Research Output 1949 2019

2019
1 Citation (Scopus)

A chemical kinetic basis for measuring translation initiation and elongation rates from ribosome profiling data

Sharma, A. K., Sormanni, P., Ahmed, N., Ciryam, P., Friedrich, U. A., Kramer, G. & O'Brien, Jr., E. P., May 1 2019, In : PLoS computational biology. 15, 5, p. e1007070

Research output: Contribution to journalArticle

Open Access
Chemical Kinetics
Elongation
Profiling
ribosomes
Stem cells

Adaptive Shape Ripening and Interparticle Bridging of L-Arginine-Stabilized Silica Nanoparticles during Evaporative Colloidal Crystal Assembly

Russell, J. L., Tran, N. L. L. & Mallouk, T. E., Jan 30 2019, In : ACS Applied Materials and Interfaces. 11, 4, p. 4568-4577 10 p.

Research output: Contribution to journalArticle

Arginine
Silicon Dioxide
Colloids
Silica
Nanoparticles

A Fluorogenic AggTag Method Based on Halo- and SNAP-Tags to Simultaneously Detect Aggregation of Two Proteins in Live Cells

Jung, K. H., Kim, S. F., Liu, Y. & Zhang, X., Apr 15 2019, In : ChemBioChem. 20, 8, p. 1078-1087 10 p.

Research output: Contribution to journalArticle

Agglomeration
Proteins
Ligands
Neurodegenerative Diseases
Bearings (structural)

Analysis of RNA Methylation by Phylogenetically Diverse Cfr Radical S-Adenosylmethionine Enzymes Reveals an Iron-Binding Accessory Domain in a Clostridial Enzyme

Gumkowski, J. D., Martinie, R. J., Corrigan, P. S., Pan, J., Bauerle, M. R., Almarei, M., Booker, S. J., Silakov, A., Krebs, C. & Boal, A. K., Jun 27 2019, In : Biochemistry. 58, 29, p. 3169-3184 16 p.

Research output: Contribution to journalArticle

Bacteriology
tRNA Methyltransferases
S-Adenosylmethionine
Clostridium
Methylation
1 Citation (Scopus)

A New Microbial Pathway for Organophosphonate Degradation Catalyzed by Two Previously Misannotated Non-Heme-Iron Oxygenases

Rajakovich, L. J., Pandelia, M. E., Mitchell, A. J., Chang, W. C., Zhang, B., Boal, A. K., Krebs, C. & Bollinger, Jr., J. M., Mar 26 2019, In : Biochemistry. 58, 12, p. 1627-1647 21 p.

Research output: Contribution to journalArticle

Organophosphonates
Oxygenases
Iron
Degradation
gamma-Butyrobetaine Dioxygenase
5 Citations (Scopus)

An N-nitrosating metalloenzyme constructs the pharmacophore of streptozotocin

Ng, T. L., Rohac, R., Mitchell, A. J., Boal, A. K. & Balskus, E. P., Feb 7 2019, In : Nature. 566, 7742, p. 94-99 6 p.

Research output: Contribution to journalLetter

Streptozocin
Iron
Synthetic Chemistry Techniques
Guanidine
Enzymes

An Ontology for Facilitating Discussion of Catalytic Strategies of RNA-Cleaving Enzymes

Bevilacqua, P. C., Harris, M. E., Piccirilli, J. A., Gaines, C., Ganguly, A., Kostenbader, K., Ekesan, Ş. & York, D. M., Jun 21 2019, In : ACS chemical biology. 14, 6, p. 1068-1076 9 p.

Research output: Contribution to journalReview article

RNA Cleavage
Catalytic RNA
Ontology
RNA
Enzymes

A Periplasmic Binding Protein for Pyrroloquinoline Quinone

Ho, J. V. & Cotruvo, Jr., J. A., Jun 11 2019, In : Biochemistry. 58, 23, p. 2665-2669 5 p.

Research output: Contribution to journalArticle

PQQ Cofactor
Periplasmic Binding Proteins
Methylobacterium extorquens
Carrier Proteins
Lanthanoid Series Elements
4 Citations (Scopus)
Lanthanoid Series Elements
Rare earth elements
Proteins
Methylobacterium extorquens
Sensors
2 Citations (Scopus)

A SNAP-tag fluorogenic probe mimicking the chromophore of the red fluorescent protein Kaede

Jung, K. H., Fares, M., Grainger, L. S., Wolstenholme, C. H., Hou, A., Liu, Y. & Zhang, X., Jan 1 2019, In : Organic and Biomolecular Chemistry. 17, 7, p. 1906-1915 10 p.

