Boston University Groups welcoming PROSTARS CC students for summer research

 

Inorganic/Bioinorganic Chemistry John Caradonna Linda Doerrer Sean Elliott Tom Tullius		Organic Chemistry   Mark Grinstaff James Panek John Porco Scott Schaus John Snyder
Theoretical Chemistry David Coker Tom Keyes John Straub Feng Wang		Physical Chemistry/Chemical Physics Rosina Georgiadis Bennett Goldberg Larry Ziegler
Biological Chemistry/Biology John Celenza Thomas Gilmore Pinghua Liu Dean Tolan

1. Understanding the Chemical Basis of the Genetic Disease Phenylketonuria (PKU) – Professor John Caradonna, Chemistry Department – Inorganic/Bioinorganic Chemistry

The Caradonna Group is investigating the chemistry of phenylalanine hydroxylase (PAH), a non-heme iron pterin-dependent monooxygenase that catalyzes the conversion of phenylalanine to tyrosine.  Defects in PAH, which cause classic phenylketonuria (PKU), increase serum phenylalanine concentrations and result in abnormal accumulation of phenylalanine-based metabolic products.  These products cause defective myelination of the central nervous system and result in postnatal brain damage and severe mental retardation.  PKU is the most common inborn error in amino acid metabolism of clinical importance (1 in 50 individuals carry the disease trait, with an average incidence of 1 in 10,000 for Caucasians).  The non-heme iron PAH-active site is of additional interest because it performs the same spectrum of chemical transformations as cytochrome P450 without benefit of a heme prosthetic group.  The Group utilizes a variety of enzyme mechanistic, molecular biological, and biophysical techniques to investigate the mechanism of both wild type enzyme and selected mutants that induce PKU in humans.  The PROSTARS CC student will be taught how to perform standard gene manipulations to generate missense mutations of PAH that are of clinical interest.  The student will then learn how to over-express, purify, and characterize the resulting PKU-inducing enzyme using protein purification methods already developed in the lab for this purpose.  Detailed enzyme kinetic studies using optical (UV/vis) spectroscopy and mass (LCMS) spectrometry will enable the description of the mechanism followed by these mutations and aid in the identification of the particular step(s) in the mechanism that the genetic mutation has altered.  These observations will then be placed in the context of crystal structures of these mutant enzymes in the presence of substrate and/or cofactor to offer a detailed description of this important genetic disease. 

2. Identification of the cellular targets of camalexin, a plant natural product with cytotoxic properties – Professor John Celenza, Biology Department – Chemical Biology

Plants synthesize a great variety of secondary metabolites from amino acids. Many of these metabolites are used as defense against pathogen attack.  In the mustard Arabidopsis thaliana, tryptophan is used as a precursor for the antimicrobial compound camalexin.  While camalexin is cytotoxic to eukaryotic cells, its mode of action is unclear.  The goal of the Celenza Group is to exploit the power of yeast genetics to learn which normal cellular mechanisms are targets of camalexin.  The yeast Saccharomyces cerevisiae is a single-celled eukaryotic organism, and it is likely that knowledge gained from studying the biological effects of camalexin in yeast will be applicable to animal cells.  Recently, the Group has established growth conditions to screen for yeast mutants with altered sensitivity to camalexin.  The PROSTARS CC student will screen through a large arrayed collection of yeast mutants to identify strains with more or less sensitivity to camalexin.  This collection contains over 5500 yeast strains, with each strain containing a loss-of-function mutation in a different yeast gene.  This collection contains mutations in all yeast genes that are not required for viability.  Any strain that has an altered response to camalexin can be traced back to a specific gene and function. 

3. Condensed Phase Excited State Dynamics – Professor David Coker, Chemistry Department - Theoretical Chemistry

When molecules are photoexcited in solution they relax by various means, including loosing energy to their environment or by breaking bonds and reacting. The Coker Group conducts research directed at understanding these processes. In their projects, they use and develop new theoretical and computational methods to explore how electronic and vibrational excitation of reactant molecules in different environments can influence the outcome of chemical reactions of these molecules. Electronic and vibrational relaxation of excited reactants is, in general, fundamentally quantum mechanical in nature so the methods they use must accurately describe the transfer of energy between the classical environment and the quantal reactive system.

