Physical Sciences and Mathematics Commons^™

Using Protein Design To Understand The Role Of Electrostatic Interactions On Calcium Binding Affinity And Molecular Recognition, Lisa Michelle Jones

Chemistry Dissertations

Calcium regulates many biological processes through interaction with proteins with different conformational, dynamic, and metal binding properties. Previous studies have shown that the electrostatic environment plays a key role in calcium binding affinity. In this research, we aim to dissect the contribution of the electrostatic environment to calcium binding affinity using protein design. Many natural calcium binding proteins undergo large conformational changes upon calcium binding which hampers the study of these proteins. In addition, cooperativity between multiple calcium binding sites makes it difficult to study site-specific binding affinity. The design of a single calcium binding site into a host system …

Determining The Site Specific Metal Binding And Structural Properties Of Ef-Hand Protein Using Grafting Approach, Hsiau-Wei Lee

Chemistry Dissertations

Calmodulin is an essential EF-hand protein with a helix-loop-helix calcium binding motif. Understanding Ca(II) dependent activation of calmodulin and other EF-hand proteins is limited by Ca(II)-induced conformational change, multiple and cooperative binding of Ca(II) ions, and interactions between the paired EF-hand motifs. The goal of this research project is to probe key determinants for calcium binding properties and pairing interactions at the site specific level using a grafting approach and high resolution NMR. An individual Ca(II) binding site of the EF-hand motifs of calmodulin was grafted into a non-calcium dependent protein, CD2, to bypass limitations associated with natural EF-hand proteins …

Structure And Energetics Of Rna - Protein Interactions For Hiv Rreiib Targeting Zinc Finger Proteins., Subrata H. Mishra

Chemistry Dissertations

RNA - protein interactions constitute a vital part of numerous biochemical processes. In the HIV life cycle, the interaction of the viral protein Rev and the Rev Responsive Element (RRE), a part of unspliced HIV RNA, is crucial for the propagation of infectious virions. Intervention of this interaction disrupts the viral life cycle. Rev - RRE interaction initially occurs at a high affinity binding site localized to a relatively small stem loop structure called RREIIB. This binding event has been well characterized by a variety of biochemical, enzymatic and structural studies. Our collaborators have previously demonstrated the efficacy of zinc …

Application Of Term-Rewriting Grammar In Chemical Reaction Prediction, Patra Volarath

Chemistry Dissertations

Synthesis planning is a critical process in chemical design. A number of computer programs have been developed to assist the chemists with this procedure. Most of the programs utilize combinations of computational approaches. These have been successfully applied to a number of the synthesis predictions. However, they require numerous rules to screen for potential targets, as well as to keep the system from reaching the combinatorial explosion. This results in the advanced algorithms becoming more complex and parameter-sensitive. This can be problematic, particularly in the cases in which a large number of the compounds are to be handled, because it …

Application Of Computer-Aided Drug Discovery Methodologies Towards The Rational Design Of Drugs Against Infectious Diseases, Prashanth Athri

Chemistry Dissertations

Computer-aided drug discovery involves the application of computer science and programming to solve chemical and biological problems. Specifically, the QSAR (Quantitative Structure Activity Relationships) methodology is used in drug development to provide a rational basis of drug synthesis, rather than a trial and error approach. Molecular dynamics (MD) studies focus on investigating the details of drug-target interactions to elucidate various biophysical characteristics of interest. Infectious diseases like Trypanosoma brucei rhodesiense (TBR) and P. falciparum (malaria) are responsible for millions of deaths annually around the globe. This necessitates an immediate need to design and develop new drugs that efficiently battle these …

I. Characterization Of Sulfonated Phthalocyanines By Mass Spectrometry. Ii. Characterization Of Siaa, A Streptococcal Heme-Binding Protein Associated With A Heme Abc Transport System, Brian R. Sook

Chemistry Dissertations

Sulfonated phthalocyanines were characterized using capillary electrophoresis and mass spectrometry. Derivatives investigated included the copper, cobalt, zinc and metal-free sulfonated phthalocyanines. The electropherograms of commercially available copper phthalocyanine-3,4',4'',4'''-tetrasulfonic acid and 4,4',4'',4'''-tetrasulfonic acid were very different, consistent with the latter compound having a structure that is not fully sulfonated. Matrix-assisted laser desorption/ionization (MALDI) and electrospray ionization (ESI) were used to characterize the sulfonated phthalocyanines. Mass spectral evidence was obtained for a pentasulfonated species of both the metal-free phthalocyanine and zinc phthalocyanine when these species were made by sulfonation of the metal-free phthalocyanine (followed by zinc insertion in the latter case). Many …

