A Transferrable Model for Chromatin Folding
Jose N. Onuchic
Center for Theoretical Biological Physics, Rice University, Houston TX
In vivo, the human genome folds into a characteristic ensemble of 3D structures. The mechanism driving the folding process remains unknown. A theoretical model for chromatin (minimal chromatin model) that explains the folding of interphase chromosomes and generates chromosome conformations consistent with experimental data will be presented. The energy landscape of the model was derived by using the maximum entropy principle and relies on two experimentally derived inputs: a classification of loci into chromatin types and a catalog of the positions of chromatin loops. First, we trained our energy function using the Hi-C contact map of chromosome 10 from human GM12878 lymphoblastoid cells. Then, we used the model to perform molecular dynamics simulations producing an ensemble of 3D structures for all GM12878 autosomes. Finally, we used these 3D structures to generate contact maps. We found that simulated contact maps closely agree with experimental results for all GM12878 autosomes. The ensemble of structures resulting from these simulations exhibited unknotted chromosomes, phase separation of chromatin types, and a tendency for open chromatin to lie at the periphery of chromosome territories.
Let’s Build Something Together: Collaborative Teaching in Science and the Technical Arts
Scott M. Ames1 and Kenneth A. Goldsby2
1. Agricultural Science Program, Ransom Middle School, Pensacola, FL 32533
2. Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306
Six years ago, at FAME 2011, we described our initial efforts to encourage collaborations between shop teachers and science teachers in the State of Florida secondary school system. Our plan was to start conversations and forge new relationships between the teachers by showing them examples of equipment that could be built in shop class and used for classroom demonstrations and laboratory experiments in science class. Beyond providing equipment for the science teachers and new projects for the shop teachers, we expected that the real winners would be the students participating in the design and construction activities. We will give a brief progress report describing the reception to this initiative and some of the challenges encountered along the way. Following this presentation, participants in the associated workshop will build two demonstrations for their classroom from reasonably priced and readily available materials, using tools found in most secondary schools with a technical arts or agricultural science program.
ANAKIN-ME: A GENERAL PURPOSE AND CHEMICALLY ACCURATE DEEP LEARNED POTENTIAL
Justin S. Smith1, Olexandr Isayev2 and Adrian E. Roitberg1
1 Department of Chemistry, University of Florida, Gainesville FL, USA
2 UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill NC, USA
In the theoretical study of molecular systems, a compromise between speed and accuracy is required to study the energetics of chemical systems. Quantum mechanical (QM) methods allow accurate energies and forces to be calculated but require massive computational effort. Classical force fields are fast but only accurate near equilibrium and are generally unusable in reactivity studies due to restrictive functional forms. A possible solution to these problems is the development of empirical potentials built through machine learning methods. Artificial neural networks have been used to develop neural network potentials (NNP), which are fit to QM reference energies. Through the development of a new methodology, known as ANAKIN-ME (ANI), we provide the tools to build a new class of NNP, which is fully transferable and chemically accurate. With the ANI method, we develop the ANI-1.2 potential for organic molecules containing H, C, N, and O. Through extensive benchmark and case studies, the ANI-1.2 potential provides evidence that the ANI method produces chemically accurate and size extensible potentials. The ANI method brings a new, highly efficient, and accurate method for the development of NNPs into the realm of reality, and opens the door for a new generation of “out-of-the-box” general purpose potentials.
SIROHEME BIOSYNTHESIS BY CYSG
Joseph M. Pennington and M. Elizabeth Stroupe
Department of Biological Science and Institute of Molecular Biophysics
Florida State University
Siroheme is the modified tetrapyrrole used by siroheme-dependent sulfite and nitrite reductases (SiR/NiRs) in catalyzing the six-electron reduction of sulfite to sulfide or nitrite to ammonia. Proteobacteria like Escherichia coli or Salmonella typhimurium use a single gene product to synthesize siroheme, CysG. CysG is the product of expressing a gene fusion between a C-terminal methyltransferase (CysGA) and an N-terminal bifunctional dehydrogenase/ferrochelatase (CysGB). CysGB is a three-domain homodimer composed of an N-terminal Rossmann fold that binds NAD+, a four-stranded β-sheet dimerization domain, and a C-terminal α-helical domain. Together, these three domains form an X-shaped molecule, where the Rossmann fold from one subunit and the helical domain from the other subunit carve out a large cavity. Although this large cavity is suggestive of a porphyrin binding site, we do not yet know the mechanism for positioning precorrin-2 for dehydrogenation at C12. Additionally, despite extensive mutagenesis in an attempt to identify a metal ligand, it is unclear how iron is selected and then inserted in the final step. We have successfully determined the X-ray crystallographic structure of S. typhimurium CysG bound to sirohydroclorin and siroheme in the dehydrogenase/chelatase domain that suggest a mechanism for hydride abstraction and iron chelation.
