April Research Round-Up

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

Bowman Group

Qu, C., & Bowman, J. M. (2019). A fragmented, permutationally invariant polynomial approach for potential energy surfaces of large molecules: Application to N-methyl acetamideThe Journal of chemical physics150(14), 141101.

Yang, B., Zhang, P., Qu, C., Stancil, P., Bowman, J., Balakrishnan, N., & Forrey, R. (2019). Full-dimensional quantum rovibrational scattering of SO with H2*Bulletin of the American Physical Society.

Dunham Group

Srinivas, P., Goralski, T. D., Keiler, K. C., & Dunham, C. M. (2019). Alternative mechanisms of ribosome stalling rescue in the gram-negative bacterium Francisella tularensisThe FASEB Journal33(1_supplement), 628-3.

Hoffer, E. D., Maehigashi, T., Fredrick, K., & Dunham, C. M. (2019). Ribosomal am biguity (ram) mutations promote 30S domain closure and thereby increase miscodingThe FASEB Journal33(1_supplement), 628-2.

Dunham, C. M., Hoffer, E. D., Nguyen, H. A., Subramanian, S., Hong, S., & Maehigashi, T. (2019). RNA-mediated Mechanisms of Translation ControlThe FASEB Journal33(1_supplement), 100-1.

Zaldana, K. S., Pavelich, I., Moller, A., & Dunham, C. M. (2019). Dissecting the gene regulation of Proteus vulgaris Rts1 HigB-HigA toxin-antitoxin systemThe FASEB Journal33(1_supplement), 458-20.

Pavelich, I., & Dunham, C. M. (2019). Mechanism and stability of type II bacterial toxin-antitoxin complexes and the role of regulated antitoxin proteolysis that releases toxinThe FASEB Journal33(1_supplement), 463-8.

Nguyen, H. A., & Dunham, C. M. (2019). Importance of the m1G37 modification and 32–38 pairing in tRNAPro (CCG) on decoding and tRNA stabilityThe FASEB Journal33(1_supplement), 630-6.

Dyer Group

Sanchez, M. K., Wu, C. H., Adams, M. W., & Dyer, R. B. (2019). Optimizing electron transfer from CdSe QDs to hydrogenase for photocatalytic H 2 productionChemical Communications.

Deng, H., Dyer, R. B., & Callender, R. (2019). Active Site Glu165 Activation in Triosephosphate Isomerase and its Deprotonation KineticsThe Journal of Physical Chemistry B.

Evangelista Group

Zhang, T., Li, C., & Evangelista, F. A. (2019). Improving the efficiency of the multireference driven similarity renormalization group via sequential transformation, density fitting, and the non-interacting virtual orbital approximationarXiv preprint arXiv:1903.11637.

Li, C., Lindh, R., & Evangelista, F. A. (2019). Dynamically weighted multireference perturbation theory: Combining the advantages of multi-state and state-averaged methodsThe Journal of Chemical Physics150(14), 144107.

Heemstra Group

Lackey, H., Peterson, E. M., Chen, Z., Harris, J. M., & Heemstra, J. M. (2019). Thermostability Trends of TNA: DNA Duplexes Reveal Strong Purine DependenceACS synthetic biology.

Ayele, T., Knutson, S. D., Ellipilli, S., Hwang, H., & Heemstra, J. M. (2019). Fluorogenic Photoaffinity Labeling of Proteins in Living CellsBioconjugate Chemistry.

Heaven Group

Le, A. T., Nakhate, S. G., Nguyen, D. T., Steimle, T. C., & Heaven, M. C. (2019). Characterization of gas-phase thorium nitride. The Journal of chemical physics150(14), 144304.

Hill Group

Tao, M., Li, Y., Geletii, Y. V., Hill, C. L., & Wang, X. (2019). Aerobic oxidation of glycerol catalyzed by M salts of PMo12O403-(M= K+, Zn2+, Cu2+, Al3+, Cr3+, Fe3+)Applied Catalysis A: General.

Tian, Y., Plonka, A. M., Ebrahim, A. M., Palomino, R. M., Senanayake, S. D., Balboa, A., … & Mitchell, M. B. (2019). A Correlated Multimodal Approach Reveals Key Details of Nerve-Agent Decomposition by Single Site Zr-Based Polyoxometalates. The journal of physical chemistry letters.

Ke Group

Wang, W., Chen, S., An, B., Huang, K., Bai, T., Xu, M., … & Wei, B. (2019). Complex wireframe DNA nanostructures from simple building blocksNature communications10(1), 1067.

Musaev Group

McLarney, B. D., Hanna, S. R., Musaev, D. G., & France, S. (2019). A Predictive Model for the [Rh2 (esp) 2]-catalyzed Intermolecular C (sp3)-H Bond Insertion of β-carbonyl Ester Carbenes: Interplay Between Theory and ExperimentACS Catalysis.

Tian, Y., Plonka, A. M., Ebrahim, A. M., Palomino, R. M., Senanayake, S. D., Balboa, A., … & Mitchell, M. B. (2019). A Correlated Multimodal Approach Reveals Key Details of Nerve-Agent Decomposition by Single Site Zr-Based PolyoxometalatesThe journal of physical chemistry letters.

Wuest Group

Zhao, W., Cross, A. R., Crowe-McAuliffe, C., Weigert-Munoz, A., Csatary, E. E., Solinski, A., … & Wuest, W. (2019). The natural product elegaphenone potentiates antibiotic effects against Pseudomonas aeruginosaAngewandte Chemie.

