Department of Biochemistry & Molecular Biophysics

2021

The catalytic mechanism of vitamin K epoxide reduction in a cellular environment

Shen, G., Cui, W., Cao, Q., Gao, M., Liu, H., Su, G., Gross, M. L. & Li, W., Jan 1 2021, In: Journal of Biological Chemistry. 296, 100145.

Research output: Contribution to journal › Article › peer-review

Open Access

9 Scopus citations

The context-dependent influence of promoter sequence motifs on transcription initiation kinetics and regulation

Jensen, D. & Galburt, E. A., Apr 2021, In: Journal of bacteriology. 203, 8, e00512-20.

Research output: Contribution to journal › Article › peer-review

Open Access

15 Scopus citations

The extensive and functionally uncharacterized mitochondrial phosphoproteome

Niemi, N. M. & Pagliarini, D. J., Jul 1 2021, In: Journal of Biological Chemistry. 297, 1, 100880.

Research output: Contribution to journal › Article › peer-review

Open Access

22 Scopus citations

The fidelity of DNA replication, particularly on GC-rich templates, is reduced by defects of the Fe-S cluster in DNA polymerase δ

Kiktev, D. A., Dominska, M., Zhang, T., Dahl, J., Stepchenkova, E. I., Mieczkowski, P., Burgers, P. M., Lujan, S., Burkholder, A., Kunkel, T. A. & Petes, T. D., Jun 4 2021, In: Nucleic acids research. 49, 10, p. 5623-5636 14 p.

Research output: Contribution to journal › Article › peer-review

Open Access

2 Scopus citations

The mechanism of micu-dependent gating of the mitochondrial ca²⁺ uniporter

Garg, V., Suzuki, J., Paranjpe, I., Unsulangi, T., Boyman, L., Milescu, L. S., Jonathan Lederer, W. & Kirichok, Y., Aug 2021, In: eLife. 10, e69312.

Research output: Contribution to journal › Article › peer-review

Open Access

43 Scopus citations

The Role of the Membrane in Transporter Folding and Activity

Ernst, M. & Robertson, J. L., Aug 6 2021, In: Journal of Molecular Biology. 433, 16, 167103.

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

Open Access

12 Scopus citations

The Role of XPB/Ssl2 dsDNA Translocase Processivity in Transcription Start-site Scanning

Tomko, E. J., Luyties, O., Rimel, J. K., Tsai, C. L., Fuss, J. O., Fishburn, J., Hahn, S., Tsutakawa, S. E., Taatjes, D. J. & Galburt, E. A., Jul 9 2021, In: Journal of Molecular Biology. 433, 14, 166813.

Research output: Contribution to journal › Article › peer-review

Open Access

7 Scopus citations

The SARS-CoV-2 nucleocapsid protein is dynamic, disordered, and phase separates with RNA

Cubuk, J., Alston, J. J., Incicco, J. J., Singh, S., Stuchell-Brereton, M. D., Ward, M. D., Zimmerman, M. I., Vithani, N., Griffith, D., Wagoner, J. A., Bowman, G. R., Hall, K. B., Soranno, A. & Holehouse, A. S., Dec 1 2021, In: Nature communications. 12, 1, 1936.

Research output: Contribution to journal › Article › peer-review

Open Access

322 Scopus citations

TMEM41B acts as an ER scramblase required for lipoprotein biogenesis and lipid homeostasis

Huang, D., Xu, B., Liu, L., Wu, L., Zhu, Y., Ghanbarpour, A., Wang, Y., Chen, F. J., Lyu, J., Hu, Y., Kang, Y., Zhou, W., Wang, X., Ding, W., Li, X., Jiang, Z., Chen, J., Zhang, X., Zhou, H. & Li, J. Z. & 7 others, Guo, C., Zheng, W., Zhang, X., Li, P., Melia, T., Reinisch, K. & Chen, X. W., Aug 3 2021, In: Cell metabolism. 33, 8, p. 1655-1670.e8

Research output: Contribution to journal › Article › peer-review

Open Access

79 Scopus citations

Using BioID to Characterize the RAS Interactome

Adhikari, H. & Counter, C. M., 2021, Methods in Molecular Biology. Humana Press Inc., p. 271-280 10 p. (Methods in Molecular Biology; vol. 2262).

Research output: Chapter in Book/Report/Conference proceeding › Chapter › peer-review

3 Scopus citations

Uveal melanoma cells use ameboid and mesenchymal mechanisms of cell motility crossing the endothelium

Onken, M. D., Blumer, K. J. & Cooper, J. A., Mar 1 2021, In: Molecular biology of the cell. 32, 5, p. 413-421 9 p.

