Research Output 1968 2019

2016

An Atypical α/β-Hydrolase Fold Revealed in the Crystal Structure of Pimeloyl-Acyl Carrier Protein Methyl Esterase BioG from Haemophilus influenzae

Shi, J., Cao, X., Chen, Y., Cronan, J. E. & Guo, Z., Dec 6 2016, In : Biochemistry. 55, 48, p. 6705-6717 13 p.

Research output: Contribution to journalArticle

Acyl Carrier Protein
Haemophilus influenzae
Hydrolases
Esterases
Crystal structure

An Engineered Switch in T Cell Receptor Specificity Leads to an Unusual but Functional Binding Geometry

Harris, DT., Singh, NK. K., Cai, Q., Smith, SN. N., Vander Kooi, CW. W., Procko, E., Kranz, D. M. & Baker, BM. M., Jul 6 2016, In : Structure. 24, 7, p. 1142-1154 13 p.

Research output: Contribution to journalArticle

T-Cell Antigen Receptor Specificity
Major Histocompatibility Complex
Peptide Receptors
Molecular Evolution
Proteins
Unfolded Protein Response
Immediate-Early Genes
Cell proliferation
Epidermal Growth Factor
Gene expression

Anticipatory UPR Activation: A Protective Pathway and Target in Cancer

Shapiro, D. J., Livezey, M., Yu, L., Zheng, X. & Andruska, N., Oct 1 2016, In : Trends in Endocrinology and Metabolism. 27, 10, p. 731-741 11 p.

Research output: Contribution to journalReview article

Unfolded Protein Response
Neoplasms
Endoplasmic Reticulum Stress
Breast Neoplasms
Protein Unfolding

Antiestrogen resistant cell lines expressing estrogen receptor α mutations upregulate the unfolded protein response and are killed by BHPI

Mao, C., Livezey, M., Kim, J. E. & Shapiro, D. J., Oct 7 2016, In : Scientific Reports. 6, 34753.

Research output: Contribution to journalArticle

Unfolded Protein Response
Estrogen Receptor Modulators
Estrogen Receptors
Up-Regulation
Cell Line

A Purple Cupredoxin from Nitrosopumilus maritimus Containing a Mononuclear Type 1 Copper Center with an Open Binding Site

Hosseinzadeh, P., Tian, S., Marshall, N. M., Hemp, J., Mullen, T., Nilges, M. J., Gao, Y. G., Robinson, H., Stahl, D. A., Gennis, R. B. & Lu, Y., May 25 2016, In : Journal of the American Chemical Society. 138, 20, p. 6324-6327 4 p.

Research output: Contribution to journalArticle

Binding sites
Copper
Binding Sites
electron spin resonance
copper

Artificial Dense Granules: A Procoagulant Liposomal Formulation Modeled after Platelet Polyphosphate Storage Pools

Donovan, A. J., Kalkowski, J., Szymusiak, M., Wang, C., Smith, S. A., Klie, R. F., Morrissey, J. H. & Liu, Y., Aug 8 2016, In : Biomacromolecules. 17, 8, p. 2572-2581 10 p.

Research output: Contribution to journalArticle

Polyphosphates
Type C Phospholipases
Platelets
Factor XII
Nanoparticles
Thioctic Acid
Biosynthetic Pathways
Keto Acids
Enzymes
Bacillus subtilis

Assignment of function to a domain of unknown function: DUF1537 is a new kinase family in catabolic pathways for acid sugars

Zhang, X., Carter, M. S., Vetting, M. W., Francisco, B. S., Zhao, S., Al-Obaidi, N. F., Solbiati, J. O., Thiaville, J. J., Crécy-Lagard, V. D., Jacobson, M. P., Almo, S. C. & Gerlt, J. A., Jul 19 2016, In : Proceedings of the National Academy of Sciences of the United States of America. 113, 29, p. E4161-E4169

Research output: Contribution to journalArticle

Sugar Acids
Phosphotransferases
Carbon
Fructose-Bisphosphate Aldolase
Membrane Transport Proteins

Asymmetric Binding and Metabolism of Polyunsaturated Fatty Acids (PUFAs) by CYP2J2 Epoxygenase

Arnold, W. R., Baylon, J. L., Tajkhorshid, E. & Das, A., Dec 20 2016, In : Biochemistry. 55, 50, p. 6969-6980 12 p.

