Research Output 1968 2019

2019

Nanoscale monitoring of mitochondria and lysosome interactions for drug screening and discovery

Chen, Q., Shao, X., Tian, Z., Chen, Y., Mondal, P., Liu, F., Wang, F., Ling, P., He, W., Zhang, K., Guo, Z. & Diao, J., Jan 1 2019, In : Nano Research.

Research output: Contribution to journalArticle

Mitochondria
Screening
Monitoring
Pharmaceutical Preparations
Cells

NMR analysis of free and lipid nanodisc anchored CEACAM1 membrane proximal peptides with Ca 2+ /CaM

Ghazarian, H., Hu, W., Mao, A., Nguyen, T., Vaidehi, N., Sligar, S. & Shively, J. E., Apr 1 2019, In : Biochimica et Biophysica Acta - Biomembranes. 1861, 4, p. 787-797 11 p.

Research output: Contribution to journalArticle

Nuclear magnetic resonance
Membranes
Lipids
Actins
Peptides

Nontranslational function of leucyl-tRNA synthetase regulates myogenic differentiation and skeletal muscle regeneration

Son, K., You, J. S., Yoon, M. S., Dai, C., Kim, J. H., Khanna, N., Banerjee, A., Martinis, S. A., Han, G., Han, J. M., Kim, S. & Chen, J., May 1 2019, In : Journal of Clinical Investigation. 129, 5, p. 2088-2093 6 p.

Research output: Contribution to journalArticle

Open Access
Amino Acyl-tRNA Synthetases
Regeneration
Skeletal Muscle
Muscle Development
Transfer RNA Aminoacylation

Novel Anti-inflammatory and Vasodilatory ω-3 Endocannabinoid Epoxide Regioisomers

Carnevale, L. N. & Das, A., Jan 1 2019, Advances in Experimental Medicine and Biology. Springer New York LLC, p. 219-232 14 p. (Advances in Experimental Medicine and Biology; vol. 1161).

Research output: Chapter in Book/Report/Conference proceedingChapter

Endocannabinoids
Epoxy Compounds
Anti-Inflammatory Agents
Acids
Metabolites

Novel functions of the ubiquitin-independent proteasome system in regulating Xenopus germline development

Hwang, H., Jin, Z., Krishnamurthy, V. V., Saha, A., Klein, P. S., Garcia, B., Mei, W., King, M. L., Zhang, K. & Yang, J., Apr 15 2019, In : Development (Cambridge). 146, 8, dev172700.

Research output: Contribution to journalArticle

Open Access
Proteasome Endopeptidase Complex
Ubiquitin
Xenopus
embryo
vertebrate

Novel metabolic pathways and regulons for hexuronate utilization in Proteobacteria

Bouvier, J. T., Sernova, N. V., Ghasempur, S., Rodionova, I. A., Vetting, M. W., Al-Obaidi, N. F., Almo, S. C., Gerlt, J. A. & Rodionov, D. A., Jan 1 2019, In : Journal of bacteriology. 201, 2, e00431-18.

Research output: Contribution to journalArticle

Regulon
Proteobacteria
Metabolic Networks and Pathways
Ralstonia pickettii
Enzymes

O-Methyltransferase-Mediated Incorporation of a β-Amino Acid in Lanthipeptides

Acedo, J. Z., Bothwell, I. R., An, L., Trouth, A., Frazier, C. & Van Der Donk, W. A., Jan 1 2019, In : Journal of the American Chemical Society. 141, 42, p. 16790-16801 12 p.

Research output: Contribution to journalArticle

Methyltransferases
Isoaspartic Acid
peptide
Peptides
Amino acids

Optogenetic Delineation of Receptor Tyrosine Kinase Subcircuits in PC12 Cell Differentiation

Khamo, J. S., Krishnamurthy, V. V., Chen, Q., Diao, J. & Zhang, K., Mar 21 2019, In : Cell chemical biology. 26, 3, p. 400-410.e3

Research output: Contribution to journalArticle

Optogenetics
PC12 Cells
Receptor Protein-Tyrosine Kinases
Cell Differentiation
Nerve Growth Factor

Phosphatidic acid induces conformational changes in Sec18 protomers that prevent SNARE priming

Starr, M. L., Sparks, R. P., Arango, A. S., Hurst, L. R., Zhao, Z., Lihan, M., Jenkins, J. L., Tajkhorshid, E. & Fratti, R., Jan 1 2019, In : Journal of Biological Chemistry. 294, 9, p. 3100-3116 17 p.

