Biochemistry and Molecular Biology

Publications 1975 2018

2018

A biosensor-based framework to measure latent proteostasis capacity

Wood, R. J., Ormsby, A. R., Radwan, M., Cox, D., Sharma, A., Vöpel, T., Ebbinghaus, S., Oliveberg, M., Reid, G. E., Dickson, A. & Hatters, D. M. Dec 1 2018 In : Nature Communications. 9, 1, 287

Research output: Contribution to journalArticle

homeostasis
gene expression
Protein Folding
heat shock
flow cytometry

A failsafe for sensing chromatid tension in mitosis with the histone H3 tail in saccharomyces cerevisiae

Buehl, C. J., Deng, X., Luo, J., Buranasudja, V., Hazbun, T. & Kuo, M. H. Feb 1 2018 In : Genetics. 208, 2, p. 565-578 14 p.

Research output: Contribution to journalArticle

Chromatids
Mitosis
Histones
Saccharomyces cerevisiae
Centromere

A Structural Model of the Urease Activation Complex Derived from Ion Mobility-Mass Spectrometry and Integrative Modeling

Eschweiler, J. D., Farrugia, M. A., Dixit, S. M., Hausinger, R. P. & Ruotolo, B. T. Apr 3 2018 In : Structure. 26, 4, p. 599-606.e3

Research output: Contribution to journalArticle

Urease
Structural Models
Mass Spectrometry
Apoproteins
Ions

Biosynthesis of bioactive diterpenoids in the medicinal plant Vitex agnus-castus

Heskes, A. M., Sundram, T. C. M., Boughton, B. A., Jensen, N. B., Hansen, N. L., Crocoll, C., Cozzi, F., Rasmussen, S., Hamberger, B., Hamberger, B., Staerk, D., Møller, B. L. & Pateraki, I. Mar 1 2018 In : Plant Journal. 93, 5, p. 943-958 16 p.

Research output: Contribution to journalArticle

Vitex agnus-castus
Vitex
Diterpenes
Medicinal Plants
diterpenoids

Breaking symmetry in viral icosahedral capsids as seen through the lenses of X-ray crystallography and cryo-electron microscopy

Parent, K. N., Schrad, J. R. & Cingolani, G. Feb 7 2018 In : Viruses. 10, 2, 67

Research output: Contribution to journalReview article

Cryoelectron Microscopy
Capsid
X Ray Crystallography
Lenses
Product Packaging

Capturing and Interconverting Embryonic Cell Fates in a Dish

Watts, J., Lokken, A., Moauro, A. & Ralston, A. Jan 1 2018 (Accepted/In press) In : Current Topics in Developmental Biology.

Research output: Contribution to journalArticle

Stem Cells
Embryonic Stem Cells
Embryonic Structures
Pluripotent Stem Cells
Endoderm

Coexpression analysis identifies two oxidoreductases involved in the biosynthesis of the monoterpene acid moiety of natural pyrethrin insecticides in Tanacetum cinerariifolium

Xu, H., Moghe, G. D., Wiegert-Rininger, K., Schilmiller, A. L., Barry, C. S., Last, R. L. & Pichersky, E. Jan 1 2018 In : Plant Physiology. 176, 1, p. 524-537 14 p.

Research output: Contribution to journalArticle

Chrysanthemum cinerariifolium
Tanacetum cinerariifolium
Pyrethrins
Monoterpenes
oxidoreductases
3 Citations

Conserved dynamics of chloroplast cytoskeletal FtsZ proteins across photosynthetic lineages

Terbush, A. D., MacCready, J. S., Chen, C., Ducat, D. C. & Osteryoung, K. W. Jan 1 2018 In : Plant Physiology. 176, 1, p. 295-306 12 p.

Research output: Contribution to journalArticle

Chloroplasts
chloroplasts
Temperature
temperature
proteins
Photosystem I Protein Complex
photosystem I
Photosynthesis
funding
Publications
Iron-Regulatory Proteins
Hepcidins
Aryl Hydrocarbon Receptors
Production control
Heme

Editorial

Blumwald, E., Grotewold, E., Okita, T., Jiang, L. & Wendehenne, D. Jan 1 2018 In : Plant Science. 266, 1 p.

