Biochemistry and Molecular Biology

Publications 1986 2018

2018

Functions of triacylglycerols during plant development and stress

Yang, Y. & Benning, C. Feb 1 2018 In : Current Opinion in Biotechnology. 49, p. 191-198 8 p.

Research output: Contribution to journalReview article

Plant Development
Triglycerides
Library Catalogs
Tissue
Pollination
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: Contribution to journalArticle

Enterohepatic Circulation
Tetrachlorodibenzodioxin
Bile Acids and Salts
Homeostasis
Taurolithocholic Acid
1 Citations
engineering
genes
proteins
protein
gene
photosystem II
mutants
thylakoids
acclimation
chloroplasts
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: Contribution to journalArticle

proteins
fluorescence
Tolypothrix
carotenoids
Synechocystis

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: Contribution to journalArticle

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: Contribution to journalArticle

Branched Chain Amino Acids
Metabolic Networks and Pathways
Arabidopsis
branched chain amino acids
Homeostasis
Fatty Acid Desaturases
Eicosapentaenoic Acid
Genetic Engineering
Unsaturated Fatty Acids
Genes

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: Contribution to journalArticle

Maltose-Binding Proteins
Bacillus subtilis
Membrane Proteins
Peptide Hydrolases
Escherichia coli
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: Contribution to journalArticle

Petunia
Solanaceae
Trichomes
Acyltransferases
Lycopersicon esculentum
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: Contribution to journalArticle

chloroplasts
Arabidopsis
Brassicaceae
Chloroplasts
Poaceae

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: Contribution to journalArticle

crowding
Spontaneous Fractures
Computer Simulation
Peptides
Proteins

Deciphering metabolic rewiring in breast cancer subtypes

Ogrodzinski, M. P., Bernard, J. J. & Lunt, S. Y. 2017 In : Translational Research.

Research output: Contribution to journalArticle

Supravalvular Aortic Stenosis
Castration
Metabolism
Breast Neoplasms
Metabolic Diseases

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: Contribution to journalArticle

membranes
Anthralin
Bronchiolo-Alveolar Adenocarcinoma
Membranes
scoring

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: Contribution to journalArticle

Single-Stranded DNA
DNA-Binding Proteins
Mitochondrial DNA
DNA
Proteins

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: Contribution to journalArticle

Protein Biosynthesis
Drosophila
Peptide Hydrolases
Mitochondrial Turnover
Unfolded Protein Response

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: Contribution to journalArticle

Proteins
Synthetic Biology
Bioengineering
Bacterial Proteins
Metabolic Networks and Pathways

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: Contribution to journalArticle

Lod Score
Metabolic Networks and Pathways
Cyclic AMP Receptor Protein
Solanaceae
Methacholine Compounds

Fighting through the darkness

Hoogstraten, C. G. Aug 4 2017 In : Science. 357, 6350, p. 522 1 p.

Research output: Contribution to journalShort survey

1 Citations
Thylakoids
Proton-Motive Force
Photosynthesis
Ions
protons

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 In : Transcription.

Research output: Contribution to journalArticle

Hand Strength
DNA-Directed RNA Polymerases
RNA
DNA
Fluorouracil

Kinetics of ligand binding through advanced computational approaches: A review

Dickson, A., Tiwary, P. & Vashisth, H. 2017 In : Current Topics in Medicinal Chemistry. 17, 23, p. 2626-2641 16 p.

Research output: Contribution to journalReview article

Ligands
Drug Design
Molecular Dynamics Simulation
Pharmacokinetics
Temperature

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: Contribution to journalArticle

Aryl Hydrocarbon Receptors
Inbred C57BL Mouse
Gene Expression
Liver
liver

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: Contribution to journalArticle

seeds
corn
genes
metabolic engineering
Arabidopsis thaliana

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: Contribution to journalArticle

activity
Meiosis
Students
student
students

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: Contribution to journalArticle

Chromatin
B-Lymphocytes
Acetylation
Lymphocyte Activation
Epigenomics
1 Citations
fluorescence
Photosystem II Protein Complex
Chlorophyll
Fluorescence
image analysis

P450s controlling metabolic bifurcations in plant terpene specialized metabolism

Banerjee, A. & Hamberger, B. Sep 12 2017 In : Phytochemistry Reviews. p. 1-31 31 p.

