Biochemistry

Research Output 1971 2020

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Review article
2019

A small-molecule competitive inhibitor of phosphatidic acid binding by the AAA+ protein NSF/Sec18 blocks the SNARE-priming stage of vacuole fusion

Sparks, R. P., Arango, A. S., Starr, M. L., Aboff, Z. L., Hurst, L. R., Rivera-Kohr, D. A., Zhang, C., Harnden, K. A., Jenkins, J. L., Guida, W. C., Tajkhorshid, E. & Fratti, R. A., Jan 1 2019, In : Journal of Biological Chemistry. 294, 46, p. 17168-17185 18 p.

Research output: Contribution to journal › Review article

Open Access
N-Ethylmaleimide-Sensitive Proteins
SNARE Proteins
Phosphatidic Acids
Vacuoles
Carrier Proteins

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 journal › Review article

Membrane Proteins
Modulation
Lipids
Proteins
Molecular dynamics

Computational Dissection of Membrane Transport at a Microscopic Level

Jiang, T., Wen, P. C., Trebesch, N., Zhao, Z., Pant, S., Kapoor, K., Shekhar, M. & Tajkhorshid, E., Jan 1 2019, (Accepted/In press) In : Trends in Biochemical Sciences.

Research output: Contribution to journal › Review article

Dissection
Membrane Transport Proteins
Membranes
Molecular Dynamics Simulation
Computational methods

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

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

Research output: Contribution to journal › Review article

Endocannabinoids
Omega-3 Fatty Acids
Derivatives
Cannabinoid Receptors
Dopamine

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 journal › Review article

Styrene
Membrane Proteins
Copolymers
Lipids
Proteins

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 journal › Review article

Vacuoles
Fusion reactions
Membranes
Lipids
Membrane Fusion
2018

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 journal › Review article

Thioctic Acid
Biotin
Methylation
Metabolism
Escherichia coli

Chemical Physics in Living Cells-using Light to Visualize and Control Intracellular Signal Transduction

Krishnamurthy, V. V. & Zhang, K., 2018, In : Chinese Journal of Chemical Physics. 31, 4, p. 375-392 18 p.

Research output: Contribution to journal › Review article

Development of Photoacoustic Probes for in Vivo Molecular Imaging

Reinhardt, C. J. & Chan, J. K. F., Jan 16 2018, In : Biochemistry. 57, 2, p. 194-199 6 p.

Research output: Contribution to journal › Review article

Molecular imaging
Biological Models
Molecular Imaging
Photoacoustic effect
Optical Imaging

Microscopic view of lipids and their diverse biological functions

Wen, P. C., Mahinthichaichan, P., Trebesch, N., Jiang, T., Zhao, Z., Shinn, E., Wang, Y., Shekhar, M., Kapoor, K., Chan, C. K. & Tajkhorshid, E., Aug 2018, In : Current Opinion in Structural Biology. 51, p. 177-186 10 p.

Research output: Contribution to journal › Review article

Lipids
Membranes
Physiological Phenomena
Lipid Bilayers
Hydrodynamics

Nanodiscs: A Controlled Bilayer Surface for the Study of Membrane Proteins

McLean, M. A., Gregory, M. C. & Sligar, S., May 20 2018, In : Annual Review of Biophysics. 47, p. 107-124 18 p.

Research output: Contribution to journal › Review article

Membrane Proteins
Proteins
Membranes
Lipids
Multiprotein Complexes

P-TEFb: Finding its ways to release promoter-proximally paused RNA polymerase II

Li, Y., Liu, M., Chen, L-F. & Chen, R., Mar 15 2018, In : Transcription. 9, 2, p. 88-94 7 p.

Research output: Contribution to journal › Review article

Positive Transcriptional Elongation Factor B
RNA Polymerase II
Small Nuclear Ribonucleoproteins
Genetic Promoter Regions
Genes

Reconstitution and substrate specificity for isopentenyl pyrophosphate of the antiviral radical SAM enzyme viperin

Chakravarti, A., Selvadurai, K., Shahoei, R., Lee, H., Fatma, S., Tajkhorshid, E. & Huang, R. H., Jan 1 2018, In : Journal of Biological Chemistry. 293, 36, p. 14122-14133 12 p.

