Research from the Dunham Lab Wins Cozzarelli Prize

Congratulations to Dr. Christine Dunham and colleagues on their recent publication in Proceedings of the National Academy of Sciences. This manuscript has won the journal’s Cozzarelli Prize, which recognizes one outstanding contribution each year to each of the six disciplines of the National Academy of Sciences and celebrates “scientific excellence and originality”.

The manuscript entitled “Mechanism of tRNA-mediated +1 ribosomal frameshifting” discusses ribosomal frameshifting, a perturbation of the protein assembly process. With an enhanced understanding of this process, we can begin to understand more about how proteins are synthesized as well as how some antibiotics can hijack this process and re-engineer it for new applications.

To read more about this, click [here]!

November Research Round-Up

Congratulations to our amazing research teams here in the Department of Chemistry for their publications this month!

Bowman Group:

Chen, Q., & Bowman, J. M. (2018). Quantum approaches to vibrational dynamics and spectroscopy: is ease of interpretation sacrificed as rigor increases?Physical Chemistry Chemical Physics.

Yang, B., Zhang, P., Chen, Q., Stancil, P., Bowman, J. M., Naduvalath, B., & Forrey, R. C. (2018). Inelastic Vibrational Dynamics of CS in Collision with H2 Using a Full-dimensional Potential Energy SurfacePhysical Chemistry Chemical Physics.

Dunham Group:

Hong, S., Sunita, S., Maehigashi, T., Hoffer, E. D., Dunkle, J. A., & Dunham, C. M. (2018). Mechanism of tRNA-mediated+ 1 ribosomal frameshiftingProceedings of the National Academy of Sciences115(44), 11226-11231.

Rivera, S., Young, P. G., Hoffer, E. D., Vansuch, G. E., Metzler, C. L., Dunham, C. M., & Weinert, E. E. (2018). Structural Insights into Oxygen-Dependent Signal Transduction within Globin Coupled SensorsInorganic chemistry.

Hoffer, E. D., Maehigashi, T., Fredrick, K., & Dunham, C. M. (2018). Ribosomal ambiguity (ram) mutations promote the open (off) to closed (on) transition and thereby increase miscodingNucleic Acids Research.

Hill Group:

Sullivan, K. P., Wieliczko, M., Kim, M., Yin, Q., Collins-Wildman, D. L., Mehta, A. K., … & Hill, C. L. (2018). Speciation and Dynamics in the [Co4V2W18O68] 10-/Co (II) aq/CoOx Catalytic Water Oxidation SystemACS Catalysis.

Kaledin, A. L., Troya, D., Karwacki, C. J., Balboa, A., Gordon, W. O., Morris, J. R., … & Musaev, D. G. (2018). Key Mechanistic Details of Paraoxon Decomposition by Polyoxometalates: Critical Role of Para-Nitro SubstitutionChemical Physics.

Lian Group:

Clark, M. L., Ge, A., Videla, P. E., Rudshteyn, B., Miller, C. J., Song, J., … & Kubiak, C. P. (2018). CO2 Reduction Catalysts on Gold Electrode Surfaces Influenced by Large Electric FieldsJournal of the American Chemical Society.

Lutz Group:

Williams, E., Jung, S. M., Coffman, J. L., & Lutz, S. (2018). Pore engineering for enhanced mass transport in encapsulin nano-compartmentsACS synthetic biology.

Musaev Group:

Kaledin, A. L., Troya, D., Karwacki, C. J., Balboa, A., Gordon, W. O., Morris, J. R., … & Musaev, D. G. (2018). Key Mechanistic Details of Paraoxon Decomposition by Polyoxometalates: Critical Role of Para-Nitro Substitution. Chemical Physics.

Salaita Group:

Hong, J., Ge, C., Jothikumar, P., Yuan, Z., Liu, B., Bai, K., … & Palin, A. (2018). A TCR mechanotransduction signaling loop induces negative selection in the thymusNature Immunology, 1.

Weinert Group

Rivera, S., Young, P. G., Hoffer, E. D., Vansuch, G. E., Metzler, C. L., Dunham, C. M., & Weinert, E. E. (2018). Structural Insights into Oxygen-Dependent Signal Transduction within Globin Coupled SensorsInorganic chemistry.

Fontaine, B. M., Duggal, Y., & Weinert, E. E. (2018). Exploring the Links Between Nucleotide Signaling and Quorum Sensing Pathways in Regulating Bacterial VirulenceACS infectious diseases.

