Research Output 1971 2019

2019

Allosteric Interactions in Human Cytochrome P450 CYP3A4: The Role of Phenylalanine 213

Denisov, I. G., Grinkova, Y. V., Nandigrami, P., Shekhar, M., Tajkhorshid, E. & Sligar, S., Mar 12 2019, In : Biochemistry. 58, 10, p. 1411-1422 12 p.

Research output: Contribution to journalArticle

Cytochrome P-450 CYP3A
Phenylalanine
Cytochrome P-450 Enzyme System
Progesterone
Carbamazepine

A novel synthesis of trans-unsaturated fatty acids by the Gram-positive commensal bacterium Enterococcus faecalis FA2-2

Kondakova, T., Kumar, S. & Cronan, J. E., Aug 1 2019, In : Chemistry and Physics of Lipids. 222, p. 23-35 13 p.

Research output: Contribution to journalArticle

Trans Fatty Acids
Enterococcus faecalis
Gram-Positive Bacteria
Unsaturated Fatty Acids
Bacteria

Assessing the Flexibility of the Prochlorosin 2.8 Scaffold for Bioengineering Applications

Hegemann, J. D., Bobeica, S. C., Walker, M. C., Bothwell, I. R. & van der Donk, W. A., May 17 2019, In : ACS synthetic biology. 8, 5, p. 1204-1214 11 p.

Research output: Contribution to journalArticle

Bioengineering
Scaffolds
Peptides
Epitopes
Cyclization

Axial shielding of Pd(II) complexes enables perfect stereoretention in Suzuki-Miyaura cross-coupling of Csp 3 boronic acids

Lehmann, J. W., Crouch, I. T., Blair, D. J., Trobe, M., Wang, P., Li, J. & Burke, M., Dec 1 2019, In : Nature communications. 10, 1, 1263.

Research output: Contribution to journalArticle

Open Access
Boronic Acids
cross coupling
Shielding
shielding
acids

Bacterial expression of membrane-associated cytochrome P450s and their activity assay in nanodiscs

Maroutsos, D., Huff, H. & Das, A., Jan 1 2019, Methods in Molecular Biology. Humana Press Inc., p. 47-72 26 p. (Methods in Molecular Biology; vol. 1927).

Research output: Chapter in Book/Report/Conference proceedingChapter

Cytochromes
Membranes
Cytochrome P-450 Enzyme System
Bacteria
Paclitaxel

Biosynthesis of the RiPP trojan horse nucleotide antibiotic microcin C is directed by the N-formyl of the peptide precursor

Dong, S. H., Kulikovsky, A., Zukher, I., Estrada, P., Dubiley, S., Severinov, K. & Nair, S. K., Jan 1 2019, In : Chemical Science. 10, 8, p. 2391-2395 5 p.

Research output: Contribution to journalArticle

Open Access
Biosynthesis
Nucleotides
Anti-Bacterial Agents
Peptides
Ubiquitin-Activating Enzymes

Breaking tolerance with engineered class I antigen-presenting molecules

Parks, C. A., Henning, K. R., Pavelko, K. D., Hansen, M. J., Van Keulen, V. P., Reed, B. K., Stone, J. D., Schrum, A. G., Gil, D., Kranz, D. M., Bordner, A. J., Barry, M. A. & Pease, L. R., Feb 19 2019, In : Proceedings of the National Academy of Sciences of the United States of America. 116, 8, p. 3136-3145 10 p.

Research output: Contribution to journalArticle

Histocompatibility Antigens Class I
Peptides
T-Lymphocytes
Autoantigens
Isoantigens

Bulk-state and single-particle imaging are central to understanding carbon dot photo-physics and elucidating the effects of precursor composition and reaction temperature

Fathi, P., Khamo, J. S., Huang, X., Srivastava, I., Esch, M. B., Zhang, K. & Pan, D., Apr 1 2019, In : Carbon. 145, p. 572-585 14 p.

Research output: Contribution to journalArticle

Carbon
Physics
Imaging techniques
Chemical analysis
Temperature

Cell-type specific polysome profiling from mammalian tissues

Seimetz, J., Arif, W., Bangru, S., Hernaez, M. & Kalsotra, A., Feb 15 2019, In : Methods. 155, p. 131-139 9 p.

Research output: Contribution to journalArticle

Polyribosomes
Tissue
Messenger RNA
Workflow
Gene Expression Regulation

Characterization of Lipid-Protein Interactions and Lipid-Mediated Modulation of Membrane Protein Function through Molecular Simulation

Muller, M. P., Jiang, T., Sun, C., Lihan, M., Pant, S., Mahinthichaichan, P., Trifan, A. & Tajkhorshid, E., May 8 2019, In : Chemical reviews. 119, 9, p. 6086-6161 76 p.

Research output: Contribution to journalReview article

Membrane Proteins
Modulation
Lipids
Proteins
Molecular dynamics

Characterization of the flavin monooxygenase involved in biosynthesis of the antimalarial FR-900098

Nguyen, K., DeSieno, M. A., Bae, B., Johannes, T. W., Cobb, R. E., Zhao, H. & Nair, S. K., Jan 1 2019, In : Organic and Biomolecular Chemistry. 17, 6, p. 1506-1518 13 p.