Research output: Contribution to journalArticle

SNARE Proteins
Phosphatidic Acids
Protein Subunits
Membranes
N-Ethylmaleimide-Sensitive Proteins

Phosphatidylinositol 3,5-bisphosphate regulates the transition between trans-SNARE complex formation and vacuole membrane fusion

Miner, G. E., Sullivan, K. D., Guo, A., Jones, B. C., Hurst, L. R., Ellis, E. C., Starr, M. L. & Fratti, R., Jan 15 2019, In : Molecular biology of the cell. 30, 2, p. 201-208 8 p.

Research output: Contribution to journalArticle

SNARE Proteins
Membrane Fusion
Phosphatidylinositols
Vacuoles
Lipids

PIP2 Influences the Conformational Dynamics of Membrane-Bound KRAS4b

McLean, M. A., Stephen, A. G. & Sligar, S., Jan 1 2019, In : Biochemistry.

Research output: Contribution to journalArticle

Phosphatidylserines
Membranes
Lipids
Phosphatidylinositols
Phospholipids

Polymorphisms of CYP2C8 alter first-electron transfer kinetics and increase catalytic uncoupling

Arnold, W. R., Zelasko, S., Meling, D. D., Sam, K. & Das, A., Sep 2 2019, In : International journal of molecular sciences. 20, 18, 4626.

Research output: Contribution to journalArticle

Open Access
cytochromes
polymorphism
Polymorphism
Cytochrome P-450 Enzyme System
electron transfer

Preface

Fratti, R., Jan 1 2019, In : Methods in Molecular Biology. 1860, p. v

Research output: Contribution to journalEditorial

Pro-Nifuroxazide Self-Assembly Leads to Triggerable Nanomedicine for Anti-cancer Therapy

Misra, S. K., Wu, Z., Ostadhossein, F., Ye, M., Boateng, K. A., Schulten, K., Tajkhorshid, E. & Pan, D., May 22 2019, In : ACS Applied Materials and Interfaces. 11, 20, p. 18074-18089 16 p.

Research output: Contribution to journalArticle

Medical nanotechnology
Self assembly
Nanoparticles
Prodrugs
Phosphorylation

Protein kinase C-α is upregulated by IMP1 in melanoma and is linked to poor survival

Mahapatra, L., Andruska, N., Mao, C., Gruber, S. B., Johnson, T. M., Fullen, D. R., Raskin, L. & Shapiro, D. J., Oct 1 2019, In : Melanoma research. 29, 5, p. 539-543 5 p.

Research output: Contribution to journalArticle

Protein Kinase C
Melanoma
Survival
Messenger RNA
Insulin-Like Growth Factor Binding Protein 2

Real-time fluorescence detection of calcium efflux during vacuolar membrane fusion

Miner, G. E. & Fratti, R., Jan 1 2019, Methods in Molecular Biology. Humana Press Inc., p. 323-331 9 p. (Methods in Molecular Biology; vol. 1860).

Research output: Chapter in Book/Report/Conference proceedingChapter

Membrane Fusion
Vacuoles
Fluorescence
Calcium
Organelles

Reiterative synthesis by the ribosome and recognition of the N-terminal formyl group by biosynthetic machinery contribute to evolutionary conservation of the length of antibiotic microcin c peptide precursor

Zukher, I., Pavlov, M., Tsibulskaya, D., Kulikovsky, A., Zyubko, T., Bikmetov, D., Serebryakova, M., Nair, S. K., Ehrenberg, M., Dubiley, S. & Severinova, K., Mar 1 2019, In : mBio. 10, 2, e00768-19.

Research output: Contribution to journalArticle

Open Access
Ribosomes
Anti-Bacterial Agents
Peptides
Amino Acids
Operon

Repurposing Protein Degradation for Optogenetic Modulation of Protein Activities

Mondal, P., Krishnamurthy, V. V., Sharum, S. R., Haack, N., Zhou, H., Cheng, J., Yang, J. & Zhang, K., Jan 1 2019, (Accepted/In press) In : ACS synthetic biology.

Research output: Contribution to journalArticle

Optogenetics
Proteolysis
Modulation
Proteins
Degradation

Ribotoxins Kill Cells by Chopping off the Head of tRNAs

Huang, R. H., Nov 5 2019, In : Structure. 27, 11, p. 1613-1614 2 p.