Research output: Contribution to journalArticle

Docosahexaenoic Acids
Unsaturated Fatty Acids
Metabolism
Arachidonic Acid
Eicosapentaenoic Acid

Atomic-level description of protein-lipid interactions using an accelerated membrane model

Baylon, J. L., Vermaas, J. V., Muller, M. P., Arcario, M. J., Pogorelov, T. V. & Tajkhorshid, E., Jul 1 2016, In : Biochimica et Biophysica Acta - Biomembranes. 1858, 7, p. 1573-1583 11 p.

Research output: Contribution to journalArticle

Membrane Proteins
Membranes
Lipids
Mobile Applications
Proteins

BET inhibition attenuates helicobacter pylori-induced inflammatory response by suppressing inflammatory gene transcription and enhancer activation

Chen, J., Wang, Z., Hu, X., Chen, R., Romero-Gallo, J., Peek, R. M. & Chen, L-F., May 15 2016, In : Journal of Immunology. 196, 10, p. 4132-4142 11 p.

Research output: Contribution to journalArticle

Helicobacter pylori
Transcriptional Activation
Genes
RNA
Messenger RNA

Binding Site Recognition and Docking Dynamics of a Single Electron Transport Protein: Cytochrome c2

Singharoy, A., Barragan, A. M., Thangapandian, S., Tajkhorshid, E. & Schulten, K., Sep 21 2016, In : Journal of the American Chemical Society. 138, 37, p. 12077-12089 13 p.

Research output: Contribution to journalArticle

Cytochromes c2
Binding sites
Electron Transport
Oxidation-Reduction
cytochrome

Biophysical and biochemical characterization of avian secretory component provides structural insights into the evolution of the polymeric Ig receptor

Stadtmueller, B. M., Yang, Z., Huey-Tubman, K. E., Roberts-Mataric, H., Hubbell, W. L. & Bjorkman, P. J., Aug 15 2016, In : Journal of Immunology. 197, 4, p. 1408-1414 7 p.

Research output: Contribution to journalArticle

Polymeric Immunoglobulin Receptors
Secretory Component
Electrons
Ligands
Surface Plasmon Resonance

Biosynthetic investigation of phomopsins reveals a widespread pathway for ribosomal natural products in Ascomycetes

Ding, W., Liu, W. Q., Jia, Y., Li, Y., Van Der Donk, W. A. & Zhang, Q., Mar 29 2016, In : Proceedings of the National Academy of Sciences of the United States of America. 113, 13, p. 3521-3526 6 p.

Research output: Contribution to journalArticle

Ascomycota
Biological Products
Methyltransferases
Fungi
Antimitotic Agents

Biosynthetic Timing and Substrate Specificity for the Thiopeptide Thiomuracin

Zhang, Z., Hudson, G. A., Mahanta, N., Tietz, J. I., van der Donk, W. A. & Mitchell, D. A., Dec 7 2016, In : Journal of the American Chemical Society. 138, 48, p. 15511-15514 4 p.

Research output: Contribution to journalArticle

Alkenes
Protein Sorting Signals
Substrate Specificity
peptide
Peptides

Cameo appearances of aminoacyl-tRNA in natural product biosynthesis

Ulrich, E. C. & van der Donk, W. A., Dec 1 2016, In : Current Opinion in Chemical Biology. 35, p. 29-36 8 p.

Research output: Contribution to journalReview article

Biosynthesis
Transfer RNA
Biological Products
Genes
Enzymes

Characterization of the stereochemical configuration of lanthionines formed by the lanthipeptide synthetase GeoM

Garg, N., Goto, Y., Chen, T. & van der Donk, W. A., Nov 1 2016, In : Biopolymers. 106, 6, p. 834-842 9 p.

Research output: Contribution to journalArticle

Ligases
Peptides
Peptide Synthases
Perforin
Bacteriocins

Colloidal Confinement of Polyphosphate on Gold Nanoparticles Robustly Activates the Contact Pathway of Blood Coagulation

Szymusiak, M., Donovan, A. J., Smith, S. A., Ransom, R., Shen, H., Kalkowski, J., Morrissey, J. H. & Liu, Y., Jan 20 2016, In : Bioconjugate Chemistry. 27, 1, p. 102-109 8 p.

Research output: Contribution to journalArticle

Polyphosphates
Blood Coagulation
Coagulation
Gold
Nanoparticles

Computationally designed high specificity inhibitors delineate the roles of BCL2 family proteins in cancer

Berger, S., Procko, E., Margineantu, D., Lee, E. F., Shen, B. W., Zelter, A., Silva, D. A., Chawla, K., Herold, M. J., Garnier, J. M., Johnson, R., Maccoss, M. J., Lessene, G., Davis, T. N., Stayton, P. S., Stoddard, B. L., Fairlie, W. D., Hockenbery, D. M. & Baker, D., Nov 2 2016, In : eLife. 5, NOVEMBER2016, e20352.

