Day 1 :
Arizona State University, USA
Sidney Hecht obtained his Ph.D. in Chemistry at the University of Illinois. He was an MIT Chemistry faculty member (1971-79) and was John Mallet Professor of Chemistry at UVa (1978-2008). He is Director of the Center for BioEnergetics in ASU’s Biodesign Institute. He was an Alfred P. Sloan Fellow, a John Simon Guggenheim Fellow and an ACS Cope Scholar Awardee. Hecht was selected as Virginia’s Outstanding Scientist for 1996. He received the 2011 ASU Faculty Achievement Award in Defining Edge Research: Innovation. He is Associate Editor of the Journal of the American Chemical Society and has published 440 research papers.
While the bacterial ribosome is remarkable for its facility of polypeptide synthesis, it has been optimized for a-L-amino acid incorporation; other types of amino acids are incorporated poorly. To expand the repertoire of amino acids capable of being incorporated into protein, we have considered strategies for ribosome modification. Since the ribosome is a ribozyme, i.e. peptide bond formation is actually mediated by ribosomal RNA rather than protein, we have focused on rRNA modification. We have created libraries of E. coli each harboring a plasmid with the operon for 23S rRNA; these plasmids have been randomized in rRNA regions important for peptide bond formation. The antibiotic puromycin consists of a modified adenosine attached to an amino acid via an amide bond; it binds to the ribosomal A-site by virtue of its resemblance to the 3′-end of aminoacyl-tRNA. Puromycin accepts growing polypeptide chains from the P-site peptidyl-tRNA, thereby terminating protein synthesis. Puromycin is internalized by bacteria; these cells are killed by protein synthesis inhibition. In the belief that a structurally modified ribosomal A-site, having a geometry conducive to recognition of an unnatural (e.g. beta) amino acid, would also bind a puromycin analogue having the same type of amino acid, we surveyed our E. coli containing ribosomal RNA libraries for colonies sensitive to puromycins containing modified amino acids. The colonies so identified make normal proteins of good quality, but also exhibit enhanced incorporation of modified amino acids. Examples of the incorporation of D-amino acids, b-amino acids, modified dipeptides and dipeptidomimetics will be discussed.
- Workshop on
St. Mary’s University, USA
Time : 13:40-14:40
José R Tormos has received a BS in Chemistry from the University of Sacred Heart in San Juan, Puerto Rico. He has earned his MS and PhD in Chemistry from the University of Iowa, where he worked on Cholinesterase Enzymes. As a Post-doctoral Research Fellow, he joined the Laboratory of Dr. Fitzpatrick in the Department of Biochemistry at the University of Texas Health Science Center at San Antonio, where he worked on flavoproteins nitroalkane oxidase and polyamine oxidase. After his post-doctoral appointment, he joined the Department of Chemistry and Biochemistry at St. Mary’s University.
Polyamine oxidases are peroxisomal flavoproteins that catalyze the oxidation of an endo carbon nitrogen bond of N1-acetylspermine in the catabolism of polyamines. While no structure has been reported for a mammalian polyamine oxidase, sequence alignments of polyamine oxidizing flavoproteins identify a conserved histidine residue. Based on the structure of a yeast polyamine oxidase, Saccharomyces cerevisiae Fms1, this residue has been proposed to hydrogen bond to the reactive nitrogen in the polyamine substrate. The corresponding histidine in mouse polyamine oxidase, His64, has been mutated to glutamine, asparagine, and alanine to determine if this residue plays a similar role in the mammalian enzymes. The kinetics of the mutant enzymes were examined with N1- acetylspermine and the slow substrates spermine and N,N’-dibenzyl-1,4-diaminobutane. On average the mutations result in a decrease of ~15- fold in the rate constant for amine oxidation. Rapid-reaction kinetic analyses established that amine oxidation is rate-limiting with spermine as substrate for the wild-type and mutant enzymes and for the H64N enzyme with N1-acetylspermine as substrate. The kcat/KO2 value was unaffected by the mutations with N1- acetylspermine as substrate, but decreased ~55-fold with the two slower substrates. The results are consistent with this residue assisting in properly positioning the amine substrate for oxidation.