Research output: Contribution to journalArticle

terpenoids
Terpenes
Synthetic Biology
Monoterpenes
Diterpenes

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: Contribution to journalArticle

Cyclic AMP Receptor Protein
Spontaneous Fractures
Airway Obstruction
Genes
Phenotype

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

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

Research output: Contribution to journalArticle

photosystem I
Photosystem I Protein Complex
Spontaneous Fractures
Thylakoids
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: Contribution to journalArticle

corn
lipid bodies
fatty acids
biosynthesis
biomass
1 Citations

Promiscuity, impersonation and accommodation: evolution of plant specialized metabolism

Leong, B. J. & Last, R. L. Dec 1 2017 In : Current Opinion in Structural Biology. 47, p. 105-112 8 p.

Research output: Contribution to journalReview article

Enzymes
Gene Duplication
Glucosinolates
Acyltransferases
Methyltransferases

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: Contribution to journalArticle

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: Contribution to journalArticle

rigidity
Proteins
drug
interaction
Ligands
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: Contribution to journalArticle

Ketoglutaric Acids
Metals
Enzymes
Ethylene
Carbazoles
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: Contribution to journalArticle

Tetrachlorodibenzodioxin
Microbiota
Microbial Drug Resistance
Genes
gene
1 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: Contribution to journalArticle

interactions
proteins
Alcuronium
Ununited Fractures
Anthralin

The Ecstasy and Agony of Assay Interference Compounds

Aldrich, C., Bertozzi, C., Georg, G. I., Kiessling, L., Lindsley, C., Liotta, D., Merz, K. M., Schepartz, A. & Wang, S. Mar 15 2017 In : ACS Chemical Neuroscience. 8, 3, p. 420-423 4 p.

Research output: Contribution to journalReview article

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: Contribution to journalArticle

Catalytic RNA
Thermodynamics
RNA
Alkynes
Eosinophil Chemotactic Factors

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: Contribution to journalArticle

H-transporting ATP synthase
thylakoids
protons
chloroplasts
imports
Neural networks
neural networks
Mutation
protein
Homology
2016
5 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: Contribution to journalArticle

enzymes
Synthetic Biology
Enzymes
synthetic biology
plant biology
2 Citations

Biolayer interferometry: A novel method to Elucidate Protein-Protein and Protein-DNA interactions in the Mitochondrial DNA Replisome

Ciesielski, G. L., Hytönen, V. P. & Kaguni, L. S. 2016 Methods in Molecular Biology. Humana Press Inc., Vol. 1351, p. 223-231 9 p. (Methods in Molecular Biology; vol. 1351)

Research output: Chapter in Book/Report/Conference proceedingChapter

Interferometry
Mitochondrial Diseases
DNA-Directed DNA Polymerase
Mitochondrial DNA
DNA
1 Citations
Xylulose
Ficus
Site-Directed Mutagenesis
Phosphates
imidazoles
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 In : Methods in Enzymology.

Research output: Contribution to journalArticle

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

Expression and purification of mitochondrial RNA polymerase and transcription factor a from drosophila melanogaster

Gajewski, J. P., Arnold, J. J., Salminen, T. S., Kaguni, L. S. & Cameron, C. E. 2016 Methods in Molecular Biology. Humana Press Inc., Vol. 1351, p. 199-210 12 p. (Methods in Molecular Biology; vol. 1351)

Research output: Chapter in Book/Report/Conference proceedingChapter

DNA-Directed RNA Polymerases
Drosophila melanogaster
Transcription Factors
Proteins
Bacteria
1 Citations

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

Opron, K., Xia, K., Burton, Z. & Wei, G. W. 2016 In : Journal of Computational Chemistry.

Research output: Contribution to journalArticle

Proteins
Flexibility
Nucleic acids
Rigidity
Gallic Acid
1 Citations

Isotopic fractionation associated with [NiFe]- and [FeFe]-hydrogenases

Yang, H., Gandhi, H., Cornish, A. J., Moran, J. J., Kreuzer, H. W., Ostrom, N. E. & Hegg, E. L. Jan 30 2016 In : Rapid communications in mass spectrometry : RCM. 30, 2, p. 285-292 8 p.

Research output: Contribution to journalArticle

Fractionation
Erythrasma
Fusobacterium
Metabolism
Electrons