Research output: Contribution to journalArticle

Proto-Oncogene Proteins c-bcl-2
Neoplasms
Proteins
Survival
Apoptosis

Conformational Dynamics of the Human Islet Amyloid Polypeptide in a Membrane Environment: Toward the Aggregation Prone Form

Skeby, K. K., Andersen, O. J., Pogorelov, T. V., Tajkhorshid, E. & Schiøtt, B., Apr 19 2016, In : Biochemistry. 55, 13, p. 2031-2042 12 p.

Research output: Contribution to journalArticle

Islet Amyloid Polypeptide
Agglomeration
Membranes
Amyloid
Membrane Lipids

Conformational equilibrium of talin is regulated by anionic lipids

Ye, X., McLean, M. A. & Sligar, S., Aug 1 2016, In : Biochimica et Biophysica Acta - Biomembranes. 1858, 8, p. 1833-1840 8 p.

Research output: Contribution to journalArticle

Talin
Integrins
Lipids
Phospholipids
Membranes

Copper regulates cyclic-AMP-dependent lipolysis

Krishnamoorthy, L., Cotruvo, J. A., Chan, J. K. F., Kaluarachchi, H., Muchenditsi, A., Pendyala, V. S., Jia, S., Aron, A. T., Ackerman, C. M., Wal, M. N. V., Guan, T., Smaga, L. P., Farhi, S. L., New, E. J., Lutsenko, S. & Chang, C. J., Aug 1 2016, In : Nature chemical biology. 12, 8, p. 586-592 7 p.

Research output: Contribution to journalArticle

Lipolysis
Cyclic AMP
Copper
Oxidation-Reduction
Metals
Erythritol
Mycobacterium smegmatis
Metabolic Networks and Pathways
threitol

CtaM is required for menaquinol oxidase aa 3 function in Staphylococcus aureus

Hammer, N. D., Schurig-Briccio, L. A., Gerdes, S. Y., Gennis, R. B. & Skaar, E. P., Jul 1 2016, In : mBio. 7, 4, e00823-16.

Research output: Contribution to journalArticle

Staphylococcus aureus
Oxidoreductases
Electron Transport
Heme
Oxygen

Deeper understanding of carboxylase

Morrissey, J. H., Apr 14 2016, In : Blood. 127, 15, p. 1841-1842 2 p.

Research output: Contribution to journalComment/debate

Glutamic Acid
Assays
Blood
Genes
Mutation

Deep mutational scans as a guide to engineering high affinity t cell receptor interactions with peptide-bound major histocompatibility complex

Harris, D. T., Wang, N., Riley, T. P., Anderson, S. D., Singh, N. K., Procko, E., Baker, B. M. & Kran, D. M., Nov 18 2016, In : Journal of Biological Chemistry. 291, 47, p. 24566-24578 13 p.

Research output: Contribution to journalArticle

T-Cell Antigen Receptor
Major Histocompatibility Complex
Cell Communication
Yeast
High-Throughput Nucleotide Sequencing

Development of poly unsaturated fatty acid derivatives of aspirin for inhibition of platelet functions

Roy, J., Adili, R., Kulmacz, R., Holinstat, M. & Das, A., Oct 2016, In : Journal of Pharmacology and Experimental Therapeutics. 359, 1, p. 134-141 8 p.

Research output: Contribution to journalArticle

Unsaturated Fatty Acids
Aspirin
Blood Platelets
Platelet Aggregation
Anhydrides
Bacteriocins
peptide
Peptides
Amino acids
amino acid

Editorial overview: Biocatalysis and Biotransformation: Esoteric, Niche Enzymology

Tawfik, D. S. & van der Donk, W. A., Apr 1 2016, In : Current Opinion in Chemical Biology. 31, p. v-vii

Research output: Contribution to journalEditorial

Sulfonium Compounds
Biocatalysis
Cyclization
Biotransformation
Biochemistry

Engineered CAR T Cells Targeting the Cancer-Associated Tn-Glycoform of the Membrane Mucin MUC1 Control Adenocarcinoma

Posey, A. D., Schwab, R. D., Boesteanu, A. C., Steentoft, C., Mandel, U., Engels, B., Stone, J. D., Madsen, T. D., Schreiber, K., Haines, K. M., Cogdill, A. P., Chen, T. J., Song, D., Scholler, J., Kranz, D. M., Feldman, M. D., Young, R., Keith, B., Schreiber, H., Clausen, H. & 2 others, Johnson, L. A. & June, C. H., Jun 21 2016, In : Immunity. 44, 6, p. 1444-1454 11 p.