- Sessions: Biochemistry & Structural Biochemistry | Clinical Glycomics, Glycoproteomics & Protein Expression | Molecular Biology and Amino Acids
University of Houston, USA
Title: Peptoid-combinatorial strategies to target non-protein biomarkers in the tumor microenvironment
Time : 11:40-12-10
Gomika Udugamasooriya has been working in the fields of Medicinal Chemistry and Chemical Biology and is trained in both Rational Drug Design and High Throughput Combinatorial Approaches. He has been exploring peptoids, an emerging class of biologically amenable and easy to synthesize peptidomimetics with great drug-like properties focusing on cancer treatment and imaging. The development of a unique on-bead two-color (OBTC) combinatorial cell screen to directly identify the highest specificity ligands for cell surface biomarkers was one of the major milestones in his career.
Chemotherapies are nonspecific and have side effects. Targeted therapies are expensive and fail on larger patient populations due to the heterogeneity of their target protein biomarkers. This suggests that effective cancer treatments need to be either personalized or find universal biomarkers - probably beyond proteins. We have been exploring peptoids as an emerging class of highly bio-compatible synthetic molecules as future drug leads. Peptoids are serum stable, non-immunogenic, cell permeable, easy to synthesize and optimize. Also, the cost of peptoid development is significantly lower than for small organic molecules, peptides and antibodies. We design and synthesize large on-bead peptoid combinatorial libraries and developed a unique on-bead two-color (OBTC) cell screen to directly identify most specific compounds
targeting biomarkers on the cell surface. As an approach to overcome the protein biomarker heterogeneity problem, we applied our OBTC assay at an unbiased fashion and identified a lipid-phosphatidylserine (PS) binding peptoid. PS is universally found on the outer layer of tumor endothelium and on many cancer cells as compared to normal cells. Our peptoid is found to be cytotoxic on various tumor types such as lung, breast and prostate and not on
normal cells, indicating a wider but tumor specific treatment method.
Darón Freedberg's research focus has been in the experience in NMR and conformational analysis. He obtained his Bachelors from UCSD in Chemistry where he worked on Stereodynamics and conformational analysis under the mentorship of Jay Siegel.
He obtained his Ph.D. from UCLA where he studied conformational isotope effects, Stereoelectronic effects, 3He NMR under the joint mentorship of Frank Anet and Craig Merlic. There was also a study of a tetrasaccharide.
He moved to the NIH where he was a postdoctoral at fellow studying Structure and dynamics of HIV Protease inhibitor complexes (and some carbohydrate structure on the side) under the mentorship of Dennis Torchia (pronounced Torsha).
Throughout his training Darón has always managed to do a few carbohydrate projects and was always intrigued with the complexity in these systems. Now he is combining his expertise in stereochemistry, conformational analysis and biomolecular structure and dynamics to converge on analyzing structure and dynamics studies of oligo- and polysaccharides at the FDA, where he has been since 1997.
Glycans are ubiquitous in nature and participate in a wide variety of cellular processes. They make up bacterial capsules, play roles in cell-cell interactions such as immune responses, fertilization, inflammation, and cell growth, influence protein folding and stability, and may be involved in signal transduction. Given the variety of monosaccharides, linkage types, and functional group modifications, oligosaccharides alone have potential structural complexity unmatched by any other biomolecule.
Despite their importance, glycan structure-function relationships, or “glycan code”, are poorly understood. We are delineating carbohydrate three-dimensional solution structure by NMR to gain insight into how glycans function, which should facilitate development of vaccines, drug delivery systems, and antibiotics of the future. Our goal is to unveil carbohydrate structure-function relationships using heteronuclear multidimensional NMR to delineate oligo- and polysaccharide conformation and dynamics. I will present results of our studies of a, 2->8 polysialic acid on cells and of a 15N, and 13C a, 2->8 labeled tetramer in-vitro. I will also discuss new methods for directly detecting and inferring hydrogen bonding in glycans dissolved in aqueous solution.
