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Prediction of New Stabilizing Mutations Based on Mechanistic Insights from Markov State Models.

ACS central science

Zimmerman MI, Hart KM, Sibbald CA, Frederick TE, Jimah JR, Knoverek CR, Tolia NH, Bowman GR.
PMID: 29296672
ACS Cent Sci. 2017 Dec 27;3(12):1311-1321. doi: 10.1021/acscentsci.7b00465. Epub 2017 Nov 21.

Protein stabilization is fundamental to enzyme function and evolution, yet understanding the determinants of a protein's stability remains a challenge. This is largely due to a shortage of atomically detailed models for the ensemble of relevant protein conformations and...

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Zimmerman MI, Hart KM, Sibbald CA, et al. Prediction of New Stabilizing Mutations Based on Mechanistic Insights from Markov State Models. ACS Cent Sci. 2017;3(12):1311-1321doi: 10.1021/acscentsci.7b00465.
Zimmerman, M. I., Hart, K. M., Sibbald, C. A., Frederick, T. E., Jimah, J. R., Knoverek, C. R., Tolia, N. H., & Bowman, G. R. (2017). Prediction of New Stabilizing Mutations Based on Mechanistic Insights from Markov State Models. ACS central science, 3(12), 1311-1321. https://doi.org/10.1021/acscentsci.7b00465
Zimmerman, Maxwell I, et al. "Prediction of New Stabilizing Mutations Based on Mechanistic Insights from Markov State Models." ACS central science vol. 3,12 (2017): 1311-1321. doi: https://doi.org/10.1021/acscentsci.7b00465
Zimmerman MI, Hart KM, Sibbald CA, Frederick TE, Jimah JR, Knoverek CR, Tolia NH, Bowman GR. Prediction of New Stabilizing Mutations Based on Mechanistic Insights from Markov State Models. ACS Cent Sci. 2017 Dec 27;3(12):1311-1321. doi: 10.1021/acscentsci.7b00465. Epub 2017 Nov 21. PMID: 29296672; PMCID: PMC5746865.
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SARS-CoV-2 Simulations Go Exascale to Capture Spike Opening and Reveal Cryptic Pockets Across the Proteome.

bioRxiv : the preprint server for biology

Zimmerman MI, Porter JR, Ward MD, Singh S, Vithani N, Meller A, Mallimadugula UL, Kuhn CE, Borowsky JH, Wiewiora RP, Hurley MFD, Harbison AM, Fogarty CA, Coffland JE, Fadda E, Voelz VA, Chodera JD, Bowman GR.
PMID: 32637963
bioRxiv. 2020 Oct 07; doi: 10.1101/2020.06.27.175430.

SARS-CoV-2 has intricate mechanisms for initiating infection, immune evasion/suppression, and replication, which depend on the structure and dynamics of its constituent proteins. Many protein structures have been solved, but far less is known about their relevant conformational changes. To...

Cite
Zimmerman MI, Porter JR, Ward MD, et al. SARS-CoV-2 Simulations Go Exascale to Capture Spike Opening and Reveal Cryptic Pockets Across the Proteome. bioRxiv. 2020;doi: 10.1101/2020.06.27.175430.
Zimmerman, M. I., Porter, J. R., Ward, M. D., Singh, S., Vithani, N., Meller, A., Mallimadugula, U. L., Kuhn, C. E., Borowsky, J. H., Wiewiora, R. P., Hurley, M. F. D., Harbison, A. M., Fogarty, C. A., Coffland, J. E., Fadda, E., Voelz, V. A., Chodera, J. D., & Bowman, G. R. (2020). SARS-CoV-2 Simulations Go Exascale to Capture Spike Opening and Reveal Cryptic Pockets Across the Proteome. bioRxiv : the preprint server for biology, . https://doi.org/10.1101/2020.06.27.175430
Zimmerman, Maxwell I, et al. "SARS-CoV-2 Simulations Go Exascale to Capture Spike Opening and Reveal Cryptic Pockets Across the Proteome." bioRxiv : the preprint server for biology vol. (2020). doi: https://doi.org/10.1101/2020.06.27.175430
Zimmerman MI, Porter JR, Ward MD, Singh S, Vithani N, Meller A, Mallimadugula UL, Kuhn CE, Borowsky JH, Wiewiora RP, Hurley MFD, Harbison AM, Fogarty CA, Coffland JE, Fadda E, Voelz VA, Chodera JD, Bowman GR. SARS-CoV-2 Simulations Go Exascale to Capture Spike Opening and Reveal Cryptic Pockets Across the Proteome. bioRxiv. 2020 Oct 07; doi: 10.1101/2020.06.27.175430. PMID: 32637963; PMCID: PMC7337393.
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SARS-CoV-2 Nsp16 activation mechanism and a cryptic pocket with pan-coronavirus antiviral potential.