Research output: Contribution to journalArticle

SNAP
Chromophores
chromophores
proteins
probes

A stepwise mechanism for aqueous two-phase system formation in concentrated antibody solutions

Rogers, B. A., Rembert, K. B., Poyton, M. F., Okur, H. I., Kale, A. R., Yang, T., Zhang, J. & Cremer, P. S., Aug 6 2019, In : Proceedings of the National Academy of Sciences of the United States of America. 116, 32, p. 15784-15791 8 p.

Research output: Contribution to journalArticle

Open Access
Temperature
Antibodies
Gels
Suspensions
Proteins

Atomistic Characterization of Plasmonic Dimers in the Quantum Size Regime

Liu, P., Chulhai, D. V. & Jensen, L., Jun 6 2019, In : Journal of Physical Chemistry C. 123, 22, p. 13900-13907 8 p.

Research output: Contribution to journalArticle

Plasmons
plasmons
Dimers
dimers
Charge transfer
5 Citations (Scopus)

Bacterial FtsZ protein forms phase-separated condensates with its nucleoid-associated inhibitor SlmA

Monterroso, B., Zorrilla, S., Sobrinos-Sanguino, M., Robles-Ramos, M. A., López-Álvarez, M., Margolin, W., Keating, C. D. & Rivas, G., Jan 1 2019, In : EMBO Reports. 20, 1, e45946.

Research output: Contribution to journalArticle

Bacterial Proteins
Phase separation
Condensation
Bacterial Physiological Phenomena
Intracellular Space

Biochemical and Structural Characterization of XoxG and XoxJ and Their Roles in Lanthanide-Dependent Methanol Dehydrogenase Activity

Featherston, E. R., Rose, H. R., McBride, M. J., Taylor, E. M., Boal, A. K. & Cotruvo, Jr., J. A., Jan 1 2019, (Accepted/In press) In : ChemBioChem.

Research output: Contribution to journalArticle

Lanthanoid Series Elements
Cytochromes c
Rare earths
Assays
Methylobacterium extorquens
1 Citation (Scopus)
S-Adenosylmethionine
Biosynthesis
Peptides
C1 peptide
Acids

Catalytic Conversion of Ethanol to Liquid Hydrocarbons by Tin-Promoted Raney Nickel Supported on Alumina

Mandal, S. & Sen, A., Apr 22 2019, In : ACS Applied Energy Materials. 2, 4, p. 2398-2401 4 p.

Research output: Contribution to journalArticle

Tin
Aluminum Oxide
Hydrocarbons
Nickel
Ethanol
1 Citation (Scopus)

Cationic Gold(I) Diarylallenylidene Complexes: Bonding Features and Ligand Effects

Sorbelli, D., Nunes dos Santos Comprido, L., Knizia, G., Hashmi, A. S. K., Belpassi, L., Belanzoni, P. & Klein, J. E. M. N., Jul 2 2019, In : ChemPhysChem. 20, 13, p. 1671-1679 9 p.

Research output: Contribution to journalArticle

Open Access
Gold
gold
Ligands
ligands
Chemical shift

Chapter 11: Collective Behaviour of Artificial Microswimmers in Response to Environmental Conditions

Altemose, A. & Sen, A., Jan 1 2019, Self-organized Motion: Physicochemical Design based on Nonlinear Dynamics. Lagzi, I., Pimienta, V., Suematsu, N. J., Nakata, S. & Kitahata, H. (eds.). 14 ed. Royal Society of Chemistry, p. 250-283 34 p. (RSC Theoretical and Computational Chemistry Series; vol. 2019-January, no. 14).

Research output: Chapter in Book/Report/Conference proceedingChapter

Biological systems
Fish

Charge Transfer Dynamics in Aqueous Dye-Sensitized Photoelectrochemical Cells: Implications for Water Splitting Efficiency

Xu, P. & Mallouk, T. E., Oct 1 2019, In : Journal of Physical Chemistry C. 123, 1, p. 299-305 7 p.