Research output: Contribution to journalArticle

Mucins
T-Cell Antigen Receptor
Adenocarcinoma
Membranes
Antigen Receptors

Enhancing Mn(II)-Binding and Manganese Peroxidase Activity in a Designed Cytochrome c Peroxidase through Fine-Tuning Secondary-Sphere Interactions

Hosseinzadeh, P., Mirts, E. N., Pfister, T. D., Gao, Y. G., Mayne, C., Robinson, H., Tajkhorshid, E. & Lu, Y., Mar 15 2016, In : Biochemistry. 55, 10, p. 1494-1502 9 p.

Research output: Contribution to journalArticle

manganese peroxidase
Cytochrome-c Peroxidase
Tuning
Metals
Mutation

Estrogen receptor alpha somatic mutations Y537S and D538G confer breast cancer endocrine resistance by stabilizing the activating function-2 binding conformation

Fanning, S. W., Mayne, C. G., Dharmarajan, V., Carlson, K. E., Martin, T. A., Novick, S. J., Toy, W., Green, B., Panchamukhi, S., Katzenellenbogen, B. S., Tajkhorshid, E., Griffin, P. R., Shen, Y., Chandarlapaty, S., Katzenellenbogen, J. A. & Greene, G. L., Feb 2 2016, In : eLife. 5, FEBRUARY2016, e12792.

Research output: Contribution to journalArticle

Estrogen Receptor alpha
Estrogen Receptor Modulators
Conformations
Breast Neoplasms
Mutation
Aryl Hydrocarbon Receptors
Estrogen Receptors
Estrogens
Gene expression
Crosstalk

Evidence that cytochrome b5 acts as a redox donor in CYP17A1 mediated androgen synthesis

Duggal, R., Liu, Y., Gregory, M. C., Denisov, I. G., Kincaid, J. R. & Sligar, S., Aug 19 2016, In : Biochemical and Biophysical Research Communications. 477, 2, p. 202-208 7 p.

Research output: Contribution to journalArticle

Cytochromes b5
Cytochrome P-450 Enzyme System
Androgens
Lyases
Oxidation-Reduction

High-resolution NMR studies of human tissue factor

Nuzzio, K. M., Watt, E. D., Boettcher, J. M., Gajsiewicz, J. M., Morrissey, J. H. & Rienstra, C. M., Sep 2016, In : PloS one. 11, 9, e0163206.

Research output: Contribution to journalArticle

Thromboplastin
Nuclear magnetic resonance
Benchmarking
Factor VIIa
blood coagulation

Inorganic polyphosphate in blood coagulation

Smith, S. A. & Morrissey, J. H., Jan 1 2016, Inorganic Polyphosphates in Eukaryotic Cells. Springer International Publishing, p. 159-176 18 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Polyphosphates
Blood Coagulation
Coagulation
Blood
Chemical activation

Interplay between steroid hormone activation of the unfolded protein response and nuclear receptor action

Zheng, X., Andruska, N., Yu, L., Mao, C., Kim, J. E., Livezey, M., Helferich, W. G. & Shapiro, D. J., Jan 1 2016, In : Steroids. 114, p. 2-6 5 p.

Research output: Contribution to journalReview article

Steroid hormones
Unfolded Protein Response
Cytoplasmic and Nuclear Receptors
Chemical activation
Steroids

Leader Peptide Establishes Dehydration Order, Promotes Efficiency, and Ensures Fidelity during Lacticin 481 Biosynthesis

Thibodeaux, C. J., Wagoner, J., Yu, Y. & van der Donk, W. A., May 25 2016, In : Journal of the American Chemical Society. 138, 20, p. 6436-6444 9 p.

Research output: Contribution to journalArticle

Chemical bonds
Biosynthesis
Ligases
Protein Sorting Signals
Dehydration

Lipoprotein Nanoplatelets: Brightly Fluorescent, Zwitterionic Probes with Rapid Cellular Entry

Lim, S. J., McDougle, D. R., Zahid, M. U., Ma, L., Das, A. & Smith, A. M., Jan 13 2016, In : Journal of the American Chemical Society. 138, 1, p. 64-67 4 p.

Research output: Contribution to journalArticle

Lipoproteins
phospholipid
Fluorescent Dyes
fluorescence
probe

Members of a Novel Kinase Family (DUF1537) Can Recycle Toxic Intermediates into an Essential Metabolite

Thiaville, J. J., Flood, J., Yurgel, S., Prunetti, L., Elbadawi-Sidhu, M., Hutinet, G., Forouhar, F., Zhang, X., Ganesan, V., Reddy, P., Fiehn, O., Gerlt, J. A., Hunt, J. F., Copley, S. D. & De Crécy-Lagard, V., Aug 19 2016, In : ACS chemical biology. 11, 8, p. 2304-2311 8 p.

