Biochemistry

Research Output

Research Output per year

1971 2021

• 2441 Article
• 198 Review article
• 48 Chapter
• 34 Short survey
• 110 More
  • 25 Comment/debate
  • 24 Editorial
  • 22 Letter
  • 16 Conference contribution
  • 14 Book
  • 5 Working paper
  • 4 Conference article

Research Output per year

Research Output per year

Search results

• 2021

  Discovery of novel pathways for carbohydrate metabolism

  Stack, T. M. M. & Gerlt, J. A., Apr 2021, In: Current Opinion in Chemical Biology. 61, p. 63-70 8 p.

  Research output: Contribution to journal › Review article › peer-review

  • Carbohydrate Metabolism
  • Metabolic Networks and Pathways
  • Molecules
  • Enzymes
  • Biosynthesis
• 2020

  Acoustic-based chemical tools for profiling the tumor microenvironment

  Yadav, A. K., Hernandez, S., Su, S. & Chan, J., Aug 2020, In: Current Opinion in Chemical Biology. 57, p. 114-121 8 p.

  Research output: Contribution to journal › Review article › peer-review

  • Tumor Microenvironment
  • Tumors
  • Acoustics
  • Ultrasonics
  • Photoacoustic effect

• Advances in Activity-Based Sensing Probes for Isoform-Selective Imaging of Enzymatic Activity

  Gardner, S. H., Reinhardt, C. J. & Chan, J., 2020, (Accepted/In press) In: Angewandte Chemie - International Edition.

  Research output: Contribution to journal › Review article › peer-review

  • Catalyst selectivity
  • Molecules
  • Protein Isoforms
  • Enzyme activity
  • Imaging techniques

• Cellular and molecular basis of liver regeneration

  Bangru, S. & Kalsotra, A., Apr 2020, In: Seminars in Cell and Developmental Biology. 100, p. 74-87 14 p.

  Research output: Contribution to journal › Review article › peer-review

  • Liver Regeneration
  • Liver
  • Genome
  • RNA Sequence Analysis
  • Proteome

• 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., Mar 2020, In: Trends in Biochemical Sciences. 45, 3, p. 202-216 15 p.

  Research output: Contribution to journal › Review article › peer-review

  • Dissection
  • Membranes
  • Membrane Transport Proteins
  • Molecular Dynamics Simulation
  • Molecular dynamics

• CYP2J2 Molecular Recognition: A New Axis for Therapeutic Design

  Das, A., Weigle, A. T., Arnold, W. R., Kim, J. S., Carnevale, L. N. & Huff, H. C., Nov 2020, In: Pharmacology and Therapeutics. 215, 107601.

  Research output: Contribution to journal › Review article › peer-review

  • arachidonate epoxygenase
  • Cytochrome P-450 Enzyme System
  • Unsaturated Fatty Acids
  • Xenobiotics
  • Cardiovascular Physiological Phenomena

• Lipid Rafts, Sphingolipids, and Ergosterol in Yeast Vacuole Fusion and Maturation

  Hurst, L. R. & Fratti, R. A., Jul 3 2020, In: Frontiers in Cell and Developmental Biology. 8, 539.

  Research output: Contribution to journal › Review article › peer-review

  Open Access

  • Ergosterol
  • Sphingolipids
  • Vacuoles
  • Yeasts
  • Lipids

• Nanodiscs: A toolkit for membrane protein science

  Sligar, S. G. & Denisov, I. G., 2020, (Accepted/In press) In: Protein Science.

  Research output: Contribution to journal › Review article › peer-review

  • Membrane Proteins
  • Lipid bilayers
  • Cell signaling
  • Signal transduction
  • Metabolic Networks and Pathways

• Natural product biosynthesis: What’s next? An introduction to the JBC Reviews Thematic Series

  Nair, S. K. & Jez, J. M., Jan 10 2020, In: Journal of Biological Chemistry. 295, 2, p. 335-336 2 p.

