Biochemistry and Molecular Biology

Publications 1981 2018

2018

Engineering nanoreactors using bacterial microcompartment architectures

Plegaria, J. S. & Kerfeld, C. A. Jun 1 2018 In : Current Opinion in Biotechnology. 51, p. 1-7 7 p.

Research output: Research - peer-reviewReview article

Nanoreactors
Enzymes
Proteins
Carbon Monoxide
Encapsulation

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: Research - peer-reviewReview article

Plant Development
Triglycerides
Tissue
Pollination
Plant Oils

Improvements to the APBS biomolecular solvation software suite

Jurrus, E. , Engel, D. , Star, K. , Monson, K. , Brandi, J. , Felberg, L. E. , Brookes, D. H. , Wilson, L. , Chen, J. , Liles, K. , Chun, M. , Li, P. , Gohara, D. W. , Dolinsky, T. , Konecny, R. , Koes, D. R. , Nielsen, J. E. , Head-Gordon, T. , Geng, W. , Krasny, R. & 4 others Wei, G. W., Holst, M. J., McCammon, J. A. & Baker, N. A. Jan 1 2018 In : Protein science : a publication of the Protein Society. 27, 1, p. 112-128 17 p.

Research output: Research - peer-reviewArticle

Solvation
Electrostatics
Static Electricity
Software
Insulator Elements

XEN and the Art of Stem Cell Maintenance: Molecular Mechanisms Maintaining Cell Fate and Self-Renewal in Extraembryonic Endoderm Stem (XEN) Cell Lines

Ralston, A. Jan 1 2018 Advances in Anatomy Embryology and Cell Biology. Springer Verlag, Vol. 229, p. 69-78 10 p. (Advances in Anatomy Embryology and Cell Biology; vol. 229)

Research output: ResearchChapter

Endoderm
Art
Stem Cells
Maintenance
Cell Line
2017
1 Citations
Enterohepatic Circulation
Bile Acids and Salts
Homeostasis
Polychlorinated Dibenzodioxins
Taurolithocholic Acid
1 Citations
engineering
metabolism
genes
proteins
protein
thylakoids
acclimation
chloroplasts
proteins
photosystem II
2 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

Altered thymocyte and T cell development in neonatal mice with hyperoxia-induced lung injury

Angusamy, S., Mansour, T., Abdulmageed, M., Han, R., Schutte, B. C., Lapres, J., Harkema, J. R. & Omar, S. A. Aug 19 2017 (Accepted/In press) In : Unknown Journal.

Research output: Research - peer-reviewArticle

Hyperoxia
Lung Injury
Thymocytes
Thymus Gland
T-Lymphocytes
1 Citations

Analysis and prediction of protein folding energy changes upon mutation by element specific persistent homology

Cang, Z. & Wei, G. W. Nov 15 2017 In : Bioinformatics. 33, 22, p. 3549-3557 9 p.

Research output: Research - peer-reviewArticle

Protein Folding
Homology
Mutation
Prediction
Energy

Anions for Near-Infrared Selective Organic Salt Photovoltaics

Traverse, C. J., Young, M., Suddard-Bangsund, J., Patrick, T., Bates, M., Chen, P., Wingate, B., Lunt, S. Y., Anctil, A. & Lunt, R. R. Dec 1 2017 In : Scientific Reports. 7, 1, 16399

Research output: Research - peer-reviewArticle

Anions
Salts
Infrared radiation
Functional groups
Borates
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)
1 Citations
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
2 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
3 Citations

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
1 Citations

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
Fremyella diplosiphon
tryptophan
Cyanobacteria
nutrients
genes

DnaC, the indispensable companion of DnaB helicase, controls the accessibility of DnaB helicase by primase

Felczak, M. M., Chodavarapu, S. & Kaguni, J. M. Jan 1 2017 In : Journal of Biological Chemistry. 292, 51, p. 20871-20882 12 p.