HYDROGEN BOND DIRECTED SELF-ASSEMBLY OF π-SYSTEMS
Ronald K. Castellano
Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, FL 32611-7200, USA
Although "ordered" organic π-conjugated assemblies outperform "disordered" ones in many optoelectronic device applications, we are far from being able to port the well-understood supramolecular recipes of π-systems from solution to solid-state device environments. For the past several years we have been exploring hydrogen bond (H-bond) directed self-assembly of π-systems along these lines, for example, to enhance their absorption and charge transport properties for organic photovoltaic (OPV) applications. Various examples of oligothiophenes outfitted with heterocycles capable of forming H-bonded "rosettes" will be discussed in this context. The second part of the talk will introduce new monomers derived from [2.2]paracyclophane (pCp) that are capable of robust H-bond directed self-assembly into one-dimensional nanostructures in solution and the solid state. The design introduces transannular (intramolecular) H-bonds between pairs of pseudo-ortho-positioned amides as a way to preorganize the molecules for intermolecular H-bonding with two neighbors. The result is formation of homochiral, one-dimensional pCp stacks that show supramolecular polymer signatures in solution.
Synthesis of Vinyl Sulfone 1,6-Enynes for [2+2+2] Cycloisomerization Methodology
Ron R. Ramsubhag1, Gregory B. Dudley2
1 - Department of Chemistry and Biochemistry, Florida State University, 102 Varsity Way, 5007 CSL, Tallahassee, FL 32306-4390, USA
1, 2 - Gregory B. Dudley - Eugene Bennett Department of Chemistry, 100 Prospect Street, 222 Clark Hall, West Virginia University, Morgantown, WV 26506-6045
1,6-Enynes have proven to be invaluable building blocks that has help innovate alkyne chemistry. Using the fragmentation/olefination methodology developed in our lab, we can now synthesize a new type of 1,6-enyne which incorporates a vinyl sulfone. Here, these vinyl sulfone enynes are used to explore and expand [2+2+2] cycloisomeriaztion methodology. Various alkynes are used as coupling partners to synthesize variety of gem-dimethyl indanes.
SPLIT DEOXYRIBOZYME SENSORS FOR NUCLEIC ACID ANALYSIS AND DIAGNOSTICS OF INFECTIOUS DISEASES
Nicole Aberdabbo,1 Rebecca Basch,1 Ryan Connelly,1 Carly Mitchell,2 Sheila Solarez1 and Yulia V. Gerasimova1
1Chemistry Department, University of Central Florida, Orlando FL 32816, USA
2Oviedo High School, Oviedo, FL 32765
Deoxyribozymes (Dz) are DNA molecules capable of catalyzing chemical reactions. Due to their structural versatility, biocompatibility, signal amplification ability and relatively low cost, Dz are widely used as scaffolds for biosensor design. Here we present a split Dz (sDz) approach for nucleic acid sensors, in which a Dz is divided into two subunits, which re-associate into the catalytically active construct only in the presence of a specific nucleic acid target. The target-inducible signal can be monitored for target detection and quantification. The advantages of sDz sensors include great selectivity of the target recognition down to a single base substitution in the target structure, as well tolerance to the secondary structure of the analyzed nucleic acid, which often represents a real challenge for conventional hybridization probes. Here, we present sDz sensors with fluorescent of colorimetric signal for highly selective recognition of bacterial and viral RNA, as well as amplified fragments of bacterial genome. The applications of the sensors for the RNA maturation monitoring and mutation analysis, as well as point-of-care compatible detection and genotyping of ZIKA virus and Mycobacterium tuberculosis are discussed.
Funding from the National Institutes of Health (NIH; 1R21AI123876-01A1) and the Florida Department of Health (7ZK33) is greatly appreciated.