Research output: Contribution to journalEditorial

1 Citations

Enabling the hypothesis-driven prioritization of ligand candidates in big databases: Screenlamp and its application to GPCR inhibitor discovery for invasive species control

Raschka, S., Scott, A. M., Liu, N., Gunturu, S., Huertas, M., Li, W. & Kuhn, L. A. Jan 30 2018 (Accepted/In press) In : Journal of Computer-Aided Molecular Design. p. 1-19 19 p.

Research output: Contribution to journalArticle

Introduced Species
Computer-Aided Design
Structure-Activity Relationship
G-Protein-Coupled Receptors
inhibitors
1 Citations

Engineered Lignin in Poplar Biomass Facilitates Cu-Catalyzed Alkaline-Oxidative Pretreatment

Bhalla, A., Bansal, N., Pattathil, S., Li, M., Shen, W., Particka, C. A., Karlen, S. D., Phongpreecha, T., Semaan, R. R., Gonzales-Vigil, E., Ralph, J., Mansfield, S. D., Ding, S. Y., Hodge, D. B. & Hegg, E. L. Mar 5 2018 In : ACS Sustainable Chemistry and Engineering. 6, 3, p. 1932-1941 10 p.

Research output: Contribution to journalArticle

copper compound
Copper compounds
hierarchical system
Hierarchical systems
Delignification
1 Citations

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: Contribution to journalReview article

Nanoreactors
Enzymes
Proteins
Carbon Cycle
Bacterial Genes

Expanding the Substrate Specificity of Thermoanaerobacter pseudoethanolicus Secondary Alcohol Dehydrogenase by a Dual Site Mutation

Musa, M. M., Bsharat, O., Karume, I., Vieille, C., Takahashi, M. & Hamdan, S. M. Feb 14 2018 In : European Journal of Organic Chemistry. 2018, 6, p. 798-805 8 p.

Research output: Contribution to journalArticle

dehydrogenases
mutations
alcohols
Ketones
ketones

Exposure Assessment of Acetamide in Milk, Beef, and Coffee Using Xanthydrol Derivatization and Gas Chromatography/Mass Spectrometry

Vismeh, R., Haddad, D., Moore, J., Nielson, C., Bals, B., Campbell, T., Julian, A., Teymouri, F., Jones, A. D. & Bringi, V. Jan 10 2018 In : Journal of Agricultural and Food Chemistry. 66, 1, p. 298-305 8 p.

Research output: Contribution to journalArticle

acetamides
Beef
Coffee
exposure assessment
derivatization

Extended Zinc AMBER Force Field (EZAFF)

Yu, Z., Li, P. & Merz, K. M. Jan 9 2018 In : Journal of Chemical Theory and Computation. 14, 1, p. 242-254 13 p.

Research output: Contribution to journalArticle

field theory (physics)
Zinc
zinc
Molecular mechanics
Organometallic Compounds

Fluorescence and Excited-State Conformational Dynamics of the Orange Carotenoid Protein

Gurchiek, J. K., Bao, H., Domínguez-Martín, M. A., McGovern, S. E., Marquardt, C. E., Roscioli, J. D., Ghosh, S., Kerfeld, C. A. & Beck, W. F. Feb 15 2018 In : Journal of Physical Chemistry B. 122, 6, p. 1792-1800 9 p.

Research output: Contribution to journalArticle

carotenoids
Carotenoids
Excited states
Fluorescence
proteins

Free-Energy-Based Protein Design: Re-Engineering Cellular Retinoic Acid Binding Protein II Assisted by the Moveable-Type Approach

Zhong, H. A., Santos, E. M., Vasileiou, C., Zheng, Z., Geiger, J. H., Borhan, B. & Merz, K. M. Mar 14 2018 In : Journal of the American Chemical Society. 140, 10, p. 3483-3486 4 p.