 

4. Synthesis of Manganese Aryloxide Compounds Relevant to O2 Production in the Water Oxidation Cluster – Professor Linda Doerrer, Chemistry Department – Inorganic/Materials Chemistry

One of the outstanding mysteries in bioinorganic chemistry is the mechanism by which the {Mn4Ca} water oxidizing complex (WOC) or oxygen evolving complex in photosystem II in plants functions.  Photosystem II is part of the photosynthetic process that brings visible light, CO2, and water together to make carbohydrates and oxygen.  It is known that a cluster of four manganese atoms and one calcium atom is critical for this functioning, as well as the participation of a tyrosine residue from the protein environment.  The reactive moiety in the tyrosine residue is a phenolic hydroxyl group.  The Doerrer Group is synthesizing first-row transition metal complexes with phenoxide anions, and they are interested in extending this chemistry to manganese to mimic WOC.  The PROSTARS CC Student will learn how to synthesize transition-metal complexes in the absence of H2O and O2 and characterize them.  Characterization techniques include NMR, UV-Vis, and IR spectroscopy, as well as solid state magnetism and single crystal X-ray diffraction.  Successful efforts in the first stages of the project could lead to more advanced work in the project such as reactivity studies. 

5. Protein Electrochemistry of Biological Disulfide Bonds – Professor Sean Elliott, Chemistry Department – Inorganic/Bioinorganic Chemistry

The Elliott Group's research centers on the use and development of protein electrochemistry to ask fundamental questions about how biological systems tune and control the redox chemistry of fast and reversible processes.  Projects study the structure-function relationship of biological electron transfer in model systems that include: simple electron transfer proteins (cytochromes c551 and thioredoxins), complex cytochromes that contain as many as ten heme units, and multi-electron redox enzymes containing several redox cofactors. The work encompasses traditional enzymology, molecular biology, surface science and electroanalysis. The Group's efforts have benefited greatly from the contribution of undergraduate researchers, and one such UROP student pioneered its studies of the disulfide bond electrochemistry of the protein thioredoxin (Trx).  A PROSTARS CC investigator will continue this work by constructing and examining novel Trx mutant proteins that are proposed to have greatly modulated redox characteristics.  The protein sequence of a single loop motif (-CXXC-) is hypothesized to act as a ‘rheostat’ of the thioredoxin midpoint potential.  Thus, the PROSTARS student will begin her/his project initially collaborating with current group members to design a mutation in this loop that should greatly perturb the potential.  In subsequent experiments, the student will generate the site-directed mutant, prepare the pure mutant protein, conduct the electrochemical analysis, and analyze the resulting data. 

6. Physical and analytical chemistry of interfaces:  Surface Plasmon Resonance Spectroscopy Laboratory – Professor Rosina Georgiadis,
Chemistry Department – Physical/Analytical Chemistry

The Georgiadis Group’s research focuses on the development and use of novel label-free detection methods based on surface plasmon resonance (SPR) spectroscopy.  Current projects involve the development of label-free DNA microarray technologies.  Areas of study include: electric field effects at interfaces (rapid mismatch discrimination by electric field induced denaturation); DNA/protein interactions (screening methods for anti-tumor aptamers as tumor targeting reagents); DNA/drug interactions (kinetics of binding novel platinum anti-tumor drugs with oligonucleotides).  A PROSTARS CC student would be assigned to a particular label-free microarray application, learning to prepare the materials for screening, to use the surface plasmon spectroscopy apparatus, and to interpret the resulting data.

