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Investigating Cryptic Binding Sites by Molecular Dynamics Simulations.

Kuzmanic A, Bowman GR, Juarez-Jimenez J, Michel J, Gervasio FL.

Acc Chem Res. 2020 Mar 17;53(3):654-661. doi: 10.1021/acs.accounts.9b00613. Epub 2020 Mar 5.


Spatial and temporal alterations in protein structure by EGF regulate cryptic cysteine oxidation.

Behring JB, van der Post S, Mooradian AD, Egan MJ, Zimmerman MI, Clements JL, Bowman GR, Held JM.

Sci Signal. 2020 Jan 21;13(615). pii: eaay7315. doi: 10.1126/scisignal.aay7315.


The Cap-Snatching SFTSV Endonuclease Domain Is an Antiviral Target.

Wang W, Shin WJ, Zhang B, Choi Y, Yoo JS, Zimmerman MI, Frederick TE, Bowman GR, Gross ML, Leung DW, Jung JU, Amarasinghe GK.

Cell Rep. 2020 Jan 7;30(1):153-163.e5. doi: 10.1016/j.celrep.2019.12.020.


Inducible asymmetric cell division and cell differentiation in a bacterium.

Mushnikov NV, Fomicheva A, Gomelsky M, Bowman GR.

Nat Chem Biol. 2019 Sep;15(9):925-931. doi: 10.1038/s41589-019-0340-4. Epub 2019 Aug 12.


SpbR overproduction reveals the importance of proteolytic degradation for cell pole development and chromosome segregation in Caulobacter crescentus.

Wang H, Bowman GR.

Mol Microbiol. 2019 Jun;111(6):1700-1714. doi: 10.1111/mmi.14247. Epub 2019 Apr 2.


Cooperative Changes in Solvent Exposure Identify Cryptic Pockets, Switches, and Allosteric Coupling.

Porter JR, Moeder KE, Sibbald CA, Zimmerman MI, Hart KM, Greenberg MJ, Bowman GR.

Biophys J. 2019 Mar 5;116(5):818-830. doi: 10.1016/j.bpj.2018.11.3144. Epub 2019 Jan 25.


Enspara: Modeling molecular ensembles with scalable data structures and parallel computing.

Porter JR, Zimmerman MI, Bowman GR.

J Chem Phys. 2019 Jan 28;150(4):044108. doi: 10.1063/1.5063794.


Advanced Methods for Accessing Protein Shape-Shifting Present New Therapeutic Opportunities.

Knoverek CR, Amarasinghe GK, Bowman GR.

Trends Biochem Sci. 2019 Apr;44(4):351-364. doi: 10.1016/j.tibs.2018.11.007. Epub 2018 Dec 14. Review.


Effects of trace mineral amount and source on aspects of oxidative metabolism and responses to intramammary lipopolysaccharide challenge in midlactation dairy cows.

Yasui T, Ehrhardt RM, Bowman GR, Vázquez-Añon M, Richards JD, Atwell CA, Overton TR.

Animal. 2019 May;13(5):1000-1008. doi: 10.1017/S1751731118002525. Epub 2018 Oct 16.


Simulation of spontaneous G protein activation reveals a new intermediate driving GDP unbinding.

Sun X, Singh S, Blumer KJ, Bowman GR.

Elife. 2018 Oct 5;7. pii: e38465. doi: 10.7554/eLife.38465.


Choice of Adaptive Sampling Strategy Impacts State Discovery, Transition Probabilities, and the Apparent Mechanism of Conformational Changes.

Zimmerman MI, Porter JR, Sun X, Silva RR, Bowman GR.

J Chem Theory Comput. 2018 Nov 13;14(11):5459-5475. doi: 10.1021/acs.jctc.8b00500. Epub 2018 Oct 23.


Remodeling the Specificity of an Endosomal CORVET Tether Underlies Formation of Regulated Secretory Vesicles in the Ciliate Tetrahymena thermophila.

Sparvoli D, Richardson E, Osakada H, Lan X, Iwamoto M, Bowman GR, Kontur C, Bourland WA, Lynn DH, Pritchard JK, Haraguchi T, Dacks JB, Turkewitz AP.

