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For: Keedy DA, Hill ZB, Biel JT, Kang E, Rettenmaier TJ, Brandão-Neto J, Pearce NM, von Delft F, Wells JA, Fraser JS. An expanded allosteric network in PTP1B by multitemperature crystallography, fragment screening, and covalent tethering. eLife 2018;7:36307. [PMID: 29877794 PMCID: PMC6039181 DOI: 10.7554/elife.36307] [Citation(s) in RCA: 116] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 06/04/2018] [Indexed: 12/28/2022]  Open
Number Cited by Other Article(s)
1
McLeod MJ, Barwell SAE, Holyoak T, Thorne RE. A structural perspective on the temperature dependent activity of enzymes. Structure 2025;33:924-934.e2. [PMID: 40120576 DOI: 10.1016/j.str.2025.02.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2024] [Revised: 12/09/2024] [Accepted: 02/25/2025] [Indexed: 03/25/2025]
2
Cavender CE, Case DA, Chen JCH, Chong LT, Keedy DA, Lindorff-Larsen K, Mobley DL, Ollila OHS, Oostenbrink C, Robustelli P, Voelz VA, Wall ME, Wych DC, Gilson MK. Structure-Based Experimental Datasets for Benchmarking Protein Simulation Force Fields [Article v0.1]. ARXIV 2025:arXiv:2303.11056v2. [PMID: 40196146 PMCID: PMC11975311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 04/09/2025]
3
Perdikari A, Woods VA, Ebrahim A, Lawler K, Bounds R, Singh NI, Mehlman T(S, Riley BT, Sharma S, Morris JW, Keogh JM, Henning E, Smith M, Farooqi IS, Keedy DA. Structures of human PTP1B variants reveal allosteric sites to target for weight loss therapy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2024.08.05.603709. [PMID: 39149290 PMCID: PMC11326154 DOI: 10.1101/2024.08.05.603709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
4
Zhu G, Didry-Barca B, Seabra L, Rice GI, Uggenti C, Touimy M, Rodero MP, Trapero RH, Bondet V, Duffy D, Gautier P, Livingstone K, Sutherland FJH, Lebon P, Parisot M, Bole-Feysot C, Masson C, Cagnard N, Nitschké P, Anderson G, Assmann B, Barth M, Boespflug-Tanguy O, D'Arco F, Dorboz I, Giese T, Hacohen Y, Hancarova M, Husson M, Lepine A, Lim M, Mancardi MM, Melki I, Neubauer D, Sa M, Sedlacek Z, Seitz A, Rottman MS, Sanquer S, Straussberg R, Vlčková M, Villéga F, Wagner M, Zerem A, Marsh JA, Frémond ML, Kaliakatsos M, Crow YJ, El-Daher MT, Lepelley A. Autoinflammatory encephalopathy due to PTPN1 haploinsufficiency: a case series. Lancet Neurol 2025;24:218-229. [PMID: 39986310 PMCID: PMC7617446 DOI: 10.1016/s1474-4422(24)00526-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2024] [Revised: 12/18/2024] [Accepted: 12/19/2024] [Indexed: 02/24/2025]
5
Tao H, Yang B, Farhangian A, Xu K, Li T, Zhang ZY, Li J. Covalent-Allosteric Inhibitors: Do We Get the Best of Both Worlds? J Med Chem 2025;68:4040-4052. [PMID: 39937154 DOI: 10.1021/acs.jmedchem.4c02760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/13/2025]
6
Huang Q, Hu L, Chen H, Yang B, Sun X, Wang M. A Medicinal Chemistry Perspective on Protein Tyrosine Phosphatase Nonreceptor Type 2 in Tumor Immunology. J Med Chem 2025;68:3995-4021. [PMID: 39936476 DOI: 10.1021/acs.jmedchem.4c01802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/13/2025]
7
Guerrero L, Ebrahim A, Riley BT, Kim SH, Bishop AC, Wu J, Han YN, Tautz L, Keedy DA. Three STEPs forward: A trio of unexpected structures of PTPN5. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2024.11.20.624168. [PMID: 39605455 PMCID: PMC11601604 DOI: 10.1101/2024.11.20.624168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2024]
8
Montserrat-Canals M, Cordara G, Krengel U. Allostery. Q Rev Biophys 2025;58:e5. [PMID: 39849666 DOI: 10.1017/s0033583524000209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2025]
9
Gao C, Hu W, Xu F, Lin Y, Chen J, Shi D, Xing P, Zhu J, Li X. Allosteric inhibition of PTP1B by bromocatechol-chalcone derivatives. Eur J Med Chem 2025;282:117053. [PMID: 39561499 DOI: 10.1016/j.ejmech.2024.117053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2024] [Revised: 10/31/2024] [Accepted: 11/11/2024] [Indexed: 11/21/2024]