Research output: Research - peer-reviewArticle

DnaB Helicases
DNA Primase
Conformations
Substitution reactions
DNA

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

Dual impact of elevated temperature on plant defence and bacterial virulence in Arabidopsis

Huot, B., Castroverde, C. D. M., Velásquez, A. C., Hubbard, E., Pulman, J. A., Yao, J., Childs, K. L., Tsuda, K., Montgomery, B. L. & He, S. Y. Dec 1 2017 In : Nature Communications. 8, 1, 1808

Research output: Research - peer-reviewArticle

Arabidopsis
Virulence
Temperature
virulence
temperature
2 Citations

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

Engaging undergraduate biology students in scientific modeling: Analysis of group interactions, sense-making, and justification

Bierema, A. M. K., Schwarz, C. V. & Stoltzfus, J. R. Dec 1 2017 In : CBE Life Sciences Education. 16, 4, ar68

Research output: Research - peer-reviewArticle

group interaction
biology
student
Students
small group
2 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
1 Citations

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

Evolution of a flipped pathway creates metabolic innovation in tomato trichomes through BAHD enzyme promiscuity

Fan, P., Miller, A. M., Liu, X., Jones, A. D. & Last, R. L. Dec 1 2017 In : Nature Communications. 8, 1, 2080

Research output: Research - peer-reviewArticle

cells and cell components
phytochemistry
trichome
biochemical composition
herb

Fibroblast growth factor receptor is a mechanistic link between visceral adiposity and cancer

Chakraborty, D., Benham, V., Bullard, B., Kearney, T., Hsia, H. C., Gibbon, D., Demireva, E. Y., Lunt, S. Y. & Bernard, J. J. Nov 30 2017 In : Oncogene. 36, 48, p. 6668-6679 12 p.

Research output: Research - peer-reviewArticle

Fibroblast Growth Factor Receptors
Intra-Abdominal Fat
Adiposity
Neoplasms
Fibroblast Growth Factor 2

Fighting through the darkness

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

Research output: Research - peer-reviewShort survey

academic research
mental health
psychology
research work
fighting
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

Hybrid All-Atom/Coarse-Grained Simulations of Proteins by Direct Coupling of CHARMM and PRIMO Force Fields

Kar, P. & Feig, M. Nov 14 2017 In : Journal of Chemical Theory and Computation. 13, 11, p. 5753-5765 13 p.

Research output: Research - peer-reviewArticle

field theory (physics)
proteins
atoms
simulation
Atoms

Inhibition of pressure-activated cancer cell adhesion by FAKderived peptides

Zeng, B., Devadoss, D., Wang, S., Vomhof-DeKrey, E. E., Kuhn, L. A. & Basson, M. D. Jan 1 2017 In : Oncotarget. 8, 58, p. 98051-98067 17 p.

Research output: Research - peer-reviewArticle

Cell Adhesion
Pressure
Peptides
Neoplasms
FAK peptide

Interaction of intramembrane metalloprotease SpoIVFB with substrate Pro-σK

Halder, S., Parrell, D., Whitten, D., Feig, M. & Kroos, L. Dec 12 2017 In : Proceedings of the National Academy of Sciences of the United States of America. 114, 50, p. E10677-E10686

Research output: Research - peer-reviewArticle

Metalloproteases
Membranes
Substrates
Peptide Hydrolases
Bacilli
1 Citations

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: Research - peer-reviewReview article

Ligands
Drug Design
Molecular Dynamics Simulation
Pharmacokinetics
Temperature

Long-Range Changes in Neurolysin Dynamics Upon Inhibitor Binding

Uyar, A., Karamyan, V. & Dickson, A. Sep 7 2017 (Accepted/In press) In : Unknown Journal.

Research output: Research - peer-reviewArticle

Neurotensin
inhibitors
Level control
Discriminant analysis
Binding sites

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
Metabolites
Pesticides
Metabolism
Liver
Fish

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
2 Citations

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