Biochemistry and Molecular Biology

Publications 1986 2018

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2017
1 Citations

2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD)-elicited effects on bile acid homeostasis: Alterations in biosynthesis, enterohepatic circulation, and microbial metabolism

Fader, K. A., Nault, R., Zhang, C., Kumagai, K., Harkema, J. R. & Zacharewski, T. R. Dec 1 2017 In : Scientific Reports. 7, 1, 5927

Research output: Research - peer-reviewArticle

Enterohepatic Circulation
Bile Acids and Salts
Homeostasis
Polychlorinated Dibenzodioxins
Taurolithocholic Acid
1 Citations
engineering
metabolism
genes
proteins
protein
thylakoids
acclimation
chloroplasts
proteins
photosystem II
1 Citations

Additional families of orange carotenoid proteins in the photoprotective system of cyanobacteria

Bao, H., Melnicki, M. R., Pawlowski, E. G., Sutter, M., Agostoni, M., Lechno-Yossef, S., Cai, F., Montgomery, B. L. & Kerfeld, C. A. Jul 10 2017 In : Nature Plants. 3, 17089

Research output: Research - peer-reviewArticle

Cyanobacteria
carotenoids
proteins
fluorescence
Tolypothrix
1 Citations

A plastid phosphatidylglycerol lipase contributes to the export of acyl groups from plastids for seed oil biosynthesis

Wang, K., Froehlich, J. E., Zienkiewicz, A., Hersh, H. L. & Benning, C. Jul 1 2017 In : Plant Cell. 29, 7, p. 1678-1696 19 p.

Research output: Research - peer-reviewArticle

Phosphatidylglycerols
Plastids
Lipase
Seeds
Oils

A regulatory hierarchy of the arabidopsis branched-chain amino acid metabolic network

Xing, A. & Last, R. L. Jun 1 2017 In : Plant Cell. 29, 6, p. 1480-1499 20 p.

Research output: Research - peer-reviewArticle

branched chain amino acids
Arabidopsis
Branched Chain Amino Acids
Metabolic Networks and Pathways
homeostasis

A synthetic, light-driven consortium of cyanobacteria and heterotrophic bacteria enables stable polyhydroxybutyrate production

Weiss, T. L., Young, E. J. & Ducat, D. C. Nov 1 2017 In : Metabolic Engineering. 44, p. 236-245 10 p.

Research output: Research - peer-reviewArticle

Cyanobacteria
Sucrose
Bacteria
Light
Sugar (sucrose)
Nannochloropsis
stearoyl-CoA desaturase
long chain polyunsaturated fatty acids
eicosapentaenoic acid
genetic engineering

Bacillus subtilis intramembrane protease RasP activity in Escherichia coli and in vitro

Parrell, D., Zhang, Y., Olenic, S. & Kroos, L. 2017 In : Journal of Bacteriology. 199, 19, e00381-17

Research output: Research - peer-reviewArticle

Maltose-Binding Proteins
Bacillus subtilis
Membrane Proteins
Peptide Hydrolases
Escherichia coli
Coenzyme A-Transferases
Paclitaxel
baccatin III
Biocatalysis
Coenzyme A

Breaking the polar-nonpolar division in solvation free energy prediction

Wang, B., Wang, C., Wu, K. & Wei, G. W. 2017 (Accepted/In press) In : Journal of Computational Chemistry.

Research output: Research - peer-reviewArticle

Feature Vector
Free Energy
Division
Molecules
Prediction
DNA
Proteins
AlkB Enzymes
Demonstrations
Cells
1 Citations

Characterization of trichome-expressed BAHD acyltransferases in petunia axillaris reveals distinct acylsugar assembly mechanisms within the solanaceae

Nadakuduti, S. S., Uebler, J. B., Liu, X., Jones, A. D. & Barry, C. S. Sep 1 2017 In : Plant Physiology. 175, 1, p. 36-50 15 p.