Machine learning approaches to study dynamic allosteric regulation of proteins
Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, Tampa, FL-33620, USA
The activities of many proteins, including GPCRs, NTFs and Igs, are regulated by small changes in structures that are comparable to thermal fluctuations. Consequently, their regulatory mechanisms cannot be modeled in terms of how their energy-minimum structures differ between states. Understanding their regulatory mechanisms requires assessment of relationships between high-dimensional conformational ensembles of different states. To realize this, we present development of a new class of approaches based on support vector machines (SVMs). However, we do not use SVMs in the traditional manner to predict group identities of unseen instances. Instead, we use the mathematical framework of SVMs to identify instances and spatial regions that overlap between pre-classified groups. We also show how this development enables us to statistically analyze relationships between multiple conformational ensembles and compute correlations in inter-site ensemble shifts, thereby providing direct insight into how regulatory signals are spread through a combination of changes in structure and dynamics.
Facile Tuning of Atropisomeric P,N-Ligands Towards Enantioselective Conjugate Addition
Sourabh Mishra, Ji Liu, Aaron Aponick
Center for Heterocyclic Compounds, Department of Chemistry, University of Florida, Gainesville, FL 32611
Catalytic asymmetric conjugate addition reactions are very important tools for the assembly of chiral compounds and Meldrum’s acid derivatives are excellent acceptors for such transformations. Facile diversification of β–alkynyl adducts makes them highly useful targets and a new synthetic method using StackPhos, an imidazole–based atropisomeric P,N–ligand has been developed. Employing a ligand modification strategy, this transformation was achieved with a broad substrate scope and excellent enantioselectivity. Recent results using modified ligands will be presented, as well as the application of the method.
Functional Biomaterials via Modification of Kraft Lignin
Anthony N. Cauley, James N. Wilson
Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, FL 33146, United States
Lignin, a cross-linked phenolic polymer found in plant cell walls, is the main contributor of strength and structure in wood. It is a byproduct of the paper and agricultural industry with several different isolation methods. Kraft lignin, with high phenolic hydroxyl content, can be readily modified via SN2 reaction to introduce numerous different functional groups. The modified lignins will self-assemble into nanostructures that can act as a “container” for organic dyes. The supramolecular assembly of lignin nanocontainer host and molecular guest lends itself to biologically relevant applications such as delivery and sequestration. Also, the substitution reactions can be used for introducing bio-orthogonal functional groups and subsequent conjugation chemistry to coat the surface in sensing molecules. This will open a new avenue towards novel polymer-bioconjugates that combine the utility of polymers with the functionality of biomolecules. Overall, lignin is a versatile material that has been underutilized as a renewable chemical resource and its amphiphilic nature can be easily modified for use in a variety of applications.
Bridge-mediated exciton transport: pathway analysis of the donor-acceptor exciton coupling
Spiros S. Skourtis
Department of Physics, University of Cyprus, Nicosia Cyprus
Dexter energy transfer (triplet-exciton transfer), is important in solar energy harvesting assemblies, damage protection schemes of photobiology, and organometallic opto-electronic materials. Triplet-exciton transfer between chemically linked donors and acceptors is bridge-mediated. If the bridge is a tunneling barrier for the transferring exciton, exciton transfer presents an enticing analogy with bridge-mediated superexchange electron transfer. We formulate a theory for exciton-transfer coupling pathways by analogy to electron-transfer coupling pathways . We show that virtual exciton intermediates with one electron or one hole on the bridge dominate the donor-acceptor coupling at shorter distances and/or high tunneling energy gaps, while virtual intermediates with an electron and a hole on the bridge (virtual bridge excitons) dominate at longer distances and /or low energy gaps. The effects of virtual bridge excitons have been neglected in earlier descriptions and may alter the distance dependence of the Dexter rate. Spiros S. Skourtis, Charoen Liu, Panayiotis Antoniou, Aaron M. Virshup and David N. Beratan. Proc. Nat. Acad. Sci. USA, 2016, 113 8115-8120.