Research output: Contribution to journalArticle

Tretinoin
Free energy
Proteins
Protein Engineering
Acids

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
Tissue
Pollination
Plant Oils

Galactoglycerolipid lipase PGD1 is involved in thylakoid membrane remodeling in response to adverse environmental conditions in chlamydomonas

Du, Z. Y., Lucker, B. F., Zienkiewicz, K., Miller, T. E., Zienkiewicz, A., Sears, B. B., Kramer, D. M. & Benning, C. Feb 1 2018 In : Plant Cell. 30, 2, p. 447-465 19 p.

Research output: Contribution to journalArticle

Chlamydomonas
Thylakoids
Plastids
Lipase
thylakoids

Genes affecting progression of bacteriophage P22 infection in Salmonella identified by transposon and single gene deletion screens

Bohm, K., Porwollik, S., Chu, W., Dover, J. A., Gilcrease, E. B., Casjens, S. R., Mcclelland, M. & Parent, K. N. Jan 1 2018 (Accepted/In press) In : Molecular Microbiology.

Research output: Contribution to journalArticle

Bacteriophage P22
Salmonella Infections
Gene Deletion
Genes
Bacteriophages
1 Citations

Genetic basis of photosynthetic responses to cold in two locally adapted populations of Arabidopsis thaliana

Oakley, C. G., Savage, L., Lotz, S., Larson, G. R., Thomashow, M. F., Kramer, D. M. & Schemske, D. W. Jan 23 2018 In : Journal of Experimental Botany. 69, 3, p. 699-709 11 p.

Research output: Contribution to journalArticle

photostability
Quantitative Trait Loci
Photosynthesis
Arabidopsis
quantitative trait loci

Identification of an algal xylan synthase indicates that there is functional orthology between algal and plant cell wall biosynthesis

Jensen, J. K., Busse-Wicher, M., Poulsen, C. P., Fangel, J. U., Smith, P. J., Yang, J. Y., Peña, M. J., Dinesen, M. H., Martens, H. J., Melkonian, M., Wong, G. K. S., Moremen, K. W., Wilkerson, C. G., Scheller, H. V., Dupree, P., Ulvskov, P., Urbanowicz, B. R. & Harholt, J. Jan 1 2018 (Accepted/In press) In : New Phytologist.

Research output: Contribution to journalArticle

xylan
algae
Plant Cells
Cell Wall
cell walls

Impact of Ultrathin C60 on Perovskite Photovoltaic Devices

Liu, D., Wang, Q., Traverse, C. J., Yang, C., Young, M., Kuttipillai, P. S., Lunt, S. Y., Hamann, T. W. & Lunt, R. R. Jan 23 2018 In : ACS Nano. 12, 1, p. 876-883 8 p.

Research output: Contribution to journalArticle

Fullerenes
Perovskite
fullerenes
solar cells
Photocurrents
4 Citations

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: Contribution to journalArticle

Solvation
Static Electricity
Electrostatics
Software
Insulator Elements

Incorporating population-level genetic variability within laboratory models in toxicology: From the individual to the population

Dornbos, P. & LaPres, J. J. Feb 15 2018 In : Toxicology. 395, p. 1-8 8 p.

Research output: Contribution to journalReview article

Population Genetics
Toxicology
Population
Risk assessment
Decision Making
1 Citations

In silico analysis of the regulation of the photosynthetic electron transport Chain in C3 plants

Morales, A., Yin, X., Harbinson, J., Driever, S. M., Molenaar, J., Kramer, D. M. & Struik, P. C. Feb 1 2018 In : Plant Physiology. 176, 2, p. 1247-1261 15 p.

Research output: Contribution to journalArticle

C3 plants
electron transport chain
Electron Transport
Computer Simulation
electron transfer
2 Citations
Protein Binding
Affine transformation
Learning systems
Homology
Machine Learning

In the grass species Brachypodium distachyon, the production of mixed-linkage (1,3;1,4)-β-glucan (MLG) occurs in the Golgi apparatus

Kim, S. J., Zemelis-Durfee, S., Jensen, J. K., Wilkerson, C. G., Keegstra, K. & Brandizzi, F. Mar 1 2018 In : Plant Journal. 93, 6, p. 1062-1075 14 p.

