The Green Center for Systems Biology

Research Output

2020

Directional allosteric regulation of protein filament length

Jermyn, A. S., Cao, W., Elam, W. A., De La Cruz, E. M. & Lin, M. M., Mar 2020, In : Physical Review E. 101, 3, 032409.

Research output: Contribution to journalArticle

Strategies for Engineering and Rewiring Kinase Regulation

McCormick, J. W., Pincus, D., Resnekov, O. & Reynolds, K. A., Mar 2020, In : Trends in biochemical sciences. 45, 3, p. 259-271 13 p.

Research output: Contribution to journalReview article

2019

4D electron microscopy of T cell activation

Lu, Y., Yoo, B. K., Ng, A. H. C., Kim, J., Yeom, S., Tang, J., Lin, M. M., Zewail, A. H. & Heath, J. R., Oct 29 2019, In : Proceedings of the National Academy of Sciences of the United States of America. 116, 44, p. 22014-22019 6 p.

Research output: Contribution to journalArticle

Open Access

A fully-automated, robust, and versatile algorithm for long-term budding yeast segmentation and tracking

Ezgi Wood, N. & Doncic, A., Mar 1 2019, In : PloS one. 14, 3, e0206395.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

A Two-Enzyme Adaptive Unit within Bacterial Folate Metabolism

Schober, A. F., Mathis, A. D., Ingle, C., Park, J. O., Chen, L., Rabinowitz, J. D., Junier, I., Rivoire, O. & Reynolds, K. A., Jun 11 2019, In : Cell Reports. 27, 11, p. 3359-3370.e7

Research output: Contribution to journalArticle

Open Access
3 Scopus citations

Functional divergence caused by mutations in an energetic hotspot in ERK2

Taylor, C. A., Cormier, K. W., Keenan, S. E., Earnest, S., Stippec, S., Wichaidit, C., Juang, Y. C., Wang, J., Shvartsman, S. Y., Goldsmith, E. J. & Cobb, M. H., Jul 30 2019, In : Proceedings of the National Academy of Sciences of the United States of America. 116, 31, p. 15514-15523 10 p.

Research output: Contribution to journalArticle

Open Access
6 Scopus citations

High-order epistasis in catalytic power of dihydrofolate reductase gives rise to a rugged fitness landscape in the presence of trimethoprim selection

Tamer, Y. T., Gaszek, I. K., Abdizadeh, H., Batur, T. A., Reynolds, K. A., Atilgan, A. R., Atilgan, C. & Toprak, E., Jan 1 2019, In : Molecular biology and evolution. 36, 7, p. 1533-1550 18 p.

Research output: Contribution to journalArticle

Open Access
2 Scopus citations

Non-antibiotic Small-Molecule Regulation of DHFR-Based Destabilizing Domains In Vivo

Peng, H., Chau, V. Q., Phetsang, W., Sebastian, R. M., Stone, M. R. L., Datta, S., Renwick, M., Tamer, Y. T., Toprak, E., Koh, A. Y., Blaskovich, M. A. T. & Hulleman, J. D., Dec 13 2019, In : Molecular Therapy - Methods and Clinical Development. 15, p. 27-39 13 p.

Research output: Contribution to journalArticle

Open Access
2 Scopus citations

Rapid ultrasensitive detection platform for antimicrobial susceptibility testing

Cansizoglu, M. F., Tamer, Y. T., Farid, M., Koh, A. & Toprak, E., May 1 2019, In : PLoS biology. 17, 5, p. e3000291

Research output: Contribution to journalArticle

Open Access
3 Scopus citations

Tau local structure shields an amyloid-forming motif and controls aggregation propensity

Chen, D., Drombosky, K. W., Hou, Z., Sari, L., Kashmer, O. M., Ryder, B. D., Perez, V. A., Woodard, D. N. R., Lin, M. M., Diamond, M. I. & Joachimiak, L. A., Dec 1 2019, In : Nature communications. 10, 1, 2493.

Research output: Contribution to journalArticle

Open Access
8 Scopus citations
2018

An evolutionary hotspot defines functional differences between CRYPTOCHROMES

Rosensweig, C., Reynolds, K. A., Gao, P., Laothamatas, I., Shan, Y., Ranganathan, R., Takahashi, J. S. & Green, C. B., Dec 1 2018, In : Nature Communications. 9, 1, 1138.