Research output: Contribution to journalShort survey

Transfer RNA
Stem Cells

Serotonin transporter–ibogaine complexes illuminate mechanisms of inhibition and transport

Coleman, J. A., Yang, D., Zhao, Z., Wen, P. C., Yoshioka, C., Tajkhorshid, E. & Gouaux, E., Jan 1 2019, In : Nature.

Research output: Contribution to journalLetter

Ibogaine
Serotonin Plasma Membrane Transport Proteins
Plasma Membrane Neurotransmitter Transport Proteins
Serotonin
Neurotransmitter Agents

Single-particle cryo-EM studies of transmembrane proteins in SMA copolymer nanodiscs

Sun, C. & Gennis, R. B., Jul 2019, In : Chemistry and Physics of Lipids. 221, p. 114-119 6 p.

Research output: Contribution to journalReview article

Styrene
Membrane Proteins
Copolymers
Lipids
Proteins

Single-vesicle measurement of protein-induced membrane tethering

Cai, B., Yu, L., Sharum, S. R., Zhang, K. & Diao, J., May 1 2019, In : Colloids and Surfaces B: Biointerfaces. 177, p. 267-273 7 p.

Research output: Contribution to journalArticle

tethering
Membrane Proteins
membranes
proteins
Proteins

Small-molecule ion channels increase host defences in cystic fibrosis airway epithelia

Muraglia, K. A., Chorghade, R. S., Kim, B. R., Tang, X. X., Shah, V. S., Grillo, A. S., Daniels, P. N., Cioffi, A. G., Karp, P. H., Zhu, L., Welsh, M. J. & Burke, M. D., Mar 21 2019, In : Nature. 567, 7748, p. 405-408 4 p.

Research output: Contribution to journalLetter

Cystic Fibrosis Transmembrane Conductance Regulator
Ion Channels
Cystic Fibrosis
Amphotericin B
Epithelium

Structural architecture of a dimeric class C GPCR based on co-trafficking of sweet taste receptor subunits

Park, J., Selvam, B., Sanematsu, K., Shigemura, N., Shukla, D. & Procko, E., Jan 1 2019, In : Journal of Biological Chemistry. 294, 13, p. 4759-4774 16 p.

Research output: Contribution to journalArticle

G-Protein-Coupled Receptors
Dimerization
Dimers
Cysteine
Cells

Structural Insights into the Lipid A Transport Pathway in MsbA

Padayatti, P. S., Lee, S. C., Stanfield, R. L., Wen, P. C., Tajkhorshid, E., Wilson, I. A. & Zhang, Q., Jul 2 2019, In : Structure. 27, 7, p. 1114-1123.e3

Research output: Contribution to journalArticle

Lipid A
ATP-Binding Cassette Transporters
Protein Transport
Salmonella typhimurium
Gram-Negative Bacteria
Depressaria pastinacella
Pastinaca
psoralens
substrate specificity
Substrate Specificity

T cell receptors for gene transfer in adoptive T cell therapy

Sharma, P. & Kranz, D. M., Jan 1 2019, In : Critical Reviews in Immunology. 39, 2, p. 105-122 18 p.

Research output: Contribution to journalArticle

T-Cell Receptor Genes
Adoptive Transfer
Cell- and Tissue-Based Therapy
T-Lymphocytes
Antigen Receptors

Temperature-Independent Kinetic Isotope Effects as Evidence for a Marcus-like Model of Hydride Tunneling in Phosphite Dehydrogenase

Howe, G. W. & Van Der Donk, W. A., Oct 15 2019, In : Biochemistry. 58, 41, p. 4260-4268 9 p.

Research output: Contribution to journalArticle

Hydrides
Isotopes
Kinetics
Temperature
NAD

The EFI Web Resource for Genomic Enzymology Tools: Leveraging Protein, Genome, and Metagenome Databases to Discover Novel Enzymes and Metabolic Pathways

Zallot, R., Oberg, N. & Gerlt, J. A., Oct 15 2019, In : Biochemistry. 58, 41, p. 4169-4182 14 p.

Research output: Contribution to journalArticle

Open Access
Metagenome
Metabolic Networks and Pathways
Genes
Genome
Databases

The hydrodynamic motion of Nanodiscs

Camp, T., McLean, M., Kato, M., Cheruzel, L. & Sligar, S., May 2019, In : Chemistry and Physics of Lipids. 220, p. 28-35 8 p.

Research output: Contribution to journalArticle

Hydrodynamics
Membrane Proteins
Lipid bilayers
Lipid Bilayers
Membranes

The Participation of Regulatory Lipids in Vacuole Homotypic Fusion

Starr, M. L. & Fratti, R., Jun 2019, In : Trends in Biochemical Sciences. 44, 6, p. 546-554 9 p.