Research output: Contribution to journalArticle

Brachypodium
Plant cell culture
Brachypodium distachyon
brefeldin A
Brefeldin A

Lignin Conversion to Low-Molecular-Weight Aromatics via an Aerobic Oxidation-Hydrolysis Sequence: Comparison of Different Lignin Sources

Das, A., Rahimi, A., Ulbrich, A., Alherech, M., Motagamwala, A. H., Bhalla, A., Da Costa Sousa, L., Balan, V., Dumesic, J. A., Hegg, E. L., Dale, B. E., Ralph, J., Coon, J. J. & Stahl, S. S. Mar 5 2018 In : ACS Sustainable Chemistry and Engineering. 6, 3, p. 3367-3374 8 p.

Research output: Contribution to journalArticle

Aromatization
Depolymerization
Catalytic oxidation
catalysis
Lignin
1 Citations

Maize w3 disrupts homogentisate solanesyl transferase (ZmHst) and reveals a plastoquinone-9 independent path for phytoene desaturation and tocopherol accumulation in kernels

Hunter, C. T., Saunders, J. W., Magallanes-Lundback, M., Christensen, S. A., Willett, D., Stinard, P. S., Li, Q. B., Lee, K., DellaPenna, D. & Koch, K. E. Mar 1 2018 In : Plant Journal. 93, 5, p. 799-813 15 p.

Research output: Contribution to journalArticle

Plastoquinone
Tocopherols
Transferases
Seedlings
transferases

Metabolism in cancer metastasis: bioenergetics, biosynthesis, and beyond

Teoh, S. T. & Lunt, S. Y. Mar 1 2018 In : Wiley Interdisciplinary Reviews: Systems Biology and Medicine. 10, 2, e1406

Research output: Contribution to journalReview article

Biosynthesis
Metabolism
Energy Metabolism
Cells
Neoplasm Metastasis

Metformin induces distinct bioenergetic and metabolic profiles in sensitive versus resistant high grade serous ovarian cancer and normal fallopian tube secretory epithelial cells

Hodeib, M., Ogrodzinski, M. P., Vergnes, L., Reue, K., Karlan, B. Y., Lunt, S. Y. & Aspuria, P. J. P. Jan 1 2018 In : Oncotarget. 9, 3, p. 4044-4060 17 p.

Research output: Contribution to journalArticle

Fallopian Tube Neoplasms
Metabolome
Metformin
Ovarian Neoplasms
Energy Metabolism

Multiscale weighted colored graphs for protein flexibility and rigidity analysis

Bramer, D. & Wei, G. W. Feb 7 2018 In : Journal of Chemical Physics. 148, 5, 054103

Research output: Contribution to journalArticle

rigidity
Rigidity
flexibility
proteins
Proteins

Novel bioengineered cassava expressing an archaeal starch degradation system and a bacterial ADP-glucose pyrophosphorylase for starch self-digestibility and yield increase

Ligaba-Osena, A., Jones, J., Donkor, E., Chandrayan, S., Pole, F., Wu, C. H., Vieille, C., Adams, M. W. W. & Hankoua, B. B. Feb 26 2018 In : Frontiers in Plant Science. 9, 192

Research output: Contribution to journalArticle

bioethanol
cassava
digestibility
genetically modified organisms
starch

Perspectives on Sharing Models and Related Resources in Computational Biomechanics Research

Erdemir, A. , Hunter, P. J. , Holzapfel, G. A. , Loew, L. M. , Middleton, J. , Jacobs, C. R. , Nithiarasu, P. , Löhner, R. , Wei, G. , Winkelstein, B. A. , Barocas, V. H. , Guilak, F. , Ku, J. P. , Hicks, J. L. , Delp, S. L. , Sacks, M. , Weiss, J. A. , Ateshian, G. A. , Maas, S. A. , McCulloch, A. D. & 1 others Peng, G. C. Y. Feb 1 2018 In : Journal of Biomechanical Engineering. 140, 2, 024701

Research output: Contribution to journalReview article

Biomechanics
Biomechanical Phenomena
Research
Software
Biological Phenomena

Plant hormones: Metabolic end run to jasmonate

Howe, G. A. Jan 16 2018 In : Nature Chemical Biology. 14, 2, p. 109-110 2 p.