  Research output: Contribution to journal › Review article › peer-review

  Open Access

  • Biosynthesis
  • Pathogens
  • Biological Products
  • Aphorisms and Proverbs
  • Polyketides

• New developments in RiPP discovery, enzymology and engineering

  Montalbán-López, M., Scott, T. A., Ramesh, S., Rahman, I. R., van Heel, A. J., Viel, J. H., Bandarian, V., Dittmann, E., Genilloud, O., Goto, Y., Grande Burgos, M. J., Hill, C., Kim, S., Koehnke, J., Latham, J. A., Link, A. J., Martínez, B., Nair, S. K., Nicolet, Y., Rebuffat, S. & 16 others, Sahl, H-G., Sareen, D., Schmidt, E. W., Schmitt, L., Severinov, K., Süssmuth, R. D., Truman, A. W., Wang, H., Weng, J-K., van Wezel, G. P., Zhang, Q., Zhong, J., Piel, J., Mitchell, D. A., Kuipers, O. P. & van der Donk, W. A., Sep 16 2020, (Accepted/In press) In: Natural Product Reports.

  Research output: Contribution to journal › Review article › peer-review

  • Genome
  • Bioengineering
  • Genes
  • Protein Sorting Signals
  • Biosynthesis

• Pinning Down the Transcription: A Role for Peptidyl-Prolyl cis-trans Isomerase Pin1 in Gene Expression

  Hu, X. & Chen, L. F., Mar 20 2020, In: Frontiers in Cell and Developmental Biology. 8, 179.

  Research output: Contribution to journal › Review article › peer-review

  Open Access

  • NIMA-Interacting Peptidylprolyl Isomerase
  • Gene Expression
  • Proline
  • Transcription Factors
  • Proteins

• Progress in the Enzymology of the Mitochondrial Diseases of Lipoic Acid Requiring Enzymes

  Cronan, J. E., May 21 2020, In: Frontiers in Genetics. 11, 510.

  Research output: Contribution to journal › Review article › peer-review

  Open Access

  • Thioctic Acid
  • Mitochondrial Diseases
  • Enzymes
  • Proteins
  • Nonsense Codon

• Structural Biology of Influenza Hemagglutinin: An Amaranthine Adventure

  Wu, N. C. & Wilson, I. A., Sep 22 2020, In: Viruses. 12, 9, 1053.

  Research output: Contribution to journal › Review article › peer-review

  Open Access

  • Hemagglutinins
  • Human Influenza
  • X Ray Crystallography
  • Glycoproteins
  • Vaccines

• Syntaxin Clustering and Optogenetic Control for Synaptic Membrane Fusion

  Li, M., Oh, T. J., Fan, H., Diao, J. & Zhang, K., Aug 7 2020, In: Journal of Molecular Biology. 432, 17, p. 4773-4782 10 p.

  Research output: Contribution to journal › Review article › peer-review

  • Qa-SNARE Proteins
  • Optogenetics
  • Synaptic Membranes
  • Cluster Analysis
  • SNARE Proteins
• 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., Nov 15 2019, In: Journal of Biological Chemistry. 294, 46, p. 17168-17185 18 p.

  Research output: Contribution to journal › Review article › peer-review

  Open Access

  • AAA Proteins
  • N-Ethylmaleimide-Sensitive Proteins
  • Phosphatidic Acids
  • SNARE Proteins
  • Vacuoles

• 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 › peer-review

  • Membrane Proteins
  • Modulation
  • Lipids
  • Molecular dynamics
  • Proteins

• 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 › peer-review

  • Endocannabinoids
  • Omega-3 Fatty Acids
  • Derivatives
  • Serotonin
  • Cannabinoid Receptors

• 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 › peer-review

  • maleic acid
  • Styrene
  • Copolymers
  • Membrane Proteins
  • Electron Transport Complex III

