Research Output 1967 2020

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2020

Probing cholesterol binding and translocation in P-glycoprotein

Thangapandian, S., Kapoor, K. & Tajkhorshid, E., Jan 1 2020, In : Biochimica et Biophysica Acta - Biomembranes. 1862, 1, 183090.

Research output: Contribution to journalArticle

P-Glycoprotein
Cholesterol
Amino Acids
Binding Sites
Molecular Dynamics Simulation
2019

A Chalcogen-Bonding Cascade Switch for Planarizable Push–Pull Probes

Macchione, M., Goujon, A., Strakova, K., Humeniuk, H. V., Licari, G., Tajkhorshid, E., Sakai, N. & Matile, S., Oct 28 2019, In : Angewandte Chemie - International Edition. 58, 44, p. 15752-15756 5 p.

Research output: Contribution to journalArticle

Chalcogens
Switches
Supramolecular chemistry
Chemical stability
Molecular dynamics

A Conformationally Restricted Aza-BODIPY Platform for Stimulus-Responsive Probes with Enhanced Photoacoustic Properties

Zhou, E. Y., Knox, H. J., Liu, C., Zhao, W. & Chan, J., Nov 6 2019, In : Journal of the American Chemical Society. 141, 44, p. 17601-17609 9 p.

Research output: Contribution to journalArticle

Photoacoustic effect
dye
Coloring Agents
probe
hypoxia

Active site rearrangement and structural divergence in prokaryotic respiratory oxidases

Safarian, S., Hahn, A., Mills, D. J., Radloff, M., Eisinger, M. L., Nikolaev, A., Meier-Credo, J., Melin, F., Miyoshi, H., Gennis, R. B., Sakamoto, J., Langer, J. D., Hellwig, P., Kühlbrandt, W. & Michel, H., Oct 4 2019, In : Science. 366, 6461, p. 100-104 5 p.

Research output: Contribution to journalArticle

Catalytic Domain
Oxidoreductases
Oxygen
Electron Transport Complex IV
Cytochromes

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. G., 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 network of phosphatidylinositol 4,5-bisphosphate binding sites regulates gating of the Ca2+-activated Cl channel ANO1 (TMEM16A)

Yu, K., Jiang, T., Cui, Y. Y., Tajkhorshid, E. & Criss Hartzell, H., Jan 1 2019, In : Proceedings of the National Academy of Sciences of the United States of America. 116, 40, p. 19952-19962 11 p.

Research output: Contribution to journalArticle

Open Access
Molecular Dynamics Simulation
Phosphatidylinositols
Binding Sites
Mutagenesis
Fluids and Secretions

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 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

A specific small-molecule inhibitor of protein kinase CI activity improves metabolic dysfunction in human adipocytes from obese individuals

Sparks, R., Lui, A., Bader, D., Patel, R., Murr, M., Guida, W., Fratti, R. & Patel, N. A., Jan 1 2019, In : Journal of Biological Chemistry. 294, 41, p. 14896-14910 15 p.

Research output: Contribution to journalArticle

Open Access
Surface plasmon resonance
Protein Kinase Inhibitors
Adipocytes
Caspase 3
Surface Plasmon Resonance

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

Atoms to Phenotypes: Molecular Design Principles of Cellular Energy Metabolism

Singharoy, A., Maffeo, C., Delgado-Magnero, K. H., Swainsbury, D. J. K., Sener, M., Kleinekathöfer, U., Vant, J. W., Nguyen, J., Hitchcock, A., Isralewitz, B., Teo, I., Chandler, D. E., Stone, J. E., Phillips, J. C., Pogorelov, T. V., Mallus, M. I., Chipot, C., Luthey-Schulten, Z., Tieleman, D. P., Hunter, C. N. & 3 others, Tajkhorshid, E., Aksimentiev, A. & Schulten, K., Nov 14 2019, In : Cell. 179, 5, p. 1098-1111.e23

Research output: Contribution to journalArticle

Chromatophores
Energy conversion
Energy Metabolism
Phenotype
Atoms

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

Bacteriophage targeting of gut bacterium attenuates alcoholic liver disease

Duan, Y., Llorente, C., Lang, S., Brandl, K., Chu, H., Jiang, L., White, R. C., Clarke, T. H., Nguyen, K., Torralba, M., Shao, Y., Liu, J., Hernandez-Morales, A., Lessor, L., Rahman, I. R., Miyamoto, Y., Ly, M., Gao, B., Sun, W., Kiesel, R. & 26 others, Hutmacher, F., Lee, S., Ventura-Cots, M., Bosques-Padilla, F., Verna, E. C., Abraldes, J. G., Brown, R. S., Vargas, V., Altamirano, J., Caballería, J., Shawcross, D. L., Ho, S. B., Louvet, A., Lucey, M. R., Mathurin, P., Garcia-Tsao, G., Bataller, R., Tu, X. M., Eckmann, L., van der Donk, W. A., Young, R., Lawley, T. D., Stärkel, P., Pride, D., Fouts, D. E. & Schnabl, B., Nov 21 2019, In : Nature. 575, 7783, p. 505-511 7 p.