Research output: Contribution to journal › Article › peer-review

Open Access

12 Scopus citations

Watt W. Webb: His measurements of the seemingly inaccessible broadened the horizons of biophysics

Elson, E., Mar 23 2021, In: Proceedings of the National Academy of Sciences of the United States of America. 118, 12

Research output: Contribution to journal › Article › peer-review

Open Access

2020

¹⁹F NMR reveals the conformational properties of free thrombin and its zymogen precursor prethrombin-2

Ruben, E. A., Gandhi, P. S., Chen, Z., Koester, S. K., DeKoster, G. T., Frieden, C. & Di Cera, E., Jun 12 2020, In: Journal of Biological Chemistry. 295, 24, p. 8227-8235 9 p.

Research output: Contribution to journal › Article › peer-review

Open Access

11 Scopus citations

2019 in review: FDA approvals of new medicines

Kinch, M. S., Kraft, Z. & Schwartz, T., Nov 2020, In: Drug Discovery Today. 25, 11, p. 1923-1929 7 p.

Research output: Contribution to journal › Short survey › peer-review

3 Scopus citations

A computational platform for high-throughput analysis of RNA sequences and modifications by mass spectrometry

Wein, S., Andrews, B., Sachsenberg, T., Santos-Rosa, H., Kohlbacher, O., Kouzarides, T., Garcia, B. A. & Weisser, H., Dec 1 2020, In: Nature communications. 11, 1, 926.

Research output: Contribution to journal › Article › peer-review

Open Access

56 Scopus citations

Adenovirus-mediated ubiquitination alters protein–RNA binding and aids viral RNA processing

Herrmann, C., Dybas, J. M., Liddle, J. C., Price, A. M., Hayer, K. E., Lauman, R., Purman, C. E., Charman, M., Kim, E. T., Garcia, B. A. & Weitzman, M. D., Oct 1 2020, In: Nature microbiology. 5, 10, p. 1217-1231 15 p.

Research output: Contribution to journal › Article › peer-review

Open Access

24 Scopus citations

Analyzing the sequences of intrinsically disordered regions with CIDER and localCIDER

Ginell, G. M. & Holehouse, A. S., 2020, Methods in Molecular Biology. Humana Press Inc., p. 103-126 24 p. (Methods in Molecular Biology; vol. 2141).

Research output: Chapter in Book/Report/Conference proceeding › Chapter › peer-review

10 Scopus citations

An integrated multi-omics approach identifies epigenetic alterations associated with Alzheimer’s disease

Nativio, R., Lan, Y., Donahue, G., Sidoli, S., Berson, A., Srinivasan, A. R., Shcherbakova, O., Amlie-Wolf, A., Nie, J., Cui, X., He, C., Wang, L. S., Garcia, B. A., Trojanowski, J. Q., Bonini, N. M. & Berger, S. L., Oct 1 2020, In: Nature Genetics. 52, 10, p. 1024-1035 12 p.

Research output: Contribution to journal › Article › peer-review

203 Scopus citations

An orally available tubulin inhibitor, VERU-111, suppresses triple-negative breast cancer tumor growth and metastasis and bypasses taxane resistance

Deng, S., Krutilina, R. I., Wang, Q., Lin, Z., Parke, D. N., Playa, H. C., Chen, H., Miller, D. D., Seagroves, T. N. & Li, W., Feb 2020, In: Molecular Cancer Therapeutics. 19, 2, p. 348-363 16 p.

Research output: Contribution to journal › Article › peer-review

Open Access

29 Scopus citations

Antagonism between substitutions in β-lactamase explains a path not taken in the evolution of bacterial drug resistance

Brown, C. A., Hu, L., Sun, Z., Patel, M. P., Singh, S., Porter, J. R., Sankaran, B., Venkataram Prasad, B. V., Bowman, G. R. & Palzkill, T., May 22 2020, In: Journal of Biological Chemistry. 295, 21, p. 7376-7390 15 p.

Research output: Contribution to journal › Article › peer-review

Open Access

14 Scopus citations

Arginine-Enriched Mixed-Charge Domains Provide Cohesion for Nuclear Speckle Condensation

Greig, J. A., Nguyen, T. A., Lee, M., Holehouse, A. S., Posey, A. E., Pappu, R. V. & Jedd, G., Mar 19 2020, In: Molecular cell. 77, 6, p. 1237-1250.e4

Research output: Contribution to journal › Article › peer-review

Open Access

119 Scopus citations

A survey-based analysis of the academic job market

Fernandes, J. D., Sarabipour, S., Smith, C. T., Niemi, N. M., Jadavji, N. M., Kozik, A. J., Holehouse, A. S., Pejaver, V., Symmons, O., Bisson Filho, A. W. & Haage, A., Jun 2020, In: eLife. 9, p. 1-30 30 p., e54097.

