Biochemistry & Molecular Biology

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Research Output 1961 2020

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2019

Activation of 6-alkoxy-substituted methylenecyclopropane nucleoside analogs requires enzymatic modification by adenosine deaminase-like protein 1

Vollmer, K. J., Burns, A. C., Sauer, H. E., Williams, J. D., Komazin-Meredith, G., Cardinale, S., Butler, M., Aron, Z., Hussein, I., Busch, M. G., Bowlin, T. L. & Gentry, B. G., Jan 1 2019, In : Antimicrobial agents and chemotherapy. 63, 10, e01301-19.

Research output: Contribution to journalArticle

Adenosine Deaminase
Nucleosides
Pentostatin
Guanine
Human Herpesvirus 1

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
1 Citation (Scopus)

A machine-learning approach for accurate detection of copy number variants from exome sequencing

Pounraja, V. K., Jayakar, G., Jensen, M., Kelkar, N. & Girirajan, S., Jan 1 2019, In : Genome research. 29, 7, p. 1134-1143 10 p.

Research output: Contribution to journalArticle

Open Access
Exome
Inborn Genetic Diseases
Base Composition
Machine Learning

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

tRNA Methyltransferases
S-Adenosylmethionine
Methylation
Accessories
Rubredoxins
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, 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
1 Citation (Scopus)

An interaction-based model for neuropsychiatric features of copy-number variants

Jensen, M. & Girirajan, S., Jan 1 2019, In : PLoS genetics. 15, 1, e1007879.

Research output: Contribution to journalArticle

phenotype
Phenotype
gene
Genes
genes

An optimal O(nm) algorithm for enumerating all walks common to all closed edge-covering walks of a graph

Cairo, M., Medvedev, P., Acosta, N. O., Rizzi, R. & Tomescu, A. I., Jul 2019, In : ACM Transactions on Algorithms. 15, 4, 48.

Research output: Contribution to journalArticle

Open Access
Walk
Covering
Closed
Graph in graph theory
Dihydroxyacetone Phosphate
Quinolinic Acid
X ray crystallography
X Ray Crystallography
Phosphates

A small-molecule inhibitor of trans-translation synergistically interacts with cathelicidin antimicrobial peptides to impair survival of staphylococcus aureus

Huang, Y., Alumasa, J., Callaghan, L. T., Samuel Baugh, R., Rae, C. D., Keiler, K. C. & McGillivray, S. M., Apr 1 2019, In : Antimicrobial agents and chemotherapy. 63, 4, e02362-18.

Research output: Contribution to journalArticle

Staphylococcus aureus
Survival
Daptomycin
Anti-Bacterial Agents
Methicillin

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
1 Citation (Scopus)

A traction force threshold signifies metastatic phenotypic change in multicellular epithelia

Zhang, Y., Shi, X., Zhao, T., Huang, C., Wei, Q., Tang, X., Santy, L. C., Saif, M. T. A. & Zhang, S., Jan 1 2019, In : Soft Matter. 15, 36, p. 7203-7210 8 p.

Research output: Contribution to journalArticle

epithelium
traction
Stiffness
Phase diagrams
thresholds
4 Citations (Scopus)

Berberine directly affects the gut microbiota to promote intestinal farnesoid X receptor activation

Tian, Y., Cai, J., Gui, W., Nichols, R. G., Koo, I., Zhang, J., Anitha, M. & Patterson, A. D., Feb 1 2019, In : Drug Metabolism and Disposition. 47, 2, p. 86-93 8 p.

Research output: Contribution to journalArticle

Berberine
Bacteria
choloylglycine hydrolase
Metabolomics
Bile Acids and Salts
2 Citations (Scopus)

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., Sep 16 2019, In : ChemBioChem. 20, 18, p. 2360-2372 13 p.

Research output: Contribution to journalArticle

Lanthanoid Series Elements
Assays
Methylobacterium extorquens
Crystal structure
Periplasmic Binding Proteins
2 Citations (Scopus)

Biochemical methods to characterize RNA polymerase II elongation complexes

Brooks Crickard, J. & Reese, J. C., Apr 15 2019, In : Methods. 159-160, p. 70-81 12 p.