Research output: Research - peer-reviewArticle

Petunia axillaris
acyltransferases
Solanaceae
trichomes
tomatoes
1 Citations

Coevolution of domain interactions in the chloroplast TGD1, 2, 3 lipid transfer complex specific to brassicaceae and poaceae plants

Yang, Y., Zienkiewicz, A., Lavell, A. & Benning, C. Jun 1 2017 In : Plant Cell. 29, 6, p. 1500-1515 16 p.

Research output: Research - peer-reviewArticle

coevolution
Brassicaceae
Poaceae
chloroplasts
Arabidopsis

Crowding in Cellular Environments at an Atomistic Level from Computer Simulations

Feig, M., Yu, I., Wang, P. H., Nawrocki, G. & Sugita, Y. Aug 31 2017 In : Journal of Physical Chemistry B. 121, 34, p. 8009-8025 17 p.

Research output: Research - peer-reviewArticle

crowding
computerized simulation
Computer simulation
Computer Simulation
Peptides

Deciphering metabolic rewiring in breast cancer subtypes

Ogrodzinski, M. P., Bernard, J. J. & Lunt, S. Y. 2017 (Accepted/In press) In : Translational Research.

Research output: Research - peer-reviewArticle

Metabolism
Cells
Breast Neoplasms
Therapeutics
Metabolic Diseases

De novo genome assembly of Camptotheca acuminata, a natural source of the anti-cancer compound camptothecin

Zhao, D., Hamilton, J. P., Pham, G. M., Crisovan, E., Wiegert-Rininger, K., Vaillancourt, B., DellaPenna, D. & Robin Buell, C. Sep 1 2017 In : GigaScience. 6, 9, gix065

Research output: Research - peer-reviewArticle

Camptotheca
Camptothecin
Genome
Neoplasms
Genes

Discrimination of Native-like States of Membrane Proteins with Implicit Membrane-based Scoring Functions

Dutagaci, B., Wittayanarakul, K., Mori, T. & Feig, M. Jun 13 2017 In : Journal of Chemical Theory and Computation. 13, 6, p. 3049-3059 11 p.

Research output: Research - peer-reviewArticle

scoring
discrimination
membranes
proteins
Membrane Proteins

DNA synthesis determines the binding mode of the human mitochondrial single-stranded DNA-binding protein

Morin, J. A., Cerrón, F., Jarillo, J., Beltran-Heredia, E., Ciesielski, G. L., Arias-Gonzalez, J. R., Kaguni, L. S., Cao, F. J. & Ibarra, B. Jul 1 2017 In : Nucleic Acids Research. 45, 12, p. 7237-7248 12 p.

Research output: Research - peer-reviewArticle

Single-Stranded DNA
DNA
human SSBP1 protein
Proteins
Salts

Drosophila protease ClpXP specifically degrades DmLRPPRC1 controlling mitochondrial mRNA and translation

Matsushima, Y., Hirofuji, Y., Aihara, M., Yue, S., Uchiumi, T., Kaguni, L. S. & Kang, D. Dec 1 2017 In : Scientific Reports. 7, 1, 8315

Research output: Research - peer-reviewArticle

Protein Biosynthesis
Drosophila
Peptide Hydrolases
mitochondrial messenger RNA
Unfolded Protein Response

Dynamic assembly of Hda and the sliding clamp in the regulation of replication licensing

Kim, J. S., Nanfara, M. T., Chodavarapu, S., Jin, K. S., Babu, V. M. P., Ghazy, M. A., Chung, S., Kaguni, J. M., Sutton, M. D. & Cho, Y. Apr 20 2017 In : Nucleic acids research. 45, 7, p. 3888-3905 18 p.