10
Zhang BW, Fajer M, Chen W, Moraca F, Wang L. Leveraging the Thermodynamics of Protein Conformations in Drug Discovery. J Chem Inf Model 2025;65:252-264. [PMID: 39681511 DOI: 10.1021/acs.jcim.4c01612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2024]
11
Orlans J, Rose SL, Ferguson G, Oscarsson M, Homs Puron A, Beteva A, Debionne S, Theveneau P, Coquelle N, Kieffer J, Busca P, Sinoir J, Armijo V, Lopez Marrero M, Felisaz F, Papp G, Gonzalez H, Caserotto H, Dobias F, Gigmes J, Lebon G, Basu S, de Sanctis D. Advancing macromolecular structure determination with microsecond X-ray pulses at a 4th generation synchrotron. Commun Chem 2025;8:6. [PMID: 39775172 PMCID: PMC11707155 DOI: 10.1038/s42004-024-01404-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2024] [Accepted: 12/30/2024] [Indexed: 01/11/2025]  Open
12
Chartier CA, Woods VA, Xu Y, van Vlimmeren AE, Johns AC, Jovanovic M, McDermott AE, Keedy DA, Shah NH. Allosteric regulation of the tyrosine phosphatase PTP1B by a protein-protein interaction. Protein Sci 2025;34:e70016. [PMID: 39723820 DOI: 10.1002/pro.70016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2024] [Revised: 11/11/2024] [Accepted: 12/13/2024] [Indexed: 12/28/2024]
13
Saeed A, Klureza MA, Hekstra DR. Mapping Protein Conformational Landscapes from Crystallographic Drug Fragment Screens. J Chem Inf Model 2024;64:8937-8951. [PMID: 39530154 PMCID: PMC11633654 DOI: 10.1021/acs.jcim.4c01380] [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: 07/31/2024] [Revised: 10/23/2024] [Accepted: 10/29/2024] [Indexed: 11/16/2024]
14
Jiang Z, van Vlimmeren AE, Karandur D, Semmelman A, Shah NH. Deep mutational scanning of a multi-domain signaling protein reveals mechanisms of regulation and pathogenicity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.13.593907. [PMID: 39091798 PMCID: PMC11291063 DOI: 10.1101/2024.05.13.593907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
15
Chartier CA, Woods VA, Xu Y, van Vlimmeren AE, Johns AC, Jovanovic M, McDermott AE, Keedy DA, Shah NH. Allosteric regulation of the tyrosine phosphatase PTP1B by a protein-protein interaction. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.16.603632. [PMID: 39071364 PMCID: PMC11275736 DOI: 10.1101/2024.07.16.603632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
16
Lazou M, Kozakov D, Joseph-McCarthy D, Vajda S. Which cryptic sites are feasible drug targets? Drug Discov Today 2024;29:104197. [PMID: 39368697 PMCID: PMC11568903 DOI: 10.1016/j.drudis.2024.104197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2024] [Revised: 09/18/2024] [Accepted: 09/30/2024] [Indexed: 10/07/2024]
17
Foos N, Florial JB, Eymery M, Sinoir J, Felisaz F, Oscarsson M, Beteva A, Bowler MW, Nurizzo D, Papp G, Soler-Lopez M, Nanao M, Basu S, McCarthy AA. In situ serial crystallography facilitates 96-well plate structural analysis at low symmetry. IUCRJ 2024;11:780-791. [PMID: 39008358 PMCID: PMC11364034 DOI: 10.1107/s2052252524005785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Accepted: 06/14/2024] [Indexed: 07/16/2024]
18
Dunge A, Phan C, Uwangue O, Bjelcic M, Gunnarsson J, Wehlander G, Käck H, Brändén G. Exploring serial crystallography for drug discovery. IUCRJ 2024;11:831-842. [PMID: 39072424 PMCID: PMC11364032 DOI: 10.1107/s2052252524006134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 06/24/2024] [Indexed: 07/30/2024]
19
Mehlman T, Ginn HM, Keedy DA. An expanded trove of fragment-bound structures for the allosteric enzyme PTP1B from computational reanalysis of large-scale crystallographic data. Structure 2024;32:1231-1238.e4. [PMID: 38861991 PMCID: PMC11316629 DOI: 10.1016/j.str.2024.05.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Revised: 04/15/2024] [Accepted: 05/15/2024] [Indexed: 06/13/2024]
20