Research output: Contribution to journalArticle

21 Scopus citations

A Precise Cdk Activity Threshold Determines Passage through the Restriction Point

Schwarz, C., Johnson, A., Kõivomägi, M., Zatulovskiy, E., Kravitz, C. J., Doncic, A. & Skotheim, J. M., Jan 18 2018, In : Molecular Cell. 69, 2, p. 253-264.e5

Research output: Contribution to journalArticle

17 Scopus citations

A regulatory circuit of two lncRNAs and a master regulator directs cell fate in yeast

Moretto, F., Wood, N. E., Kelly, G., Doncic, A. & Van Werven, F. J., Dec 1 2018, In : Nature Communications. 9, 1, 780.

Research output: Contribution to journalArticle

7 Scopus citations

A simplified mechanism for anisotropic constriction in Drosophila mesoderm

Doubrovinski, K., Tchoufag, J. & Mandadapu, K., Dec 10 2018, In : Development (Cambridge, England). 145, 24

Research output: Contribution to journalArticle

1 Scopus citations

Breaking down cellulose fibrils with a mid-infrared laser

Domin, D., Man, V. H., Van-Oanh, N. T., Wang, J., Kawasaki, T., Derreumaux, P. & Nguyen, P. H., Oct 1 2018, In : Cellulose. 25, 10, p. 5553-5568 16 p.

Research output: Contribution to journalArticle

1 Scopus citations

Cheminformatic Insight into the Differences between Terrestrial and Marine Originated Natural Products

Shang, J., Hu, B., Wang, J., Zhu, F., Kang, Y., Li, D., Sun, H., Kong, D. X. & Hou, T., Jun 25 2018, In : Journal of Chemical Information and Modeling. 58, 6, p. 1182-1193 12 p.

Research output: Contribution to journalArticle

13 Scopus citations

Coevolution-based inference of amino acid interactions underlying protein function

Salinas, V. H. & Ranganathan, R., Jul 19 2018, In : eLife. 7, e34300.

Research output: Contribution to journalArticle

21 Scopus citations

Computational systems pharmacology analysis of cannabidiol: a combination of chemogenomics-knowledgebase network analysis and integrated in silico modeling and simulation

Bian, Y. M., He, X. B., Jing, Y. K., Wang, L. R., Wang, J. M. & Xie, X. Q., Jan 1 2018, (Accepted/In press) In : Acta Pharmacologica Sinica.

Research output: Contribution to journalArticle

9 Scopus citations

Crystal Structures of Human Orexin 2 Receptor Bound to the Subtype-Selective Antagonist EMPA

Suno, R., Kimura, K. T., Nakane, T., Yamashita, K., Wang, J., Fujiwara, T., Yamanaka, Y., Im, D., Horita, S., Tsujimoto, H., Tawaramoto, M. S., Hirokawa, T., Nango, E., Tono, K., Kameshima, T., Hatsui, T., Joti, Y., Yabashi, M., Shimamoto, K., Yamamoto, M. & 4 others, Rosenbaum, D. M., Iwata, S., Shimamura, T. & Kobayashi, T., Jan 2 2018, In : Structure. 26, 1, p. 7-19.e5

Research output: Contribution to journalArticle

22 Scopus citations

Engineering allosteric regulation in protein kinases

Pincus, D., Pandey, J. P., Feder, Z. A., Creixell, P., Resnekov, O. & Reynolds, K. A., Nov 6 2018, In : Science Signaling. 11, 555, eaar3250.

Research output: Contribution to journalArticle

7 Scopus citations

Hierarchical Organization Endows the Kinase Domain with Regulatory Plasticity

Creixell, P., Pandey, J. P., Palmeri, A., Bhattacharyya, M., Creixell, M., Ranganathan, R., Pincus, D. & Yaffe, M. B., Oct 24 2018, In : Cell Systems. 7, 4, p. 371-383.e4

Research output: Contribution to journalArticle

7 Scopus citations

Integration of Multiple Metabolic Signals Determines Cell Fate Prior to Commitment

Argüello-Miranda, O., Liu, Y., Wood, N. E., Kositangool, P. & Doncic, A., Sep 6 2018, In : Molecular Cell. 71, 5, p. 733-744.e11

Research output: Contribution to journalArticle

6 Scopus citations

Molecular Dynamics Simulations Revealed the Regulation of Ligands to the Interactions between Androgen Receptor and Its Coactivator

Liu, N., Zhou, W., Guo, Y., Wang, J., Fu, W., Sun, H., Li, D., Duan, M. & Hou, T., Aug 27 2018, In : Journal of Chemical Information and Modeling. 58, 8, p. 1652-1661 10 p.

Research output: Contribution to journalArticle

14 Scopus citations

Putting Evolution to Work

Ranganathan, R., Nov 29 2018, In : Cell. 175, 6, p. 1449-1451 3 p.