Research output: Contribution to journalReview article

Vacuoles
Fusion reactions
Membranes
Lipids
Membrane Fusion
Isomerases
Pseudomonas putida
isomerization
isomerases
soil bacteria

Use of a scaffold peptide in the biosynthesis of amino acid-derived natural products

Ting, C. P., Funk, M. A., Halaby, S. L., Zhang, Z., Gonen, T. & van der Donk, W. A., Jul 19 2019, In : Science. 365, 6450, p. 280-284 5 p.

Research output: Contribution to journalArticle

Peptide Biosynthesis
Biological Products
Amino Acids
Peptides
RNA, Transfer, Amino Acyl

Use of microscale thermophoresis (MST) to measure binding affinities of components of the fusion machinery

Sparks, R. P. & Fratti, R., Jan 1 2019, Methods in Molecular Biology. Humana Press Inc., p. 191-198 8 p. (Methods in Molecular Biology; vol. 1860).

Research output: Chapter in Book/Report/Conference proceedingChapter

SNARE Proteins
Proteins
Aromatic Amino Acids
Tryptophan
Ligands

Use of surface plasmon resonance (SPR) to determine binding affinities and kinetic parameters between components important in fusion machinery

Sparks, R. P., Jenkins, J. L. & Fratti, R., Jan 1 2019, Methods in Molecular Biology. Humana Press Inc., p. 199-210 12 p. (Methods in Molecular Biology; vol. 1860).

Research output: Chapter in Book/Report/Conference proceedingChapter

Surface Plasmon Resonance
Ligands
SNARE Proteins
Soluble N-Ethylmaleimide-Sensitive Factor Attachment Proteins
Carrier Proteins

Use of the dehydrophos biosynthetic enzymes to prepare antimicrobial analogs of alaphosphin

Bougioukou, D. J., Ting, C. P., Peck, S. C., Mukherjee, S. & van der Donk, W. A., Jan 1 2019, In : Organic and Biomolecular Chemistry. 17, 4, p. 822-829 8 p.

Research output: Contribution to journalArticle

enzymes
analogs
Enzymes
RNA, Transfer, Leu
peptides
2018
Isotopes
isotope
kinetics
Kinetics
Hydrides
8-amino-7-oxononanoate synthase
coenzyme A
biotin
Biotin
Bacillus subtilis

Acoustogenic Probes: A New Frontier in Photoacoustic Imaging

Knox, H. J. & Chan, J. K. F., Nov 20 2018, In : Accounts of chemical research. 51, 11, p. 2897-2905 9 p.

Research output: Contribution to journalArticle

Photoacoustic effect
Polyamideimides
Imaging techniques
Tissue
Molecules

A "cross-stitched" peptide with improved helicity and proteolytic stability

Speltz, T. E., Mayne, C. G., Fanning, S. W., Siddiqui, Z., Tajkhorshid, E., Greene, G. L. & Moore, T. W., Jan 1 2018, In : Organic and Biomolecular Chemistry. 16, 20, p. 3702-3706 5 p.

Research output: Contribution to journalArticle

peptides
estrogens
Lactams
Peptides
X ray crystallography

Advances in synthesis of biotin and assembly of lipoic acid

Cronan, J. E., Dec 2018, In : Current Opinion in Chemical Biology. 47, p. 60-66 7 p.

Research output: Contribution to journalReview article

Thioctic Acid
Biotin
Methylation
Metabolism
Escherichia coli

A lanthipeptide library used to identify a protein-protein interaction inhibitor article

Yang, X., Lennard, K. R., He, C., Walker, M. C., Ball, A. T., Doigneaux, C., Tavassoli, A. & van der Donk, W. A., Apr 1 2018, In : Nature chemical biology. 14, 4, p. 375-380 6 p.

Research output: Contribution to journalArticle

Libraries
Proteins
Human Immunodeficiency Virus Proteins
Ligases
Biological Products

Allele-defined genome of the autopolyploid sugarcane Saccharum spontaneum L.