7. Thiol-reactive inhibitors of the NF-kB signal transduction pathway –Professor Thomas Gilmore, Biology Department – Chemical Biology

The NF-kB signal transduction pathway regulates a variety of key organismal and cellular processes, including various immune responses, certain developmental processes, and cell proliferation and survival.  In addition, the NF-kB pathway is mis-regulated in many human diseases, including a variety of inflammatory diseases and cancers.  As such, there is great interest in developing chemical probes to understand the proteins involved in this pathway and chemicals that can specifically modulate NF-kB activity.  In collaborative studies with Professor John Porco (Chemistry), the Gilmore Group has been characterizing the anti-NF-kB activity of several natural product-derived compounds.  In these studies, they seek to identify the targets for these drugs in the NF-kB pathway and to understand how these compounds affect NF-kB signaling.  Several of these compounds appear to target thiol groups in cysteine residues on target proteins.  Therefore, in this project, a PROSTARS CC student would use a variety of cellular, molecular, and biochemical assays to identify and characterize novel natural product-based inhibitors of the NF-kB pathway.  These approaches include tissue culture experiments, Western blotting, DNA-binding assays, site-directed mutagenesis, and in vitro kinase assays.

8. Nanoscience and Nanotechnology - Professor Bennett Goldberg, Physics Department – Chemical Physics

Current research focus includes nanoscale imaging of subcellular processes and interferometric determination of DNA dynamics on surfaces. Near-field imaging of photonic bandgap, ring microcavity and single-mode waveguide devices identifies internal mode structure and informs resonant biosensor fabrication and development of waveguide evanescent bio-imaging techniques. Subsurface solid immersion microscopy for Si inspection and thermal imaging is being extended to high collection efficiency for quantum information processing in single quantum dots.  Room and low-temperature resonant Raman scattering and fluorescence of single nanotubes allows unprecedented spectroscopic study.

9. New Polymeric Materials for Medicine - Professor Mark Grinstaff, Chemistry Department – Organic/Macromolecular Chemistry

In one of its current research projects, the Grinstaff Group is designing, synthesizing, and characterizing novel dendrimers, termed “biodendrimers,” for tissue engineering and biotechnological applications. Currently, they are evaluating these novel biomaterials for the repair of corneal lacerations, for the delivery of anti-cancer drugs, for the delivery of DNA, and as temporary biodegradable scaffolds for cartilage repair. In a second project, they are creating novel polymeric coatings termed “interfacial biomaterials” that control biology on plastic, metal, and ceramic surfaces. In a third project, they are designing electrochemical-based sensors/devices using conducting polymer nanostructures and specific DNA structural motifs.

10.  Theoretical Biophysical Chemistry - Professor Tom Keyes, Chemistry Department - Theoretical Chemistry

The Keyes Group research focus is theoretical biophysical chemistry. Current projects are the mechanism and dynamics of protein folding, binding of ligands to proteins, properties of bulk and interfacial water, all-atom descriptions of viruses, and 'theory of experiment' for the associated spectral probes. Overall themes are: 1) the idea that classical mechanics is more broadly applicable than is generally realized, so long as induction, or polarization - the creation of dipoles by local electric fields - is accurately included. Thus they construct classical theories of nonlinear IR and Raman spectroscopy,  consider that ligand binding occurs via classical 'electrostatic bonds', and have developed the POLIR polarizable potential for water; 2) formulating theories in terms of the multidimensional potential energy surface, or landscape; and 3) developing intelligent or accelerated simulation algorithms for these computationally intensive problems.

11. Mechanistic studies on C-P bond containing natural products –Professor Pinghua Liu, Chemistry Department – Biological Chemistry

Synthetic C-P bond containing compounds (phosphonates) have been widely used as pesticides.  Phosphonates are also found in nature and most of them have biological activities.  The mechanistic studies on C-P bond-containing natural products in the Liu Laboratory are addressing the following two questions: 

1. How is the C-P bond formed enzymatically? and

2. How are these phosphonates degraded in nature? 

The only C-P bond formation enzyme characterized to date is phosphoenolpyruvate mutase.  The analysis of C-P containing natural products indicates that there must be other enzymatic methods to form the C-P bonds.  The PROSTARS CC student would learn the basic molecular biology skills to clone a C-P bond formation enzyme discovered in one of collaborators’ laboratory, the fortimicin KL1 methyltransferase.  He/she would then work with one of the post-doctoral fellows (Dr. Youli Xiao) in the laboratory to learn organic synthesis in aqueous solution, which is different from traditional organic synthesis.  The success of the proposed studies will lay the groundwork for more detailed mechanistic studies of these unique transformations in the future.

