Biochemistry – Research Output — University of Illinois at Urbana-Champaign

2019

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

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 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 1 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 1 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 1 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 1 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 1 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., 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 1 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., 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., 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 othersHaines, 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

2014

Multitarget drug discovery for tuberculosis and other infectious diseases

Li, K., Schurig-Briccio, L. A., Feng, X., Upadhyay, A., Pujari, V., Lechartier, B., Fontes, F. L., Yang, H., Rao, G., Zhu, W., Gulati, A., No, J. H., Cintra, G., Bogue, S., Liu, Y. L., Molohon, K., Orlean, P. A., Mitchell, D. A., Freitas-Junior, L., Ren, F. & 8 othersSun, H., Jiang, T., Li, Y., Guo, R. T., Cole, S. T., Gennis, R. B., Crick, D. C. & Oldfield, E., Apr 10 2014, In : Journal of Medicinal Chemistry. 57, 7, p. 3126-3129 4 p.

Research output: Contribution to journal › Review article

Drug Discovery

Malaria

Communicable Diseases

Parasites

Tuberculosis

Soluble T cell receptor Vβ domains engineered for high-affinity binding to staphylococcal or streptococcal superantigens

Sharma, P., Wang, N. & Kranz, D. M., Feb 13 2014, In : Toxins. 6, 2, p. 556-574 19 p.

Research output: Contribution to journal › Review article

Superantigens

T-Cell Antigen Receptor

T-cells

T-Lymphocytes

Staphylococcus aureus