Possible Undergraduate Research Projects

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List of types of available research projects

Your summer research project will enhance your educational experience by integrating research and education in active and collaborative research, and through individual mentoring and support networks.

Below are examples of research projects within the Chemistry Summer Undergraduate Research program. These change annually based on the interests of students and faculty. Please also see chem.psu.edu for the faculty research pages for more information.  Each summer, we have projects that emphasize synthesis, exploration and discovery, analysis, and computation, as well as combinations of these in collaborative teams of scientists.  We encourage you to consider not only projects of interest but also those that extend and enhance your learning.

Project 1: Functional Annotation and Characterization of Enzymes within the Radical S-Adenosylmethionine Superfamily
Faculty Mentors: Squire Booker, Carsten Krebs, Alexey Silakov, and Amie Boal

Project Description: Enzymes within the radical S-adenosylmethionine (SAM) superfamily catalyze a dazzling array of chemical transformations that proceed via free radical intermediates. Radical SAM (RS) enzymes use radicals derived from SAM to initiate catalysis by abstracting hydrogen atoms from their respective substrates. This project will focus on developing methods to annotate the functions of RS enzymes catalyzing unknown reactions. Students will learn how to generate sequence similarity and genome neighborhood networks to provide insight into function via 9 bioinformatics methods. They will also learn molecular biological techniques, such as cloning and site directed mutagenesis and gene expression. Lastly, they will learn how to purify and manipulate these oxygen-sensitive proteins under anaerobic conditions and characterize them using UVvis, EPR, ENDOR, HYSCORE and Mössbauer spectroscopies, x-ray crystallography and techniques.

Project 2: Catalytic Mechanisms of RNA Enzymes
Faculty Mentors: Philip Bevilacqua and Christine Keating

Project Description: It is well known that protein enzymes catalyze a diverse array of chemical reactions with exceptional rates and specificity. RNA is comprised of only four similar nitrogenous heterocycles, yet it too can catalyze chemical reactions and do so with remarkable rate acceleration and specificity. The surprising discovery that RNA can catalyze reactions is relatively recent and led to the Nobel Prize in Chemistry in 1989. Moreover, because RNA can also store genetic information, the notion of an RNA World in which RNA, or a related polymer, was key to the emergence of life has been advanced. This project will employ interdisciplinary approaches to understand how RNA catalyzes reactions. Students will be engaged in a combination of molecular biology, chemical kinetics, and bioanalytical techniques. In addition, there is the option to study chemical reactions that may have formed the first RNAs that were then copied to begin life.

Project 3: Elucidating the broad reaction profiles of iron and 2-(oxo)glutarate-dependent enzymes
Faculty Mentors: Amie Boal, Carsten Krebs, Marty Bollinger

Project Description. Iron- and 2-(oxo)glutarate-dependent (Fe/2OG) enzymes activate dioxygen and couple oxidative decarboxylation of 2OG to many reactions of importance to agriculture, bioremediation, and even blockbuster natural-product drugs. The Bollinger/Krebs and Boal research groups are deploying an arsenal of structural, biochemical, spectroscopic, and computational approaches to understand the structures and mechanisms of these and similar enzymes. The most exciting new directions concern several enzymes that mediate two or three distinct reaction types (e.g., hydroxylation followed by cyclization and/or desaturation) or drastically different outcomes in parallel (e.g., production of ethylene and three equivalents CO2 from 2OG in parallel with a "standard" hydroxylation of L-arginine). These sequential and divergent reactivities are certain to involve dynamic repositioning of substrates within the enzyme active sites to enable different substrates, different positions on the same substrates, or different outcomes to be targeted within the same active site. The combination of novel chemical mechanisms and active-site structural dynamics will make for rich vehicles for excited, aspiring young biochemists and biophysicists to study modern enzymology.

Project 4: Trapping and spectroscopic investigation of metalloenzyme reaction intermediates
Faculty Mentor: Alexey Silakov

Project Description. Metalloenzymes catalyze a wide variety of difficult reactions that, in a majority of cases, require a chain of chemical transformations. The Silakov group is interested in a novel hybrid class of metalloenzymes containing two catalytically active domains: a hydrogen-utilizing [Fe-Fe] hydrogenase and a rubrerythrin. It is hypothesized that hydrogen is heterolytically cleaved by the [Fe-Fe] hydrogenase domain to provide electrons and protons, which in turn are used by the di-iron site of rubrerythrin to reduce hydrogen peroxide to water. This REU project will focus on understanding the interaction between the two domains by means of trapping and characterizing intermediates in the reaction. REU students will learn to overexpress and isolate metalloenzymes, perform rapid-freeze quench experiments and characterize intermediates by electron paramagnetic resonance (EPR) and/or fourier-transform infrared spectroscopies. Students will also be provided with an opportunity to perform theoretical modeling of the experimental data using EPR simulation software and perform density functional theory calculations.