Binding Studies Of Near Infrared Cyanine Dyes With Human Serum Albumin And Poly-L-Lysine Using Optical Spectroscopy Methods, Amy Dawn Watson

Chemistry Dissertations

The sensitivity of biological studies performed between 190 and 650 nm is greatly reduced due to the autofluorescence of biomolecules and impurities in this region. Therefore, the enhanced signal-to-noise ratios encountered at longer wavelengths makes biological analysis within the near infrared (NIR) region from 650 nm to 1100 nm far more advantageous. This dissertation describes the noncovalent binding interactions of near-infrared (NIR) carbocyanine dyes with human serum albumin (HSA) and poly-L-lysine (PLL) using UV-Vis/NIR absorption spectroscopy, emission spectroscopy, circular dichroism (CD), and fluorescence detected circular dichroism (FDCD). The optical spectroscopy methods used in this work are described in detail in …

Exploring The Role Of Calcium Ions In Biological Systems By Computational Prediction And Protein Engineering, Yubin Zhou

Chemistry Dissertations

Ca2+, a signal for death and life, is closely involved in the regulation of numerous important cellular events. Ca2+ carries out its function through its binding to Ca2+-receptors or Ca2+-binding proteins. The EF-hand protein, with a helix-loop-helix Ca2+-binding motif, constitutes one of the largest protein families. To facilitate our understanding of the role of Ca2+ in biological systems (denoted as calciomics) using genomic information, an improved pattern search method (http://www.chemistry.gsu.edu/faculty/Yang/Calciomics.htm) for the identification of EF-hand and EF-like Ca2+-binding proteins was developed. This fast and robust method allows us to analyze putative EF-hand proteins at the genome-wide level and further visualize …

Electrokinetic Modeling Of Free Solution Electrophoresis, Yao Xin

Chemistry Dissertations

Modeling electrophoresis of peptides, proteins, DNA, blood cells and colloids is based on classical electrokinetic theory. The coupled field equations-Poisson, Navier-Stokes or Brinkman, and ion transport equations are solved numerically to calculate the electrophoretic mobilities. First, free solution electrophoretic mobility expressions are derived for weakly charged rigid bead arrays. Variables include the number of beads (N), their size (radius), charge, distribution (configuration), salt type, and salt concentration. We apply these mobility expressions to rings, rigid rods, and wormlike chain models and then apply the approach to the electrophoretic mobilities and translational diffusion constants of weakly charged peptides. It is shown …

Capillary Electrochromatography-Mass Spectrometry (Cec-Ms) Of Surfactants, Dean Stephen Norton

Chemistry Dissertations

This research presents advancements in the coupling of capillary electrochromatography (CEC) to mass spectrometry (MS) for the analysis of different chemical classes of surfactants. Chapter 1 provides a brief introduction that summarizes the mechanics and fundamentals of CEC, including instrumentation and applications for CEC-MS. Chapter 2 describes the on-line hyphenation of a packed CEC column with an internally tapered tip coupled to electrospray ionization-mass spectrometry (ESI-MS) and atmospheric pressure chemical ionization-mass spectrometry (APCI-MS) for the analysis of betaine-type amphoteric or zwitterionic surfactants (Zwittergent®). The interesting aspects include CEC-MS column manufacture and charaterization, as well as a comparison between the CEC-ACPI-MS …

New Techniques For The Qualitative And Quantitative Measurement Of Naturally-Ocurring Gonadotropin-Releasing Hormone Analogues By Mass Spectrometry, Tanya R. Myers

Chemistry Dissertations

GnRH peptides have been discovered in a wide variety of vertebrate and invertebrate organisms, and work is ongoing to characterize additional unique isoforms. This dissertation describes the investigation of reversed-phase chromatographic and mass spectrometric behavior of GnRH peptides, the development and application of an LC-MS/MS method for qualitative identification of GnRH peptides, and the comprehensive validation of an LC-MS/MS method for simultaneous, quantitative measurement of hydroxyproline9GnRH (Hyp9GnRH) and mammalian GnRH (mGnRH) in rat brain tissues. Chromatographic and mass spectrometric behavior of GnRH isoforms was characterized for six GnRH model peptides. Using reversed-phase high performance liquid chromatography (HPLC), nearly complete separation …

The Extent Of Perturbation Of Skin Models By Transdermal Penetration Enhancers Investigated By 31p Nmr And Fluorescence Spectroscopy, Charmita Patricia Burch

Chemistry Dissertations

The molecular basis of the potent transdermal enhancement activity of a series of iminosulfuranes, structure provided where X = H, Cl, Br, and I, is being investigated skin models. It has been shown (J. Lipid Res. 46(2005), 2192-2201.) that correlations exist between the activity of the aforementioned transdermal penetration enhancers (TPE) and the extent to which these agents bind to DMPC vesicles and perturb the gel to liquid crystal phase transition measured by calorimetry. The degree to which the perturbation of these compounds extends into the bilayer interior in contrast to surface activity is unclear. To gain insight into this …