bioRxiv : the preprint server for biology

Vithani N, Ward MD, Zimmerman MI, Novak B, Borowsky JH, Singh S, Bowman GR.
PMID: 33330873
bioRxiv. 2020 Dec 10; doi: 10.1101/2020.12.10.420109.

Coronaviruses have caused multiple epidemics in the past two decades, in addition to the current COVID-19 pandemic that is severely damaging global health and the economy. Coronaviruses employ between twenty and thirty proteins to carry out their viral replication...

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Vithani N, Ward MD, Zimmerman MI, et al. SARS-CoV-2 Nsp16 activation mechanism and a cryptic pocket with pan-coronavirus antiviral potential. bioRxiv. 2020;doi: 10.1101/2020.12.10.420109.
Vithani, N., Ward, M. D., Zimmerman, M. I., Novak, B., Borowsky, J. H., Singh, S., & Bowman, G. R. (2020). SARS-CoV-2 Nsp16 activation mechanism and a cryptic pocket with pan-coronavirus antiviral potential. bioRxiv : the preprint server for biology, . https://doi.org/10.1101/2020.12.10.420109
Vithani, Neha, et al. "SARS-CoV-2 Nsp16 activation mechanism and a cryptic pocket with pan-coronavirus antiviral potential." bioRxiv : the preprint server for biology vol. (2020). doi: https://doi.org/10.1101/2020.12.10.420109
Vithani N, Ward MD, Zimmerman MI, Novak B, Borowsky JH, Singh S, Bowman GR. SARS-CoV-2 Nsp16 activation mechanism and a cryptic pocket with pan-coronavirus antiviral potential. bioRxiv. 2020 Dec 10; doi: 10.1101/2020.12.10.420109. PMID: 33330873; PMCID: PMC7743098.
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SARS-CoV-2 Simulations Go Exascale to Capture Spike Opening and Reveal Cryptic Pockets Across the Proteome.

bioRxiv : the preprint server for biology

Zimmerman MI, Porter JR, Ward MD, Singh S, Vithani N, Meller A, Mallimadugula UL, Kuhn CE, Borowsky JH, Wiewiora RP, Hurley MFD, Harbison AM, Fogarty CA, Coffland JE, Fadda E, Voelz VA, Chodera JD, Bowman GR.
PMID: 32637963
bioRxiv. 2020 Oct 07; doi: 10.1101/2020.06.27.175430.

SARS-CoV-2 has intricate mechanisms for initiating infection, immune evasion/suppression, and replication, which depend on the structure and dynamics of its constituent proteins. Many protein structures have been solved, but far less is known about their relevant conformational changes. To...

