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For: Boras BW, Kornev A, Taylor SS, McCulloch AD. Using Markov state models to develop a mechanistic understanding of protein kinase A regulatory subunit RIα activation in response to cAMP binding. J Biol Chem 2014;289:30040-51. [PMID: 25202018 DOI: 10.1074/jbc.m114.568907] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]  Open
Number Cited by Other Article(s)
1
Hirakis SP, Bartol TM, Autin L, Amaro RE, Sejnowski TJ. Electrophysical cardiac remodeling at the molecular level: Insights into ryanodine receptor activation and calcium-induced calcium release from a stochastic explicit-particle model. Biophys J 2024;123:3812-3831. [PMID: 39369273 PMCID: PMC11560313 DOI: 10.1016/j.bpj.2024.09.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 07/03/2024] [Accepted: 09/26/2024] [Indexed: 10/07/2024]  Open
2
Lyons AC, Mehta S, Zhang J. Fluorescent biosensors illuminate the spatial regulation of cell signaling across scales. Biochem J 2023;480:1693-1717. [PMID: 37903110 PMCID: PMC10657186 DOI: 10.1042/bcj20220223] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 10/11/2023] [Accepted: 10/13/2023] [Indexed: 11/01/2023]
3
Thomas T, Roux B. TYROSINE KINASES: COMPLEX MOLECULAR SYSTEMS CHALLENGING COMPUTATIONAL METHODOLOGIES. THE EUROPEAN PHYSICAL JOURNAL. B 2021;94:203. [PMID: 36524055 PMCID: PMC9749240 DOI: 10.1140/epjb/s10051-021-00207-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 09/14/2021] [Indexed: 05/28/2023]
4
McCabe KJ, Rangamani P. Computational modeling approaches to cAMP/PKA signaling in cardiomyocytes. J Mol Cell Cardiol 2021;154:32-40. [PMID: 33548239 DOI: 10.1016/j.yjmcc.2021.01.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 01/11/2021] [Accepted: 01/15/2021] [Indexed: 12/12/2022]
5
Lu TW, Aoto PC, Weng JH, Nielsen C, Cash JN, Hall J, Zhang P, Simon SM, Cianfrocco MA, Taylor SS. Structural analyses of the PKA RIIβ holoenzyme containing the oncogenic DnaJB1-PKAc fusion protein reveal protomer asymmetry and fusion-induced allosteric perturbations in fibrolamellar hepatocellular carcinoma. PLoS Biol 2020;18:e3001018. [PMID: 33370777 PMCID: PMC7793292 DOI: 10.1371/journal.pbio.3001018] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 01/08/2021] [Accepted: 12/18/2020] [Indexed: 12/31/2022]  Open
6
Tenner B, Getz M, Ross B, Ohadi D, Bohrer CH, Greenwald E, Mehta S, Xiao J, Rangamani P, Zhang J. Spatially compartmentalized phase regulation of a Ca2+-cAMP-PKA oscillatory circuit. eLife 2020;9:e55013. [PMID: 33201801 PMCID: PMC7671691 DOI: 10.7554/elife.55013] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 10/07/2020] [Indexed: 01/31/2023]  Open
7
Zhang JZ, Lu TW, Stolerman LM, Tenner B, Yang JR, Zhang JF, Falcke M, Rangamani P, Taylor SS, Mehta S, Zhang J. Phase Separation of a PKA Regulatory Subunit Controls cAMP Compartmentation and Oncogenic Signaling. Cell 2020;182:1531-1544.e15. [PMID: 32846158 PMCID: PMC7502557 DOI: 10.1016/j.cell.2020.07.043] [Citation(s) in RCA: 203] [Impact Index Per Article: 40.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 03/30/2020] [Accepted: 07/30/2020] [Indexed: 12/25/2022]
8
Histamine-induced biphasic activation of RhoA allows for persistent RhoA signaling. PLoS Biol 2020;18:e3000866. [PMID: 32881857 PMCID: PMC7494096 DOI: 10.1371/journal.pbio.3000866] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 09/16/2020] [Accepted: 08/12/2020] [Indexed: 12/30/2022]  Open