Research output: Contribution to journalArticle

dimethylaniline monooxygenase (N-oxide forming)
Flavin-Adenine Dinucleotide
biosynthesis
Biosynthesis
Antimalarials

Chronic Exposure of Mice to Bisphenol-A Alters Uterine Fibroblast Growth Factor Signaling and Leads to Aberrant Epithelial Proliferation

Neff, A. M., Blanco, S. C., Flaws, J. A., Bagchi, I. C. & Bagchi, M. K., May 1 2019, In : Endocrinology. 160, 5, p. 1234-1246 13 p.

Research output: Contribution to journalArticle

Open Access
Fibroblast Growth Factors
Uterus
Endometrial Hyperplasia
Neural Crest
Steroids

Combined ∆ 9 -tetrahydrocannabinol and moderate alcohol administration: effects on ingestive behaviors in adolescent male rats

Nelson, N. G., Law, W. X., Weingarten, M. J., Carnevale, L. N., Das, A. & Liang, N-C., Feb 14 2019, In : Psychopharmacology. 236, 2, p. 671-684 14 p.

Research output: Contribution to journalArticle

Adolescent Behavior
Dronabinol
Alcohols
Alcohol Drinking
Saccharin

Conformational engineering of HIV-1 Env based on mutational tolerance in the CD4 and PG16 bound states

Heredia, J. D., Park, J., Choi, H., Gill, K. S. & Procko, E., Jan 1 2019, In : Journal of virology. 93, 11, e0021919.

Research output: Contribution to journalArticle

Human immunodeficiency virus 1
HIV-1
engineering
mutation
Mutation
Lysogeny
Bacteriophages
Escherichia coli
Temperature
Microbiological Attachment Sites

Correction to: Allosteric interactions in human cytochrome P450 CYP3A4: The role of phenylalanine 213 (Biochemistry (2019) 58: 10 (1411-1422) DOI: 10.1021/acs.biochem.8b01268)

Denisov, I. G., Grinkova, Y. V., Nandigrami, P., Shekhar, M., Tajkhorshid, E. & Sligar, S. G., Jun 18 2019, In : Biochemistry. 58, 24, 1 p.

Research output: Contribution to journalComment/debate

Cytochrome P-450 CYP3A
Biochemistry
Phenylalanine
Cytochrome P-450 Enzyme System

CylA is a sequence-specific protease involved in toxin biosynthesis

Tang, W., Bobeica, S. C., Wang, L. & van der Donk, W. A., Mar 29 2019, In : Journal of Industrial Microbiology and Biotechnology. 46, 3-4, p. 537-549 13 p.

Research output: Contribution to journalArticle

Perforin
Biosynthesis
Peptide Hydrolases
Peptides
Subtilisin

Determination of sec18-lipid interactions by liposome-binding assay

Starr, M. L. & Fratti, R., Jan 1 2019, Methods in Molecular Biology. Humana Press Inc., p. 211-220 10 p. (Methods in Molecular Biology; vol. 1860).

Research output: Chapter in Book/Report/Conference proceedingChapter

Liposomes
Lipids
Proteins
SNARE Proteins
Unilamellar Liposomes

Emerging class of omega-3 fatty acid endocannabinoids & their derivatives

Watson, J. E., Kim, J. S. & Das, A., Aug 1 2019, In : Prostaglandins and Other Lipid Mediators. 143, 106337.

Research output: Contribution to journalReview article

Endocannabinoids
Omega-3 Fatty Acids
Derivatives
Cannabinoid Receptors
Dopamine

Enterococcus faecalis encodes an atypical auxiliary acyl carrier protein required for efficient regulation of fatty acid synthesis by exogenous fatty acids

Zhu, L., Zou, Q., Cao, X. & Cronan, J. E., May 1 2019, In : mBio. 10, 3, e00577-19.

Research output: Contribution to journalArticle

Open Access
Acyl Carrier Protein
Enterococcus faecalis
Fatty Acids
Operon
Oleic Acid

Escherichia coli vectors having stringently repressible replication origins allow a streamlining of Crispr/Cas9 gene editing

Srinivas, S., Hu, Z. & Cronan, J. E., May 1 2019, In : Plasmid. 103, p. 53-62 10 p.

Research output: Contribution to journalArticle

Replication Origin
Plasmids
Escherichia coli
Isopropyl Thiogalactoside
Clustered Regularly Interspaced Short Palindromic Repeats

Estrogen-independent Myc overexpression confers endocrine therapy resistance on breast cancer cells expressing ERαY537S and ERαD538G mutations

Yu, L., Wang, L., Mao, C., Duraki, D., Kim, J. E., Huang, R., Helferich, W. G., Nelson, E., Park, B. H. & Shapiro, D. J., Feb 1 2019, In : Cancer Letters. 442, p. 373-382 10 p.