Curr Biol. 2018 Mar 5;28(5):697-710.e13. doi: 10.1016/j.cub.2018.01.047. Epub 2018 Feb 22.


Electron Cryo-microscopy Structure of Ebola Virus Nucleoprotein Reveals a Mechanism for Nucleocapsid-like Assembly.

Su Z, Wu C, Shi L, Luthra P, Pintilie GD, Johnson B, Porter JR, Ge P, Chen M, Liu G, Frederick TE, Binning JM, Bowman GR, Zhou ZH, Basler CF, Gross ML, Leung DW, Chiu W, Amarasinghe GK.

Cell. 2018 Feb 22;172(5):966-978.e12. doi: 10.1016/j.cell.2018.02.009.


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

Zimmerman MI, Hart KM, Sibbald CA, Frederick TE, Jimah JR, Knoverek CR, Tolia NH, Bowman GR.

ACS Cent Sci. 2017 Dec 27;3(12):1311-1321. doi: 10.1021/acscentsci.7b00465. Epub 2017 Nov 21.


Bladder-cancer-associated mutations in RXRA activate peroxisome proliferator-activated receptors to drive urothelial proliferation.

Halstead AM, Kapadia CD, Bolzenius J, Chu CE, Schriefer A, Wartman LD, Bowman GR, Arora VK.

Elife. 2017 Nov 16;6. pii: e30862. doi: 10.7554/eLife.30862.


Endogenous retinoid X receptor ligands in mouse hematopoietic cells.

Niu H, Fujiwara H, di Martino O, Hadwiger G, Frederick TE, Menéndez-Gutiérrez MP, Ricote M, Bowman GR, Welch JS.

Sci Signal. 2017 Oct 31;10(503). pii: eaan1011. doi: 10.1126/scisignal.aan1011.


Mechanistic Basis for ATP-Dependent Inhibition of Glutamine Synthetase by Tabtoxinine-β-lactam.

Patrick GJ, Fang L, Schaefer J, Singh S, Bowman GR, Wencewicz TA.

Biochemistry. 2018 Jan 9;57(1):117-135. doi: 10.1021/acs.biochem.7b00838. Epub 2017 Oct 31.


Polar Organizing Protein PopZ Is Required for Chromosome Segregation in Agrobacterium tumefaciens.

Ehrle HM, Guidry JT, Iacovetto R, Salisbury AK, Sandidge DJ, Bowman GR.

J Bacteriol. 2017 Aug 8;199(17). pii: e00111-17. doi: 10.1128/JB.00111-17. Print 2017 Sep 1.


Absence of the Polar Organizing Protein PopZ Results in Reduced and Asymmetric Cell Division in Agrobacterium tumefaciens.

Howell M, Aliashkevich A, Salisbury AK, Cava F, Bowman GR, Brown PJB.

J Bacteriol. 2017 Aug 8;199(17). pii: e00101-17. doi: 10.1128/JB.00101-17. Print 2017 Sep 1.


Designing small molecules to target cryptic pockets yields both positive and negative allosteric modulators.

Hart KM, Moeder KE, Ho CMW, Zimmerman MI, Frederick TE, Bowman GR.

PLoS One. 2017 Jun 1;12(6):e0178678. doi: 10.1371/journal.pone.0178678. eCollection 2017.


Quantifying Allosteric Communication via Both Concerted Structural Changes and Conformational Disorder with CARDS.

Singh S, Bowman GR.

J Chem Theory Comput. 2017 Apr 11;13(4):1509-1517. doi: 10.1021/acs.jctc.6b01181. Epub 2017 Mar 22.


Propagation of the Allosteric Modulation Induced by Sodium in the δ-Opioid Receptor.

Sun X, Laroche G, Wang X, Ågren H, Bowman GR, Giguère PM, Tu Y.

Chemistry. 2017 Apr 3;23(19):4615-4624. doi: 10.1002/chem.201605575. Epub 2017 Mar 20.


Warfarin traps human vitamin K epoxide reductase in an intermediate state during electron transfer.

Shen G, Cui W, Zhang H, Zhou F, Huang W, Liu Q, Yang Y, Li S, Bowman GR, Sadler JE, Gross ML, Li W.