Cite
Zimmerman MI, Porter JR, Ward MD, et al. SARS-CoV-2 Simulations Go Exascale to Capture Spike Opening and Reveal Cryptic Pockets Across the Proteome. bioRxiv. 2020;doi: 10.1101/2020.06.27.175430.
Zimmerman, M. I., Porter, J. R., Ward, M. D., Singh, S., Vithani, N., Meller, A., Mallimadugula, U. L., Kuhn, C. E., Borowsky, J. H., Wiewiora, R. P., Hurley, M. F. D., Harbison, A. M., Fogarty, C. A., Coffland, J. E., Fadda, E., Voelz, V. A., Chodera, J. D., & Bowman, G. R. (2020). SARS-CoV-2 Simulations Go Exascale to Capture Spike Opening and Reveal Cryptic Pockets Across the Proteome. bioRxiv : the preprint server for biology, . https://doi.org/10.1101/2020.06.27.175430
Zimmerman, Maxwell I, et al. "SARS-CoV-2 Simulations Go Exascale to Capture Spike Opening and Reveal Cryptic Pockets Across the Proteome." bioRxiv : the preprint server for biology vol. (2020). doi: https://doi.org/10.1101/2020.06.27.175430
Zimmerman MI, Porter JR, Ward MD, Singh S, Vithani N, Meller A, Mallimadugula UL, Kuhn CE, Borowsky JH, Wiewiora RP, Hurley MFD, Harbison AM, Fogarty CA, Coffland JE, Fadda E, Voelz VA, Chodera JD, Bowman GR. SARS-CoV-2 Simulations Go Exascale to Capture Spike Opening and Reveal Cryptic Pockets Across the Proteome. bioRxiv. 2020 Oct 07; doi: 10.1101/2020.06.27.175430. PMID: 32637963; PMCID: PMC7337393.
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Opening of a cryptic pocket in β-lactamase increases penicillinase activity.

Proceedings of the National Academy of Sciences of the United States of America

Knoverek CR, Mallimadugula UL, Singh S, Rennella E, Frederick TE, Yuwen T, Raavicharla S, Kay LE, Bowman GR.
PMID: 34799442
Proc Natl Acad Sci U S A. 2021 Nov 23;118(47). doi: 10.1073/pnas.2106473118.

Understanding the functional role of protein-excited states has important implications in protein design and drug discovery. However, because these states are difficult to find and study, it is still unclear if excited states simply result from thermal fluctuations and...

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Knoverek CR, Mallimadugula UL, Singh S, et al. Opening of a cryptic pocket in β-lactamase increases penicillinase activity. Proc Natl Acad Sci U S A. 2021;118(47)doi: 10.1073/pnas.2106473118.
Knoverek, C. R., Mallimadugula, U. L., Singh, S., Rennella, E., Frederick, T. E., Yuwen, T., Raavicharla, S., Kay, L. E., & Bowman, G. R. (2021). Opening of a cryptic pocket in β-lactamase increases penicillinase activity. Proceedings of the National Academy of Sciences of the United States of America, 118(47), . https://doi.org/10.1073/pnas.2106473118
Knoverek, Catherine R, et al. "Opening of a cryptic pocket in β-lactamase increases penicillinase activity." Proceedings of the National Academy of Sciences of the United States of America vol. 118,47 (2021). doi: https://doi.org/10.1073/pnas.2106473118
Knoverek CR, Mallimadugula UL, Singh S, Rennella E, Frederick TE, Yuwen T, Raavicharla S, Kay LE, Bowman GR. Opening of a cryptic pocket in β-lactamase increases penicillinase activity. Proc Natl Acad Sci U S A. 2021 Nov 23;118(47). doi: 10.1073/pnas.2106473118. PMID: 34799442; PMCID: PMC8617505.
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Choice of Adaptive Sampling Strategy Impacts State Discovery, Transition Probabilities, and the Apparent Mechanism of Conformational Changes.

Journal of chemical theory and computation

Zimmerman MI, Porter JR, Sun X, Silva RR, Bowman GR.
PMID: 30240203
J Chem Theory Comput. 2018 Nov 13;14(11):5459-5475. doi: 10.1021/acs.jctc.8b00500. Epub 2018 Oct 23.