Research output: Contribution to journalArticle

Photoelectrochemical cells
water splitting
Charge transfer
Coloring Agents
Dyes

C-O Bond Dissociation and Induced Chemical Ionization Using High Energy (CO2)n+ Gas Cluster Ion Beam

Tian, H., Maciążek, D., Postawa, Z., Garrison, B. J. & Winograd, N., Mar 15 2019, In : Journal of the American Society for Mass Spectrometry. 30, 3, p. 476-481 6 p.

Research output: Contribution to journalArticle

Ion beams
Ionization
Gases
Ions
Oxygen
1 Citation (Scopus)

Competing Polar and Antipolar Structures in the Ruddlesden-Popper Layered Perovskite Li2SrNb2O7

Uppuluri, R., Akamatsu, H., Sen Gupta, A., Wang, H., Brown, C. M., Agueda Lopez, K. E., Alem, N., Gopalan, V. & Mallouk, T. E., Jun 25 2019, In : Chemistry of Materials. 31, 12, p. 4418-4425 8 p.

Research output: Contribution to journalArticle

Perovskite
Antiferroelectric materials
Ferroelectricity
Neutron diffraction
Synchrotrons
4 Citations (Scopus)

Conjugated Block Copolymers as Model Systems to Examine Mechanisms of Charge Generation in Donor–Acceptor Materials

Aplan, M. P., Grieco, C., Lee, Y., Munro, J. M., Lee, W., Gray, J. L., Seibers, Z. D., Kuei, B., Litofsky, J. H., Kilbey, S. M., Wang, Q., Dabo, I., Asbury, J. B. & Gomez, E. D., Jan 4 2019, In : Advanced Functional Materials. 29, 1, 1804858.

Research output: Contribution to journalArticle

block copolymers
Block copolymers
Charge transfer
charge transfer
Nanoparticles

Controlled Rapid Formation of Polyurethane at 700 K: Thermodynamic and Kinetic Consequences of Extreme Photothermal Heating

Van Burns, E. N. & Lear, B. J., Jun 13 2019, In : Journal of Physical Chemistry C. 123, 23, p. 14774-14780 7 p.

Research output: Contribution to journalArticle

Polyurethanes
Thermodynamics
Heating
thermodynamics
Kinetics

Coordinated Network Changes across the Catalytic Cycle of Alpha Tryptophan Synthase

O'Rourke, K. F., Sahu, D., Bosken, Y. K., D'Amico, R. N., Chang, C. E. A. & Boehr, D. D., Sep 3 2019, In : Structure. 27, 9, p. 1405-1415.e5

Research output: Contribution to journalArticle

Tryptophan Synthase
Protein Engineering
Magnetic Resonance Spectroscopy
Proteins
Enzymes
Catalytic RNA
Nucleotides
Catalysis
Molecules

Correlated spatially resolved two-dimensional electronic and linear absorption spectroscopy

Steves, M. A., Zheng, H. & Knappenberger, K., Apr 15 2019, In : Optics Letters. 44, 8, p. 2117-2120 4 p.

Research output: Contribution to journalArticle

absorption spectroscopy
spatial resolution
temporal resolution
electronics
optical spectrum
1 Citation (Scopus)

Counter Cations Affect Transport in Aqueous Hydroxide Solutions with Ion Specificity

Drexler, C. I., Miller, T. C., Rogers, B. A., Li, Y. C., Daly, C. A., Yang, T., Corcelli, S. A. & Cremer, P. S., May 1 2019, In : Journal of the American Chemical Society. 141, 17, p. 6930-6936 7 p.

Research output: Contribution to journalArticle

Cations
Protons
Lithium
Positive ions
Sodium

Design of highly active double-pseudoknotted ribozymes: A combined computational and experimental study

Yamagami, R., Kayedkhordeh, M., Mathews, D. H. & Bevilacqua, P. C., Jan 10 2019, In : Nucleic acids research. 47, 1, p. 29-42 14 p.

Research output: Contribution to journalArticle

Catalytic RNA
RNA Folding
Riboswitch
RNA
Synthetic Biology
1 Citation (Scopus)

Domain topology, stability, and translation speed determine mechanical force generation on the ribosome

Leininger, S. E., Trovato, F., Nissley, D. A. & O'Brien, Jr., E. P., Jan 1 2019, In : Proceedings of the National Academy of Sciences of the United States of America. 116, 12, p. 5523-5532 10 p.