9
Hao Y, England JP, Bellucci L, Paci E, Hodges HC, Taylor SS, Maillard RA. Activation of PKA via asymmetric allosteric coupling of structurally conserved cyclic nucleotide binding domains. Nat Commun 2019;10:3984. [PMID: 31484930 PMCID: PMC6726620 DOI: 10.1038/s41467-019-11930-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 08/12/2019] [Indexed: 12/16/2022]  Open
10
Lu TW, Wu J, Aoto PC, Weng JH, Ahuja LG, Sun N, Cheng CY, Zhang P, Taylor SS. Two PKA RIα holoenzyme states define ATP as an isoform-specific orthosteric inhibitor that competes with the allosteric activator, cAMP. Proc Natl Acad Sci U S A 2019;116:16347-16356. [PMID: 31363049 PMCID: PMC6697891 DOI: 10.1073/pnas.1906036116] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
11
Sengupta U, Strodel B. Markov models for the elucidation of allosteric regulation. Philos Trans R Soc Lond B Biol Sci 2019;373:rstb.2017.0178. [PMID: 29735732 DOI: 10.1098/rstb.2017.0178] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/14/2018] [Indexed: 11/12/2022]  Open
12
Coggan JS, Keller D, Calì C, Lehväslaiho H, Markram H, Schürmann F, Magistretti PJ. Norepinephrine stimulates glycogenolysis in astrocytes to fuel neurons with lactate. PLoS Comput Biol 2018;14:e1006392. [PMID: 30161133 PMCID: PMC6160207 DOI: 10.1371/journal.pcbi.1006392] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 09/27/2018] [Accepted: 07/24/2018] [Indexed: 12/20/2022]  Open
13
Switching of the folding-energy landscape governs the allosteric activation of protein kinase A. Proc Natl Acad Sci U S A 2018;115:E7478-E7485. [PMID: 30038016 DOI: 10.1073/pnas.1802510115] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
14
Isensee J, Kaufholz M, Knape MJ, Hasenauer J, Hammerich H, Gonczarowska-Jorge H, Zahedi RP, Schwede F, Herberg FW, Hucho T. PKA-RII subunit phosphorylation precedes activation by cAMP and regulates activity termination. J Cell Biol 2018;217:2167-2184. [PMID: 29615473 PMCID: PMC5987717 DOI: 10.1083/jcb.201708053] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 02/18/2018] [Accepted: 03/15/2018] [Indexed: 11/22/2022]  Open
15
Haushalter KJ, Casteel DE, Raffeiner A, Stefan E, Patel HH, Taylor SS. Phosphorylation of protein kinase A (PKA) regulatory subunit RIα by protein kinase G (PKG) primes PKA for catalytic activity in cells. J Biol Chem 2018;293:4411-4421. [PMID: 29378851 PMCID: PMC5868259 DOI: 10.1074/jbc.m117.809988] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 01/23/2018] [Indexed: 01/26/2023]  Open
16
Akimoto M, VanSchouwen B, Melacini G. The structure of the apo cAMP-binding domain of HCN4 - a stepping stone toward understanding the cAMP-dependent modulation of the hyperpolarization-activated cyclic-nucleotide-gated ion channels. FEBS J 2018;285:2182-2192. [PMID: 29444387 DOI: 10.1111/febs.14408] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Revised: 01/31/2018] [Accepted: 02/09/2018] [Indexed: 12/14/2022]
17
He D, Lorenz R, Kim C, Herberg FW, Lim CJ. Switching Cyclic Nucleotide-Selective Activation of Cyclic Adenosine Monophosphate-Dependent Protein Kinase Holoenzyme Reveals Distinct Roles of Tandem Cyclic Nucleotide-Binding Domains. ACS Chem Biol 2017;12:3057-3066. [PMID: 29111666 DOI: 10.1021/acschembio.7b00732] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