Research output: Contribution to journal › Article › peer-review

Open Access

35 Scopus citations

Author Correction: An integrated multi-omics approach identifies epigenetic alterations associated with Alzheimer’s disease (Nature Genetics, (2020), 52, 10, (1024-1035), 10.1038/s41588-020-0696-0)

Nativio, R., Lan, Y., Donahue, G., Sidoli, S., Berson, A., Srinivasan, A. R., Shcherbakova, O., Amlie-Wolf, A., Nie, J., Cui, X., He, C., Wang, L. S., Garcia, B. A., Trojanowski, J. Q., Bonini, N. M. & Berger, S. L., Nov 1 2020, In: Nature Genetics. 52, 11, p. 1266 1 p.

Research output: Contribution to journal › Comment/debate

Open Access

5 Scopus citations

A Workflow for Ultra-rapid Analysis of Histone Post-translational Modifications with Direct-injection Mass Spectrometry

Bhanu, N. V., Sidoli, S. & Garcia, B. A., 2020, In: Bio-protocol. 10, 18, e3756.

Research output: Contribution to journal › Article › peer-review

Open Access

12 Scopus citations

Bacterial colonization reprograms the neonatal gut metabolome

Bittinger, K., Zhao, C., Li, Y., Ford, E., Friedman, E. S., Ni, J., Kulkarni, C. V., Cai, J., Tian, Y., Liu, Q., Patterson, A. D., Sarkar, D., Chan, S. H. J., Maranas, C., Saha-Shah, A., Lund, P., Garcia, B. A., Mattei, L. M., Gerber, J. S. & Elovitz, M. A. & 9 others, Kelly, A., DeRusso, P., Kim, D., Hofstaedter, C. E., Goulian, M., Li, H., Bushman, F. D., Zemel, B. S. & Wu, G. D., Jun 1 2020, In: Nature microbiology. 5, 6, p. 838-847 10 p.

Research output: Contribution to journal › Article › peer-review

Open Access

76 Scopus citations

Bullet points to evaluate the performance of the middle-down proteomics workflow for histone modification analysis

Coradin, M., Mendoza, M. R., Sidoli, S., Alpert, A. J., Lu, C. & Garcia, B. A., Dec 1 2020, In: Methods. 184, p. 86-92 7 p.

Research output: Contribution to journal › Article › peer-review

15 Scopus citations

Bypass of DNA interstrand crosslinks by a Rev1-DNA polymerase ζ complex

Bezalel-Buch, R., Cheun, Y. K., Roy, U., Schärer, O. D. & Burgers, P. M., Sep 4 2020, In: Nucleic acids research. 48, 15, p. 8461-8473 13 p.

Research output: Contribution to journal › Article › peer-review

Open Access

12 Scopus citations

Characterization of missense mutations in the signal peptide and propeptide of FIX in hemophilia B by a cell-based assay

Gao, W., Xu, Y., Liu, H., Gao, M., Cao, Q., Wang, Y., Cui, L., Huang, R., Shen, Y., Li, S., Yang, H., Chen, Y., Li, C., Yu, H., Li, W. & Shen, G., Aug 11 2020, In: Blood Advances. 4, 15, p. 3659-3667 9 p.

Research output: Contribution to journal › Article › peer-review

Open Access

6 Scopus citations

Characterization of serotonin and N-acetylserotonin systems in the human epidermis and skin cells

Slominski, A. T., Kim, T. K., Kleszczyński, K., Semak, I., Janjetovic, Z., Sweatman, T., Skobowiat, C., Steketee, J. D., Lin, Z., Postlethwaite, A., Li, W., Reiter, R. J. & Tobin, D. J., Mar 1 2020, In: Journal of Pineal Research. 68, 2, e12626.

Research output: Contribution to journal › Article › peer-review

Open Access

44 Scopus citations

Characterization of Warfarin Inhibition Kinetics Requires Stabilization of Intramembrane Vitamin K Epoxide Reductases

Li, S., Liu, S., Yang, Y. & Li, W., Aug 21 2020, In: Journal of Molecular Biology. 432, 18, p. 5197-5208 12 p.