Research output: Contribution to journalArticle

Pyridoxal Phosphate
Poisons
Metabolites
Phosphotransferases
Genes

Microscopic Characterization of Membrane Transporter Function by In Silico Modeling and Simulation

Vermaas, J. V., Trebesch, N., Mayne, C. G., Thangapandian, S., Shekhar, M., Mahinthichaichan, P., Baylon, J. L., Jiang, T., Wang, Y., Muller, M. P., Shinn, E., Zhao, Z., Wen, P. C. & Tajkhorshid, E., 2016, Methods in Enzymology. Academic Press Inc., p. 373-428 56 p. (Methods in Enzymology; vol. 578).

Research output: Chapter in Book/Report/Conference proceedingChapter

Membrane Transport Proteins
Computer Simulation
Biological membranes
Membranes
Chemical Phenomena

MIDA boronates are hydrolysed fast and slow by two different mechanisms

Gonzalez, J. A., Ogba, O. M., Morehouse, G. F., Rosson, N., Houk, K. N., Leach, A. G., Cheong, P. H. Y., Burke, M. D. & Lloyd-Jones, G. C., Nov 1 2016, In : Nature Chemistry. 8, 11, p. 1067-1075 9 p.

Research output: Contribution to journalArticle

Boronic Acids
Hydrolysis
Esters
Acids
Water

Molecular basis for differential anion binding and proton coupling in the Cl-/H+ exchanger ClC-ec1

Jiang, T., Han, W., Maduke, M. & Tajkhorshid, E., Mar 9 2016, In : Journal of the American Chemical Society. 138, 9, p. 3066-3075 10 p.

Research output: Contribution to journalArticle

Ion exchangers
Anions
Protons
anion
Negative ions

Molecular basis for resistance against phosphonate antibiotics and herbicides

Chekan, J. R., Cogan, D. P. & Nair, S. K., Jan 1 2016, In : MedChemComm. 7, 1, p. 28-36 9 p.

Research output: Contribution to journalReview article

glyphosate
Fosfomycin
Organophosphonates
Herbicides
Bioactivity

Molecular basis for the broad substrate selectivity of a peptide prenyltransferase

Hao, Y., Pierce, E., Roe, D., Morita, M., McIntosh, J. A., Agarwal, V., Cheatham, T. E., Schmidt, E. W. & Nair, S. K., Dec 6 2016, In : Proceedings of the National Academy of Sciences of the United States of America. 113, 49, p. 14037-14042 6 p.

Research output: Contribution to journalArticle

Dimethylallyltranstransferase
Peptides
Prenylation
Terpenes
Enzymes

Motif-driven design of protein–protein interfaces

Silva, D. A., Correia, B. E. & Procko, E., May 1 2016, Methods in Molecular Biology. Humana Press Inc., p. 285-304 20 p. (Methods in Molecular Biology; vol. 1414).

Research output: Chapter in Book/Report/Conference proceedingChapter

Proteins
Synthetic Biology
Aptitude
Learning Curve

Multiple beneficial roles of repressor of estrogen receptor activity (REA) in suppressing the progression of endometriosis

Zhao, Y., Chen, Y., Kuang, Y., Bagchi, M. K., Taylor, R. N., Katzenellenbogen, J. A. & Katzenellenbogen, B. S., Feb 2016, In : Endocrinology. 157, 2, p. 900-912 13 p.

Research output: Contribution to journalArticle

Endometriosis
Estrogen Receptors
Tissue Donors
Estradiol Receptors
Choristoma

Multiple P-TEFbs cooperatively regulate the release of promoter-proximally paused RNA polymerase II

Lu, X., Zhu, X., Li, Y., Liu, M., Yu, B., Wang, Y., Rao, M., Yang, H., Zhou, K., Wang, Y., Chen, Y., Chen, M., Zhuang, S., Chen, L. F., Liu, R. & Chen, R., Aug 19 2016, In : Nucleic acids research. 44, 14, p. 6853-6867 15 p.

Research output: Contribution to journalArticle

Positive Transcriptional Elongation Factor B
RNA Polymerase II
Phosphorylation

Nanodiscs for structural and functional studies of membrane proteins

Denisov, I. G. & Sligar, S., Jun 7 2016, In : Nature Structural and Molecular Biology. 23, 6, p. 481-486 6 p.

Research output: Contribution to journalReview article

Membrane Proteins
Multiprotein Complexes
Technology
Membranes