration studies, NMR studies and studies with DNA oligonucleotides have suggested that the carcinogen 4-nitroquinoline-1-oxide binds to DNA with marked sequence selectivity and cooperativity and that its binding affects the reactivity of enzymes with DNA. The observed cooperativity and enzyme effects suggest that the binding alters DNA structure. Using Mung Bean nuclease, an enzyme that recognizes regions of altered DNA structure, and Topoisomerase I, an enzyme which probes the unwinding of DNA, the binding effects of NQO to DNA phiX174 structure will be observed. To examine the effects of NQO on phiX 174, samples of supercoiled DNA are incubated …

The Investigation Of The Analysis Of Flakka, Carolina Brea

Undergraduate Research at FIU (URFIU) Conference

The synthetic drug craze, which began taking root just a few years ago, has been sweeping the nation. South Florida in particular has become an epicenter for synthetic drug use with its lively nightlife and vibrant club scenes. As of today, one of the most popular, and equally dangerous drugs, on the market is α-PVP, commonly known as Flakka. Flakka is unique in its domination of Miami-Dade and Broward communities while hardly appearing anywhere else in the country. Flakka’s influence in South Florida will be investigated in order to shed light on the origins of its popularity, its effects on …

Bio-Inspired Dinuclear Copper Oxygenation Catalysts: Synthesis, Characterization, And Reactivity Studies, Susana Herrera

Undergraduate Research at FIU (URFIU) Conference

Dinuclear copper assemblies are encountered in the active centers of various oxidases involved in the oxidation of organic substrates by dioxygen. The role of the protein backbone in these metalloproteins is to hold the two Cu-centers in close proximity as to allow a two-electron oxidation of the Cu (I) rest state to the Cu (II) catalytically active form. The objective is to synthesize a dinuclear copper complex by different approaches using a pyrazole ligand and introducing substituents on the bipy site. Furthermore, the investigation of the reactivity of the Cu (I) complex towards oxidants other than dioxygen and the reactivity …

Conformational Dynamics In Vertebrate Hexa-Coordinate Hemoglobins, Jessica Lopez

Undergraduate Research at FIU (URFIU) Conference

Cytoglobin, a recently discovered hemeprotein, is part of a globin protein family including hemoglobin, myoglobin, and neuroglobin. Numerous studies have reported the role of cytoglobin in tissue protection as well as a tumor suppression. However, the molecular mechanism of how cytoglobin carries out its protective functions under physiological and pathological conditions remains unclear. The cytoglobin structure includes a globin core that is homologous to myoglobin and a 20 amino acid residue extension at the N terminus and the C terminus that is unique among vertebrate globins. This study aims to provide a molecular insight into the cytoglobin folding mechanism with …

A Rapid And Sensitive High-Throughput Screening Method To Identify Compounds Targeting Protein–Nucleic Acids Interactions, Nicole Alonso, Roboan Guillen

Undergraduate Research at FIU (URFIU) Conference

DNA-binding and RNA-binding proteins are usually considered ‘undruggable’ partly due to the lack of an efficient method to identify inhibitors from existing small molecule repositories. Here we report a rapid and sensitive high-throughput screening approach to identify compounds targeting protein–nucleic acids interactions based on protein–DNA or protein–RNA interaction enzyme-linked immunosorbent assays (PDI-ELISA or PRI-ELISA). We validated the PDI-ELISA method using the mammalian highmobility- group protein AT-hook 2 (HMGA2) as the protein of interest and netropsin as the inhibitor of HMGA2–DNA interactions. With this method we successfully identified several inhibitors and an activator for HMGA2–DNA interactions from a collection of 29 …

Screening For Ampr-Specific Inhibitors To Combat P. Aeruginosa Infections, Kevin Morales

Undergraduate Research at FIU (URFIU) Conference

Pseudomonas aeruginosa, a Gram-negative bacterium, an opportunistic pathogen that infects individuals suffering from reduced immunity or damaged tissue. The treatment of these infections has become a major problem due to its increasing antibiotic resistance. Many multi-drug resistant isolates of P. aeruginosa can thwart most antibiotic classes including ?- lactams, fluoroquinolones, and aminoglycosides. Its ability to combat ?-lactams is in part due to expression of AmpC, a major chromosomally encoded ?-lactamase. The expression of ampC is positively regulated by AmpR. Besides antibiotic resistance, AmpR is an important regulator of various factors that are required for establishing acute and chronic infections. Loss …

Conformational Kinetics Study Of Mp-11 Using Tims-Ms And Molecular Dynamics, Christopher Harrilal, Jaroslava Miksovska, Emily R. Schenk

Undergraduate Research at FIU (URFIU) Conference

In the present work, we studied the conformational kinetics of microperoxidase 11 (MP-11), a digest fragment of cytochrome C that contains 11 amino acids with a covalently attached heme group. In particular, a novel technique recently developed at FIU in collaboration with Bruker Daltonics Inc. combined with theoretical calculation was used for the characterization of MP- 11 conformational space [1-3]. Accurate ion-neutral collision cross sections were measured for all MP-11 generated charge states. Since MP-11 (like cytochrome C) undergoes conformational changes as a function of the solvent state, MP-11 ions were produced by electrospray ionization (ESI) in order to preserve …

Validation Of An Analytical Method For The Identification Of Smartwater Csi Forensic Marking Technology, Demi Moreda, Claudia Martinez

Undergraduate Research at FIU (URFIU) Conference

SmartWater is a chemical taggant used as a crime deterrent. The chemical taggant is a colorless liquid that fluoresces yellow under ultra-violet (UV) light and contains distinctive, identifiable and traceable elemental composition. For instance, upon a break and entry scenario, the burglar is sprayed with a solution that has an elemental signature custom-made to a specific location. The residues of this taggant persist on skin and other objects and can be easily recovered for further analysis. The product has been effectively used in Europe as a crime deterrent and has been recently introduced in South Florida. In 2014, Fourt Lauderdale …