12. Advances in the Stereocontrolled Synthesis of Complex Natural Products – Professor James Panek, Chemistry Department – Organic/Synthetic Chemistry

Research in the Panek Laboratory centers on the design and development of new methods for the stereocontrolled synthesis of complex organic molecules. Serving as inspiration for reaction development, natural product targets are chosen based on their novel architecture and biological activities.  Once the scope of a methodology is determined, it is utilized in the stereocontrolled synthesis of a natural product or a group of related natural product targets.  These natural product targets then provide opportunities for the preparation of chemical entities through diversity-oriented synthesis.  The objectives are to enhance structural diversity available from Nature and to prepare molecules with novel chemical or biological properties. These studies are often carried out in conjunction with the Center for Methodology and Library Development at Boston University (CMLD-BU).  The PROSTARS CC student’s experience would include experiments involving methodology development and the stereocontrolled synthesis of complex natural products.  Other options include the synthesis of chemical libraries in collaboration with the CMLD-BU. The PROSTARS CC student would be actively involved in contemporary synthetic methods and using modern analytical techniques.

13. Studies Towards the Synthesis of Complex Molecules – Professor John Porco, Chemistry Department – Organic/Synthetic Chemistry

The Porco Laboratory focuses on the development of new methodologies for chemical synthesis of complex molecules.  Natural product targets are selected based on the presence of novel, challenging functionality and the likelihood for development of new methodologies (A). This functionality ultimately drives development of new reaction processes (B). Utility of methodologies is then demonstrated in the context of complex, target-directed synthesis (C.)  Complex target molecules then provide opportunities for the preparation of new structures (D, “diversity exploration”) with a goal to increase the structural diversity available from Nature and prepare molecules with novel chemical or biological properties. A key aspect is parallel synthesis for development and optimization of chemical transformations. The latter studies are conducted in conjunction with the CMLD-BU.  The PROSTARS CC project will involve complex natural product synthesis or the synthesis of chemical libraries in collaboration with the CMLD-BU. The PROSTARS CC student would learn synthetic organic techniques, including running reactions under inert conditions, as well as running and interpreting NMR spectra.

14. Research in the Chemical and Biological Sciences – Professor Scott Schaus, Chemistry Department – Organic/Chemical Genomics

The Schaus Laboratory develops new chemical methodologies, synthesizes natural products and small molecules that possess interesting biological activities, and applies techniques in chemical genomics to study the effects of compounds on cellular processes.  The group uses chemical synthesis, functional genomics, and bioinformatics to gain further understanding into the effects of antiproliferative compounds on cellular processes. The research approach creates an integrated training environment, encouraging students to identify and develop research projects that address fundamental questions in chemistry and biology.  The diverse array of research projects undertaken in the Schaus Group work synergistically toward the development of a new asymmetric methodology and its subsequent application as they synthesize interesting natural products and develop and use techniques in genomics and biology to understand how these compounds affect cellular processes. Their work in chemical methodology has focused on the development of direct asymmetric carbon-carbon bond-forming reactions. A reaction they have been studying is the Morita-Baylis-Hillman (MBH) reaction; a long-standing challenge in asymmetric catalysis. Their approach has been to concentrate on the phosphine-promoted reaction. They have successfully identified a highly enantioselective Brønsted-acid catalyzed MBH reaction.  The reaction not only addresses a gap in asymmetric synthetic methodology but also identified a unique example of chiral Brønsted acid catalysis. Future work will focus on developing the reaction for use in synthesis.  They plan to use the reaction as a key step in the synthesis of the pycnanthuquinones, natural products with a unique mode of overcoming the symptoms of type 2 diabetes mellitus. A PROSTARS CC student working on this project would learn the basic techniques of synthesis and purification, chiral HPLC analysis, preparative LC methods, and multinuclear NMR analytical techniques.