Nat Struct Mol Biol. 2017 Jan;24(1):69-76. doi: 10.1038/nsmb.3333. Epub 2016 Dec 5.


Defining NADH-Driven Allostery Regulating Apoptosis-Inducing Factor.

Brosey CA, Ho C, Long WZ, Singh S, Burnett K, Hura GL, Nix JC, Bowman GR, Ellenberger T, Tainer JA.

Structure. 2016 Dec 6;24(12):2067-2079. doi: 10.1016/j.str.2016.09.012. Epub 2016 Nov 3.


Caulobacter PopZ forms an intrinsically disordered hub in organizing bacterial cell poles.

Holmes JA, Follett SE, Wang H, Meadows CP, Varga K, Bowman GR.

Proc Natl Acad Sci U S A. 2016 Nov 1;113(44):12490-12495. Epub 2016 Oct 18.


Modelling proteins' hidden conformations to predict antibiotic resistance.

Hart KM, Ho CM, Dutta S, Gross ML, Bowman GR.

Nat Commun. 2016 Oct 6;7:12965. doi: 10.1038/ncomms12965.


Structure and Dynamics of PD-L1 and an Ultra-High-Affinity PD-1 Receptor Mutant.

Pascolutti R, Sun X, Kao J, Maute RL, Ring AM, Bowman GR, Kruse AC.

Structure. 2016 Oct 4;24(10):1719-1728. doi: 10.1016/j.str.2016.06.026. Epub 2016 Sep 8.


How to Run FAST Simulations.

Zimmerman MI, Bowman GR.

Methods Enzymol. 2016;578:213-25. doi: 10.1016/bs.mie.2016.05.032. Epub 2016 Jun 16. Review.


FAST Conformational Searches by Balancing Exploration/Exploitation Trade-Offs.

Zimmerman MI, Bowman GR.

J Chem Theory Comput. 2015 Dec 8;11(12):5747-57. doi: 10.1021/acs.jctc.5b00737. Epub 2015 Nov 20.


Corrigendum: Cloud-based simulations on Google Exacycle reveal ligand modulation of GPCR activation pathways.

Kohlhoff KJ, Shukla D, Lawrenz M, Bowman GR, Konerding DE, Belov D, Altman RB, Pande VS.

Nat Chem. 2015 Sep;7(9):759. doi: 10.1038/nchem.2272. No abstract available.


Transposon Mutagenesis Paired with Deep Sequencing of Caulobacter crescentus under Uranium Stress Reveals Genes Essential for Detoxification and Stress Tolerance.

Yung MC, Park DM, Overton KW, Blow MJ, Hoover CA, Smit J, Murray SR, Ricci DP, Christen B, Bowman GR, Jiao Y.

J Bacteriol. 2015 Oct;197(19):3160-72. doi: 10.1128/JB.00382-15. Epub 2015 Jul 20.


Accurately modeling nanosecond protein dynamics requires at least microseconds of simulation.

Bowman GR.

J Comput Chem. 2016 Mar 5;37(6):558-66. doi: 10.1002/jcc.23973. Epub 2015 Jun 16.


Discovery of multiple hidden allosteric sites by combining Markov state models and experiments.

Bowman GR, Bolin ER, Hart KM, Maguire BC, Marqusee S.

Proc Natl Acad Sci U S A. 2015 Mar 3;112(9):2734-9. doi: 10.1073/pnas.1417811112. Epub 2015 Feb 17.


Fluctuations within folded proteins: implications for thermodynamic and allosteric regulation.

DuBay KH, Bowman GR, Geissler PL.

Acc Chem Res. 2015 Apr 21;48(4):1098-105. doi: 10.1021/ar500351b. Epub 2015 Feb 17. Review.


Meta-analysis of lactation performance in dairy cows receiving supplemental dietary methionine sources or postruminal infusion of methionine.

Zanton GI, Bowman GR, Vázquez-Añón M, Rode LM.

J Dairy Sci. 2014 Nov;97(11):7085-101. doi: 10.3168/jds.2014-8220. Epub 2014 Sep 18.