Wuest Group:

Kontos, R. C., Schallenhammer, S. A., Bentley, B. S., Morrison, K. R., Feliciano, J. A., Tasca, J. A., … & Minbiole, K. P. (2018). An Investigation Into Rigidity‐Activity Relationships in bisQAC Amphiphilic AntisepticsChemMedChem.

Shapiro, J. A., Varga, J. J., Parsonage, D., Walton, W., Redinbo, M. R., Ross, L. J., … & Goldberg, J. B. (2018). Identification of Specific and Non‐specific Inhibitors of Bacillus anthracis Type III Pantothenate Kinase (PanK)ChemMedChem.

Kilgore, M. B., Morrison, K. R., Wuest, W. M., & Chandler, J. D. (2018). Influence of pH on the reactions of heme peroxidase-derived oxidants with R19SFree Radical Biology and Medicine128, S101-S102.

October Research Round-Up

Congratulations to our amazing research teams here in the Department of Chemistry for their publications this month!

Bowman Group:

Nandi, A., Qu, C., & Bowman, J. M. (2018). Diffusion Monte Carlo Calculations of Zero‐Point Energies of Methanol and Deuterated Methanol. Journal of computational chemistry.

Davies Group:

Davies, H. M., Itami, K., & Stoltz, B. M. (2018). New directions in natural product synthesisChemical Society Reviews.

Evangelista Group:

Huang, Y., Xu, Z., Jin, S., Li, C., Warncke, K., Evangelista, F. A., … & Egap, E. (2018). Conjugated Oligomers with Stable Radical Substituents: Synthesis, Single Crystal Structures, Electronic Structure and Excited State DynamicsChemistry of Materials.

Heaven Group

Torbin, A., Pershin, A., Zagidullin, M., Heaven, M., Mebel, A., & Azyazov, V. (2018). Ozone recovery in the presence of CO and N2O. In MATEC Web of Conferences(Vol. 209, p. 00016). EDP Sciences.

Tolstov, G. I., Zagidullin, M. V., Khvatov, N. A., Medvedkov, I. A., Mebel, A. M., Heaven, M. C., & Azyazov, V. N. (2018). Measurements of rate constants of O2 (b) quenching by CH4, NO, N2O at temperatures 300-800 K. In MATEC Web of Conferences(Vol. 209, p. 00006). EDP Sciences.

Heaven, M. C. (2018, October). Optically pumped rare gas lasers (Conference Presentation). In High-Power Lasers: Technology and Systems, Platforms, and Effects II(Vol. 10798, p. 1079806). International Society for Optics and Photonics.

Heemstra Group

Wilson, C. J., Bommarius, A. S., Champion, J. A., Chernoff, Y. O., Lynn, D. G., Paravastu, A. K., … & Heemstra, J. M. (2018). Biomolecular Assemblies: Moving from Observation to Predictive DesignChemical reviews.

Morris, F. D., Peterson, E. M., Heemstra, J. M., & Harris, J. M. (2018). Single-Molecule Kinetic Investigation of Cocaine-Dependent Split-Aptamer AssemblyAnalytical chemistry.

Hill Group

Kaledin, A. L., Hill, C. L., Lian, T., & Musaev, D. G. (2018). A bulk adjusted linear combination of atomic orbitals (BA‐LCAO) approach for nanoparticlesJournal of computational chemistry.

Ke Group

Wang, P., & Ke, Y. (2018). Attack on the Cell Membrane: The Pointy Ends of DNA Nanostructures Lead the Way.

Wang, D., Song, J., Wang, P., Pan, V., Zhang, Y., Cui, D., & Ke, Y. (2018). Design and operation of reconfigurable two-dimensional DNA molecular arraysNature protocols, 1.

Kindt Group

Patel, L. A., & Kindt, J. T. (2018). Simulations of NaCl Aggregation from Solution: Solvent Determines Topography of Free Energy LandscapeJournal of computational chemistry.

Guo, Z., & Kindt, J. T. (2018). Partitioning of Size-mismatched Impurities to Grain Boundaries in 2-d Solid Hard Sphere MonolayersLangmuir.

Lian Group

Kaledin, A. L., Hill, C. L., Lian, T., & Musaev, D. G. (2018). A bulk adjusted linear combination of atomic orbitals (BA‐LCAO) approach for nanoparticlesJournal of computational chemistry.