Research output: Contribution to journalArticle

Ribosomes
Proteins
Statistical Models
Proteome
Phenotype

Doubly resonant sum frequency spectroscopy of mixed photochromic isomers on surfaces reveals conformation-specific vibronic effects

Raab, M., Becca, J. C., Heo, J., Lim, C. K., Baev, A., Jensen, L., Prasad, P. N. & Velarde, L., Mar 21 2019, In : Journal of Chemical Physics. 150, 11, 114704.

Research output: Contribution to journalArticle

Isomers
Conformations
Natural frequencies
isomers
Spectroscopy

Dual approach for effective potentials that accurately model structure and energetics

Lebold, K. M. & Noid, W. G., Jun 21 2019, In : Journal of Chemical Physics. 150, 23, 234107.

Research output: Contribution to journalArticle

Open Access
Model structures
degrees of freedom
Degrees of freedom (mechanics)
Potential energy
Nuclear energy
2 Citations (Scopus)

Effect of Micromorphology on Alkaline Polymer Electrolyte Stability

Han, J., Pan, J., Chen, C., Wei, L., Wang, Y., Pan, Q., Zhao, N., Xie, B., Xiao, L., Lu, J. & Zhuang, L., Jan 9 2019, In : ACS Applied Materials and Interfaces. 11, 1, p. 469-477 9 p.

Research output: Contribution to journalArticle

Chemical stability
Electrolytes
Polymers
Cations
Positive ions

Enhanced Ion Yields Using High Energy Water Cluster Beams for Secondary Ion Mass Spectrometry Analysis and Imaging

Sheraz, S., Tian, H., Vickerman, J. C., Blenkinsopp, P., Winograd, N. & Cumpson, P., May 28 2019, In : Analytical Chemistry. 91, 14, p. 9058-9068 11 p.

Research output: Contribution to journalArticle

Secondary ion mass spectrometry
Ions
Imaging techniques
Water
Argon

Epitaxial graphene/silicon carbide intercalation: A minireview on graphene modulation and unique 2D materials

Briggs, N., Gebeyehu, Z. M., Vera, A., Zhao, T., Wang, K., De La Fuente Duran, A., Bersch, B., Bowen, T., Knappenberger, K. & Robinson, J. A., Sep 7 2019, In : Nanoscale. 11, 33, p. 15440-15447 8 p.

Research output: Contribution to journalReview article

Silver Compounds
Silver compounds
Gallium nitride
Refractory metals
Graphite

Epoxidation of Alkenes by Peracids: From Textbook Mechanisms to a Quantum Mechanically Derived Curly-Arrow Depiction

Klein, J. E. M. N., Knizia, G. & Rzepa, H. S., Jan 1 2019, In : ChemistryOpen.

Research output: Contribution to journalArticle

Open Access
Peracetic Acid
Epoxidation
Textbooks
Alkenes
Teaching

Erratum: Dynamic Disorder Dominates Delocalization, Transport, and Recombination in Halide Perovskites (Chem (2018) 4(12) (2826–2843), (S2451929418304108), (10.1016/j.chempr.2018.09.001))

Munson, K. T., Kennehan, E. R., Doucette, G. S. & Asbury, J. B., Sep 12 2019, In : Chem. 5, 9, 1 p.

Research output: Contribution to journalComment/debate

halide
Genetic Recombination
recombination
2 Citations (Scopus)

Ferredoxins as interchangeable redox components in support of MiaB, a radical S-adenosylmethionine methylthiotransferase

Arcinas, A. J., Maiocco, S. J., Elliott, S. J., Silakov, A. & Booker, S. J., Jan 1 2019, In : Protein Science. 28, 1, p. 267-282 16 p.

Research output: Contribution to journalArticle

Flavodoxin
Thermotoga maritima
Ferredoxins
S-Adenosylmethionine
Oxidation-Reduction

Fight the flow: The role of shear in artificial rheotaxis for individual and collective motion

Baker, R., Kauffman, J. E., Laskar, A., Shklyaev, O. E., Potomkin, M., Dominguez-Rubio, L., Shum, H., Cruz-Rivera, Y., Aronson, I., Balazs, A. C. & Sen, A., Jun 14 2019, In : Nanoscale. 11, 22, p. 10944-10951 8 p.

Research output: Contribution to journalArticle

Nanorods
Microfluidics
Fluids
Biomimetics
Platinum

General Solution-Phase Synthesis of Nanoscale Transition Metal Tellurides Using Metal Nanoparticle Reagents

Fenton, J. L., Fagan, A. M. & Schaak, R. E., Jan 1 2019, In : European Journal of Inorganic Chemistry. 2019, 30, p. 3490-3493 4 p.