Qinghua Wang has her expertise in structural biology with a focus on mechanistic studies of actin-mediated signal transduction. She has pioneered a novel double-mutant strategy that for the first time allowed the capture of stable actin nuclei for structural studies. By applying this novel strategy, she has elucidated the molecular mechanisms of mammalian tandem-actin-binding nucleators.
Actin is one of the most abundant and conserved eukayotic proteins. Actin nucleation, defined as the formation of actin oligomers from G-actin monomers, is the rate-limiting step for de novo actin assembly in many fundamental cellular processes. In cells, actin nucleation is precisely and tightly regulated through a diverse set of actin nucleators. However, due to their fleeting nature, actin nuclei have long eluded structural investigation. Our lab has developed a novel double-mutant strategy, which allows the capture of actin nuclei in action. In the seminar, I will discuss the molecular mechanisms of actin nucleation based on the crystal structures and functional studies of multiple mammalian tandem-actin-binding nucleators.
Middle Tennessee State University, USA
Title: Structural analysis of a novel protein from C. neoformans reveals its unusual virulence and alternative energy production pathway
Time : 15:10-15:40
Dr. Moses Prabu completed his bachelors in Physics from The American College, Madurai, India. He continued his education in the same institution and received a Master’s degree in Advanced Physics with specialization in Quantum Optics and Solid State Physics. Around this time his passion for understanding biomolecules using modern physics grew deep and he switched fields to pursue his graduate research in determining structure function of proteins. He received his PhD in biophysics from Indian Institute of Science, Bangalore, India, where his contributions revealed new insights into plant lectins, microbial RecA and chemical evolution. He joined Dr. Celia Schiffer at UMASS Medical School, Worcester, MA, to conduct his postdoctoral research in HIV. His research led to the discovery of a “substrate-envelope” hypothesis which revealed the structural rationale for substrate specificity, drug resistance and coevolution of HIV-1 protease. This elegant approach has attracted several researchers to rationalize proteins with promiscuous specificity for molecular recognition. He subsequently accepted a faculty position at the Commonwealth Medical College, Scranton, PA, where his research projects include the characterization of a variety of aspartyl proteases using X-ray crystallography, tissue culture, biophysical techniques, and collaborative clinical research. As a founding faculty member of the Medical College, he played a pivotal role in establishing the Institution’s educational and research enterprises. He continues to serve the community by developing student internship programs that bridge industry and academia. In addition to his current role as a Protein Scientist, he also offers professional consultation services on regulatory implications on clinical application of biological drug compounds and preclinical testing of investigative drugs.
The pathogenic yeast Cryptococcus neoformans causes cryptococcosis, a life-threatening fungal disease. It has multiple virulence mechanisms that are non-host specific, induce damage and interfere with immune clearance. Microarray analysis of C. neoformansstrains serially passaged in mice associated a small gene (HVA1 – hypervirulence-associated protein 1 gene) with virulence. HVA1 encodes a protein that has homologs of unknown function in plant and animal fungi, consistent with a conserved mechanism. Expression of HVA1 was negatively correlated with virulence and was reduced in vitro and in vivo in both mouse- and Galleria-passaged strains of C. neoformans. Phenotypic analysis in hva1Δ and hva1Δ+HVA1 strains revealed no significant differences in established virulence factors. Mice infected intravenously with the hva1Δ strain experienced higher fungal burden in the spleen and brain, but lower fungal burden in the lungs, and died faster than mice infected with H99W or the hva1Δ+HVA1 strain. Metabolomics analysis demonstrated a general increase in all amino acids measured in the disrupted strain and a block in the TCA cycle at isocitrate dehydrogenase, possibly due to alterations in the nicotinamide cofactor pool. Macrophage fungal burden experiments recapitulated the mouse hypervirulent phenotype of the hva1Δstrain only in the presence of exogenous NADPH. The crystal structure of the HVA1 protein was solved, and a comparison of structurally similar proteins correlated with the metabolomics data and potential interactions with NADPH. We report a new gene that modulates virulence through a mechanism associated with changes in fungal metabolism.