Research output: Research - peer-reviewArticle

Licensure
Adenosine Triphosphate
Fingers
Arginine
Catalytic Domain
1 Citations

Engineering the bacterial microcompartment domain for molecular scaffolding applications

Young, E. J., Burton, R., Mahalik, J. P., Sumpter, B. G., Fuentes-Cabrera, M., Kerfeld, C. A. & Ducat, D. C. Jul 31 2017 In : Frontiers in Microbiology. 8, JUL, 1441

Research output: Research - peer-reviewArticle

Research
Proteins
Synthetic Biology
Bioengineering
Bacterial Proteins

Evolutionary routes to biochemical innovation revealed by integrative analysis of a plant-defense related specialized metabolic pathway

Moghe, G. D., Leong, B. J., Hurney, S. M., Jones, A. D. & Last, R. L. Aug 30 2017 In : eLife. 6, e28468

Research output: Research - peer-reviewArticle

Innovation
Metabolic Networks and Pathways
Genes
Biosynthetic Pathways
Solanaceae
1 Citations
photosynthesis
partitioning
ion
rate
thylakoids

Hinge action versus grip in translocation by RNA polymerase

Nedialkov, Y. A., Opron, K., Caudill, H. L., Assaf, F., Anderson, A. J., Cukier, R. I., Wei, G. & Burton, Z. F. Aug 28 2017 (Accepted/In press) In : Transcription.

Research output: Research - peer-reviewArticle

DNA-Directed RNA Polymerases
Hinges
RNA
Hand Strength
DNA

Loss of liver-specific and sexually dimorphic gene expression by aryl hydrocarbon receptor activation in C57BL/6 mice

Nault, R., Fader, K. A., Harkema, J. R. & Zacharewski, T. Sep 1 2017 In : PLoS ONE. 12, 9, e0184842

Research output: Research - peer-reviewArticle

hydrocarbons
gene expression
liver
receptors
mice

Metabolic engineering to increase the corn seed storage lipid quantity and change its compositional quality

Alameldin, H., Izadi-Darbandi, A., Smith, S. A., Balan, V., Jones, A. D., Ebru Orhun, G. & Sticklen, M. 2017 In : Crop Science. 57, 4, p. 1854-1864 11 p.

Research output: Research - peer-reviewArticle

metabolic engineering
seed storage
corn
lipids
seeds

Models in the Biology Classroom: An in-Class Modeling Activity on Meiosis

Hubbs, N. B., Parent, K. N. & Stoltzfus, J. R. Aug 1 2017 In : American Biology Teacher. 79, 6, p. 482-491 10 p.

Research output: Research - peer-reviewArticle

biology
classroom
meiosis
students
Biological Sciences

Myc Regulates Chromatin Decompaction and Nuclear Architecture during B Cell Activation

Kieffer-Kwon, K. R. , Nimura, K. , Rao, S. S. P. , Xu, J. , Jung, S. , Pekowska, A. , Dose, M. , Stevens, E. , Mathe, E. , Dong, P. , Huang, S. C. , Ricci, M. A. , Baranello, L. , Zheng, Y. , Ardori, F. T. , Resch, W. , Stavreva, D. , Nelson, S. , McAndrew, M. , Casellas, A. & 18 others Finn, E., Gregory, C., St. Hilaire, B. G., Johnson, S. M., Dubois, W., Cosma, M. P., Batchelor, E., Levens, D., Phair, R. D., Misteli, T., Tessarollo, L., Hager, G., Lakadamyali, M., Liu, Z., Floer, M., Shroff, H., Aiden, E. L. & Casellas, R. Aug 17 2017 In : Molecular Cell. 67, 4, p. 566-578.e10

Research output: Research - peer-reviewArticle

Chromatin
B-Lymphocytes
Acetylation
Lymphocyte Activation
Epigenomics

Novel loci underlie natural variation in vitamin E levels in maize grain

Diepenbrock, C. H., Kandianis, C. B., Lipka, A. E., Magallanes-Lundback, M., Vaillancourt, B., Góngora-Castillo, E., Wallace, J. G., Cepela, J., Mesberg, A., Bradbury, P. J., Ilut, D. C., Mateos-Hernandez, M., Hamilton, J., Owens, B. F., Tiede, T., Buckler, E. S., Rocheford, T., Buell, C. R., Gore, M. A. & DellaPenna, D. Oct 1 2017 In : Plant Cell. 29, 10, p. 2374-2392 19 p.