Analyzing complex behavior of α7 nAChR binding sites
Alican Gulsevin1, Clare Stokes2, Roger L. Papke2, Nicole A. Horenstein1
1 - Department of Chemistry, University of Florida, Gainesville, FL, USA
2 - Department of Pharmacology and Therapeutics, University of Florida, Gainesville, FL, USA
The α7 nicotinic acetylcholine receptor (nAChR) is an important ion channel involved in functions ranging from cognition and memory to inflammation. This receptor has a propensity to enter ligand induced desensitized states which are hypothesized to elicit anti-inflammatory effects. In many cases ion currents are not detectable, leading to the idea of metabotropic-like signaling from the receptor. In this study, computational chemistry and electrophysiology are used to explore the complex behavior of a group of molecules called silent agonists, that selectively place the α7 nAChR in a desensitized state that can be detected by co-application of positive allosteric modulators such as PNU-120596. Our findings suggest that ligands may bind the orthosteric binding domain with different “flipped” poses, and there is another possible binding site in the vestibule of the extracellular domain. The CRC and iCRC data generated for eight diethyl phenyl piperazines (DiEPPs) (partial agonists, silent agonists and an antagonist) on WT and Q57T receptor showed nearly half the potency relative to WT and a slight decrease in response. However, Q57T was able to nearly abolish silent agonist activity for DiEPP meta carboxamide. We discuss these results in the context of possible modes of action for silent agonists.
STRUCTURE AND FUNCTION OF SULFITE REDUCTASE: IMPORTANCE OF DYNAMIC INTERACTIONS IN A MULTIMERIC COMPLEX
Isabel Askenasy1, Rachel Andrews2, and M. Elizabeth Stroupe1,2
1 Department of Biological Science, Florida State University, Tallahassee FL 32306 - 4295, USA.
2 Institute of Molecular Biophysics, Florida State University, Tallahassee FL 32306 - 4380, USA.
Sulfite Reductase (SiR) is a key enzyme in sulfur assimilation, performing the six electrons reduction of sulfite to sulfide. In Enterobacteria, SiR is dodecameric complex with eight copies of the α subunit, or Flavoprotein, and four copies of the β subunit, or Hemoprotein. We aim to understand how electron transfer occurs in the context of SiR’s unique stoichiometry and structure. From our biochemical analysis, we have discovered that SiR’s subunits share two interfaces: one functional and one structural. Surprisingly, the structural interface is far from where electron transfer is known to occur. Therefore, we hypothesize that the functional interface occurs through a transient interaction between the subunits. To test our hypothesis, we synthesized four Flavoprotein point variants. The variations were introduced in the structural interface, the functional interface or the flexible region that connects the domains where the interfaces are located. We then measured binding affinities using ITC and enzyme activity through in vivo and in vitro experiments. Electron transfer is, indeed, independent from tight binding.
Virtual Biomolecular Target Identification for Drug Discovery and Beyond
Wayne C. Guida, Wesley Brooks, Kenyon Daniel, Yuri Pevzner, and H. Lee Woodcock
Department of Chemistry, University of South Florida
Identification of bioactive compounds with desired therapeutic effects is still a laborious, expensive process. Moreover, once a compound has been identified, which acts against a particular biomolecular target, the question still remains as to whether all relevant protein targets for the compound have been identified. Thus, it is desirable to understand the breadth of biomolecular targets with which a particular compound interacts in order to establish the compound’s selectivity or lack thereof (polypharmacology). Such an endeavor would also be of utility for re-purposing known drugs and elucidation of the possible metabolic fate of a compound of interest. Previously, we developed Virtual Target Screening (VTS) methodology that allows one to computationally screen a compound of interest against a collection of protein targets. By scoring each compound‑protein interaction, we can compare against averaged scores of a collection of drug-like molecules docked to the same proteins to determine if a particular protein would be a potential target of the compound of interest. We have validated our VTS system using kinase inhibitors and natural products. In this talk, we discuss our work in progress.
STABLE PICKERING EMULSIONS USING JANUS PARTICLES VIA MICROFLUIDICS
Bobby Haney1, Liheng Cai2, Dong Chen2, David A. Weitz2, Subramanian Ramakrishnan1
1Chemical and Biomedical Engineering - FAMU-FSU College of Engineering, Tallahassee FL 32310
2Department of Physics, Harvard University, Cambridge MA 02138
Stable Pickering emulsions are important to systems where controlled confinement of an oil or water phase is critical to its applications (enhanced oil recovery). The stability of the Pickering emulsions depends on the wetting properties of the particle and hence there is a need to control the chemistry of the particles and tune the surface tensions to enhance stability. In this regard, “Janus” particles with both hydrophobic (hb) and hydrophilic(hl) portions have recently been used to form stable emulsions. Stability can be enhanced and controlled by tuning the hb/hl ratios, concentration of particles, and size.