Research output: Contribution to journal › Review article

Substrate Specificity
Antiviral Agents
Substrates
Enzymes
Mevalonic Acid

Sensitivity of peripheral membrane proteins to the membrane context: A case study of phosphatidylserine and the TIM proteins

Kerr, D., Tietjen, G. T., Gong, Z., Tajkhorshid, E., Adams, E. J. & Lee, K. Y. C., Oct 2018, In : Biochimica et Biophysica Acta - Biomembranes. 1860, 10, p. 2126-2133 8 p.

Research output: Contribution to journal › Review article

T-cells
Phosphatidylserines
Mucins
Immunoglobulins
Membrane Proteins

The Molecular Industrial Revolution: Automated Synthesis of Small Molecules

Trobe, M. & Burke, M. D., Apr 9 2018, In : Angewandte Chemie - International Edition. 57, 16, p. 4192-4214 23 p.

Research output: Contribution to journal › Review article

3D printers
Automation
Molecules
Innovation
Direction compound

Towards the generalized iterative synthesis of small molecules

Lehmann, J. W., Blair, D. J. & Burke, M., Jan 1 2018, In : Nature Reviews Chemistry. 2, 2, 0115.

Research output: Contribution to journal › Review article

Molecules
Tall buildings
Biological Products
Macromolecules
Drug products

‘Democratized’ genomic enzymology web tools for functional assignment

Zallot, R., Oberg, N. O. & Gerlt, J. A., Dec 2018, In : Current Opinion in Chemical Biology. 47, p. 77-85 9 p.

Research output: Contribution to journal › Review article

Protein Databases
Genome
Genes
Proteins
Costs and Cost Analysis
2017

Applications of Optobiology in Intact Cells and Multicellular Organisms

Khamo, J. S., Krishnamurthy, V. V., Sharum, S. R., Mondal, P. & Zhang, K., Oct 13 2017, In : Journal of Molecular Biology. 429, 20, p. 2999-3017 19 p.

Research output: Contribution to journal › Review article

Light
Cell Differentiation
Signal Transduction
Cell Proliferation
Apoptosis

Bromodomain and extraterminal proteins - A novel class of therapeutic targets in epigenetics

Chen, J. J., Zhao, X. L., Wang, Z. & Chen, L-F., Jan 1 2017, In : Yaoxue Xuebao. 52, 8, p. 1209-1215 7 p.

Research output: Contribution to journal › Review article

Staphylococcal Protein A
Epigenomics
Proteins
Therapeutic Uses
Therapeutics

Disproportionate impact of named reactions on chemical biology

Bearrood, T. E. & Chan, J. K. F., Jan 1 2017, In : Aldrichimica Acta. 50, 2, p. 31-41 11 p.

Research output: Contribution to journal › Review article

Organic Chemistry

Drive the car(go)s—new modalities to control cargo trafficking in live cells

Mondal, P., Khamo, J. S., Krishnamurthy, V. V., Cai, Q. & Zhang, K., Jan 20 2017, In : Frontiers in Molecular Neuroscience. 10, 4.

Research output: Contribution to journal › Review article

Synaptic Transmission
Synapses
Neurotransmitter Receptor
Peptide Receptors
Active Biological Transport

Go it alone: four-electron oxidations by mononuclear non-heme iron enzymes

Peck, S. C. & van der Donk, W. A., Apr 1 2017, In : Journal of Biological Inorganic Chemistry. 22, 2-3, p. 381-394 14 p.

Research output: Contribution to journal › Review article

Iron
Electrons
Oxidation
Enzymes
Biosynthesis

Intersections of post-transcriptional gene regulatory mechanisms with intermediary metabolism

Arif, W., Datar, G. & Kalsotra, A., Mar 1 2017, In : Biochimica et Biophysica Acta - Gene Regulatory Mechanisms. 1860, 3, p. 349-362 14 p.

Research output: Contribution to journal › Review article

Regulator Genes
Metabolism
Genes
Enzymes
Allosteric Regulation

Mitochondrial VDAC1: A key gatekeeper as potential therapeutic target

Camara, A. K. S., Zhou, Y. F., Wen, P. C., Tajkhorshid, E. & Kwok, W. M., Jun 30 2017, In : Frontiers in Physiology. 8, JUN, 460.