Research output: Contribution to journalArticle

Metal nanoparticles
Transition metals
Nanoparticles
Metals
Tellurium

High-resolution tip-enhanced Raman scattering probes sub-molecular density changes

Chen, X., Liu, P., Hu, Z. & Jensen, L., Dec 1 2019, In : Nature communications. 10, 1, 2567.

Research output: Contribution to journalArticle

Open Access
Molecular Probes
Raman Spectrum Analysis
Raman spectroscopy
Raman scattering
Raman spectra

How Protein Binding Sensitizes the Nucleosome to Histone H3K56 Acetylation

Lee, J. & Lee, T., Mar 15 2019, In : ACS chemical biology. 14, 3, p. 506-515 10 p.

Research output: Contribution to journalArticle

Acetylation
Nucleosomes
Protein Binding
Histones
DNA

Hydrogen Donation but not Abstraction by a Tyrosine (Y68) during Endoperoxide Installation by Verruculogen Synthase (FtmOx1)

Dunham, N. P., Del Río Pantoja, J. M., Zhang, B., Rajakovich, L. J., Allen, B. D., Krebs, C., Boal, A. K. & Bollinger, Jr., J. M., Jun 26 2019, In : Journal of the American Chemical Society. 141, 25, p. 9964-9979 16 p.

Research output: Contribution to journalArticle

Tyrosine
Hydrogen
Atoms
Carbon
Iron

Identifying A- and P-site locations on ribosome-protected mRNA fragments using Integer Programming

Ahmed, N., Sormanni, P., Ciryam, P., Vendruscolo, M., Dobson, C. M. & O'Brien, Jr., E. P., Dec 1 2019, In : Scientific reports. 9, 1, 6256.

Research output: Contribution to journalArticle

Open Access
Ribosomes
Messenger RNA
Codon
Camellia
Reading Frames

In Vivo Genome-Wide RNA Structure Probing with Structure-seq

Ritchey, L. E., Su, Z., Assmann, S. M. & Bevilacqua, P. C., Jan 1 2019, Methods in Molecular Biology. Humana Press Inc., p. 305-341 37 p. (Methods in Molecular Biology; vol. 1933).

Research output: Chapter in Book/Report/Conference proceedingChapter

Genome
RNA
Glyoxal
Transcriptome
Bacteria
2 Citations (Scopus)

In vivo RNA structural probing of uracil and guanine base-pairing by 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide (EDC)

Mitchell, D., Renda, A. J., Douds, C. A., Babitzke, P. L., Assmann, S. M. & Bevilacqua, P. C., Jan 1 2019, In : RNA. 25, 1, p. 147-157 11 p.

Research output: Contribution to journalArticle

Ethyldimethylaminopropyl Carbodiimide
Uracil
Guanine
Base Pairing
Glyoxal
1 Citation (Scopus)

Ionization probability of sputtered indium under irradiation with 20-keV fullerene and argon gas cluster projectiles

Wucher, A., Breuer, L. & Winograd, N., Apr 1 2019, In : International Journal of Mass Spectrometry. 438, p. 13-21 9 p.

Research output: Contribution to journalArticle

Fullerenes
Indium
Argon
Projectiles
fullerenes

Lattice Anharmonicity: A Double-Edged Sword for 3D Perovskite-Based Optoelectronics

Munson, K. T., Swartzfager, J. R. & Asbury, J. B., Aug 9 2019, In : ACS Energy Letters. 4, 8, p. 1888-1897 10 p.

Research output: Contribution to journalArticle

Optical lattices
Optoelectronic devices
Perovskite
Ions
Carrier lifetime

Light-Induced Convective Segregation of Different Sized Microparticles

Manna, R. K., Shklyaev, O. E., Kauffman, J., Tansi, B., Sen, A. & Balazs, A. C., May 15 2019, In : ACS Applied Materials and Interfaces. 11, 19, p. 18004-18012 9 p.

Research output: Contribution to journalArticle

Gold
Nanoparticles
Sorting
Fluids
Buoyancy

Lipid Vesicle-Coated Complex Coacervates

Pir Cakmak, F., Grigas, A. T. & Keating, C. D., Jun 18 2019, In : Langmuir. 35, 24, p. 7830-7840 11 p.

Research output: Contribution to journalArticle

Phospholipids
RNA
Lipids
lipids
bioreactors