Research output: Contribution to journal › Article › peer-review

Open Access

8 Scopus citations

Charge Reduction of Membrane Proteins in Native Mass Spectrometry Using Alkali Metal Acetate Salts

Petroff, J. T., Tong, A., Chen, L. J., Dekoster, G. T., Khan, F., Abramson, J., Frieden, C. & Cheng, W. W. L., May 5 2020, In: Analytical Chemistry. 92, 9, p. 6622-6630 9 p.

Research output: Contribution to journal › Article › peer-review

Open Access

10 Scopus citations

Chloroquine sensitizes GNAQ/11-mutated melanoma to MEK1/2 inhibition

Truong, A., Yoo, J. H., Scherzer, M. T., Sanchez, J. M. S., Dale, K. J., Kinsey, C. G., Richards, J. R., Shin, D., Ghazi, P. C., Onken, M. D., Blumer, K. J., Odelberg, S. J. & McMahon, M., Dec 2020, In: Clinical Cancer Research. 26, 23, p. 6374-6386 13 p.

Research output: Contribution to journal › Article › peer-review

Open Access

35 Scopus citations

Comparative Analysis of CPI-Motif Regulation of Biochemical Functions of Actin Capping Protein

McConnell, P., Mekel, M., Kozlov, A. G., Mooren, O. L., Lohman, T. M. & Cooper, J. A., Mar 24 2020, In: Biochemistry. 59, 11, p. 1202-1215 14 p.

Research output: Contribution to journal › Article › peer-review

9 Scopus citations

Comparative differential cuproproteomes of: Rhodobacter capsulatus reveal novel copper homeostasis related proteins

Selamoglu, N., Önder, Ö., Öztürk, Y., Khalfaoui-Hassani, B., Blaby-Haas, C. E., Garcia, B. A., Koch, H. G. & Daldal, F., Apr 2020, In: Metallomics. 12, 4, p. 572-591 20 p.

Research output: Contribution to journal › Article › peer-review

Open Access

9 Scopus citations

Competitive tight-binding inhibition of VKORC1 underlies warfarin dosage variation and antidotal efficacy

Li, S., Liu, S., Liu, X. R., Zhang, M. M. & Li, W., May 26 2020, In: Blood Advances. 4, 10, p. 2202-2212 11 p.

Research output: Contribution to journal › Article › peer-review

Open Access

14 Scopus citations

Comprehensive Map of the Artemisia annua Proteome and Quantification of Differential Protein Expression in Chemotypes Producing High versus Low Content of Artemisinin

Chen, M., Yan, T., Ji, L., Dong, Y., Sidoli, S., Yuan, Z., Cai, C., Chen, J., Tang, Y., Shen, Q., Pan, Q., Fu, X., Ku, X., Liao, L., Garcia, B. A., Yan, W. & Tang, K., May 1 2020, In: Proteomics. 20, 10, 1900310.

Research output: Contribution to journal › Article › peer-review

9 Scopus citations

Computational and Spectroscopic Characterization of the Photocycle of an Artificial Rhodopsin

Manathunga, M., Jenkins, A. J., Orozco-Gonzalez, Y., Ghanbarpour, A., Borhan, B., Geiger, J. H., Larsen, D. S., Olivucci, M., Olivucci, M. & Olivucci, M., Jun 4 2020, In: Journal of Physical Chemistry Letters. 11, 11, p. 4245-4252 8 p.

Research output: Contribution to journal › Article › peer-review

Open Access

6 Scopus citations

Computing and optimizing over all fixed-points of discrete systems on large networks: Computing and optimizing over all fixed-points of discrete systems on large networks

Riehl, J. R., Zimmerman, M. I., Singh, M. F., Bowman, G. R. & Ching, S., Sep 1 2020, In: Journal of the Royal Society Interface. 17, 170, 20200126.

Research output: Contribution to journal › Article › peer-review

Open Access

1 Scopus citations

Conformational distributions of isolated myosin motor domains encode their mechanochemical properties

Porter, J. R., Meller, A., Zimmerman, M. I., Greenberg, M. J. & Bowman, G. R., May 2020, In: eLife. 9, e55132.

Research output: Contribution to journal › Article › peer-review

Open Access

22 Scopus citations

Connecting Coil-to-Globule Transitions to Full Phase Diagrams for Intrinsically Disordered Proteins

Zeng, X., Holehouse, A. S., Chilkoti, A., Mittag, T. & Pappu, R. V., Jul 21 2020, In: Biophysical Journal. 119, 2, p. 402-418 17 p.