Research Topic: Dynamics of Biological Processes

Project 5: Viral RNA replication in motion
Faculty Mentors: David Boehr, Craig Cameron

Project Description: RNA viruses, including Zika, Ebola, hepatitis C and poliovirus, cause a number of acute and chronic diseases. The viral RNA-dependent RNA polymerase (RdRp) is the catalytic machinery responsible for the replication of these RNA genomes. The central objective of this project is to exploit our ability to use solution-state NMR to “watch” the RdRp reaction to elucidate the conformational states governing each step of the nucleotide addition cycle. Our insights can be leveraged towards the rational design of new anti-viral drugs and vaccines. REU students on this project will learn state-of-theart, high-dimensional NMR techniques as they pertain to understanding protein structure and dynamics. These NMR methods will be complemented by other spectroscopic and calorimetric methods, along with other biochemical and molecular biology techniques.

Project 6: Engineering new regulatory activities into enzyme catalysts
Faculty Mentor: David Boehr

Project Description: The Boehr lab is interested in the development and engineering of new stimulusresponsive enzyme catalysts. Enzymes can be viewed as small-world networks of amino acid residues connected through noncovalent interactions. Using solution-state NMR methods, we have identified amino acid networks that stretch from the surface of enzymes into their active sites. These networkassociated, surface residues are potential attachment points for new regulatory modules, which would tune catalysis in response to ligand-binding and/or changes to physical parameters (e.g. pH, lightactivation). An REU student on this project will learn approaches to covalently modify proteins, protein NMR methods to identify changes to the amino acid network, and kinetic and biological methods to determine changes to enzyme function. These studies can be leveraged towards designing new biological systems for improving applications in industry and biomedical research, including the biological syntheses of new fuels and pharmaceuticals.

Project 7: Probing glutathione trafficking in cell
Faculty Mentor: Joseph Cotruvo

Project Description: Glutathione (GSH) is a ubiquitous thiol-containing tripeptide present at millimolar concentrations in eukaryotes and many prokaryotes. Although the effects of alterations in GSH redox potential are well known, dramatic yet regulated fluctuations in total GSH levels also occur during apoptosis and as a part of the normal cell cycle in nuclei. GSH is also elevated in many cancers. The mechanisms and physiological targets of these redistributions are almost completely unknown. The Cotruvo lab has developed protein-based fluorescent sensors that respond to GSH selectively and that can be targeted to organelles to probe the proteins involved in GSH movement within cells. In this project, students would aid in sensor optimization and targeting to organelles of interest, and investigate putative transporters via genetic knockdown. The REU student would gain experience in a variety of biochemical and chemical biology methods such as protein engineering, protein purification, molecular biology, mammalian cell culture and transfection, and confocal microscopy.

Project 8: Understanding Macromolecular dynamics
Faculty Mentors: Scott Showalter and Will Noid

Project Description. A central problem in modern physical biochemistry is to quantify the conformational dynamics of highly flexible biological macromolecules, such as intrinsically disordered proteins, and then to establish the connection between those dynamics and molecular function. This REU project will focus specifically on the role of conformational dynamics in producing specific and reversible proteinprotein and protein-nucleic acid interactions that drive the process of gene transcription. REU students will gain experience with recombinant protein expression in bacterial cell culture as well as protein purification and characterization. Depending on the interests and background of the individual student, projects will emphasize different areas of analytical and physical chemistry, including high-resolution NMR spectroscopy, mass spectrometry, micro-calorimetry, and functional assays involving introductory mammalian cell culture, as well as computational analyses to generated detailed molecular structure sets for highly flexible biomolecules.

Project 9: Unraveling the Molecular Mechanism of Chemotaxis
Faculty Mentors: Paul Cremer, Ayusman Sen

Project Description. It has been found that receptor molecules, such as porphyrins, nanoparticles and proteins, can migrate up a concentration gradient of their corresponding ligands. This phenomenon, which is called chemotaxis, may have physiological consequences and can be exploited to create a new generation of nanomotors that respond to subtle changes in the chemical environment of the surrounding medium. We are exploring ligand-receptor binding systems to determine the underlying molecular mechanism of this process as well as to build a new generation of devices that can produce chromatographic separation of receptor materials. Significantly, many of the proteins that display chemotaxis are also enzyme-based catalysts wherein their ligand fuel may provide a direction of motion for the substrate. Students involved in this project will obtain a unique opportunity to study the motion of nanomaterials using novel spectroscopic techniques as well as help in the development of microfluidic platforms and assays.