In this work we demonstrate a simple and reproducible method using glass capillary microfluidics to synthesize “Janus” particles with varying hb and hl domains. Flowrates of the chemical constituents were varied to control particle sizes (125- 400 microns) and hb/hl domain volume ratios (0.7 – 5.8). Using UV light, these droplets were cross-linked via photo-polymerization to form fairly monodispersed particles. These particles were used to make very stable water in oil and oil in water Pickering emulsions where the size of the emulsions were controlled by changing the size of the Janus particles. These large particle sizes permit un-aided visualization of particle stabilized emulsions.
DESIGN AND SYNTHESIS OF HYDROGEN—BONDING CAPABLE 1,4-DIHYDROPYRAZINO[2,3-b]QUINOXALINE-2,3-DIONES FOR APPLICATIONS IN ORGANIC FIELD-EFFECT TRANSISTORS
Tural N. Akhmedov,1 Daken J. Starkenburg,2 Kyle J. Chesney,1 Jiangeng Xue,2 and Ronald K. Castellano1
1Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, FL 32611-7200, USA
2Department of Materials Science and Engineering, University of Florida, P.O. Box 116400, Gainesville, FL 32611-6400, USA
Up and coming technology in π-conjugated organic field-effect transistors (OFETs) can in principle allow for cost-effective production of small scale electronics. In order to effectively compete with widely used inorganic materials such as silicon, field-effect transistors of organic origin must be properly tuned for good charge mobility. It is known that ordered π-π stacking among organic molecules is essential for efficient charge transport; however, the desired order is not always achieved. To be able to better control π-stacking arrangements in the solid state, introduction of heterocycles to the π-backbone capable of strong hydrogen -bonding has recently been shown to be a promising approach. Reported here is the synthesis of a family of electron deficient N-heteroacenes containing the H-bonding capable 1,4-dihydropyrazine-2,3-dione moiety towards improvement of charge carrier mobility in OFETs.
Influence of proximal heme pocket on the oxygen insertion reactions of heme thiolate enzymes: Theoretical studies of epoxidation and hydroxylation by CPO and P450CAM
David C. Chatfield and Alexander N. Morozov
Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199
Cytochrome P450cam from P. putida (P450cam) and chloroperoxidase from C. fumago (CPO) are highly versatile enzymes capable of catalyzing a broad spectrum of oxidation reactions, including the epoxidation and hydroxylation of organic substrates. These reactions can be highly enantiospecific, making engineered CPO variants potentially useful biocatalysts. We have previously reported a body of simulation work on the structure-function relationships of CPO. Here we report work on CPO and P450cam that traces the difference between the epoxidation and hydroxylation activities to the environment of the heme’s proximal thiolate ligand. We show, on the basis of QM and QM/MM models, that this environment can favor epoxidation over hydroxylation by up to 5 kcal/mol, even though the reaction takes place on the opposite heme face (distal binding pocket), resolving a long-standing discrepancy between experiment and simulation. We also provide evidence that the proximal environment can, via electronic effects, be a significant factor in controlling the enantiospecificity of CPO-catalyzed epoxidation reactions.
Amphiphilic Homopolymers via Successive Post-Polymerization Modification Reactions
Tomohiro Kubo,a Maxym Tansky,a Kyle C. Bentz,a Kristin C. Powell,b C. Adrian Figg,a Jeremy L. Swartz,a Anuj Chauhan,b Daniel A. Savin,a Brent S. Sumerlin*a
a George & Josephine Butler Polymer Research Laboratory, Center for Macromolecular Science & Engineering, Department of Chemistry, University of Florida, PO Box 117200, Gainesville, Florida 32611, United States
b Department of Chemical Engineering, University of Florida, 1030 Center Drive, Gainesville, Florida 32611, United States
We demonstrated the systematic preparation of amphiphilic homopolymers, which exhibit greater tunability of their self-assembly behaviors, via post-polymerization modification. Successive nucleophilic aromatic substitution of 2,4,6-trichloro-1,3,5-triazine made a modular and facile synthesis possible, allowing for the systematic investigation of structure-property relationships. Light scattering measurements, dye encapsulation, and water-oil interfacial tension measurements indicated successful formation of amphiphilic homopolymers and provided greater insight into their solution properties.