Huang CY, Aumonier S, Olieric V, Wang M. Cryo2RT: a high-throughput method for room-temperature macromolecular crystallography from cryo-cooled crystals. Acta Crystallogr D Struct Biol 2024;80:620-628. [PMID: 39052318 DOI: 10.1107/s2059798324006697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Accepted: 07/08/2024] [Indexed: 07/27/2024]  Open
21
Saeed AA, Klureza MA, Hekstra DR. Mapping protein conformational landscapes from crystallographic drug fragment screens. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.29.605395. [PMID: 39131376 PMCID: PMC11312500 DOI: 10.1101/2024.07.29.605395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/13/2024]
22
Hekstra DR, Wang HK, Klureza MA, Greisman JB, Dalton KM. Sensitive Detection of Structural Differences using a Statistical Framework for Comparative Crystallography. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.22.604476. [PMID: 39091831 PMCID: PMC11291090 DOI: 10.1101/2024.07.22.604476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
23
Schanda P, Haran G. NMR and Single-Molecule FRET Insights into Fast Protein Motions and Their Relation to Function. Annu Rev Biophys 2024;53:247-273. [PMID: 38346243 DOI: 10.1146/annurev-biophys-070323-022428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2024]
24
Wankowicz SA, Fraser JS. Comprehensive encoding of conformational and compositional protein structural ensembles through the mmCIF data structure. IUCRJ 2024;11:494-501. [PMID: 38958015 PMCID: PMC11220883 DOI: 10.1107/s2052252524005098] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 05/29/2024] [Indexed: 07/04/2024]
25
Wankowicz SA, Ravikumar A, Sharma S, Riley B, Raju A, Hogan DW, Flowers J, van den Bedem H, Keedy DA, Fraser JS. Automated multiconformer model building for X-ray crystallography and cryo-EM. eLife 2024;12:RP90606. [PMID: 38904665 PMCID: PMC11192534 DOI: 10.7554/elife.90606] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/22/2024]  Open
26
Zhuang C, Yang S, Gonzalez CG, Ainsworth RI, Li S, Kobayashi MT, Wierzbicki I, Rossitto LAM, Wen Y, Peti W, Stanford SM, Gonzalez DJ, Murali R, Santelli E, Bottini N. A novel gain-of-function phosphorylation site modulates PTPN22 inhibition of TCR signaling. J Biol Chem 2024;300:107393. [PMID: 38777143 PMCID: PMC11237943 DOI: 10.1016/j.jbc.2024.107393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 04/20/2024] [Accepted: 05/07/2024] [Indexed: 05/25/2024]  Open
27
Brookner DE, Hekstra DR. MatchMaps: non-isomorphous difference maps for X-ray crystallography. J Appl Crystallogr 2024;57:885-895. [PMID: 38846758 PMCID: PMC11151677 DOI: 10.1107/s1600576724003510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 04/19/2024] [Indexed: 06/09/2024]  Open
28
Woods VA, Abzalimov RR, Keedy DA. Native dynamics and allosteric responses in PTP1B probed by high-resolution HDX-MS. Protein Sci 2024;33:e5024. [PMID: 38801229 PMCID: PMC11129624 DOI: 10.1002/pro.5024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 03/27/2024] [Accepted: 05/02/2024] [Indexed: 05/29/2024]
29
Wankowicz SA, Ravikumar A, Sharma S, Riley BT, Raju A, Flowers J, Hogan D, van den Bedem H, Keedy DA, Fraser JS. Uncovering Protein Ensembles: Automated Multiconformer Model Building for X-ray Crystallography and Cryo-EM. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.06.28.546963. [PMID: 37425870 PMCID: PMC10327213 DOI: 10.1101/2023.06.28.546963] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
30
Day JEH, Berdini V, Castro J, Chessari G, Davies TG, Day PJ, St Denis JD, Fujiwara H, Fukaya S, Hamlett CCF, Hearn K, Hiscock SD, Holvey RS, Ito S, Kandola N, Kodama Y, Liebeschuetz JW, Martins V, Matsuo K, Mortenson PN, Muench S, Nakatsuru Y, Ochiiwa H, Palmer N, Peakman T, Price A, Reader M, Rees DC, Rich SJ, Shah A, Shibata Y, Smyth T, Twigg DG, Wallis NG, Williams G, Wilsher NE, Woodhead A, Shimamura T, Johnson CN. Fragment-Based Discovery of Allosteric Inhibitors of SH2 Domain-Containing Protein Tyrosine Phosphatase-2 (SHP2). J Med Chem 2024;67:4655-4675. [PMID: 38462716 DOI: 10.1021/acs.jmedchem.3c02118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