18
Lorenz R, Bertinetti D, Herberg FW. cAMP-Dependent Protein Kinase and cGMP-Dependent Protein Kinase as Cyclic Nucleotide Effectors. Handb Exp Pharmacol 2017;238:105-122. [PMID: 27885524 DOI: 10.1007/164_2015_36] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
19
Hirakis SP, Malmstrom RD, Amaro RE. Molecular Simulations Reveal an Unresolved Conformation of the Type IA Protein Kinase A Regulatory Subunit and Suggest Its Role in the cAMP Regulatory Mechanism. Biochemistry 2017;56:3885-3888. [PMID: 28661131 PMCID: PMC5751417 DOI: 10.1021/acs.biochem.7b00461] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
20
Meng Y, Pond MP, Roux B. Tyrosine Kinase Activation and Conformational Flexibility: Lessons from Src-Family Tyrosine Kinases. Acc Chem Res 2017;50:1193-1201. [PMID: 28426203 DOI: 10.1021/acs.accounts.7b00012] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
21
Igamberdiev AU, Shklovskiy-Kordi NE. The quantum basis of spatiotemporality in perception and consciousness. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2017;130:15-25. [PMID: 28232245 DOI: 10.1016/j.pbiomolbio.2017.02.008] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 02/16/2017] [Indexed: 12/21/2022]
22
Bruystens JG, Wu J, Fortezzo A, Del Rio J, Nielsen C, Blumenthal DK, Rock R, Stefan E, Taylor SS. Structure of a PKA RIα Recurrent Acrodysostosis Mutant Explains Defective cAMP-Dependent Activation. J Mol Biol 2016;428:4890-4904. [PMID: 27825928 PMCID: PMC5149412 DOI: 10.1016/j.jmb.2016.10.033] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 10/08/2016] [Accepted: 10/31/2016] [Indexed: 01/03/2023]
23
Meng Y, Shukla D, Pande VS, Roux B. Transition path theory analysis of c-Src kinase activation. Proc Natl Acad Sci U S A 2016;113:9193-8. [PMID: 27482115 PMCID: PMC4995974 DOI: 10.1073/pnas.1602790113] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]  Open
24
Ribeiro AAST, Ortiz V. A Chemical Perspective on Allostery. Chem Rev 2016;116:6488-502. [DOI: 10.1021/acs.chemrev.5b00543] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
25
Mapping the Free Energy Landscape of PKA Inhibition and Activation: A Double-Conformational Selection Model for the Tandem cAMP-Binding Domains of PKA RIα. PLoS Biol 2015;13:e1002305. [PMID: 26618408 PMCID: PMC4664472 DOI: 10.1371/journal.pbio.1002305] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 10/22/2015] [Indexed: 01/31/2023]  Open
26
Boras BW, Hirakis SP, Votapka LW, Malmstrom RD, Amaro RE, McCulloch AD. Bridging scales through multiscale modeling: a case study on protein kinase A. Front Physiol 2015;6:250. [PMID: 26441670 PMCID: PMC4563169 DOI: 10.3389/fphys.2015.00250] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 08/24/2015] [Indexed: 12/21/2022]  Open
27
Malmstrom RD, Kornev AP, Taylor SS, Amaro RE. Allostery through the computational microscope: cAMP activation of a canonical signalling domain. Nat Commun 2015;6:7588. [PMID: 26145448 PMCID: PMC4504738 DOI: 10.1038/ncomms8588] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2014] [Accepted: 05/22/2015] [Indexed: 11/09/2022]  Open
28
Zhang P, Kornev AP, Wu J, Taylor SS. Discovery of Allostery in PKA Signaling. Biophys Rev 2015;7:227-238. [PMID: 26097522 DOI: 10.1007/s12551-015-0170-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]  Open
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