UNIFESP-Escola Paulista de Medicina, Brazil
Title: From discovering “calcium paradox” to Ca2+/cAMP interaction: Impact in human health and disease
Time : 15:40-16:10
Leandro Bueno Bergantin received his academic education at UNIFESP-EPM (Brazil) and UAM (Spain) i.e., degree in Biomedicine in 2008, MSc in 2010 and PhD in 2014. His research involves cell signaling mediated by Ca2+ and cAMP, skeletal and smooth muscles, peripheral and central nervous systems. His research work solved the enigma of the paradoxical effects produced by L-type Ca2+ channel blockers. He is currently pursuing Post-doctoral fellowship (FAPESP) at UNIFESP-EPM.
The hypothesis of the so-called “calcium paradox” phenomenon in the sympathetic neurotransmission has its origin in experiments done in models of neurotransmission since 1970´s. Historically, “calcium paradox” originated several clinical studies reporting that acute and chronic administration of L-type Ca2+ Channel Blockers (CCBs), drugs largely used for antihypertensive therapy such as verapamil and nifedipine, produces reduction in peripheral vascular resistance and arterial pressure, associated with a paradoxical sympathetic hyperactivity. Despite this sympathetic hyperactivity has been initially attributed to adjust reflex of arterial pressure, the cellular and molecular mechanisms involved in this paradoxical effect of the L-type CCBs remained unclear for four decades. Also, experimental studies using isolated tissues richly innervated by sympathetic nerves showed that neurogenic responses were completely inhibited by L-type CCBs in high concentrations, but paradoxically potentiated in low concentrations, characterized as a “calcium paradox” phenomenon. We discovered in 2013 that this paradoxical increase in sympathetic activity produced by L-type CCBs is due to Ca2+/cAMP interaction. Then, the pharmacological manipulation of this interaction could represent a potential cardiovascular risk for hypertensive patients due to increase of sympathetic hyperactivity. In contrast, this pharmacological manipulation could be a new therapeutic strategy for increasing neurotransmission in psychiatric disorders such as depression, and producing neuroprotection in the neurodegenerative diseases such as Alzheimer´s and Parkinson’s diseases.
Niger Delta University, Nigeria
Time : 16:30-17:00
C. Madukosiri has a PhD in Biochemistry in the year 2003 from University of Jos, Nigeria. At present she is an Associate Professor of Nutritional Biochemistry in Niger Delta University. She has published twenty-two papers relating to Nutrition, Agriculture, and Clinical Biochemistry in both local and international Journals. Before joining the University she had worked as a Nutritionist / Dietician for eighteen years in Federal Ministry of Defence.
The present study compared the fatty acids, cholesterol, low density lipoprotein (LDL), and high density lipoprotein (HDL) of four commercially important fresh-water fish species, Clarias gariepinus (CG), Oreochromis niloticus (ON), Synodontis budgetti (SB), and Mormyrops deliciosus (MD), using Gas Chromatographic and High Performance Lipid Chromatographic methods. Results showed that the percent polyunsaturated fatty acids (PUFAs) determined from CG were, 35.709, 14.310, 45.845 and 32.345, from Amassoma, Swali, Tombia (in Bayelsa State, South-South of Nigeria) and Lagos rivers respectively. The prominent omega-3 fatty acid determined were eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA); while the major omega-6 fatty acid was eicosatetraenoic acid (AA). Cholesterol content of fishes from the study rivers ranged from 5.080 to 5.570 (mg/100g DW) and was more or less significantly lower than that from Lagos river (in a populous city in the Southwest of Nigeria), (p < 0.05). Cholesterol, HDL and LDL content in the four fish species were according to the decreasing order CG > ON >SB>MD. For the HDL content of fish, higher value was obtained from Amassoma than those of Swali and Tombia rivers but (with the exception of that of O. niloticus in Amassoma) were all found to be significantly lower than that of Lagos, (p < 0.05). Fishes from Amassoma and Lagos rivers were prominent in n-3 PUFA particularly DHA and EPA; while those from SR showed the lowest levels. This information should find application not only for personal and institutional nutrition practices, but also for development and processing in fish cultures.