An anti-microbial peptide based intracellular delivery of nanocrystals
Anshika Kapur@, Scott Medina#, Wentao Wang@, Goutam Palui@, Xin Ji@, Joel P. Schneider# and Hedi Mattoussi@
@Department of Chemistry and Biochemistry, Florida State University, 95 Chieftan Way, Tallahassee, Florida 32306, USA
# Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201
Engineered inorganic nanomaterials with tunable composition and controllable surface functionalization have emerged as potential imaging and diagnostic tools for integration with biological systems. However, little is known about the strategies to facilitate the movement of nanocrystals (NCs) across the cell membrane while circumventing endocytosis. We show that an anti-microbial peptide, SVS-1, can potentially be utilized to promote non-endocytic uptake of nanocrystals including luminescent quantum dots (QDs), metallic gold nanoparticles (AuNPs) and gold nanorods (AuNRs). The N-terminal cysteine residue of the chemically synthesized peptide allows for covalent coupling to amine-functionalized NCs. Fluorescence imaging data show homogeneous distribution of the rapidly internalized NC-SVS-1 conjugates throughout the cytoplasm of different mammalian cell lines. The internalized NCs do not show any co-localization with labelled endosomes or nucleii. More importantly, additional endocytosis inhibition experiments imply that the conjugates are primarily internalized through physical translocation of the membrane rather than endocytosis. Live cell imaging data along with quantification by flow cytometry analysis also support our conclusions.
CONFORMATIONAL DYNAMICS OF GROWTH HORMONE – RELEASING HORMONE PEPTIDE ANALOGS USING COLLISION INDUCED ACTIVATION – TRAPPED ION MOBILITY – MASS SPECTROMETRY
Kevin Jeanne Dit Fouque,1 Luis M. Salgueiro,2 Renzhi Cai,2 Wei Sha,2 Andrew V. Schally,2 and Francisco Fernandez-Lima.1
1 Department of Chemistry and Biochemistry, Florida International University, Miami, FL.
2 Departments of Pathology and Medicine, Divisions of Hematology/Oncology and Endocrinology, Miller School of Medicine, University of Miami, Miami, FL.
Growth hormone – releasing hormone (GHRH) is a 44 residue hypothalamic peptide hormone that specifically stimulates the secretion and release of growth hormone from the anterior pituitary gland upon binding to its receptor. GHRH and its receptor are expressed in many human cancer cell lines and tumors as well as in other tissues including myocardium and pancreatic β cells. Understanding the action of GHRH on its target cells is important for the use of synthetic GHRH analogs, with prolonged half-lives, which may provide a promising scaffold for drug development. In the present work, a set of three GHRH agonists, MR-356, MR-406 and MR-409 and three GHRH antagonists, MIA-602, MIA-606 and MIA-690 were investigated using trapped ion mobility spectrometry coupled to mass spectrometry (TIMS-MS) to study the kinetically trapped intermediates species of these analogs as a function of the starting solution conditions (native conditions vs denaturing conditions) and as a function of the collision induced activation (CIA) prior the TIMS-MS measurements. Comparison between GHRH (1-29) and its synthetic agonist and antagonist conformational spaces and dynamics are described as a way to gain a better understanding of the conformation involved in the biological activity.
Synthesis of Ketene Dithioacetals
Jin Wang, Teng Yuan, Xiaodong Shi*
University of South Florida
ketene dithioacetals can be accessed using a gold-catalyzed reaction. Substrate scope, mechanism as well as synthetic applications of this transformation will be discussed.
Molecular Conductance and Electrochemical Studies of Nucleic Acids and Peptides
David H. Waldeck, Edward Beall, and Emil Wierzbinski
University of Pittsburgh
We present new results on charge transport in nucleic acids and chiral symmetry effects on electron transfer. Molecular conductance and electrochemical charge transfer are different manifestations of a molecule’s ability to transmit electric charge, and we report on experiments that compare the molecular conductance to the charge transfer rates. We present recent findings on the chiral induced spin-selectivity effect and its importance for understanding the fundamental nature of charge transfer and charge displacement
STRUCTURAL CHARACTERIZATION OF THE INTRINSICALLY DISORDER HMGA2 PROTEIN AND THEIR DNA COMPLEXES USING NANOESI-CIA-HDX-TIMS-MS
Alyssa Garabedian1; Prem Chapagain2; Fenfei Leng1,3; and Francisco Fernandez-Lima1,3*.