Huang, Y., Xu, Z., Jin, S., Li, C., Warncke, K., Evangelista, F. A., … & Egap, E. (2018). Conjugated Oligomers with Stable Radical Substituents: Synthesis, Single Crystal Structures, Electronic Structure and Excited State DynamicsChemistry of Materials.

Lynn Group

Wilson, C. J., Bommarius, A. S., Champion, J. A., Chernoff, Y. O., Lynn, D. G., Paravastu, A. K., … & Heemstra, J. M. (2018). Biomolecular Assemblies: Moving from Observation to Predictive DesignChemical reviews.

Musaev Group

Kaledin, A. L., Hill, C. L., Lian, T., & Musaev, D. G. (2018). A bulk adjusted linear combination of atomic orbitals (BA‐LCAO) approach for nanoparticles. Journal of computational chemistry.

Haines, B. E., Nelson, B. M., Grandner, J. M., Kim, J., Houk, K. N., Movassaghi, M., & Musaev, D. G. (2018). Mechanism of Permanganate-Promoted Dihydroxylation of Complex Diketopiperazines: Critical Roles of Counter-cation and Ion-PairingJournal of the American Chemical Society.

Wuest Group

Ernouf, G., Wilt, I., Zahim, S., & Wuest, W. M. (2018). Epoxy isonitriles, a unique class of antibiotics–Synthesis of their metabolites and biological investigationsChemBioChem.

 

New Catalyst Developed by CCHF

Side view of the new catalyst. Graphic image by Kuangbiao Liao via escienceommons.

Chemists have developed another catalyst that can selectively activate a carbon-hydrogen bond, part of an ongoing strategy to revolutionize the field of organic synthesis and open up new chemical space.

The journal Nature is publishing the work by chemists at Emory University, following on their development of a similar catalyst last year. Both of the catalysts are able to selectively functionalize the unreactive carbon-hydrogen (C-H) bonds of an alkane without using a directing group, while also maintaining virtually full control of site selectivity and the three-dimensional shape of the molecules produced.

Read the full story by Carol Clark on the Emory esciencecommons blog!

Dunham Group Publication in Nature Chemical Biology

Graduate student Ha An Nguyen of the Dunham Group recently published a News and Views article for the journal Nature Chemical Biology entitled, “Genome Mining: Digging the Tunnel for Chemical Space” based on a July article published in the same journal, “Klebsazolicin Inhibits 70S Ribosome by Obstructing the Peptide Exit Tunnel”.

In her review, Ha An summarizes the major findings of the Metelev et al. paper and emphasizes the value of genome mining in the discovery of new antimicrobials. “We previously thought we had beaten bacterial infections with ‘miracle drugs’ but if you look at the numbers from the CDC, at least 2 million people become infected with bacteria that are resistant to antibiotics and at least 23,000 people die each year as a direct result of these infections in the United States alone,” Ha An says. “Techniques such as genome mining used in this paper can help sift through tons of sequencing data and can lead us to places we would have never thought of to look.”

Beyond its scientific contributions to the field, this manuscript held particular value to Ha An. “As a novice scientist, this paper on klebsazolicin provides a nice story of a scientific study that walks through the project from conception in silico and into the laboratory for mechanistic and structural investigation,” she says. “It also let me dip my toes into making figures of ribosomes structures, which I am hoping to do a lot of during my time in the Dunham lab to tease out the details of bacterial translation with atomic-level resolution.”

Wuest Group Featured in ChemBioChem

Research from the Wuest Group is featured on the cover of the August issue of ChemBioChem. The article is “Efflux Pumps Might Not Be the Major Drivers of QAC Resistance in Methicillin-Resistant Staphylococcus aureus.”

The inside cover picture shows that
cell-membrane composition might be
the primary driver of bacterial resistance to quaternary ammonium compounds (QACs). Our findings shed light on this daunting phenomenon with world-wide impact as QACs are ubiquitous in household cleaners and typically serve as the last line of defense in home sanitation.

AIDS Quilt Returns to Chemistry

Two of the three AIDS Quilt panels on display in the Science Commons.
Two of the AIDS Quilt panels on display in the Science Commons.

The Department of Chemistry is honored to once again host panels from the AIDS quilt. Chemistry hosted four panels in 2015 in the new Atwood Science Commons, marking the first time the quilt had been displayed in the new building. This year, the quilt panels will be on display in the Science Commons through World AIDS Day, December 1st, 2016. On World AIDS Day, quilt panels will also be displayed on the quad as part of Emory’s Quilt on the Quad.