Research output: Contribution to journal › Article › peer-review

Open Access

69 Scopus citations

Controlling Structural Bias in Intrinsically Disordered Proteins Using Solution Space Scanning

Holehouse, A. S. & Sukenik, S., Mar 10 2020, In: Journal of Chemical Theory and Computation. 16, 3, p. 1794-1805 12 p.

Research output: Contribution to journal › Article › peer-review

Open Access

26 Scopus citations

Correction: Discovery of 6-Phenylhexanamide Derivatives as Potent Stereoselective Mitofusin Activators for the Treatment of Mitochondrial Diseases (Journal of Medicinal Chemistry (2020) 63:13 (7033−7051) DOI: 10.1021/acs.jmedchem.0c00366)

Dang, X., Zhang, L., Franco, A., Li, J., Rocha, A. G., Devanathan, S., Dolle, R. E., Bernstein, P. R. & Dorn, G. W., Sep 10 2020, In: Journal of Medicinal Chemistry. 63, 17, p. 10086 1 p.

Research output: Contribution to journal › Comment/debate

Cryo-EM Structure of Nucleotide-Bound Tel1^ATM Unravels the Molecular Basis of Inhibition and Structural Rationale for Disease-Associated Mutations

Yates, L. A., Williams, R. M., Hailemariam, S., Ayala, R., Burgers, P. & Zhang, X., Jan 7 2020, In: Structure. 28, 1, p. 96-104.e3

Research output: Contribution to journal › Article › peer-review

Open Access

31 Scopus citations

Depletion interactions modulate the binding between disordered proteins in crowded environments

Zosel, F., Soranno, A., Buholzer, K. J., Nettels, D. & Schuler, B., Jun 16 2020, In: Proceedings of the National Academy of Sciences of the United States of America. 117, 24, p. 13480-13489 10 p.

Research output: Contribution to journal › Article › peer-review

Open Access

88 Scopus citations

Development of a single-stranded DNA-binding protein fluorescent fusion toolbox

Dubiel, K., Henry, C., Spenkelink, L. M., Kozlov, A. G., Wood, E. A., Jergic, S., Dixon, N. E., van Oijen, A. M., Cox, M. M., Lohman, T. M., Sandler, S. J. & Keck, J. L., 2020, In: Nucleic acids research. 48, 11, p. 6053-6067 15 p.

Research output: Contribution to journal › Article › peer-review

Open Access

16 Scopus citations

Discovery of 6-Phenylhexanamide Derivatives as Potent Stereoselective Mitofusin Activators for the Treatment of Mitochondrial Diseases

Dang, X., Zhang, L., Franco, A., Li, J., Rocha, A. G., Devanathan, S., Dolle, R. E., Bernstein, P. R. & Dorn, G. W., Jul 9 2020, In: Journal of Medicinal Chemistry. 63, 13, p. 7033-7051 19 p.

Research output: Contribution to journal › Article › peer-review

Open Access

29 Scopus citations

Discovery of Electrophiles and Profiling of Enzyme Cofactors

Dettling, S. E., Ahmadi, M., Lin, Z., He, L. & Matthews, M. L., Dec 2020, In: Current protocols in chemical biology. 12, 4, e86.

Research output: Contribution to journal › Article › peer-review

Open Access

7 Scopus citations

Disruption of ATRX-RNA interactions uncovers roles in ATRX localization and PRC2 function

Ren, W., Medeiros, N., Warneford-Thomson, R., Wulfridge, P., Yan, Q., Bian, J., Sidoli, S., Garcia, B. A., Skordalakes, E., Joyce, E., Bonasio, R. & Sarma, K., Dec 1 2020, In: Nature communications. 11, 1, 2219.

Research output: Contribution to journal › Article › peer-review

Open Access

18 Scopus citations

Emerging Roles for Phase Separation in Plants

Emenecker, R. J., Holehouse, A. S. & Strader, L. C., Oct 12 2020, In: Developmental cell. 55, 1, p. 69-83 15 p.

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

Open Access

81 Scopus citations

Exon and protein positioning in a pre-catalytic group II intron RNP primed for splicing

Liu, N., Dong, X., Hu, C., Zeng, J., Wang, J., Wang, J., Wang, H. W. & Belfort, M., Nov 4 2020, In: Nucleic acids research. 48, 19, p. 11185-11198 14 p.

Research output: Contribution to journal › Article › peer-review

Open Access

9 Scopus citations

Department of Biochemistry & Molecular Biophysics

Research output

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