Research output: Contribution to journalShort survey

1 Scopus citations
2017

A Continuum Poisson-Boltzmann Model for Membrane Channel Proteins

Xiao, L., Diao, J., Greene, DA., Wang, J. & Luo, R., Jul 11 2017, In : Journal of Chemical Theory and Computation. 13, 7, p. 3398-3412 15 p.

Research output: Contribution to journalArticle

9 Scopus citations

A DREAM challenge to build prediction models for short-term discontinuation of docetaxel in metastatic castration- resistant prostate cancer

Prostate Cancer DREAM Challenge Community, Jan 1 2017, In : JCO Clinical Cancer Informatics. 2017, 1, p. 1-15 15 p.

Research output: Contribution to journalArticle

Open Access
6 Scopus citations

An evolution-based strategy for engineering allosteric regulation

Pincus, D., Resnekov, O. & Reynolds, K. A., Apr 28 2017, In : Physical Biology. 14, 2, 025002.

Research output: Contribution to journalArticle

8 Scopus citations

Conserved amino acid networks modulate discrete functional properties in an enzyme superfamily

Narayanan, C., Gagné, D., Reynolds, K. A. & Doucet, N., Dec 1 2017, In : Scientific reports. 7, 1, 3207.

Research output: Contribution to journalArticle

10 Scopus citations

Deconstruction of the ras switching cycle through saturation mutagenesis

Bandaru, P., Shah, N. H., Bhattacharyya, M., Barton, J. P., Kondo, Y., Cofsky, J. C., Gee, C. L., Chakraborty, A. K., Kortemme, T., Ranganathan, R. & Kuriyan, J., Jul 7 2017, In : eLife. 6, e27810.

Research output: Contribution to journalArticle

20 Scopus citations

Epithelial Patterning, Morphogenesis, and Evolution: Drosophila Eggshell as a Model

Osterfield, M., Berg, C. A. & Shvartsman, S. Y., May 22 2017, In : Developmental Cell. 41, 4, p. 337-348 12 p.

Research output: Contribution to journalReview article

Open Access
10 Scopus citations

Fighting against evolution of antibiotic resistance by utilizing evolvable antimicrobial drugs

Cansizoglu, M. F. & Toprak, E., May 11 2017, (Accepted/In press) In : Current Genetics. p. 1-4 4 p.

Research output: Contribution to journalArticle

13 Scopus citations

Increased substrate affinity in the Escherichia coli L28R dihydrofolate reductase mutant causes trimethoprim resistance

Abdizadeh, H., Tamer, Y. T., Acar, O., Toprak, E., Atilgan, A. R. & Atilgan, C., 2017, In : Physical Chemistry Chemical Physics. 19, 18, p. 11416-11428 13 p.

Research output: Contribution to journalArticle

8 Scopus citations

Leveraging symmetry to predict self-assembly of multiple polymers

Lin, M. M., Sep 1 2017, In : Chemical Physics Letters. 683, p. 347-351 5 p.

Research output: Contribution to journalArticle

1 Scopus citations

Measurement of cortical elasticity in Drosophila melanogaster embryos using ferrofluids

Doubrovinski, K., Swan, M., Polyakov, O. & Wieschaus, E. F., Jan 31 2017, In : Proceedings of the National Academy of Sciences of the United States of America. 114, 5, p. 1051-1056 6 p.

Research output: Contribution to journalArticle

27 Scopus citations

On the Race to Starvation: How Do Bacteria Survive High Doses of Antibiotics?

Tamer, Y. T. & Toprak, E., Jan 1 2017, In : Molecular Cell. 68, 6, p. 1134-1146.e6

Research output: Contribution to journalShort survey

2 Scopus citations
2016

An electrostatic selection mechanism controls sequential kinase signaling downstream of the T cell receptor

Shah, N. H., Wang, Q., Yan, Q., Karandur, D., Kadlecek, T. A., Fallahee, I. R., Russ, W. P., Ranganathan, R., Weiss, A. & Kuriyan, J., Oct 4 2016, In : eLife. 5, OCTOBER2016, e20105.

Research output: Contribution to journalArticle

30 Scopus citations

A protocol for functional assessment of whole-protein saturation mutagenesis libraries utilizing high-throughput sequencing

Stiffler, M. A., Subramanian, S. K., Salinas, V. H. & Ranganathan, R., Jul 3 2016, In : Journal of Visualized Experiments. 2016, 113, e54119.