Research output: Contribution to journal › Review article

Voltage-Dependent Anion Channel 1
Mitochondria
Therapeutics
Apoptosis
Apoptosis Regulatory Proteins

Myotonic dystrophy: disease repeat range, penetrance, age of onset, and relationship between repeat size and phenotypes

Yum, K., Wang, E. T. & Kalsotra, A., Jun 1 2017, In : Current Opinion in Genetics and Development. 44, p. 30-37 8 p.

Research output: Contribution to journal › Review article

Myotonic Dystrophy
Penetrance
Genetic Testing
Age of Onset
Myotonia

Nanodiscs in Membrane Biochemistry and Biophysics

Denisov, I. G. & Sligar, S. G., Mar 22 2017, In : Chemical reviews. 117, 6, p. 4669-4713 45 p.

Research output: Contribution to journal › Review article

Biophysics
Biochemistry
Membrane Proteins
Membranes
Cell signaling

Recent advances in nanodisc technology for membrane protein studies (2012–2017)

Rouck, J. E., Krapf, J. E., Roy, J., Huff, H. C. & Das, A., Jul 1 2017, In : FEBS Letters. 591, 14, p. 2057-2088 32 p.

Research output: Contribution to journal › Review article

Membrane Proteins
Technology
Nanotechnology
Fluorescence microscopy
Scintillation

Ribosomally synthesized and post-translationally modified peptide natural product discovery in the genomic era

Hetrick, K. J. & van der Donk, W. A., Jun 1 2017, In : Current Opinion in Chemical Biology. 38, p. 36-44 9 p.

Research output: Contribution to journal › Review article

Biological Products
Genes
Genome
Bacterial Genomes
Peptides

RNA modifications and structures cooperate to guide RNA-protein interactions

Lewis, C. J. T., Pan, T. & Kalsotra, A., Mar 1 2017, In : Nature Reviews Molecular Cell Biology. 18, 3, p. 202-210 9 p.

Research output: Contribution to journal › Review article

Guide RNA
RNA
Proteins
Transcriptome
Gene Expression
2016

Adoptive T Cell Therapies: A Comparison of T Cell Receptors and Chimeric Antigen Receptors

Harris, D. T. & Kranz, D. M., Mar 1 2016, In : Trends in Pharmacological Sciences. 37, 3, p. 220-230 11 p.

Research output: Contribution to journal › Review article

Antigen Receptors
T-cells
Cell- and Tissue-Based Therapy
T-Cell Antigen Receptor
T-Lymphocytes

Advances in analyzing RNA diversity in eukaryotic transcriptomes: Peering through the Omics lens [version 1; referees: 3 approved]

Bangru, S. & Kalsotra, A., Jan 1 2016, In : F1000Research. 5, 2668.

Research output: Contribution to journal › Review article

Transcriptome
Lenses
RNA
Polyadenylation
Data handling

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 journal › Review article

Unfolded Protein Response
Neoplasms
Endoplasmic Reticulum Stress
Breast Neoplasms
Protein Unfolding

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 journal › Review article

Biosynthesis
Transfer RNA
Biological Products
Genes
Enzymes

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 journal › Review article

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

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 journal › Review article

glyphosate
Fosfomycin
Organophosphonates
Herbicides
Bioactivity

Nanodiscs for structural and functional studies of membrane proteins

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

Research output: Contribution to journal › Review article

Membrane Proteins
Multiprotein Complexes
Technology
Membranes

New Insights into the Biosynthetic Logic of Ribosomally Synthesized and Post-translationally Modified Peptide Natural Products

Ortega, M. A. & van der Donk, W. A., Jan 21 2016, In : Cell chemical biology. 23, 1, p. 31-44 14 p.

Research output: Contribution to journal › Review article

Biosynthesis
Biological Products
Synthetic Biology
Peptides
Biosynthetic Pathways

The many roles of glutamate in metabolism

Walker, M. C. & van der Donk, W. A., Mar 1 2016, In : Journal of Industrial Microbiology and Biotechnology. 43, 2-3, p. 419-430 12 p.