California State University, USA
Title: Post-translational click-based labeling of unnatural amino acid-tagged ribosome-bound nascent polypeptide chains for high-throughput structural biophysics and single-molecule spectroscopy applications
Time : 17:00-17:30
Kambiz M Hamadani is primarily interested in studying protein folding on the ribosome using single molecule fluorescence methods. The methods he has developed to study this fundamental process have a wide range of applications in molecular evolution, structural biochemistry/biophysics, and glycobiology. He is very interested in collaborating with industry and academic partners that could possible make use of the labeling methods he’s developed for their own applications.
"Tag-and-modify" strategies to protein labeling often employ various combinations of unnatural amino acid incorporation and bio-orthogonal click chemistries to post-translationally attach fluorescent reporters, carbohydrates, or other functional groups onto purified target proteins. However, cell-based expression can limit the scope of such approaches. Purified and reconstituted in-vitro translation systems (prIVT) overcome many of these limitations at the expense of reduced product yield. Here we demonstrate that by combining prIVT technology, quantitative unnatural amino acid incorporation via sense codon reassignment, and either strain-promoted or copper-catalyzed azide-alkyne cycloaddition we can overcome the major hurdles which currently limit the scope and throughput of single molecule protein biophysics applications. Singlemolecule methods access biomolecular distributions, transient states, and asynchronous dynamics inaccessible to standard ensemble techniques. Although extremely powerful, the ability to screen large biomolecular libraries using fluorescence-based single-molecule detection platforms is still a challenge due to the lack of high-throughput methods for the generation and screening of large libraries of dye-labeled proteins. Here, we present a purificationfree and parallelizable in-vitro approach to generating dual-labeled proteins and ribosome-nascent-chain (RNC) libraries suitable for single-molecule FRET-based structural phenotyping. Importantly, dual-labeled RNC libraries enable single molecule co-localization of genotypes with phenotypes, and thus multiplexed single molecule screening of protein libraries. Such an approach to high-throughput posttranslational modification of large libraries of proteins may be useful for the in-vitro directed evolution of proteins with designer (single molecule) phenotypes.
Payame Noor University, Iran
Title: Preparation and properties of sheets of reduced graphene oxide anchored with Nd-La doped Sr2CuMgFe28O46 nanoparticles
Time : 17:30-18:00
My name is Paransa Alimard. I was born in 1981. I live in Tehran, Iran. After I finished my high school I started my education in the field of chemistry. I got my Bachelors in Applied chemistry and then I started working in a cosmetic and hygienic company named Sufin and after 6 years I got my master of science in Inorganic chemistry. I earned my PhD in Inorganic chemistry 2 years ago. My PhD thesis was about magnetic nanocomposites and the investigation of their physical and chemical properties. My interest is about synthesis of nano particles and nano composites. Now I work for Surfin Company again and I hope to attend the conference.
The Nd-La doped Sr2CuMgFe28O46 magnetic nanoparticles were successfully prepared by green sol-gel method. Decorating the magnetic nanoparticles on reduced graphene oxide (RGO) sheets was performed via a facile green chemical reaction strategy, where the reduction of graphene oxide and connection of magnetic nanoparticles with RGO by dopamine, occurred simultaneously. The as-fabricated magnetic nanoparticles were characterized systematically through the use of an X-ray diffraction (XRD), energy dispersive X-ray spectroscopy (EDS), scanning electron microscope (SEM), fourier transform infrared spectroscopy (FT-IR), network analyzer, particle size analyzer (PSA) and a vibrating sampling magnetometer (VSM). The results revealed that the magnetic nanoparticles were spherical-shaped with hexagonal ferrite structure and a grain size of 10 to 98 nm, approximately. Characterization of RGO/Nd-La doped Sr2CuMgFe28O46 nanocomposite using FT-IR clearly demonstrates the successful covalent attachment of magnetic nanoparticles to RGO sheets. Magnetic measurement revealed that the saturation magnetization (Ms) and coercivity (Hc) of magnetic nanoparticles were 44.3 Am2/Kg and 354.6 KA/m, respectively. As expected, the magnetic response of the nanocomposite was dramatically reduced in comparison with that in magnetic nanoparticles. Microwave absorption of the nanocomposite was evidently enhanced compared to that of pure graphite and magnetic nanoparticles.