Research output: Contribution to journalArticle

3 Scopus citations

Crystal structure of the human sterol transporter ABCG5/ABCG8

Lee, J. Y., Kinch, L. N., Borek, D. M., Wang, J., Wang, J., Urbatsch, I. L., Xie, X. S., Grishin, N. V., Cohen, J. C., Otwinowski, Z., Hobbs, H. H. & Rosenbaum, D. M., May 4 2016, In : Nature. 533, 7604, p. 561-564 4 p.

Research output: Contribution to journalArticle

112 Scopus citations

Dihydrostreptomycin Directly Binds to, Modulates, and Passes through the MscL Channel Pore

Wray, R., Iscla, I., Gao, Y., Li, H., Wang, J. & Blount, P., Jun 9 2016, In : PLoS Biology. 14, 6, e1002473.

Research output: Contribution to journalArticle

9 Scopus citations

Electric-field-stimulated protein mechanics

Hekstra, D. R., White, K. I., Socolich, M. A., Henning, R. W., Šrajer, V. & Ranganathan, R., Dec 15 2016, In : Nature. 540, 7633, p. 400-405 6 p.

Research output: Contribution to journalArticle

58 Scopus citations

Erratum: Mechanical slowing-down of cytoplasmic diffusion allows in vivo counting of proteins in individual cells (Nature Communications (2016) 7 (11641) DOI: 10.1038/ncomms11641)

Okumus, B., Landgraf, D., Lai, G. C., Bakshi, S., Arias-Castro, J. C., Yildiz, S., Huh, D., Fernandez-Lopez, R., Peterson, C. N., Toprak, E., El Karoui, M. & Paulsson, J., Jun 24 2016, In : Nature Communications. 7, 12130.

Research output: Contribution to journalComment/debate

Evolution-Based Functional Decomposition of Proteins

Rivoire, O., Reynolds, K. A. & Ranganathan, R., Jun 2016, In : PLoS Computational Biology. 12, 6, e1004817.

Research output: Contribution to journalArticle

31 Scopus citations

High-resolution crystal structure of the human CB1 cannabinoid receptor

Shao, Z., Yin, J., Chapman, K., Grzemska, M., Clark, L., Wang, J. & Rosenbaum, D. M., Dec 22 2016, In : Nature. 540, 7634, p. 602-606 5 p.

Research output: Contribution to journalArticle

148 Scopus citations

In Silico Chemogenomics Knowledgebase and Computational System Neuropharmacology Approach for Cannabinoid Drug Research

Xie, X. Q., Wang, L., Wang, J., Xie, Z., Yang, P. & Ouyang, Q., May 13 2016, General Processes and Mechanisms, Prescription Medications, Caffeine and Areca, Polydrug Misuse, Emerging Addictions and Non-Drug Addictions. Elsevier Inc., Vol. 3. p. 183-195 13 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

2 Scopus citations

Mechanical slowing-down of cytoplasmic diffusion allows in vivo counting of proteins in individual cells

Okumus, B., Landgraf, D., Lai, G. C., Bakhsi, S., Arias-Castro, J. C., Yildiz, S., Huh, D., Fernandez-Lopez, R., Peterson, C. N., Toprak, E., El Karoui, M. & Paulsson, J., May 18 2016, In : Nature communications. 7, 11641.

Research output: Contribution to journalArticle

20 Scopus citations

Origins of Allostery and Evolvability in Proteins: A Case Study

Raman, A. S., White, K. I. & Ranganathan, R., Jul 14 2016, In : Cell. 166, 2, p. 468-480 13 p.

Research output: Contribution to journalArticle

45 Scopus citations

Sequence-Specific Targeting of Bacterial Resistance Genes Increases Antibiotic Efficacy

Ayhan, D. H., Tamer, Y. T., Akbar, M., Bailey, S. M., Wong, M., Daly, S. M., Greenberg, D. E. & Toprak, E., Sep 15 2016, In : PLoS Biology. 14, 9, e1002552.

Research output: Contribution to journalArticle

24 Scopus citations

Switch-like Transitions Insulate Network Motifs to Modularize Biological Networks

Atay, O., Doncic, A. & Skotheim, J. M., Aug 24 2016, In : Cell Systems. 3, 2, p. 121-132 12 p.

Research output: Contribution to journalArticle

8 Scopus citations

The Context-Dependence of Mutations: A Linkage of Formalisms

Poelwijk, F. J., Krishna, V. & Ranganathan, R., Jun 1 2016, In : PLoS Computational Biology. 12, 6, e1004771.

Research output: Contribution to journalArticle

25 Scopus citations

Timing Correlations in Proteins Predict Functional Modules and Dynamic Allostery

Lin, M. M., May 4 2016, In : Journal of the American Chemical Society. 138, 15, p. 5036-5043 8 p.

Research output: Contribution to journalArticle

6 Scopus citations