Bacterial scaffold directs pole-specific centromere segregation.

Ptacin JL, Gahlmann A, Bowman GR, Perez AM, von Diezmann AR, Eckart MR, Moerner WE, Shapiro L.

Proc Natl Acad Sci U S A. 2014 May 13;111(19):E2046-55. doi: 10.1073/pnas.1405188111. Epub 2014 Apr 28.


Extensive conformational heterogeneity within protein cores.

Bowman GR, Geissler PL.

J Phys Chem B. 2014 Jun 19;118(24):6417-23. doi: 10.1021/jp4105823. Epub 2014 Mar 12.


Shotgun proteomic analysis unveils survival and detoxification strategies by Caulobacter crescentus during exposure to uranium, chromium, and cadmium.

Yung MC, Ma J, Salemi MR, Phinney BS, Bowman GR, Jiao Y.

J Proteome Res. 2014 Apr 4;13(4):1833-47. doi: 10.1021/pr400880s. Epub 2014 Mar 7.


Cloud-based simulations on Google Exacycle reveal ligand modulation of GPCR activation pathways.

Kohlhoff KJ, Shukla D, Lawrenz M, Bowman GR, Konerding DE, Belov D, Altman RB, Pande VS.

Nat Chem. 2014 Jan;6(1):15-21. doi: 10.1038/nchem.1821. Epub 2013 Dec 15. Erratum in: Nat Chem. 2015 Sep;7(9):759.


Software for building Markov state models.

Bowman GR, Noé F.

Adv Exp Med Biol. 2014;797:139. doi: 10.1007/978-94-007-7606-7_11. Review. No abstract available.


An overview and practical guide to building Markov state models.

Bowman GR.

Adv Exp Med Biol. 2014;797:7-22. doi: 10.1007/978-94-007-7606-7_2. Review. No abstract available.


Introduction and overview of this book.

Bowman GR, Pande VS, Noé F.

Adv Exp Med Biol. 2014;797:1-6. doi: 10.1007/978-94-007-7606-7_1. No abstract available.


Oligomerization and higher-order assembly contribute to sub-cellular localization of a bacterial scaffold.

Bowman GR, Perez AM, Ptacin JL, Ighodaro E, Folta-Stogniew E, Comolli LR, Shapiro L.

Mol Microbiol. 2013 Nov;90(4):776-95. doi: 10.1111/mmi.12398. Epub 2013 Oct 7.


Quantitative comparison of alternative methods for coarse-graining biological networks.

Bowman GR, Meng L, Huang X.

J Chem Phys. 2013 Sep 28;139(12):121905. doi: 10.1063/1.4812768.


A tutorial on building markov state models with MSMBuilder and coarse-graining them with BACE.

Bowman GR.

Methods Mol Biol. 2014;1084:141-58. doi: 10.1007/978-1-62703-658-0_8.


Dynamics of an intrinsically disordered protein reveal metastable conformations that potentially seed aggregation.

Qiao Q, Bowman GR, Huang X.

J Am Chem Soc. 2013 Oct 30;135(43):16092-101. doi: 10.1021/ja403147m. Epub 2013 Oct 17.


Hierarchical Nyström methods for constructing Markov state models for conformational dynamics.

Yao Y, Cui RZ, Bowman GR, Silva DA, Sun J, Huang X.

J Chem Phys. 2013 May 7;138(17):174106. doi: 10.1063/1.4802007.


Mechanistic and structural insight into the functional dichotomy between IL-2 and IL-15.

Ring AM, Lin JX, Feng D, Mitra S, Rickert M, Bowman GR, Pande VS, Li P, Moraga I, Spolski R, Ozkan E, Leonard WJ, Garcia KC.

Nat Immunol. 2012 Dec;13(12):1187-95. doi: 10.1038/ni.2449. Epub 2012 Oct 28.


Equilibrium fluctuations of a single folded protein reveal a multitude of potential cryptic allosteric sites.

Bowman GR, Geissler PL.

Proc Natl Acad Sci U S A. 2012 Jul 17;109(29):11681-6. doi: 10.1073/pnas.1209309109. Epub 2012 Jul 2.

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