Research output: Contribution to journalArticle

RNA Polymerase II
Elongation
Transcription
Peptide Elongation Factors
DNA

Bioresponsive peptide-polysaccharide nanogels — A versatile delivery system to augment the utility of bioactive cargo

Simonson, A. W., Lawanprasert, A., Goralski, T. D. P., Keiler, K. C. & Medina, S. H., Apr 1 2019, In : Nanomedicine: Nanotechnology, Biology, and Medicine. 17, p. 391-400 10 p.

Research output: Contribution to journalArticle

Hyaluronic acid
Polysaccharides
Peptides
Cells
Proteins

Bipartite graphs of small readability

Chikhi, R., Jovičić, V., Kratsch, S., Medvedev, P., Milanič, M., Raskhodnikova, S. & Varma, N., Jan 1 2019, In : Theoretical Computer Science.

Research output: Contribution to journalArticle

Bioinformatics
Bipartite Graph
Chain Graph
Graph in graph theory
Polynomials
1 Citation (Scopus)

"Candidates thermonerobacter thiotrophicus," a non-phototrophic member of the Bacteroidetes/Chlorobi with dissimilatory sulfur metabolism in hot spring mat communities

Thiel, V., Costas, A. M. G., Fortney, N. W., Martinez, J. N., Tank, M., Roden, E. E., Boyd, E. S., Ward, D. M., Hanada, S. & Bryant, D. A., Jan 1 2019, In : Frontiers in Microbiology. 10, JAN, 3159.

Research output: Contribution to journalArticle

Open Access
Chlorobi
Hot Springs
Bacteroidetes
Sulfur
Sulfates
1 Citation (Scopus)
S-Adenosylmethionine
Biosynthesis
Peptides
C1 peptide
Acids
1 Citation (Scopus)

Ccr4–not maintains genomic integrity by controlling the ubiquitylation and degradation of arrested RNAPII

Jiang, H., Wolgast, M., Beebe, L. M. & Reese, J. C., Jun 1 2019, In : Genes and Development. 33, 11-12, p. 705-717 13 p.

Research output: Contribution to journalArticle

Open Access
RNA Polymerase II
Ubiquitination
DNA Damage
Ligases
Ubiquitin

Cellular Concentrations of Nucleotide Diphosphate-Chelated Magnesium Ions Accelerate Catalysis by RNA and DNA Enzymes

Yamagami, R., Huang, R. & Bevilacqua, P. C., Sep 24 2019, In : Biochemistry. 58, 38, p. 3971-3979 9 p.

Research output: Contribution to journalArticle

Diphosphates
Catalysis
Magnesium
Nucleotides
RNA
6 Citations (Scopus)

Characterization of chlorophyll f synthase heterologously produced in Synechococcus sp. PCC 7002

Shen, G., Canniffe, D. P., Ho, M. Y., Kurashov, V., van der Est, A., Golbeck, J. H. & Bryant, D. A., Apr 1 2019, In : Photosynthesis research. 140, 1, p. 77-92 16 p.

Research output: Contribution to journalArticle

Synechococcus sp. PCC 7002
Synechococcus
chlorophyll
Genes
Light

Characterizing protein-DNA binding event subtypes in ChIP-exo data

Yamada, N., Lai, W., Farrell, N., Pugh, B. F. & Mahony, S. A., Mar 15 2019, In : Bioinformatics. 35, 6, p. 903-913 11 p.

Research output: Contribution to journalArticle

DNA-binding Protein
Chromatin Immunoprecipitation
Chromatin
DNA-Binding Proteins
DNA
2 Citations (Scopus)

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

Comparative genomics of the genus Methanohalophilus, including a newly isolated strain from Kebrit deep in the Red Sea

Guan, Y., Ngugi, D. K., Vinu, M., Blom, J., Alam, I., Guillot, S., Ferry, J. G. & Stingl, U., Jan 1 2019, In : Frontiers in Microbiology. 10, APR, 839.

Research output: Contribution to journalArticle

Open Access
Indian Ocean
Genomics
Genome
Carbon Cycle
Archaea
2 Citations (Scopus)

Comparison of herpes simplex virus 1 strains circulating in Finland demonstrates the uncoupling of whole-genome relatedness and phenotypic outcomes of viral infection

Bowen, C. D., Paavilainen, H., Renner, D. W., Palomäki, J., Lehtinen, J., Vuorinen, T., Norberg, P., Hukkanen, V. & Szpara, M. L., Jan 1 2019, In : Journal of virology. 93, 8, Y.