1 Department of Chemistry and Biochemistry, Florida International University, Miami, USA
2 Department of Physics, Florida International University, Miami, USA
3 Biomolecular Science Institute, Florida International University, Miami, USA
The mammalian high mobility group AT-hook 2 (HMGA2) is an architectural transcription factor traditionally characterized as being unstructured. This disordered-to-ordered transition has implicated HMGA2 as a protein actively involved in many biological processes. Additionally, the abnormal expression of HMGA2 has been linked to a variety of health problems including diabetes, obesity and oncogenesis. In this work, for the first time we take advantage of trapped ion mobility spectrometry coupled to mass spectrometry to study the conformational space of HMGA2 and their DNA-complexes, not accessible using traditional structural biology tools. Our experiments showed that HMGA2 monomer can exist as multiple kinetic intermediates with varying tridimensional structure (folded to unfolded transitions), regardless of the starting solution conditions. Moreover, HMGA2 complex with a short 22 base hairpin DNA can be preserved in the gas phase and shows multiple kinetically trapped conformational states. In contrast, HMGA2 complex with a longer 50 base hairpin DNA complex can also be preserved in the gas-phase and the number of kinetically trapped conformational states is greatly reduced by the higher number of intramolecular interactions (e.g. binding sites). When combined with molecular dynamics, for the first time, candidate structures were proposed for the HMGA2 and HMGA2-DNA kinetically trapped intermediates.
Computational Modeling of Human 3'-phosphoadenosine 5'-phosphosulfate Synthase HNGH motif
Chris Soha, Rudiger Ettrich, K.V. Venkatachalam
College of Medical Sciences, Health Professions Division, Nova Southeastern University, Ft. Lauderdale, FL-33328
The sulfur nucleotide PAPS (3’-phosphoadenosine 5’-phosphosulfate) is the universal sulfuryl donor of the cell. In mammals 3’-phosphoadenosine 5’-phosphosulfate Synthase (PAPSS), using ATP, converts biochemically inert inorganic sulfate to metabolically active PAPS. PAPS synthase is a bi-functional enzyme and catalyzes the formation of PAPS in two sequential steps. Prior experimental, site selected mutagenesis of human PAPSS HNGH motif (amino acid residues 425-428) revealed drastic changes in enzymatic activity. With this prior knowledge, retrospectively we first set out to calculate in silico, the binding energies of the wild type and the mutants using molecular modeling and dynamics. The binding of ATP in wild type was exothermic that required -40 kJ/mol energy. In mutant H425A, H428A it required 524 kJ/mol of energy for ATP binding, and change into alanine made it very endothermic and inactive as a catalyst. G427A mutant was endothermic, requiring binding energy of 218 kJ/mol. Interestingly, N426K was very exothermic which required even less binding energy (-70kJ/mol), matching with increased activity. With autodocking program, the pre-reaction position of inorganic sulfate was predicted. Two arginine (R522 and R421) of PAPSS1 were well poised with sulfate for nucleophilic attack with ATP.
ANALOG ORIENTED SYNTHESIS OF TERPENOID CORES: TOWARDS DOLESTANE AND PSEUDO-GUAIANOLIDE ARCHITECTURES
Fabien Emmetiere and Alexander J. Grenning
Department of Chemistry, University of Florida, Gainesville FL 32611-7200, USA
Terpene molecules are abundant in nature and a lot of them are relevant from a pharmaceutical standpoint. Unfortunately, the isolation of these terpenes remains very challenging since they must be extracted from living organisms allowing for no more than few milligrams to be recovered. In order to tackle this limitation, we have recently reported a simple and scalable methodology to access terpenoid cores using readily available reagents. Using this approach, simple cyclic ketones were converted to decorated 5-7 or 6-7 fused ring systems in only 4 steps. From these preliminary results, we were able to devise a strategy toward tricyclic natural products. Among them, dolestane and pseudo-guaianolide architectures are of particular interest in terms of synthetic challenges and potential latent biological activities. Recent results demonstrate that analogs of the targeted natural products can be synthesized.