31
Zinovjev K, Guénon P, Ramos-Guzmán CA, Ruiz-Pernía JJ, Laage D, Tuñón I. Activation and friction in enzymatic loop opening and closing dynamics. Nat Commun 2024;15:2490. [PMID: 38509080 PMCID: PMC10955111 DOI: 10.1038/s41467-024-46723-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 03/04/2024] [Indexed: 03/22/2024]  Open
32
McCullagh M, Zeczycki TN, Kariyawasam CS, Durie CL, Halkidis K, Fitzkee NC, Holt JM, Fenton AW. What is allosteric regulation? Exploring the exceptions that prove the rule! J Biol Chem 2024;300:105672. [PMID: 38272229 PMCID: PMC10897898 DOI: 10.1016/j.jbc.2024.105672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 01/09/2024] [Accepted: 01/12/2024] [Indexed: 01/27/2024]  Open
33
Greisman JB, Dalton KM, Brookner DE, Klureza MA, Sheehan CJ, Kim IS, Henning RW, Russi S, Hekstra DR. Perturbative diffraction methods resolve a conformational switch that facilitates a two-step enzymatic mechanism. Proc Natl Acad Sci U S A 2024;121:e2313192121. [PMID: 38386706 PMCID: PMC10907320 DOI: 10.1073/pnas.2313192121] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 12/18/2023] [Indexed: 02/24/2024]  Open
34
Welsh CL, Madan LK. Allostery in Protein Tyrosine Phosphatases is Enabled by Divergent Dynamics. J Chem Inf Model 2024;64:1331-1346. [PMID: 38346324 PMCID: PMC11144062 DOI: 10.1021/acs.jcim.3c01615] [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] [Indexed: 02/27/2024]
35
Ly HT, Pham KD, Le PH, Do THT, Nguyen TTH, Le VM. Pharmacological properties of Ensete glaucum seed extract: Novel insights for antidiabetic effects via modulation of oxidative stress, inflammation, apoptosis and MAPK signaling pathways. JOURNAL OF ETHNOPHARMACOLOGY 2024;320:117427. [PMID: 37992883 DOI: 10.1016/j.jep.2023.117427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 11/06/2023] [Accepted: 11/12/2023] [Indexed: 11/24/2023]
36
Crean RM, Corbella M, Calixto AR, Hengge AC, Kamerlin SCL. Sequence - dynamics - function relationships in protein tyrosine phosphatases. QRB DISCOVERY 2024;5:e4. [PMID: 38689874 PMCID: PMC11058592 DOI: 10.1017/qrd.2024.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 09/20/2023] [Accepted: 10/24/2023] [Indexed: 05/02/2024]  Open
37
Guo M, Li Z, Gu M, Gu J, You Q, Wang L. Targeting phosphatases: From molecule design to clinical trials. Eur J Med Chem 2024;264:116031. [PMID: 38101039 DOI: 10.1016/j.ejmech.2023.116031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 12/03/2023] [Accepted: 12/04/2023] [Indexed: 12/17/2023]
38
Guerrero L, Ebrahim A, Riley BT, Kim M, Huang Q, Finke AD, Keedy DA. Pushed to extremes: distinct effects of high temperature versus pressure on the structure of STEP. Commun Biol 2024;7:59. [PMID: 38216663 PMCID: PMC10786866 DOI: 10.1038/s42003-023-05609-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 11/20/2023] [Indexed: 01/14/2024]  Open
39
Mehlman T(S, Ginn HM, Keedy DA. An expanded view of ligandability in the allosteric enzyme PTP1B from computational reanalysis of large-scale crystallographic data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.05.574428. [PMID: 38260327 PMCID: PMC10802458 DOI: 10.1101/2024.01.05.574428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
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Sharma S, Skaist Mehlman T, Sagabala RS, Boivin B, Keedy DA. High-resolution double vision of the allosteric phosphatase PTP1B. Acta Crystallogr F Struct Biol Commun 2024;80:1-12. [PMID: 38133579 PMCID: PMC10833341 DOI: 10.1107/s2053230x23010749] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 12/14/2023] [Indexed: 12/23/2023]  Open