Research output: Contribution to journalArticle

Open Access
Human herpesvirus 1
Human Herpesvirus 1
Virus Diseases
Finland
Genome
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

Convergent evolution of hetero-oligomeric cellulose synthesis complexes in mosses and seed plants

Li, X., Speicher, T. L., Dees, D. C. T., Mansoori, N., McManus, J. B., Tien, M., Trindade, L. M., Wallace, I. S. & Roberts, A. W., Jan 1 2019, In : Plant Journal. 99, 5, p. 862-876 15 p.

Research output: Contribution to journalArticle

Bryophyta
convergent evolution
Spermatophytina
Cellulose
mosses and liverworts
Toll-Like Receptor 2
Acylation
Listeria monocytogenes
Lipoproteins
Copper
4 Citations (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

Crossing the Thauer limit: Rewiring cyanobacterial metabolism to maximize fermentative H2 production

Kumaraswamy, K. G., Krishnan, A., Ananyev, G., Zhang, S., Bryant, D. A. & Dismukes, G. C., Mar 1 2019, In : Energy and Environmental Science. 12, 3, p. 1035-1045 11 p.

Research output: Contribution to journalArticle

Metabolism
Glucose
glucose
Pentoses
metabolism

Cryo-EM of multiple cage architectures reveals a universal mode of clathrin self-assembly

Morris, K. L., Jones, J. R., Halebian, M., Wu, S., Baker, M., Armache, J. P., Avila Ibarra, A., Sessions, R. B., Cameron, A. D., Cheng, Y. & Smith, C. J., Oct 1 2019, In : Nature Structural and Molecular Biology. 26, 10, p. 890-898 9 p.

Research output: Contribution to journalArticle

Clathrin
Endocytosis
Coated Vesicles
Molecular Models
Structural Models
1 Citation (Scopus)

Cryo-EM structures of remodeler-nucleosome intermediates suggest allosteric control through the nucleosome

Armache, J-P., Gamarra, N., Johnson, S. L., Leonard, J. D., Wu, S., Narlikar, G. J. & Cheng, Y., Jun 1 2019, In : eLife. 8, e46057.

Research output: Contribution to journalArticle

Open Access
Nucleosomes
Protein Subunits
Histones
Adenosine Diphosphate
Reaction intermediates
Open Access
adducts
Crystal structure
chlorides
Atoms
crystal structure

Crystal structures of three hexakis(fluoroaryloxy)cyclotriphosphazenes

Yennawar, H. P., Hess, A. R. & Allcock, H. R., Oct 1 2019, In : Acta Crystallographica Section E: Crystallographic Communications. 75, p. 1525-1530 6 p.

Research output: Contribution to journalArticle

Open Access
Crystal structure
Atoms
crystal structure
rings
phosphazene

Crystal structures of two isomeric 2-aryl-3-phenyl-1,3-thiazepan-4-ones

Yennawar, H. P., Peterson, S. D. & Silverberg, L. J., Jan 1 2019, In : Acta Crystallographica Section E: Crystallographic Communications. 75, p. 1270-1276 7 p.

Research output: Contribution to journalArticle

Open Access
Crystal structure
crystal structure
Molecules
Conformations
rings
1 Citation (Scopus)

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
3 Citations (Scopus)

Dissociation rate compensation mechanism for budding yeast pioneer transcription factors

Donovan, B. T., Chen, H., Jipa, C., Bai, L. & Poirier, M. G., Mar 1 2019, In : eLife. 8, e43008.

Research output: Contribution to journalArticle

Open Access
Saccharomycetales
Nucleosomes
Yeast
Transcription Factors
Yeasts
1 Citation (Scopus)

Draft genome sequences of type VI secretion system-encoding vibrio fischeri strains FQ-A001 and ES401

Bultman, K. M., Cecere, A. G., Miyashiro, T. I., Septer, A. N. & Mandel, M. J., May 16 2019, In : Microbiology Resource Announcements. 8, 20, e00385-19.

Research output: Contribution to journalArticle

Open Access
Aliivibrio fischeri
Genome
Decapodiformes
Genomics
Bacteria
1 Citation (Scopus)
Protein Isoforms
Phosphotransferases
Growth
Neoplasms
Drosophila
3 Citations (Scopus)
Photosystem I Protein Complex
far-red light
Energy Transfer
photosystem I
energy transfer
4 Citations (Scopus)

Engineering of B800 bacteriochlorophyll binding site specificity in the Rhodobacter sphaeroides LH2 antenna

Swainsbury, D. J. K., Faries, K. M., Niedzwiedzki, D. M., Martin, E. C., Flinders, A. J., Canniffe, D. P., Shen, G., Bryant, D. A., Kirmaier, C., Holten, D. & Hunter, C. N., Mar 1 2019, In : Biochimica et Biophysica Acta - Bioenergetics. 1860, 3, p. 209-223 15 p.