Research output: Contribution to journalArticle

Estrogen Receptors
Estrogens
Breast Neoplasms
Mutation
Neoplasm Metastasis

Global analysis of osteosarcoma lipidomes reveal altered lipid profiles in metastatic versus nonmetastatic cells

Roy, J., Dibaeinia, P., Fan, T. M., Sinha, S. & Das, A., Jan 1 2019, In : Journal of Lipid Research. 60, 2, p. 375-387 13 p.

Research output: Contribution to journalArticle

Osteosarcoma
Lipids
Diglycerides
Bone Neoplasms
Sphingolipids

High-throughput stability screening of neoantigen/HLA complexes improves immunogenicity predictions

Blaha, D. T., Anderson, S. D., Yoakum, D. M., Hager, M. V., Zha, Y., Gajewski, T. F. & Kranz, D. M., Jan 1 2019, In : Cancer immunology research. 7, 1, p. 50-61 12 p.

Research output: Contribution to journalArticle

Peptides
T-Lymphocytes
HLA-A2 Antigen
Fluorometry
Cancer Vaccines

Influence of Transmembrane Helix Mutations on Cytochrome P450-Membrane Interactions and Function

Mustafa, G., Nandekar, P. P., Camp, T. J., Bruce, N. J., Gregory, M. C., Sligar, S. & Wade, R. C., Feb 5 2019, In : Biophysical journal. 116, 3, p. 419-432 14 p.

Research output: Contribution to journalArticle

Cytochrome P-450 Enzyme System
Mutation
Membranes
Catalytic Domain
Cytochromes b5

Insights into AMS/PCAT transporters from biochemical and structural characterization of a double Glycine motif protease

Bobeica, S. C., Dong, S. H., Huo, L., Mazo, N., McLaughlin, M. I., Jiménez-Osés, G., Nair, S. K. & van der Donk, W. A., Jan 14 2019, In : eLife. 8

Research output: Contribution to journalArticle

Protein Sorting Signals
Glycine
Peptide Hydrolases
Bacteria
Peptides

Intrinsically cell-penetrating multivalent and multitargeting ligands for myotonic dystrophy type 1

Lee, J. Y., Bai, Y., Chembazhi, U. V., Peng, S., Yum, K., Luu, L. M., Hagler, L. D., Serrano, J. F., Edwin Chan, H. Y., Kalsotra, A. & Zimmerman, S. C., Apr 30 2019, In : Proceedings of the National Academy of Sciences of the United States of America. 116, 18, p. 8709-8714 6 p.

Research output: Contribution to journalArticle

Myotonic Dystrophy
Ligands
Permeability
Cell-Penetrating Peptides
RNA

Investigations into the Mechanism of Action of Sublancin

Wu, C., Biswas, S., Garcia De Gonzalo, C. V. & van der Donk, W. A., Mar 8 2019, In : ACS Infectious Diseases. 5, 3, p. 454-459 6 p.

Research output: Contribution to journalArticle

Glucose
Biological Products
DNA Replication
Cell Wall
Carbon

Lipid composition and macromolecular crowding effects on CYP2J2-mediated drug metabolism in nanodiscs

Huff, H. C., Maroutsos, D. & Das, A., May 1 2019, In : Protein Science. 28, 5, p. 928-940 13 p.

Research output: Contribution to journalArticle

NADPH-Ferrihemoprotein Reductase
Metabolism
Lipids
Chemical analysis
Pharmaceutical Preparations

Mechanistic Basis for Ribosomal Peptide Backbone Modifications

Dong, S. H., Liu, A., Mahanta, N., Mitchell, D. A. & Nair, S. K., Jan 1 2019, In : ACS Central Science.

Research output: Contribution to journalArticle

Open Access
Peptides
Enzymes
Thioamides
Substrates
Coenzymes

Microcin J25 inhibits ubiquinol oxidase activity of purified cytochrome bd-I from Escherichia coli

Galván, A. E., Chalón, M. C., Ríos Colombo, N. S., Schurig-Briccio, L. A., Sosa-Padilla, B., Gennis, R. B. & Bellomio, A., May 1 2019, In : Biochimie. 160, p. 141-147 7 p.

Research output: Contribution to journalArticle

Cytochromes
Escherichia coli
Peptides
Cyanides
Electron Transport

Modular Syntheses of Phenanthroindolizidine Natural Products

Jo, Y. I., Burke, M. & Cheon, C. H., Jun 7 2019, In : Organic Letters. 21, 11, p. 4201-4204 4 p.

Research output: Contribution to journalArticle

Boronic Acids
Vanadium
Biological Products
Bromides
Alkaloids

Molecular Basis of Bacillus subtilis ATCC 6633 Self-Resistance to the Phosphono-oligopeptide Antibiotic Rhizocticin

Petronikolou, N., Ortega, M. A., Borisova, S. A., Nair, S. K. & Metcalf, W. W., Apr 19 2019, In : ACS chemical biology. 14, 4, p. 742-750 9 p.

Research output: Contribution to journalArticle

Oligopeptides
Bacilli
Bacillus subtilis
Anti-Bacterial Agents
Threonine

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 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

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

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., 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

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
Ribosomes
Anti-Bacterial Agents
Peptides
Amino Acids
Operon

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

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 1 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., 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