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Wolff AM, Nango E, Young ID, Brewster AS, Kubo M, Nomura T, Sugahara M, Owada S, Barad BA, Ito K, Bhowmick A, Carbajo S, Hino T, Holton JM, Im D, O'Riordan LJ, Tanaka T, Tanaka R, Sierra RG, Yumoto F, Tono K, Iwata S, Sauter NK, Fraser JS, Thompson MC. Mapping protein dynamics at high spatial resolution with temperature-jump X-ray crystallography. Nat Chem 2023;15:1549-1558. [PMID: 37723259 PMCID: PMC10624634 DOI: 10.1038/s41557-023-01329-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 08/17/2023] [Indexed: 09/20/2023]
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Friedman AJ, Padgette HM, Kramer L, Liechty ET, Donovan GW, Fox JM, Shirts MR. Biophysical Rationale for the Selective Inhibition of PTP1B over TCPTP by Nonpolar Terpenoids. J Phys Chem B 2023;127:8305-8316. [PMID: 37729547 PMCID: PMC10694825 DOI: 10.1021/acs.jpcb.3c03791] [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] [Indexed: 09/22/2023]
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Thompson MC. Combining temperature perturbations with X-ray crystallography to study dynamic macromolecules: A thorough discussion of experimental methods. Methods Enzymol 2023;688:255-305. [PMID: 37748829 DOI: 10.1016/bs.mie.2023.07.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/27/2023]
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Yeh CY, Izaguirre JA, Greisman JB, Willmore L, Maragakis P, Shaw DE. A Conserved Local Structural Motif Controls the Kinetics of PTP1B Catalysis. J Chem Inf Model 2023. [PMID: 37378552 DOI: 10.1021/acs.jcim.3c00286] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2023]
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Hardie A, Cossins BP, Lovera S, Michel J. Deconstructing allostery by computational assessment of the binding determinants of allosteric PTP1B modulators. Commun Chem 2023;6:125. [PMID: 37322137 PMCID: PMC10272186 DOI: 10.1038/s42004-023-00926-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 06/08/2023] [Indexed: 06/17/2023]  Open
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Greisman JB, Dalton KM, Brookner DE, Klureza MA, Sheehan CJ, Kim IS, Henning RW, Russi S, Hekstra DR. Resolving conformational changes that mediate a two-step catalytic mechanism in a model enzyme. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.02.543507. [PMID: 37398233 PMCID: PMC10312612 DOI: 10.1101/2023.06.02.543507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
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Hong SH, Xi SY, Johns AC, Tang LC, Li A, Hum MN, Chartier CA, Jovanovic M, Shah NH. Mapping the Chemical Space of Active-Site Targeted Covalent Ligands for Protein Tyrosine Phosphatases. Chembiochem 2023;24:e202200706. [PMID: 36893077 PMCID: PMC10192133 DOI: 10.1002/cbic.202200706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 03/05/2023] [Accepted: 03/09/2023] [Indexed: 03/10/2023]
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Hekstra DR. Emerging Time-Resolved X-Ray Diffraction Approaches for Protein Dynamics. Annu Rev Biophys 2023;52:255-274. [PMID: 37159292 PMCID: PMC10687665 DOI: 10.1146/annurev-biophys-111622-091155] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
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Guerrero L, Ebrahim A, Riley BT, Kim M, Huang Q, Finke AD, Keedy DA. Pushed to extremes: distinct effects of high temperature vs. pressure on the structure of an atypical phosphatase. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.02.538097. [PMID: 37205580 PMCID: PMC10187168 DOI: 10.1101/2023.05.02.538097] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
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Steiner RA. Introduction to the virtual thematic issue on room-temperature biological crystallography. IUCRJ 2023;10:248-250. [PMID: 37000491 PMCID: PMC10161770 DOI: 10.1107/s2052252523002968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
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