Insights Into Sulfonated Phthalocyanines; Insights Into Anionic Tetraaryl Porphyrins; Irradiation Of Cationic Metalloporphyrins Bound To Dna, Anila Fiaz Gill

Chemistry Dissertations

Sulfonated porphyrins and phthalocyanines have been under consideration as microbicides, compounds which, when used in a topical formulation, can prevent transmission of the human immunodeficiency virus. Our studies have been directed toward the characterization of members of these classes. For the sulfonated phthalocyanines, matrix-assisted laser desorption/ionization (MALDI) mass spectrometry was helpful in determining the extent of sulfonation. We present the first report of spectroscopic characterization of a pentasulfonated phthalocyanine. Capillary electrophoresis data were sensitive to the concentration of the compounds (Chapter 1). Mass spectrometry was also very useful for establishing the extent of sulfonation in series of sulfonated porphyrins. Capillary …

Syntheses And Dna Interactions Of Acridine And Phenothiazine Based Photosensitizers, Beth Wilson

Chemistry Dissertations

Photosensitizing molecules and/or metal complexes that interact with DNA via intercalation and groove binding have potential applications as molecular structural probes, as footprinting reagents and in photodynamic therapeutics. To this regard, small molecules that bind to DNA and the energetics involved in these interactions, acridine-based therapeutics, photosensitization, photodynamic therapy, phenothiazine-mediated photosensitization, DNA photocleavage reaction mechanisms and photosensitizing metal complexes are introduced in Chapter I. Next, in Chapter II, the synthesis of a photonuclease consisting of a 3,6-acridinediamine chromophore attached to four metal-coordinating imidazole rings is described. The DNA photocleavage yields, emission quantum yields, and thermal denaturation studies by this acridine-imadazole …

Selective Recognition Of Quadruplex Dna By Small Molecules, Elizabeth W. White

Chemistry Dissertations

Structure-specific recognition of nucleic acids is a promising method to reduce the size of the recognition unit required to achieve the necessary selectivity and binding affinity for small molecules. It has been demonstrated recently that G-quadruplex DNA structures can be targeted by organic cations in a structure-specific manner. Structural targets of quadruplexes include the planar end surfaces of the G-tetrad stacked columns as well as four grooves. The significant structural differences between quadruplex DNA and duplex DNA make quadruplex DNA a very attractive target for highly selective, structure-specific drug design. We have used a variety of biophysical techniques including circular …

Synthesis Of Boronic Acid Based Sensors For Glucose And Sialic Acid And Synthesis Of Novel And Selective Pde4 Enzyme Inhibitors, Gurpreet Kaur

Chemistry Dissertations

The boronic acid functional group is known to bind compounds with the diol group tightly and reversibly in aqueous environment and has been used as a recognition moiety for the design of carbohydrate sensors. The first chapter of the dissertation studies the synthesis and substitution effect on the affinity and selectivity of a known boronic acid-based glucose sensor. In such a sensor design effort, the availability of a signaling event, whether it is fluorescence or UV, is crucial. The second chapter studies the detailed mechanism on how a well-known fluorescent boronic acid compound changes fluorescent properties upon binding. A new …

Design Of Novel Molecular Micelles For Capillary Electrophoresis, Syed Asad Ali Rizvi

Chemistry Dissertations

The research presented in this dissertation involves the synthesis, characterization, and application of novel anionic and cationic chiral molecular micelles in capillary electrophoresis (CE) for the separation of diverse chiral compounds. Chapter 1 presents brief overview of the surfactants, micelle polymer, CE and micellar electrokinetic chromatography (MEKC). Chapter 2 describes the simultaneous enantioseparation of eight single chiral center â-blockers using two novel leucine and isoleucine based polymeric surfactants. The simultaneous enantioseparation of multichiral center bearing â-blockers, nadolol and labetalol is described in chapter 3. A synergistic approach, using a combination of polysodium N-undecenoxycarbonyl-L-isoleucinate (poly-L-SUCIL) and sulfated â-CD showed dramatic enantioseparation …

Shape-Dependent Molecular Recognition Of Specific Sequences Of Dna By Heterocyclic Cations, Yi Miao

