Publications

  • 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 Aug 13;116(33):16347-16356. doi: 10.1073/pnas.1906036116. Epub 2019 Jul 30. PubMed PMID: 31363049; PubMed Central PMCID: PMC6697891

  • Ahuja LG, Aoto PC, Kornev AP, Veglia G, Taylor SS. Dynamic allostery-based molecular workings of kinase:peptide complexes. Proc Natl Acad Sci U S A. 2019 Jul 23;116(30):15052-15061. doi: 10.1073/pnas.1900163116. Epub 2019 Jul 8. PubMed PMID: 31285328; PubMed Central PMCID: PMC6660753.

  • Ahuja LG, Taylor SS, Kornev AP. Tuning the "violin" of protein kinases: The role of dynamics-based allostery. IUBMB Life. 2019 Jun;71(6):685-696. doi: 10.1002/iub.2057. Epub 2019 May 7. Review. PubMed PMID: 31063633; PubMed Central PMCID: PMC6690483.

  • Wang Y, V S M, Kim J, Li G, Ahuja LG, Aoto P, Taylor SS, Veglia G. Globally correlated conformational entropy underlies positive and negative cooperativity in a kinase's enzymatic cycle. Nat Commun. 2019 Feb 18;10(1):799. doi: 10.1038/s41467-019-08655-7. PubMed PMID: 30778078; PubMed Central PMCID: PMC6379427.

  • Meng Y, Ahuja LG, Kornev AP, Taylor SS, Roux B. Corrigendum to "A Catalytically-Disabled Double Mutant of Src Tyrosine Kinase Can Be Stabilized into an Active-Like Conformation." J. Mol. Biol. 430(6) (Mar 16 2018), 881-889. J Mol Biol. 2018 Oct 19;430(21):4439. doi: 10.1016/j.jmb.2018.09.001. Epub 2018 Sep 13. PubMed PMID: 30220583.

  • Meng Y, Ahuja LG, Kornev AP, Taylor SS, Roux B. A Catalytically Disabled Double Mutant of Src Tyrosine Kinase Can Be Stabilized into an Active-Like Conformation. J Mol Biol. 2018 Mar 16;430(6):881-889. doi: 10.1016/j.jmb.2018.01.019. Epub 2018 Feb 2. PubMed PMID: 29410316; PubMed Central PMCID: PMC6279248.

  • Ahuja LG. Protein Tyrosine Phosphatases: Structure Signaling and Drug Discovery. Germany: De Gryuters; 2018.

  • Kim J, Ahuja LG, Chao FA, Xia Y, McClendon CL, Kornev AP, Taylor SS, Veglia G. A dynamic hydrophobic core orchestrates allostery in protein kinases. Sci Adv. 2017 Apr;3(4):e1600663. doi: 10.1126/sciadv.1600663. eCollection 2017 Apr. PubMed PMID: 28435869; PubMed Central PMCID: PMC5384802.

  • Ahuja LG, Kornev AP, McClendon CL, Veglia G, Taylor SS. Mutation of a kinase allosteric node uncouples dynamics linked to phosphotransfer. Proc Natl Acad Sci U S A. 2017 Feb 7;114(6):E931-E940. doi: 10.1073/pnas.1620667114. Epub 2017 Jan 23. PubMed PMID: 28115705; PubMed Central PMCID: PMC5307475.

  • Meharena HS, Fan X, Ahuja LG, Keshwani MM, McClendon CL, Chen AM, Adams JA, Taylor SS. Decoding the Interactions Regulating the Active State Mechanics of Eukaryotic Protein Kinases. PLoS Biol. 2016 Nov;14(11):e2000127. doi: 10.1371/journal.pbio.2000127. eCollection 2016 Nov. PubMed PMID: 27902690; PubMed Central PMCID: PMC5130182.

  • Knape MJ, Ahuja LG, Bertinetti D, Burghardt NC, Zimmermann B, Taylor SS, Herberg FW. Divalent Metal Ions Mg²⁺ and Ca²⁺ Have Distinct Effects on Protein Kinase A Activity and Regulation. ACS Chem Biol. 2015 Oct 16;10(10):2303-15. doi: 10.1021/acschembio.5b00271. Epub 2015 Aug 5. PubMed PMID: 26200257; PubMed Central PMCID: PMC4714867.