Research output: Contribution to journalArticle

Alcoholic Hepatitis
Alcoholic Liver Diseases
Bacteriophages
Liver Diseases
Bacteria

Binding partner- and force-promoted changes in αE-catenin conformation probed by native cysteine labeling

Terekhova, K., Pokutta, S., Kee, Y. S., Li, J., Tajkhorshid, E., Fuller, G., Dunn, A. R. & Weis, W. I., Dec 1 2019, In : Scientific reports. 9, 1, 15375.

Research output: Contribution to journalArticle

Open Access
Catenins
Cysteine
Vinculin
Actins
Cadherins

Biodegradable Biliverdin Nanoparticles for Efficient Photoacoustic Imaging

Fathi, P., Knox, H. J., Sar, D., Tripathi, I., Ostadhossein, F., Misra, S. K., Esch, M. B., Chan, J. & Pan, D., Jul 23 2019, In : ACS Nano. 13, 7, p. 7690-7704 15 p.

Research output: Contribution to journalArticle

Biliverdine
Photoacoustic effect
Nanoparticles
Imaging techniques
nanoparticles

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

Biotransformation of the mycotoxin enniatin b1 by CYP P450 3A4 and potential for drug-drug interactions

Ivanova, L., Denisov, I. G., Grinkova, Y. V., Sligar, S. G. & Fæste, C. K., Aug 2019, In : Metabolites. 9, 8, 158.

Research output: Contribution to journalArticle

Open Access
Drug interactions
Cytochrome P-450 CYP3A
Mycotoxins
Biotransformation
Drug Interactions

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 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 and X-ray structure of the NADH-dependent coenzyme A disulfide reductase from Thermus thermophilus

Lencina, A. M., Koepke, J., Preu, J., Muenke, C., Gennis, R. B., Michel, H. & Schurig-Briccio, L. A., Nov 1 2019, In : Biochimica et Biophysica Acta - Bioenergetics. 1860, 11, 148080.

Research output: Contribution to journalArticle

Thermus thermophilus
Vitamin K 3
NAD
Oxidoreductases
X-Rays

Characterization of a Dehydratase and Methyltransferase in the Biosynthesis of Ribosomally Synthesized and Post-translationally Modified Peptides in Lachnospiraceae

Huo, L., Zhao, X., Acedo, J. Z., Estrada, P., Nair, S. K. & van der Donk, W. A., Jan 1 2019, (Accepted/In press) In : ChemBioChem.

Research output: Contribution to journalArticle

Hydro-Lyases
Biosynthesis
Methyltransferases
Bacteria
Genes

Characterization of glutamyl-tRNA–dependent dehydratases using nonreactive substrate mimics

Bothwell, I. R., Cogan, D. P., Kim, T., Reinhardt, C. J., van der Donk, W. A. & Nair, S. K., Aug 27 2019, In : Proceedings of the National Academy of Sciences of the United States of America. 116, 35, p. 17245-17250 6 p.

Research output: Contribution to journalArticle

Open Access
Hydro-Lyases
RNA, Transfer, Glu
Peptides
Nisin
Glutamic Acid

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

Coaction of Electrostatic an Hyrophobic Interactions: Dynamic Constraints on Disorere TrkA Juxtamembrane Domain

Wang, Z., Fan, H., Hu, X., Khamo, J., Diao, J., Zhang, K. & Pogorelov, T. V., Dec 19 2019, In : Journal of Physical Chemistry B. 123, 50, p. 10709-10717 9 p.

Research output: Contribution to journalArticle

Tropomyosin
Electrostatics
Phosphotransferases
electrostatics
Membranes

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

Copper blocks V-ATPase activity and SNARE complex formation to inhibit yeast vacuole fusion

Miner, G. E., Sullivan, K. D., Zhang, C., Hurst, L. R., Starr, M. L., Rivera-Kohr, D. A., Jones, B. C., Guo, A. & Fratti, R., Nov 1 2019, In : Traffic. 20, 11, p. 841-850 10 p.

Research output: Contribution to journalArticle

SNARE Proteins
Vacuoles
Yeast
Adenosine Triphosphatases
Copper

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

Discovery of novel bacterial queuine salvage enzymes and pathways in human pathogens

Yuan, Y., Zallot, R., Grove, T. L., Payan, D. J., Martin-Verstraete, I., Šepić, S., Balamkundu, S., Neelakandan, R., Gadi, V. K., Liu, C. F., Swairjo, M. A., Dedon, P. C., Almo, S. C., Gerlt, J. A. & de Crécy-Lagard, V., Sep 17 2019, In : Proceedings of the National Academy of Sciences of the United States of America. 116, 38, p. 19126-19135 10 p.