Cheng, A. V., & Wuest, W. M. (2019). Signed, Sealed, Delivered: Conjugate and Prodrug Strategies as Targeted Delivery Vectors for AntibioticsACS infectious diseases.

Wilt, I. K., Hari, T. P. A., & Wuest, W. M. (2019). Hijacking the Bacterial Circuitry of Biofilm Processes via Chemical” Hot-Wiring”: An Under-explored Avenue for Therapeutic DevelopmentACS infectious diseases.

Dunham Lab Paper Selected as Editor’s Pick

Ha An Nguyen

The Dunham Lab recent paper in the Journal of Biological Chemistry has been named an Editor’s Pick. The paper, “Importance of a tRNA anticodon loop modification and a conserved, noncanonical anticodon stem pairing in tRNACGGPro for decoding” is also the first paper for graduate research Ha An Nguyen who is featured in an author profile. In the profile, Ha An shares one of the most exciting parts of the research process:

“It was when we saw diffraction spots at high resolution for the first time! I spent a year setting up about one hundred crystallization trials and subsequently screening hundreds of beautiful crystals with not much success. It was very emotionally taxing to be sleep-deprived (most of our synchrotron times were during the night) and have your precious crystals diffract poorly. While I understood spending a year attempting to perform X-ray crystallography is not much time, as a starting graduate student, I couldn’t help but feel that I was a failed crystallographer. That one crystal ended up being all I needed, and the structure, along with the biochemistry, seemed to fall into place. We collected the X-ray data in October 2018 and wrote the paper in 3 months.”

Congratulations to Ha An and the Dunham Lab!

Further Reading

February Research Round-Up

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

Conticello Group

Kreutzberger, M. A., Hughes, S., Conticello, V., & Egelman, E. H. (2019). Structural Studies of the T-and RP4-Pili using Cryo-EMBiophysical Journal116(3), 573a.

Dunham Group

Mehrani, A., Hoffer, E. D., Goralski, T. D., Keiler, K. C., Dunham, C. M., & Stagg, S. (2019). Investigating the Structural Mechanism of the Stalled Bacterial Ribosome Bound to a Drug that Targets Trans-TranslationBiophysical Journal116(3), 573a-574a.

Nguyen, H. A., Hoffer, E. D., & Dunham, C. M. (2019). Importance of tRNA anticodon loop modification and a conserved, noncanonical anticodon stem pairing in tRNAProCGG for decodingJournal of Biological Chemistry, jbc-RA119.

Schureck, M. A., Meisner, J., Hoffer, E. D., Wang, D., Onuoha, N., Ei Cho, S., … & Dunham, C. M. (2019). Structural basis of transcriptional regulation by the HigA antitoxinMolecular microbiology.

Heaven Group

Khvatov, N. A., Zagidullin, M. V., Tolstov, G. I., Medvedkov, I. A., Mebel, A. M., Heaven, M. C., & Azyazov, V. N. (2019). Product Channels of the reactions of O2 (b1Σg+)Chemical Physics.

Hill Group

Hill, C., & Sullivan, K. (2019). U.S. Patent Application No. 16/061,327.

Lian Group

Lian, T., Koper, M. T., Reuter, K., & Subotnik, J. E. (2019). Special Topic on Interfacial Electrochemistry and Photo (electro) catalysis.

Musaev Group

Gair, J., Haines, B. E., Filatov, A. S., Musaev, D. G., & Lewis, J. C. (2019). Di-Palladium Complexes are Active Catalysts for Mono-N-Protected Amino Acid Accelerated Enantioselective CH Functionalization.

Salaita Group

Brockman, J. M., & Salaita, K. (2019). Mechanical Proofreading: A General Mechanism to Enhance the Fidelity of Information Transfer Between Cells Phys. 7: 14. doi: 10.3389/fphy.

Blanchard, A., & Salaita, K. (2019). Autochemophoretic DNA Motors Generate 100+ Piconewton ForcesBiophysical Journal116(3), 292a-293a.

Rao, T. C., Ma, V. P. Y., Urner, T. M., Grandhi, S., Salaita, K., & Mattheyses, A. L. (2019). EGFR Activation Enables Increased Integrin Forces and Organization of Mature Focal AdhesionsBiophysical Journal116(3), 413a.

Quach, M. E., Combs, D., Salaita, K., & Li, R. (2019). Force-Induced Unfolding of a Mechanosensory Domain in Platelet Glycoprotein (Gp) Ib-IX under Solution and Adherent ConditionsBiophysical Journal116(3), 376a.

Weinert Group

Cary, S. P., Boon, E. M., Weinert, E., Winger, J. A., & Marletta, M. A. (2019). U.S. Patent Application No. 10/202,428.

 

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.

Christine Dunham Receives ASBMB Young Investigator Award

Dr. Christine Dunham, associate professor of Biochemistry at the Emory University School of Medicine and Associated Faculty in Chemistry, has been awarded the American Society for Biochemistry and Molecular Biology Young Investigator Award. The award includes a $5,000 cash prize and recognizes outstanding research contributions to biochemistry and molecular biology by a scientist who has no more than 15 years postdoctoral experience. In addition to her research and teaching, Christine is an editorial board member of the Journal of Biological Chemistry, which the ASBMB publishes and has served on the ASBMB’s meeting program planning committee

Congratulations, Christine!