The Atwood Chemistry Center addition, opened in August 2015, was funded in large part by proceeds from the intellectual settlement for Emtriva, an HIV treatment discovered by chemistry professor Dr. Dennis C. Liotta and colleagues. Over 90% of AIDS patients take Emtriva as part of their medication regimen.

Emory’s commitment to treating and eradicating AIDS is also reflected by an investment in the Emory Center for AIDS Research. The Center provides support for 245 Emory and affiliated faculty, research fellows and post-doctoral fellows who conduct research throughout Emory University, the United States and globally.

Student Spotlight: PN Ligands and Parks at Penn

By: Juan D. Cisneros (EC ’17)

I had the pleasure of spending this past summer at the University of Pennsylvania in the lab of Professor Daniel J. Mindiola as a visiting scholar. My time in the lab was insightful and inspiring; I worked with some brilliant minds on some fascinating chemistry and left with a new knowledge of lab techniques and fond memories.

Having visited Philly briefly just once before, I wasn’t quite sure what to expect of the city. I was pleasantly surprised at how vibrant and friendly West Philadelphia welcomed me. City streets were trafficked by commuters and delicious food trucks. In order to keep my close relationship to the food trucks healthy, I began to run every evening.

Boathouse Row on my evening run. Photo by Juan D. Cisneros.
Boathouse Row on my evening run. Photo by Juan D. Cisneros.

Fairmount Park and the Philadelphia Park system is the largest landscaped urban park in the world and I explored a good bit of it during my stay. I also ran with the West Philly chapter of BoMF (Back on My Feet) on Monday mornings and participated in the Papa Gary 10k that finished at the historic Rocky Steps!

Finish Line at the Rocky Steps – 2016 Papa Gary Father’s Day Run. Photo by Juan D. Cisneros
Finish Line at the Rocky Steps – 2016 Papa Gary Father’s Day Run. Photo by Juan D. Cisneros.

When I wasn’t running off the calories to keep a Kfoodtruck, I was adapting to the new layer of neoprene hugging my hands and arms. I worked with Group IV metals with the goal of creating nitride complexes supported by a varying PN ligand. Working with highly pyrophoric compounds taught me valuable safety protocol and also some new techniques (Electron Paramagnetic Resonance, Variable Temperature NMR, et al.).  The bulk of my synthetic trials involved scaling up varying PN ligands and the constructing the complexes supported by these ligands. I began with Titanium and the Mesitylene substituted PN ligand and later worked with the 1,3,5-triisopropylbenzene substituted PN Ligand in hopes of obtaining better crystals further down the synthesis. I also experimented my trials with Hafnium and Zirconium, below are some x-rays of aforementioned complexes.

Ti-nitride (left) and ZrNH (right)
Ti-nitride (left) and ZrNH (right). Click here to view Juan’s research poster.

The workload in the Mindiola Lab was intense, but the people were friendly and supportive. Through our countless hours in lab, we developed a covalent level of friendship and I am looking forward to the point where our careers cross paths again.

Glove box in the Mindiola Lab. Photo by Juan D. Cisneros.
Glove box in the Mindiola Lab. Photo by Juan D. Cisneros.

My last day at Penn, a few of us drove to the MetLife Stadium in the boss’s Passat and watched the sold-out FC Bayern Munich vs. Real Madrid match with 82,000 other soccer enthusiasts. It was the perfect outing to celebrate a summer of hard work and breakthrough (Real unsurprisingly won).

Metlife Stadium. Photo by Juan D. Cisneros.
Metlife Stadium. Photo by Juan D. Cisneros.

orange line

metlife-stadiumJuan D. Cisneros (pictured far left) is a chemistry and Spanish double major at Emory from Coconut Creek, Florida. Previously, he wrote for The Lab Report about his experiences studying abroad in Salamanca, Spain. Juan is also an IMSD undergraduate scholar and edits the IMSD blog.

Stefan Lutz Discusses Everest Trip in The Emory Wheel

Stefan Lutz. Photo by Jessica Lily Photography.
Stefan Lutz. Photo by Jessica Lily Photography.

Stefan Lutz spoke to The Emory Wheel about his summer Everest trip. From the article:

“Mountain climbing requires a certain stubbornness in pursuit of your goals. It requires a commitment, a dedication, time wise, effort wise, and I think that is a quality that comes through in when you do research,” Lutz said. “Research involves a lot of failure. [But] to be able to go back and pick yourself up after a setback, those are qualities that I think mountaineering and research can share.”

[Full Article]