Research output: Contribution to journalArticle

Open Access
Bacteria
queuine tRNA-ribosyltransferase
Enzymes
Eukaryota
Nucleoside Q

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 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

Federating Structural Models and Data: Outcomes from A Workshop on Archiving Integrative Structures

Berman, H. M., Adams, P. D., Bonvin, A. A., Burley, S. K., Carragher, B., Chiu, W., DiMaio, F., Ferrin, T. E., Gabanyi, M. J., Goddard, T. D., Griffin, P. R., Haas, J., Hanke, C. A., Hoch, J. C., Hummer, G., Kurisu, G., Lawson, C. L., Leitner, A., Markley, J. L., Meiler, J. & 18 others, Montelione, G. T., Phillips, G. N., Prisner, T., Rappsilber, J., Schriemer, D. C., Schwede, T., Seidel, C. A. M., Strutzenberg, T. S., Svergun, D. I., Tajkhorshid, E., Trewhella, J., Vallat, B., Velankar, S., Vuister, G. W., Webb, B., Westbrook, J. D., White, K. L. & Sali, A., Dec 3 2019, In : Structure. 27, 12, p. 1745-1759 15 p.

Research output: Contribution to journalArticle

Open Access
Structural Models
Education

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

Herring roe oil supplementation alters microglial cell gene expression and reduces peripheral inflammation after immune activation in a neonatal piglet model

Caputo, M. P., Radlowski, E. C., Lawson, M. A., Antonson, A. M., Watson, J. E., Matt, S. M., Leyshon, B. J., Das, A. & Johnson, R. W., Oct 2019, In : Brain, Behavior, and Immunity. 81, p. 455-469 15 p.

Research output: Contribution to journalArticle

Oils
Inflammation
Gene Expression
Unsaturated Fatty Acids
Occipital Lobe

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 2019, In : Cancer Immunology Research. 7, 1, p. 50-61 12 p.

Research output: Contribution to journalArticle

Peptides
T-Lymphocytes
Peptide T
HLA-A2 Antigen
Fluorometry

Influence of Electron Acceptor and Electron Donor on the Photophysical Properties of Carbon Dots: A Comparative Investigation at the Bulk-State and Single-Particle Level

Srivastava, I., Khamo, J. S., Pandit, S., Fathi, P., Huang, X., Cao, A., Haasch, R. T., Nie, S., Zhang, K. & Pan, D., Jul 4 2019, In : Advanced Functional Materials. 29, 37, 1902466.

Research output: Contribution to journalArticle

Carbon
Electrons
carbon
electrons
bleaching

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. G. & 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

Integrating hydrogen–deuterium exchange mass spectrometry with molecular dynamics simulations to probe lipid-modulated conformational changes in membrane proteins

Martens, C., Shekhar, M., Lau, A. M., Tajkhorshid, E. & Politis, A., Nov 1 2019, In : Nature Protocols. 14, 11, p. 3183-3204 22 p.

Research output: Contribution to journalArticle

Open Access
Molecular Dynamics Simulation
Mass spectrometry
Molecular dynamics
Mass Spectrometry
Membrane Proteins

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 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., May 22 2019, In : ACS Central Science. 5, 5, p. 842-851 10 p.

Research output: Contribution to journalArticle

Open Access
Peptides
Enzymes
Thioamides
Substrates
Coenzymes

Mechanistic Studies of the Kinase Domains of Class IV Lanthipeptide Synthetases

Hegemann, J. D., Shi, L., Gross, M. L. & Van Der Donk, W. A., Jun 5 2019, In : ACS chemical biology. 14, 7, p. 1583-1592 10 p.

Research output: Contribution to journalArticle

Ligases
Phosphotransferases
Protein Sorting Signals
Proteins
Enzymes

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 2019, In : Biochimie. 160, p. 141-147 7 p.

Research output: Contribution to journalArticle

Cytochromes
Escherichia coli
Peptides
Cyanides
Electron Transport

Microscopic Characterization of GRP1 PH Domain Interaction with Anionic Membranes

Pant, S. & Tajkhorshid, E., Jan 1 2019, (Accepted/In press) In : Journal of Computational Chemistry.

Research output: Contribution to journalArticle

Homology
Membrane
Membranes
Interaction
Lipids

Modular Syntheses of Phenanthroindolizidine Natural Products

Jo, Y. I., Burke, M. D. & 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 for enantioselective herbicide degradation imparted by aryloxyalkanoate dioxygenases in transgenic plants

Chekan, J. R., Ongpipattanakul, C., Wright, T. R., Zhang, B., Martin Bollinger, J., Rajakovich, L. J., Krebs, C., Cicchillo, R. M. & Nair, S. K., Jan 1 2019, In : Proceedings of the National Academy of Sciences of the United States of America. 116, 27, p. 13299-13304 6 p.

Research output: Contribution to journalArticle

Open Access
Dioxygenases
Genetically Modified Plants
Herbicides
2,4-Dichlorophenoxyacetic Acid
Indoleacetic Acids