Research output: Research - peer-reviewArticle

vitamin E
loci
corn
Vitamin E
Zea mays
1 Citations
antennae
photosystem II
image analysis
fluorescence
chlorophyll

P450s controlling metabolic bifurcations in plant terpene specialized metabolism

Banerjee, A. & Hamberger, B. Sep 12 2017 (Accepted/In press) In : Phytochemistry Reviews. p. 1-31 31 p.

Research output: Research - peer-reviewArticle

terpenoids
metabolism
Terpenes
synthetic biology
structure-activity relationships

PhenoCurve: Capturing dynamic phenotype-environment relationships using phenomics data

Yang, Y., Xu, L., Feng, Z., Cruz, J. A., Savage, L. J., Kramer, D. M. & Chen, J. May 1 2017 In : Bioinformatics. 33, 9, p. 1370-1378 9 p.

Research output: Research - peer-reviewArticle

Phenotype
Relationships
Genes
Gene
Photosynthesis

Photosystem I-LHCII megacomplexes respond to high light and aging in plants

Schwarz, E. M., Tietz, S. & Froehlich, J. E. Oct 3 2017 (Accepted/In press) In : Photosynthesis Research. p. 1-18 18 p.

Research output: Research - peer-reviewArticle

Photosystem I Protein Complex
Light
Aging of materials
photosystem I
Thylakoids

Production of Seed-Like Storage Lipids and Increase in Oil Bodies in Corn (Maize; Zea mays L.) Vegetative Biomass

Alameldin, H., Izadi-Darbandi, A., Smith, S. A., Balan, V., Jones, A. D. & Sticklen, M. Dec 1 2017 In : Industrial Crops and Products. 108, p. 526-534 9 p.

Research output: Research - peer-reviewArticle

lipid bodies
seed crop production
Zea mays
fatty acids
corn

Raman Optical Activity Reveals Carotenoid Photoactivation Events in the Orange Carotenoid Protein in Solution

Fujisawa, T., Leverenz, R. L., Nagamine, M., Kerfeld, C. A. & Unno, M. Aug 2 2017 In : Journal of the American Chemical Society. 139, 30, p. 10456-10460 5 p.

Research output: Research - peer-reviewArticle

Optical Rotation
Carotenoids
Proteins
Chromophores
Crystal structure

Rigidity Strengthening: A Mechanism for Protein-Ligand Binding

Nguyen, D. D., Xiao, T., Wang, M. & Wei, G. W. Jul 24 2017 In : Journal of Chemical Information and Modeling. 57, 7, p. 1715-1721 7 p.

Research output: Research - peer-reviewArticle

rigidity
drug
interaction
Rigidity
Ligands

Spectroanalysis in native gels (SING): rapid spectral analysis of pigmented thylakoid membrane complexes separated by CN–PAGE

Lucker, B., Schwarz, E., Kuhlgert, S., Ostendorf, E. & Kramer, D. M. Nov 1 2017 In : Plant Journal. 92, 4, p. 744-756 13 p.

Research output: Research - peer-reviewArticle

thylakoids
spectral analysis
polyacrylamide gel electrophoresis
gels
Thylakoids

Structural and Functional Characterization of a Short-Chain Flavodoxin Associated with a Noncanonical 1,2-Propanediol Utilization Bacterial Microcompartment

Plegaria, J. S., Sutter, M., Ferlez, B., Aussignargues, C., Niklas, J., Poluektov, O. G., Fromwiller, C., Teravest, M., Utschig, L. M., Tiede, D. M. & Kerfeld, C. A. Oct 24 2017 In : Biochemistry. 56, 42, p. 5679-5690 12 p.