15. New Chemistries for Scaffold Synthesis for Small Molecule Libraries - Professor John Snyder, Chemistry Department – Organic/Synthetic Chemistry

The discovery of new drug candidates and biological probes often begins with the discovery of new chemistry and compounds of unusual structure rich in stereochemistry that go beyond what nature can manufacture.  The Snyder Group focuses on the discovery of new chemistries for the synthesis of unusual heterocycles and natural product-like scaffolds that can be exploited in the preparation of small molecule libraries.  Thus, it is important that these new scaffolds have a minimum of three possible diversification points for library development.  One project is automated reaction prospecting whereby eight or more different catalysts will be screened in parallel for their ability to promote unusual reactivity between a standard reactant, for example alkynyl nitrile 1 (Scheme), with a series of up to ten co-reactants. This protocol creates an 8 X 10 reaction matrix. The PROSTARS student would learn to run these screening arrays and analyze the products by LC-MS.  After identifying chemistry of interest, the student will scale-up the reaction for more accurate structure identification (NMR) and then expand the scope of the chemistry with a greater variety of co-reactants to create a small molecule library. Once prepared, these libraries will be submitted for bioactivity screening through the CMLD-BU for a variety of activities, including antiviral and antituberculosis activities, CNS related receptors and others.

16. Computer simulation of amyloid peptide aggregation using all atom protein models – Professor John Straub, Chemistry Department – Theoretical Chemistry/Bioinformatics

Human islet amylin polypeptide (IAPP) is a 37-residue peptide produced in the pancreas.  Amylin is cosecreted with insulin and its normal function is associated with glucose metabolism. In certain individuals, it contributes to insulin resistance, thereby playing a key role in the initiation of non-insulin-dependent diabetes (type II) mellitin (NIDDM).  It is believed that individuals with NIDDM have amyloid deposits formed by the association of human amylin.  While human amylin peptide aggregates, rat amylin does not aggregate under similar conditions.  Based on sequence comparison between human and rat amylin, it is suspected that the ten residues in the region 20-29 are largely responsible for the association of human amylins.  Fragment 20-29 can form fibrilar structures that have a distinct morphology; fragment 30-37 was also shown to be critical for fibril formation.  A PROSTARS CC student would be directly mentored by a senior graduate student in the Straub Laboratory in working to simulate the aggregation of human and rat IAPP.  A goal of the study will be to simulate the system at length to characterize the conformational fluctuations that may lead to the “nucleation” of secondary structural elements, and to understand in detail the role of sequence in aggregation of the peptide.  Simulations of the amylin aggregation equilibrium will be carried out as a function of the temperature and solution conditions.   State-of-the-art computational algorithms and computing resources in the Boston University Center for Computational Science will be employed.  The PROSTARS CC student would be involved in discussions with the experimental collaborators to develop a good knowledge of both practical and theoretical aspects of our studies.

17. Substituted polyhydroxylated pyrrolidines as substrate analogs for glycolytic enzymes –Professor Dean Tolan, Biology Department –
Chemical Biology

The Tolan Group research focuses on the chemistry at the active site of the glycolytic enzyme, fructose 1,6-bisphosphate aldolase.  The enzyme catalyzes the opening of the hemiketal ring of b-D-fructose-furanose 1,6-(bis)phosphate prior to covalent catalysis resulting in the cleavage of the C3-C4 bond.  Little is known about the site or mechanism of ring opening catalyzed by aldolase.  They have developed both steady-state and pre-steady state kinetic assays, as well as the ability to determine structures by X-ray crystallography so that they can study this activity of the enzyme.  Substrate analogs where the ring cannot be opened are required for this work, which can be synthesized as a deoxy-pyrrolidine ring at the hemiketal carbon.  The PROSTARS student in this program would be assigned to an individual series of synthetic steps leading to specific labeling of the carbon skeleton.  The synthesis, purification, and product analysis will allow the student to apply her/his basic organic chemistry knowledge to the research laboratory setting.  The use of the purified final product in pre-steady state kinetic analysis, X-ray crystallography, and data collection will also be conducted.