Project 10: Chemically-Powered Autonomous Active Matter
Faculty Mentor: Ayusman Sen

Project Description. Self-powered nano and microscale moving systems are currently the subject of intense interest due in part to their potential applications in nanomachinery, nanoscale assembly, robotics, fluidics, and chemical/biochemical sensing. REU projects will involve the design, characterization, and study of autonomous, chemically powered, particles. One of the projects will involve the fabrication of bimetallic nanorods and the examination of their movement arising from redox reactions occurring at the two-ends of the rods. The second project will involve the synthesis of enzyme-anchored particles powered by catalytic reactions and the study of their collective behavior in the presence of external and internal stimuli. Such systems can be further configured to observe predator-prey behavior among the swimmers, where groups of particles functionalized with different enzymes will form interaction cascades and display emergent dynamic patterns. The projects will expose the REU students to a variety of synthesis and materials characterization techniques, More broadly, the students will learn how chemistry, physics, nanotechnology, and fluid dynamics can be integrated to create synthetic materials that exhibit unprecedented biologically-inspired behavior.

Project 11: How Translation Kinetics Alters Enzyme Activity
Faculty Mentor: Ed O’Brien

Project Description: The specific activity of enzymes changes depending on the rate at which the ribosome synthesizes the enzyme during the elongation phase of translation. The molecular origins of this phenomenon is unknown, although the most likely hypothesis is that translation kinetics alters cotranslational folding events that influence the population of soluble, but kinetically-trapped non-functional protein molecules. The goal of this project is to understand the extent to which protein structure around the active sites of enzymes can be perturbed by changes in codon translation rates. REU students working on this project will use in-silico coarse-grained models developed in the O’Brien Lab to simulate the synthesis of different cytosolic enzymes, such as Luciferase and EgFABP1, that have been experimentally shown to exhibit altered specific activity. REU students will gain experience in computer coding, molecular dynamics simulations, and statistical and kinetic analyses of simulation trajectories. And ultimately, they will help contribute to the emerging paradigm about how kinetics more than thermodynamics determines protein structure and function.

Research Topic: New Insights into Chemical Catalysis

Project 12: Discovery of New Heterogeneous Catalysts

Faculty Mentor: Ray Schaak

Project Description: Catalysts can facilitate chemical reactions that otherwise would be kinetically and/or economically prohibitive. The discovery of new catalysts can therefore enable new types of reactions and also improve the efficiency and/or selectivity of existing reactions, which in turn can lead to new applications. In this project, REU students will engage in multi-disciplinary efforts to discover new heterogeneous catalysts that are relevant to applications in solar energy conversion, fuel cells, and target-oriented organic synthesis. Representative types of catalytic transformations include the oxygen evolution reaction, the oxygen reduction reaction, CO2 reduction, and selective hydrogenations and oxidations. Students will first synthesize a variety of solid-state materials as nanoparticles, films, powders, and single crystals, and then analyze them using a suite of materials characterization and catalytic testing techniques. Inspiration for target catalytic materials will be drawn from computational and mechanistic predictions, as well as from structural and compositional analogies with known homogeneous and biological catalysts.

Project 13: Molecular Scale Heat for Catalysis of Molecular Transformations
Faculty Mentor: Benjamin Lear

Project Description: Catalysis is the foundation of the modern chemical economy, allowing the accomplishment and commercialization of reactions that would otherwise be cost and energy prohibitive. The traditional means of increasing catalytic efficiency is to modify the catalyst to lower the barrier for any given specific reaction. The Lear laboratory’s approach is different: they modify the means by which heat is distributed to the catalyst. This REU project will focus on understanding how to use the properties of nanoparticles to control more precisely the distribution of this heat, and to understand the impact that this increased control has over the efficiency of catalyzed reactions. Students involved in this project will design and synthesize nanoparticle systems and characterize these systems using microscopy and diffraction techniques. They will then incorporate the nanoparticles into catalytically primed reaction mixtures and measure the efficacy of the photothermal effect for driving catalysis using a variety of analytical techniques.