Interest in atomically detailed simulations has grown significantly with recent advances in computational hardware and Markov state modeling (MSM) methods, yet outstanding questions remain that hinder their widespread adoption. Namely, how do alternative sampling strategies explore conformational space and...

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Zimmerman MI, Porter JR, Sun X, et al. Choice of Adaptive Sampling Strategy Impacts State Discovery, Transition Probabilities, and the Apparent Mechanism of Conformational Changes. J Chem Theory Comput. 2018;14(11):5459-5475doi: 10.1021/acs.jctc.8b00500.
Zimmerman, M. I., Porter, J. R., Sun, X., Silva, R. R., & Bowman, G. R. (2018). Choice of Adaptive Sampling Strategy Impacts State Discovery, Transition Probabilities, and the Apparent Mechanism of Conformational Changes. Journal of chemical theory and computation, 14(11), 5459-5475. https://doi.org/10.1021/acs.jctc.8b00500
Zimmerman, Maxwell I, et al. "Choice of Adaptive Sampling Strategy Impacts State Discovery, Transition Probabilities, and the Apparent Mechanism of Conformational Changes." Journal of chemical theory and computation vol. 14,11 (2018): 5459-5475. doi: https://doi.org/10.1021/acs.jctc.8b00500
Zimmerman MI, Porter JR, Sun X, Silva RR, Bowman GR. Choice of Adaptive Sampling Strategy Impacts State Discovery, Transition Probabilities, and the Apparent Mechanism of Conformational Changes. J Chem Theory Comput. 2018 Nov 13;14(11):5459-5475. doi: 10.1021/acs.jctc.8b00500. Epub 2018 Oct 23. PMID: 30240203; PMCID: PMC6571142.
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SARS-CoV-2 Nsp16 activation mechanism and a cryptic pocket with pan-coronavirus antiviral potential.

Biophysical journal

Vithani N, Ward MD, Zimmerman MI, Novak B, Borowsky JH, Singh S, Bowman GR.
PMID: 33794150
Biophys J. 2021 Jul 20;120(14):2880-2889. doi: 10.1016/j.bpj.2021.03.024. Epub 2021 Mar 29.

Coronaviruses have caused multiple epidemics in the past two decades, in addition to the current COVID-19 pandemic that is severely damaging global health and the economy. Coronaviruses employ between 20 and 30 proteins to carry out their viral replication...

Cite
Vithani N, Ward MD, Zimmerman MI, et al. SARS-CoV-2 Nsp16 activation mechanism and a cryptic pocket with pan-coronavirus antiviral potential. Biophys J. 2021;120(14):2880-2889doi: 10.1016/j.bpj.2021.03.024.
Vithani, N., Ward, M. D., Zimmerman, M. I., Novak, B., Borowsky, J. H., Singh, S., & Bowman, G. R. (2021). SARS-CoV-2 Nsp16 activation mechanism and a cryptic pocket with pan-coronavirus antiviral potential. Biophysical journal, 120(14), 2880-2889. https://doi.org/10.1016/j.bpj.2021.03.024
Vithani, Neha, et al. "SARS-CoV-2 Nsp16 activation mechanism and a cryptic pocket with pan-coronavirus antiviral potential." Biophysical journal vol. 120,14 (2021): 2880-2889. doi: https://doi.org/10.1016/j.bpj.2021.03.024
Vithani N, Ward MD, Zimmerman MI, Novak B, Borowsky JH, Singh S, Bowman GR. SARS-CoV-2 Nsp16 activation mechanism and a cryptic pocket with pan-coronavirus antiviral potential. Biophys J. 2021 Jul 20;120(14):2880-2889. doi: 10.1016/j.bpj.2021.03.024. Epub 2021 Mar 29. PMID: 33794150; PMCID: PMC8007187.
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Showing 1 to 7 of 7 entries