18. A structural map of the human genome - Professor Thomas Tullius, Chemistry Department – Bioinorganic Chemistry/Bioinformatics

The hydroxyl radical is a powerful chemical probe of DNA structure, which can be used to obtain detailed information on the structure of long stretches of DNA.  The Tullius Group has recently constructed a database of hydroxyl radical-generated DNA structural data.  In research supported by the ENCODE Project of the National Human Genome Research Institute of the NIH, they are using this database to make a structural map of the human genome.  They are concentrating their efforts on understanding the role of the noncoding regions of the human genome that are involved in the regulation of gene expression, and in directing the architecture of chromosomes. The structural maps of genomic DNA that their work will produce will add a new dimension to understanding of the workings of the human genome.  An PROSTARS CC student would work with graduate students in the group to add new data to the hydroxyl radical cleavage pattern database by performing the hydroxyl radical DNA cleavage reaction on new DNA sequences and analyzing the reaction products using an advanced capillary electrophoresis-based automated DNA sequencing instrument. A PROSTARS student with a background and interest in computers and computation could work with members of the Tullius Group who are part of the Boston University Graduate Training Program in Bioinformatics, to devise new computational methods to find and understand structural patterns in the human genome.

19. New Methodology for Simulation of Very Slow Biological Processes - Professor Feng Wang, Chemistry Department– Theoretical Chemistry/Computer Simulation

One of the research interests of the Wang Group is the development of the Basin Hopping Kinetic Monte Carlo (BHKMC) methodology to simulate slow dynamic processes.  Standard molecular dynamics simulations usually cannot properly address processes that occur over a time period of more than a few nano-seconds.  This limitation rules out straightforward application of these methods to many biological processes that are taking place at a much slower rate.  The Wang Group is developing a method that combines basin hopping Monte Carlo, a transition state search algorithm, and Kinetic Monte Carlo to model very slow reactions.  Biological applications of the method include modeling of ion channels and protein-ligand docking. In the flexible protein-flexible ligand docking problem, the docked geometry is usually not known a priori.  The theoretical determination of the docking rate of such a process is challenging since most methods that calculate reaction rate would require the prior knowledge of the initial and final structures. The BHKMC method does not require the prior knowledge of the final structure, which makes it a very powerful tool for studying such docking problems. The BHKMC is being implemented and tested on simple model systems in our group. The PROSTARS student would learn to use the BHKMC code and to test it by running simulations of ion transport through biological channels and comparing with experimental results.

20. Professor Larry Ziegler, Chemistry Department and PhotonicsCenter - Physical Chemistry

The Ziegler Group has three projects on which the PROSTARS CC student can engage in research: “Surface-Enhanced Raman Scattering (SERS) Detection of Pathogens” -- SERS is being exploited for the detection and identification of bacterial cells and viruses.  A novel gold or silver nanoparticle substrate has been developed which allows the observation of SERS spectra down to the single cell level, in about 10 seconds of data acquisition time using just milliwatts of incident laser power.  The unique vibrational fingerprints allow numerical algorithms to be used for diagnostic purposes much faster than currently employed culturing or PCR based methods. "Ultrafast carrier dynamics in wide band gap semiconductor materials" -- Femtosecond measurements are carried out on wide band gap materials, such as pure and doped GaN in order to learn about the properties of these semi-conductors in their conduction bands.  These materials are of importance for the development of blue-UV LEDs, lasers and solar energy devices.  Following femtosecond pulse excitation, a large variety of electronic and nuclear frame phenomena spanning time scales from 10's of femtoseconds to 10's of nanoseconds result before equilibrium is re-established in these novel materials. "Ultrafast IR spectroscopy" -- Femtosecond pulses tunable throughout the IR are used to study a wide variety of phenomena using pump-probe and multidimensional techniques.  These methods are applied to: a. the study of energy relaxation in water, the most ubiquitous solvent;  b. the study of fluctuations in super critical fluids, which are central to understanding their special solvation properties on a molecular level and c. the role of lipids and proteins in unraveling the mechanism of generalized anesthetics.