Research output: Contribution to journalArticle

Light-Harvesting Protein Complexes
Bacteriochlorophylls
Rhodobacter sphaeroides
Binding Sites
Antennas

Evaluating the structural complexity of isomeric bile acids with ion mobility spectrometry

Zheng, X., Smith, F. B., Aly, N. A., Cai, J., Smith, R. D., Patterson, A. D. & Baker, E. S., Jul 19 2019, In : Analytical and Bioanalytical Chemistry. 411, 19, p. 4673-4682 10 p.

Research output: Contribution to journalArticle

Bile Acids and Salts
Spectrometry
Spectrum Analysis
Ions
Isomers
1 Citation (Scopus)

Examination and reconstruction of three ancient endogenous parvovirus capsid protein gene remnants found in rodent genomes

Callaway, H. M., Subramanian, S., Urbina, C. A., Barnard, K. N., Dick, R. A., Bator, C. M., Hafenstein, S., Gifford, R. J. & Parrish, C. R., Mar 1 2019, In : Journal of virology. 93, 6, e01542-18.

Research output: Contribution to journalArticle

Parvovirus
Protoparvovirus
Capsid Proteins
coat proteins
capsid

Extensive remodeling of the photosynthetic apparatus alters energy transfer among photosynthetic complexes when cyanobacteria acclimate to far-red light

Ho, M. Y., Niedzwiedzki, D. M., MacGregor-Chatwin, C., Gerstenecker, G., Hunter, C. N., Blankenship, R. E. & Bryant, D. A., Jan 1 2019, (Accepted/In press) In : Biochimica et Biophysica Acta - Bioenergetics. 148064.

Research output: Contribution to journalArticle

Photosynthetic Reaction Center Complex Proteins
Energy Transfer
Cyanobacteria
Energy transfer
Light
3 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 2019, In : Protein Science. 28, 1, p. 267-282 16 p.

Research output: Contribution to journalArticle

Flavodoxin
Thermotoga maritima
Ferredoxins
S-Adenosylmethionine
Oxidation-Reduction

Formation of water-soluble organic matter through fungal degradation of lignin

Khatami, S., Deng, Y., Tien, M. & Hatcher, P. G., Sep 1 2019, In : Organic Geochemistry. 135, p. 64-70 7 p.

Research output: Contribution to journalArticle

Lignin
Biological materials
lignin
organic matter
Degradation
Photosystem I Protein Complex
Fourier Analysis
Spectrum Analysis
Fourier transforms
Cells
1 Citation (Scopus)

Gdf15 regulates murine stress erythroid progenitor proliferation and the development of the stress erythropoiesis niche

Hao, S., Xiang, J., Wu, D. C., Fraser, J. W., Ruan, B., Cai, J., Patterson, A. D., Lai, Z. & Paulson, R., Jul 23 2019, In : Blood Advances. 3, 14, p. 2205-2217 13 p.

Research output: Contribution to journalArticle

Open Access
Growth Differentiation Factor 15
Erythropoiesis
Erythroid Cells
Monocytes
Homeostasis
1 Citation (Scopus)

Genetic analysis of the RNA polymerase II CTD in Drosophila

Lu, F. & Gilmour, D. S., Apr 15 2019, In : Methods. 159-160, p. 129-137 9 p.

Research output: Contribution to journalArticle

RNA Polymerase II
Transcription
Eukaryota
Gene expression
Drosophila
2 Citations (Scopus)

Genome-wide colocalization of RNA–DNA interactions and fusion RNA pairs

Yan, Z., Huang, N., Wu, W., Chen, W., Jiang, Y., Chen, J., Huang, X., Wen, X., Xu, J., Jin, Q., Zhang, K., Chen, Z., Chien, S. & Zhong, S., Feb 19 2019, In : Proceedings of the National Academy of Sciences of the United States of America. 116, 8, p. 3328-3337 10 p.

Research output: Contribution to journalArticle

Open Access
Genome
RNA
Neoplasms
RNA Sequence Analysis
Cell Fusion