Research output: Contribution to journalShort survey

Plant Growth Regulators
jasmonic acid

PREFMD: A web server for protein structure refinement via molecular dynamics simulations

Heo, L. & Feig, M. Mar 15 2018 In : Bioinformatics. 34, 6, p. 1063-1065 3 p.

Research output: Contribution to journalArticle

Web Server
Protein Structure
Molecular Dynamics Simulation
Computational Biology
Molecular dynamics
Hydrogen
Hydrogen bonds
Ligands
hydrogen bonds
proteins

Quantitative Toxicity Prediction Using Topology Based Multitask Deep Neural Networks

Wu, K. & Wei, G. W. Feb 26 2018 In : Journal of Chemical Information and Modeling. 58, 2, p. 520-531 12 p.

Research output: Contribution to journalArticle

neural network
Toxicity
Topology
learning method
abstraction

RAF2 is a RuBisCO assembly factor in Arabidopsis thaliana

Fristedt, R., Hu, C., Wheatley, N., Roy, L. M., Wachter, R. M., Savage, L., Harbinson, J., Kramer, D. M., Merchant, S. S., Yeates, T. & Croce, R. Jan 1 2018 (Accepted/In press) In : Plant Journal.

Research output: Contribution to journalArticle

Oxygenases
Abscisic Acid
ribulose 1,5-diphosphate
Chloroplasts
oxygenases
Cues
Carbon Cycle
Cyanobacteria
Light
Thylakoids

Recovery from N deprivation is a transcriptionally and functionally distinct state in chlamydomonas

Tsai, C. H., Uygun, S., Roston, R., Shiu, S. H. & Benning, C. Mar 1 2018 In : Plant physiology. 176, 3, p. 2007-2023 17 p.

Research output: Contribution to journalArticle

Chlamydomonas
algae
Hydrolysis
hydrolysis
Chloroplast Proteins
1 Citations

Representability of algebraic topology for biomolecules in machine learning based scoring and virtual screening

Cang, Z., Mu, L. & Wei, G. W. Jan 1 2018 In : PLoS Computational Biology. 14, 1, e1005929

Research output: Contribution to journalArticle

Virtual Screening
Algebraic topology
Representability
Biomolecules
artificial intelligence

Resolution of growth–defense conflict: mechanistic insights from jasmonate signaling

Guo, Q., Major, I. T. & Howe, G. A. Aug 1 2018 In : Current Opinion in Plant Biology. 44, p. 72-81 10 p.

Research output: Contribution to journalArticle

metabolism
induced resistance
vegetative growth
signal transduction
transcription factors

Rooted tRNAomes and evolution of the genetic code

Pak, D., Du, N., Kim, Y., Sun, Y. & Burton, Z. F. Feb 1 2018 (Accepted/In press) In : Transcription.

Research output: Contribution to journalArticle

Genetic Code
Transfer RNA
Anticodon
Codon
Messenger RNA

Shigella phages isolated during a dysentery outbreak reveal uncommon structures and broad species diversity

Doore, S. M., Schrad, J. R., Dean, W. F., Dover, J. A. & Parent, K. N. Apr 1 2018 In : Journal of Virology. 92, 8, e02117-17

Research output: Contribution to journalArticle

dysentery
Dysentery
Shigella
bacteriophages
Bacteriophages

The evolutionary unZIPping of a dimerization motif—a comparison of ZIP and PrP architectures

Hu, J., Wille, H. & Schmitt-Ulms, G. Mar 1 2018 In : Pathogens. 7, 1, 4

Research output: Contribution to journalArticle

Dimerization
Proteins
Recombinant Proteins
Amino Acid Motifs
Staphylococcal Protein A
3 Citations

The molecular machinery of chloroplast division

Chen, C., MacCready, J. S., Ducat, D. C. & Osteryoung, K. W. Jan 1 2018 In : Plant Physiology. 176, 1, p. 138-151 14 p.

Research output: Contribution to journalComment/debate

Chloroplasts
chloroplasts