• The Participation of Regulatory Lipids in Vacuole Homotypic Fusion

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

  Research output: Contribution to journal › Review article › peer-review

  • Vacuoles
  • Membranes
  • Fusion reactions
  • Lipids
  • Membrane Fusion Proteins
• 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 › peer-review

  • 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 › peer-review

• Development of Photoacoustic Probes for in Vivo Molecular Imaging

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

  Research output: Contribution to journal › Review article › peer-review

  • Molecular imaging
  • Photoacoustic effect
  • Biological Models
  • Molecular Imaging
  • 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 › peer-review

  • Lipids
  • Membranes
  • Lipid Bilayers
  • Hydrodynamics
  • Molecular Dynamics Simulation

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

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

  Research output: Contribution to journal › Review article › peer-review

  • Proteins
  • Membranes
  • Membrane Proteins
  • 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 › peer-review

  • 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., Sep 7 2018, In: Journal of Biological Chemistry. 293, 36, p. 14122-14133 12 p.

  Research output: Contribution to journal › Review article › peer-review

  • isopentenyl pyrophosphate
  • Substrate Specificity
  • Antiviral Agents
  • Substrates
  • Enzymes

• 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 › peer-review

  • T-cells
  • phosphatidylserine receptor
  • Phosphatidylserines
  • Mucins
  • Immunoglobulins

• 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 › peer-review

  • Molecules
  • Automation
  • 3D printers
  • Direction compound

• Towards the generalized iterative synthesis of small molecules

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

  Research output: Contribution to journal › Review article › peer-review

  • Molecules
  • Macromolecules
  • Tall buildings
  • Drug products
  • Biological 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 › peer-review

  • Protein Databases
  • Dark Matter
  • Genome
  • Genes
  • Data Accuracy
• 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 › peer-review

  • Light
  • Signal Transduction
  • Cell Differentiation
  • Kinetics
  • Cell Proliferation

• 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 › peer-review

  • Staphylococcal Protein A
  • Epigenomics
  • Proteins
  • Drug Development
  • Histones

• Disproportionate impact of named reactions on chemical biology

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

  Research output: Contribution to journal › Review article › peer-review

  • 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 › peer-review

  • Drive
  • Synaptic Transmission
  • Synapses
  • Peptide Receptors
  • Neurotransmitter Receptor

• 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 › peer-review

  • Oxidation
  • Iron
  • Electrons
  • 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 › peer-review

  • Metabolism
  • Regulator Genes
  • 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 › peer-review

  • Voltage-Dependent Anion Channel 1
  • Mitochondria
  • Hexokinase
  • 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 › peer-review

  • 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 › peer-review

  • Biophysics
  • Biochemistry
  • Membranes
  • Membrane Proteins
  • 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 › peer-review

  • Membrane Proteins
  • Technology
  • X ray scattering
  • 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 › peer-review

  • 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 › peer-review

  • 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 › peer-review

  • T-cells
  • Chimeric Antigen Receptors
  • T-Cell Antigen Receptor
  • Cell- and Tissue-Based Therapy
  • Tumors

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

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

  Research output: Contribution to journal › Review article › peer-review

  • Lenses
  • Transcriptome
  • RNA
  • Chemical modification
  • Big Data

• 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 › peer-review

  • Unfolded Protein Response
  • Neoplasms
  • Endoplasmic Reticulum Stress
  • Protein Unfolding
  • Proteostasis

• 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 › peer-review

  • 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., 2016, In: Steroids. 114, p. 2-6 5 p.

  Research output: Contribution to journal › Review article › peer-review

  • 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 › peer-review

  • 3-(N-acetyl-N-hydroxy)aminopropylphosphonic acid
  • fosmidomycin
  • phosphonic acid
  • glyphosate
  • Organophosphonates

• 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 › peer-review

  • 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 › peer-review

  • Biosynthesis
  • Biological Products
  • Biosynthetic Pathways
  • Synthetic biology
  • Synthetic Biology