Project 14: Earth Abundant Nanocrystalline Catalytic Materials for Solar Fuels
Faculty Mentors: John Asbury and Ray Schaak

Project Description: A central problem in the development of solar power as an alternative energy supply is the ability to store the energy for later use when the sun is not shining. Catalytic materials based on inexpensive and earth-abundant elements are attractive alternatives to noble metal and rare-earth catalysts. This REU project will work toward development of new earth abundant nanocrystalline materials systems that enable high efficiency photocatalysts for hydrogen production and oxygen evolution. This REU project will involve use of inorganic solution chemistry methods to synthesize novel metal-phosphide catalysts with a variety of structures. These catalysts will be coupled to light absorbing copper-zinc-tin-sulfide nanocrystals to combine light harvesting and catalysis together in the same system. A variety of materials characterization methods (TEM, XRD, FTIR, UV-Vis, and TGA/DSC) and time-resolved spectroscopies will be used to examine photocatalytic reactions at the catalyst surfaces. The corresponding surface chemistry and photocatalytic activity will be characterized by monitoring the evolution of hydrogen and oxygen gases.

Project 15: Exploring the Oxidation of Membrane Lipids upon Transition Metal Ion Binding
Faculty Mentor: Paul Cremer

Project Description: Phosphatidylserine and phosphatidylethanolamine lipid headgroups both contain amine moieties that can bind tightly to first row transition metal ions. In the presence of an oxidant, such as hydrogen peroxide, ions like Cu2+ will catalyze the generation of hydroxyl radicals, which can lead to the oxidation of membrane double bonds through a combination of the Fenton and Haber Weiss reactions. Such oxidative damage ultimately leads to the lysis of the membrane and may be associated with neurodegenerative diseases like Alzheimer’s and Parkinson’s as well as developmental disorders like autism. Oxidative damage is more likely to occur in vivo when the concentration of metal ions is no longer tightly regulated (i.e. metal ion dyshomeostasis).  An REU student working on this project will get the opportunity to explore membrane oxidation chemistry as a function of the lipid headgroup identity, the charge on the membrane, and the positions of double bonds. Specifically, the REU student will learn to use microfluidic platforms and fluorescence microscopy to explore the kinetics of membrane oxidation. Skills will be taught concerning the fabrication of supported membranes, the use of fluorescence recovery after photobleaching (FRAP), and the making of kinetics measurements at interfaces.

Project 16: Folded Polymer Nanoreactors for Photocatalysis
Faculty Mentor: Beth Elacqua

Project Description: Compartmentalization is one of Nature’s design principles:  enzymes are ‘catalogued’ and can be shielded from reactive/incompatible environments, or partitioned such that synergistic functions like catalysis are optimized.  Generally, enzymes are attractive catalysts for synthetic organic transformations, yet, despite the emergence of highly-evolved biocatalysts, many are limited to the stepwise catalysis of naturally-occurring reactions and demonstrate markedly less selectivity in synthetic systems.  Artificially-constructed metalloenzymes continue to provide systems that are scalable for practical synthetic methods.  Although the diversity and complexity of natural systems is extraordinary, limitations on building blocks do exist, while synthetic systems equip chemists with an unlimited functional building units to engineer robust materials.  Coupled with the continued development of supramolecular approaches to mediate self-assembly, synthetic approaches that comprise enzyme-like features are realizable.  The Elacqua lab aims to develop Nature-inspired polymer nanoreactors that function in photo-controlled self-assembly and dual/tandem catalysis.  The REU student would gain experience in organic and polymer synthesis, photochemistry, and catalysis, along with spectroscopic and light scattering techniques.

Project 17: Systematic coarse-graining of polymers and complex fluids
Faculty Mentor: Will Noid

Project Description: Computational studies with atomically detailed models have contributed profound insight into molecular structure, dynamics, and interactions on the nano-scale.  However, many important phenomena occur on length- and time-scales that are inaccessible to atomically detailed simulations.  Consequently, lower-resolution "coarse-grained" (CG) models play an essential role in understanding phenomenon on meso- and macro-scales.  In this project, students will gain experience in developing and applying CG models that are not only exceedingly efficient, but also provide a remarkably accurate description of molecular structure and interactions.  Additionally, students may gain insight into how "generic" CG models can provide powerful, albeit qualitative, insight into the fundamental mechanisms driving many emergent phenomena.  Participating students can gain experience in rigorous statistical mechanical theories, software development for advanced computational methodologies, and state-of-the art molecular simulations.