Research output: Research - peer-reviewArticle

Flavodoxin
Propylene Glycol
Enzymes
Flavoproteins
Recycling
Pyrophosphatases
Sulfur
Adenosine Triphosphate
Cysteine
Ligands

Structures and Mechanisms of the Non-Heme Fe(II)- and 2-Oxoglutarate-Dependent Ethylene-Forming Enzyme: Substrate Binding Creates a Twist

Martinez, S., Fellner, M., Herr, C. Q., Ritchie, A., Hu, J. & Hausinger, R. P. Aug 30 2017 In : Journal of the American Chemical Society. 139, 34, p. 11980-11988 9 p.

Research output: Research - peer-reviewArticle

Metals
Substrates
ethylene forming enzyme
alpha-ketoglutaric acid
Ethylene
2 Citations

TCDD influences reservoir of antibiotic resistance genes in murine gut microbiome

Stedtfeld, R. D., Stedtfeld, T. M., Fader, K. A., Williams, M. R., Bhaduri, P., Quensen, J., Zacharewski, T. R., Tiedje, J. M. & Hashsham, S. A. 2017 In : FEMS Microbiology Ecology. 93, 5, fix058

Research output: Research - peer-reviewArticle

Microbial Drug Resistance
Genes
Polychlorinated Dibenzodioxins
Gastrointestinal Microbiome
antibiotic resistance
2 Citations

The BioFragment Database (BFDb): An open-data platform for computational chemistry analysis of noncovalent interactions

Burns, L. A., Faver, J. C., Zheng, Z., Marshall, M. S., Smith, D. G. A., Vanommeslaeghe, K., MacKerell, A. D., Merz, K. M. & Sherrill, C. D. Oct 28 2017 In : Journal of Chemical Physics. 147, 16, 161727

Research output: Research - peer-reviewArticle

computational chemistry
platforms
interactions
Computational chemistry
Proteins
Proton Pumps
Plastids
Chloroplasts
NAD
Oxidoreductases

Thermodynamics and kinetics of RNA tertiary structure formation in the junctionless hairpin ribozyme

White, N. A. & Hoogstraten, C. G. Sep 1 2017 In : Biophysical Chemistry. 228, p. 62-68 7 p.

Research output: Research - peer-reviewArticle

Thermodynamics
RNA
Kinetics
hairpin ribozyme
Catalytic RNA

The role of light–dark regulation of the chloroplast ATP synthase

Kohzuma, K., Froehlich, J. E., Davis, G. A., Temple, J. A., Minhas, D., Dhingra, A., Cruz, J. A. & Kramer, D. M. Jul 24 2017 In : Frontiers in Plant Science. 8, 1248

Research output: Research - peer-reviewArticle

H-transporting ATP synthase
chloroplasts
thylakoids
proton-motive force
imports
Homology
Mutation
Neural Networks
Topology
Protein
2016
6 Citations

Bacterial microcompartments as metabolic modules for plant synthetic biology

Gonzalez-Esquer, C. R., Newnham, S. E. & Kerfeld, C. A. Jul 1 2016 In : Plant Journal. 87, 1, p. 66-75 10 p.

Research output: Research - peer-reviewArticle

synthetic biology
plant biology
enzymes
Synthetic Biology
Enzymes
1 Citations

De Novo Deep Transcriptome Analysis of Medicinal Plants for Gene Discovery in Biosynthesis of Plant Natural Products

Han, R., Rai, A., Nakamura, M., Suzuki, H., Takahashi, H., Yamazaki, M. & Saito, K. 2016 (Accepted/In press) In : Methods in Enzymology.

Research output: Research - peer-reviewArticle

High-Throughput Nucleotide Sequencing
Plant Genes
Genetic Association Studies
Gene Expression Profiling
Medicinal Plants
1 Citations

Flexibility-rigidity index for protein-nucleic acid flexibility and fluctuation analysis

Opron, K., Xia, K., Burton, Z. & Wei, G. W. 2016 (Accepted/In press) In : Journal of Computational Chemistry.

Research output: Research - peer-reviewArticle

Rigidity
Flexibility
Fluctuations
Protein
Nucleic acids