Research output: Contribution to journal › Review article

Metabolism
Amino acids
Glutamic Acid
Bioremediation
Biosynthesis
2015

2013 Scientific Sessions Sol Sherry Distinguished Lecture in Thrombosis Polyphosphate: A Novel Modulator of Hemostasis and Thrombosis

Smith, S. A. & Morrissey, J. H., Jun 27 2015, In : Arteriosclerosis, Thrombosis, and Vascular Biology. 35, 6, p. 1298-1305 8 p.

Research output: Contribution to journal › Review article

Polyphosphates
Polymethyl Methacrylate
Hemostasis
Thrombosis
Blood Coagulation

Computational characterization of structural dynamics underlying function in active membrane transporters

Li, J., Wen, P. C., Moradi, M. & Tajkhorshid, E., Apr 1 2015, In : Current Opinion in Structural Biology. 31, p. 96-105 10 p.

Research output: Contribution to journal › Review article

Membrane Transport Proteins
Active Biological Transport
Molecular Dynamics Simulation
Hydrolysis
Adenosine Triphosphate

Developmental insights into the pathology of and therapeutic strategies for DM1: Back to the basics

Chau, A. & Kalsotra, A., Mar 1 2015, In : Developmental Dynamics. 244, 3, p. 377-390 14 p.

Research output: Contribution to journal › Review article

Poisons
Trinucleotide Repeat Expansion
RNA
Fetal Proteins
Pathology

Endocannabinoid metabolism by cytochrome P450 monooxygenases

Zelasko, S., Arnold, W. R. & Das, A., Jan 1 2015, In : Prostaglandins and Other Lipid Mediators. 116-117, p. 112-123 12 p.

Research output: Contribution to journal › Review article

Endocannabinoids
Mixed Function Oxygenases
Metabolism
Cytochrome P-450 Enzyme System
Lipoxygenase

Enzyme function initiative-enzyme similarity tool (EFI-EST): A web tool for generating protein sequence similarity networks

Gerlt, J. A., Bouvier, J. T., Davidson, D. B., Imker, H. J., Sadkhin, B., Slater, D. R. & Whalen, K. L., Aug 1 2015, In : Biochimica et Biophysica Acta - Proteins and Proteomics. 1854, 8, p. 1019-1037 19 p.

Research output: Contribution to journal › Review article

Enzymes
Proteins
National Institute of General Medical Sciences (U.S.)
Orotidine-5'-Phosphate Decarboxylase
Biota

How it all starts: Initiation of the clotting cascade

Smith, S. A., Travers, R. J. & Morrissey, J. H., Jul 4 2015, In : Critical Reviews in Biochemistry and Molecular Biology. 50, 4, p. 326-336 11 p.