Chemistry Dissertations

SHAPE-DEPENDENT MOLECULAR RECOGNITION OF SPECIFIC SEQUENCES OF DNA BY HETEROCYCLIC CATIONS by YI MIAO Under the Direction of Dr. W. David Wilson ABSTRACT DB921 and DB911 are biphenyl-benzimidazole-diamidine isomers with a central para- and meta-substituted phenyl group, respectively. Unexpectedly, linear DB921 has much stronger binding affinity with DNA than its curved isomer, DB911. This is quite surprising and intriguing since DB911 has the classical curved shape generally required for strong minor groove binding while DB921 clearly does not match the groove shape. Several biophysical techniques including thermal melting (Tm), circular dichroism (CD), biosensor-surface plasmon resonance (SPR), and isothermal titration calorimetry …

Crystallographic Analysis And Kinetic Studies Of Hiv-1 Protease And Drug-Resistant Mutants, Yunfeng Tie

Chemistry Dissertations

HIV-1 protease is the most effective target for drugs to treat AIDS, however, the long-term therapeutic efficiency is restricted by the rapid development of drug resistant variants. To better understand the molecular basis of drug resistance, crystallographic and kinetic studies were applied to wild-type HIV-1 protease (PR) and drug-resistant mutants, PRV82A, and PRI84V, in complex with substrate analogues, the current drug saquinavir and the new inhibitor UIC-94017 (TMC-114). UIC-94017 was also studied with mutants PRD30N and PRI50V. The drug-resistant mutations V82A, I84V, D30N and I50V participate in substrate binding. Eighteen crystal structures were refined at resolutions of 0.97-1.60A. The high …

On The Mechanistic Roles Of The Protein Positive Charge Close To The N(1)Flavin Locus In Choline Oxidase, Mahmoud Ghanem

Chemistry Dissertations

Choline oxidase catalyzes the oxidation of choline to glycine betaine. This reaction is of considerable medical and biotechnological applications, because the accumulation of glycine betaine in the cytoplasm of many plants and human pathogens enables them to counteract hyperosmotic environments. In this respect, the study of choline oxidase has potential for the development of a therapeutic agent that can specifically inhibit the formation of glycine betaine, and therefore render pathogens more susceptible to conventional treatment. The study of choline oxidase has also potential for the improvement of the stress resistance of plant by introducing an efficient biosynthetic pathway for glycine …

Ecoscale, A Semi-Quantitative Tool To Select An Organic Preparation Based On Economical And Ecological Parameters, Koen Van Aken, Lucjan Strekowski, Luc Patiny

Chemistry Faculty Publications

A novel post-synthesis analysis tool is presented which evaluates quality of the organic preparation based on yield, cost, safety, conditions and ease of workup/purification. The proposed approach is based on assigning a range of penalty points to these parameters. This semi-quantitative analysis can easily be modified by other synthetic chemists who may feel that some parameters should be assigned different relative penalty points. It is a powerful tool to compare several preparations of the same product based on safety, economical and ecological features.

Ventrolateral Prefrontal Cortex Activation And Attentional Bias In Response To Angry Faces In Adolescents With Generalized Anxiety Disorder, Christopher Monk, Eric E. Nelson, Erin B. Mcclure, Karin Mogg, Brendan P. Bradley, Ellen Leibenluft, James R. Blair, Geng Chen, Dennis S. Charney, Monique Ernst, Daniel S. Pine

Chemistry Faculty Publications

Objective: While adolescent anxiety disorders represent prevalent, debilitating conditions, few studies explore their brain physiology. Using event-related functional MRI (fMRI) and a behavioral measure of attention to angry faces, we evaluated differences in response between healthy adolescents and adolescents with generalized anxiety disorder (GAD). Method: In the primary trials of interest, 18 adolescents with GAD and 15 comparisons of equivalent age/gender/IQ viewed angry/neutral face pairs during fMRI acquisition. Following the presentation of each face pair, subjects pressed a button to a probe that was either on the same (congruent) or opposite (incongruent) side as the angry face. Reaction time differences …

Prevention Of Poxvirus Infection By Tetrapyrroles, Avril Rm Chen-Collins, Dabney W. Dixon, Andrei N. Vzorov, Luigi G. Marzilli, Richard W. Compans

Chemistry Faculty Publications

Background: Prevention of poxvirus infection is a topic of great current interest. We report inhibition of vaccinia virus in cell culture by porphyrins and phthalocyanines. Most previous work on the inhibition of viruses with tetrapyrroles has involved photodynamic mechanisms. The current study, however, investigates light-independent inhibition activity.

Methods: The Western Reserve (WR) and International Health Department-J (IHD-J) strains of vaccinia virus were used. Virucidal and antiviral activities as well as the cytotoxicity of test compounds were determined.

Results: Examples of active compounds include zinc protoporphyrin, copper hematoporphyrin, meso(2,6-dihydroxyphenyl)porphyrin, the sulfonated tetra-1-naphthyl and tetra-1- anthracenylporphyrins, selected sulfonated derivatives of halogenated tetraphenyl …