Zhang, J., Zhang, X., Tang, H., Zhang, Q., Hua, X., Ma, X., Zhu, F., Jones, T., Zhu, X., Bowers, J., Wai, C. M., Zheng, C., Shi, Y., Chen, S., Xu, X., Yue, J., Nelson, D. R., Huang, L., Li, Z., Xu, H. & 88 others, Zhou, D., Wang, Y., Hu, W., Lin, J., Deng, Y., Pandey, N., Mancini, M., Zerpa, D., Nguyen, J. K., Wang, L., Yu, L., Xin, Y., Ge, L., Arro, J., Han, J. O., Chakrabarty, S., Pushko, M., Zhang, W., Ma, Y., Ma, P., Lv, M., Chen, F., Zheng, G., Xu, J., Yang, Z., Deng, F., Chen, X., Liao, Z., Zhang, X., Lin, Z., Lin, H., Yan, H., Kuang, Z., Zhong, W., Liang, P., Wang, G., Yuan, Y., Shi, J., Hou, J., Lin, J., Jin, J., Cao, P., Shen, Q., Jiang, Q., Zhou, P., Ma, Y., Zhang, X., Xu, R., Liu, J., Zhou, Y., Jia, H., Ma, Q., Qi, R., Zhang, Z., Fang, J., Fang, H., Song, J., Wang, M., Dong, G., Wang, G., Chen, Z., Ma, T., Liu, H., Dhungana, S. R., Huss, S. E., Yang, X., Sharma, A., Trujillo, J. H., Martinez, M. C., Hudson, M., Riascos, J. J., Schuler, M. A., Chen, L., Braun, D. M., Li, L., Yu, Q., Wang, J., Wang, K., Schatz, M. C., Heckerman, D., Van Sluys, M. A., Souza, G. M., Moore, P. H., Sankoff, D., VanBuren, R., Paterson, A. H., Nagai, C. & Ming, R. R., Nov 1 2018, In : Nature Genetics. 50, 11, p. 1565-1573 9 p.

Research output: Contribution to journalArticle

Saccharum
Alleles
Genome
Chromosomes, Human, Pair 4
Disease Resistance

An Emerging Pathway of Doxorubicin Cardiotoxicity Mediated through CYP2J2

Arnold, W. R. & Das, A., Apr 24 2018, In : Biochemistry. 57, 16, p. 2294-2296 3 p.

Research output: Contribution to journalComment/debate

Naphthacenes
Gene expression regulation
Arachidonic Acid
Doxorubicin
Cytochrome P-450 Enzyme System

A new role for estrogen receptor a in cell proliferation and cancer: Activating the anticipatory unfolded protein response

Livezey, M., Kim, J. E. & Shapiro, D. J., Jun 15 2018, In : Frontiers in Endocrinology. 9, JUN, 325.

Research output: Contribution to journalShort survey

Unfolded Protein Response
Estrogen Receptors
Cell Proliferation
Neoplasms
Protein Folding

Antitumorigenic Properties of Omega-3 Endocannabinoid Epoxides

Roy, J., Watson, J. E., Hong, I. S., Fan, T. M. & Das, A., Jul 12 2018, In : Journal of Medicinal Chemistry. 61, 13, p. 5569-5579 11 p.

Research output: Contribution to journalArticle

Endocannabinoids
Epoxy Compounds
Cannabinoid Receptors
Docosahexaenoic Acids
Osteosarcoma

A Ratiometric Acoustogenic Probe for in Vivo Imaging of Endogenous Nitric Oxide

Reinhardt, C. J., Zhou, E. Y., Jorgensen, M. D., Partipilo, G. & Chan, J. K. F., Jan 24 2018, In : Journal of the American Chemical Society. 140, 3, p. 1011-1018 8 p.

Research output: Contribution to journalArticle

Photoacoustic effect
Nitric oxide
nitric oxide
Nitric Oxide
probe

A Single Amino Acid Switch Alters the Isoprene Donor Specificity in Ribosomally Synthesized and Post-Translationally Modified Peptide Prenyltransferases

Estrada, P., Morita, M., Hao, Y., Schmidt, E. W. & Nair, S. K., Jul 5 2018, In : Journal of the American Chemical Society. 140, 26, p. 8124-8127 4 p.

Research output: Contribution to journalArticle

Dimethylallyltranstransferase
Isoprene
isoprene
Biological Products
peptide
Oxidoreductases
Nitric Oxide
Substrates
Catalytic Domain
Tunnels

Biosynthetic capacity, metabolic variety and unusual biology in the CPR and DPANN radiations

Castelle, C. J., Brown, C. T., Anantharaman, K., Probst, A. J., Huang, R. H. & Banfield, J. F., Oct 1 2018, In : Nature Reviews Microbiology. 16, 10, p. 629-645 17 p.

Research output: Contribution to journalArticle

Archaea
Radiation
Bacteria
Genome Size
Metagenomics