Research output: Contribution to journal › Review article

Thrombosis
Blood
Blood Coagulation
Hemostasis
Thromboplastin

Minimum Information about a Biosynthetic Gene cluster

Medema, M. H., Kottmann, R., Yilmaz, P., Cummings, M., Biggins, J. B., Blin, K., De Bruijn, I., Chooi, Y. H., Claesen, J., Coates, R. C., Cruz-Morales, P., Duddela, S., Düsterhus, S., Edwards, D. J., Fewer, D. P., Garg, N., Geiger, C., Gomez-Escribano, J. P., Greule, A., Hadjithomas, M. & 134 others, Haines, A. S., Helfrich, E. J. N., Hillwig, M. L., Ishida, K., Jones, A. C., Jones, C. S., Jungmann, K., Kegler, C., Kim, H. U., Kötter, P., Krug, D., Masschelein, J., Melnik, A. V., Mantovani, S. M., Monroe, E. A., Moore, M., Moss, N., Nützmann, H. W., Pan, G., Pati, A., Petras, D., Reen, F. J., Rosconi, F., Rui, Z., Tian, Z., Tobias, N. J., Tsunematsu, Y., Wiemann, P., Wyckoff, E., Yan, X., Yim, G., Yu, F., Xie, Y., Aigle, B., Apel, A. K., Balibar, C. J., Balskus, E. P., Barona-Gómez, F., Bechthold, A., Bode, H. B., Borriss, R., Brady, S. F., Brakhage, A. A., Caffrey, P., Cheng, Y. Q., Clardy, J., Cox, R. J., De Mot, R., Donadio, S., Donia, M. S., Van Der Donk, W. A., Dorrestein, P. C., Doyle, S., Driessen, A. J. M., Ehling-Schulz, M., Entian, K. D., Fischbach, M. A., Gerwick, L., Gerwick, W. H., Gross, H., Gust, B., Hertweck, C., Höfte, M., Jensen, S. E., Ju, J., Katz, L., Kaysser, L., Klassen, J. L., Keller, N. P., Kormanec, J., Kuipers, O. P., Kuzuyama, T., Kyrpides, N. C., Kwon, H. J., Lautru, S., Lavigne, R., Lee, C. Y., Linquan, B., Liu, X., Liu, W., Luzhetskyy, A., Mahmud, T., Mast, Y., Méndez, C., Metsä-Ketelä, M., Micklefield, J., Mitchell, D. A., Moore, B. S., Moreira, L. M., Müller, R., Neilan, B. A., Nett, M., Nielsen, J., O'Gara, F., Oikawa, H., Osbourn, A., Osburne, M. S., Ostash, B., Payne, S. M., Pernodet, J. L., Petricek, M., Piel, J., Ploux, O., Raaijmakers, J. M., Salas, J. A., Schmitt, E. K., Scott, B., Seipke, R. F., Shen, B., Sherman, D. H., Sivonen, K., Smanski, M. J., Sosio, M., Stegmann, E., Süssmuth, R. D., Tahlan, K., Thomas, C. M., Tang, Y., Truman, A. W., Viaud, M., Walton, J. D., Walsh, C. T., Weber, T., Van Wezel, G. P., Wilkinson, B., Willey, J. M., Wohlleben, W., Wright, G. D., Ziemert, N., Zhang, C., Zotchev, S. B., Breitling, R., Takano, E. & Glöckner, F. O., Aug 18 2015, In : Nature chemical biology. 11, 9, p. 625-631 7 p.

Research output: Contribution to journal › Review article

Multigene Family
Information Storage and Retrieval
Fungi
Bacteria

Optogenetic control of intracellular signaling pathways

Zhang, K. & Cui, B., Feb 1 2015, In : Trends in Biotechnology. 33, 2, p. 92-100 9 p.

Research output: Contribution to journal › Review article

Optogenetics
Aptitude
Molecular Biology
Light

Polyphosphate, platelets, and coagulation

Travers, R. J., Smith, S. A. & Morrissey, J. H., May 1 2015, In : International Journal of Laboratory Hematology. 37, S1, p. 31-35 5 p.

Research output: Contribution to journal › Review article

Polyphosphates
Platelets
Coagulation
Blood Platelets
Inflammation

Polyphosphate as modulator of hemostasis, thrombosis, and inflammation

Morrissey, J. H. & Smith, S. A., Jun 1 2015, In : Journal of Thrombosis and Haemostasis. 13, S1, p. S92-S97

Research output: Contribution to journal › Review article

Polyphosphates
Hemostasis
Thrombosis
Polyps
Inflammation

Review and Hypothesis. New insights into the reaction mechanism of transhydrogenase: Swivelling the dIII component may gate the proton channel

Jackson, J. B., Leung, J. H., Stout, C. D., Schurig-Briccio, L. A. & Gennis, R. B., Jul 20 2015, In : FEBS Letters. 589, 16, p. 2027-2033 7 p.

Research output: Contribution to journal › Review article

NADP
Protons
Thermus thermophilus
Mitochondria
Enzymes

TCR affinity for p/MHC formed by tumor antigens that are self-proteins: Impact on efficacy and toxicity

Stone, J. D., Harris, D. T. & Kranz, D. M., Apr 1 2015, In : Current Opinion in Immunology. 33, p. 16-22 7 p.

Research output: Contribution to journal › Review article

Neoplasm Antigens
T-Cell Antigen Receptor
Peptides
Proteins
T-Lymphocytes