  • Zhang P, Knape MJ, Ahuja LG, Keshwani MM, King CC, Sastri M, Herberg FW, Taylor SS. Single Turnover Autophosphorylation Cycle of the PKA RIIβ Holoenzyme. PLoS Biol. 2015 Jul;13(7):e1002192. doi: 10.1371/journal.pbio.1002192. eCollection 2015 Jul. PubMed PMID: 26158466; PubMed Central PMCID: PMC4497662.

  • Hu J, Ahuja LG, Meharena HS, Kannan N, Kornev AP, Taylor SS, Shaw AS. Kinase regulation by hydrophobic spine assembly in cancer. Mol Cell Biol. 2015 Jan;35(1):264-76. doi: 10.1128/MCB.00943-14. Epub 2014 Oct 27. PubMed PMID: 25348715; PubMed Central PMCID: PMC4295384.

  • Moretti DM, Ahuja LG, Nunes RD, Cudischevitch CO, Daumas-Filho CR, Medeiros-Castro P, Ventura-Martins G, Jablonka W, Gazos-Lopes F, Senna R, Sorgine MH, Hartfelder K, Capurro M, Atella GC, Mesquita RD, Silva-Neto MA. Molecular analysis of Aedes aegypti classical protein tyrosine phosphatases uncovers an ortholog of mammalian PTP-1B implicated in the control of egg production in mosquitoes. PLoS One. 2014;9(8):e104878. doi: 10.1371/journal.pone.0104878. eCollection 2014. PubMed PMID: 25137153; PubMed Central PMCID: PMC4138107.

  • Ahuja LG, Gopal B. Bi-domain protein tyrosine phosphatases reveal an evolutionary adaptation to optimize signal transduction. Antioxid Redox Signal. 2014 May 10;20(14):2141-59. doi: 10.1089/ars.2013.5721. Epub 2013 Dec 21. Review. PubMed PMID: 24206235.

  • Shaw AS, Kornev AP, Hu J, Ahuja LG, Taylor SS. Kinases and pseudokinases: lessons from RAF. Mol Cell Biol. 2014 May;34(9):1538-46. doi: 10.1128/MCB.00057-14. Epub 2014 Feb 24. Review. PubMed PMID: 24567368; PubMed Central PMCID: PMC3993607.

  • Madan LL, Goutam K, Gopal B. Inter-domain interactions influence the stability and catalytic activity of the bi-domain protein tyrosine phosphatase PTP99A. Biochim Biophys Acta. 2012 Aug;1824(8):983-90. doi: 10.1016/j.bbapap.2012.05.001. Epub 2012 May 15. PubMed PMID: 22595398.

  • Madan LL, Gopal B. Conformational basis for substrate recruitment in protein tyrosine phosphatase 10D. Biochemistry. 2011 Nov 22;50(46):10114-25. doi: 10.1021/bi201092q. Epub 2011 Oct 27. PubMed PMID: 22007620; PubMed Central PMCID: PMC3667199.

  • Madan LL, Veeranna S, Shameer K, Reddy CC, Sowdhamini R, Gopal B. Modulation of catalytic activity in multi-domain protein tyrosine phosphatases. PLoS One. 2011;6(9):e24766. doi: 10.1371/journal.pone.0024766. Epub 2011 Sep 13. PubMed PMID: 21931847; PubMed Central PMCID: PMC3172300.

  • Shameer K, Madan LL, Veeranna S, Gopal B, Sowdhamini R. PeptideMine--a webserver for the design of peptides for protein-peptide binding studies derived from protein-protein interactomes. BMC Bioinformatics. 2010 Sep 22;11:473. doi: 10.1186/1471-2105-11-473. PubMed PMID: 20858292; PubMed Central PMCID: PMC2955050.

  • Raghava S, Barua B, Singh PK, Das M, Madan LL, Bhattacharyya S, Bajaj K, Gopal B, Varadarajan R, Gupta MN. Refolding and simultaneous purification by three-phase partitioning of recombinant proteins from inclusion bodies. Protein Sci. 2008 Nov;17(11):1987-97. doi: 10.1110/ps.036939.108. Epub 2008 Sep 9. PubMed PMID: 18780821; PubMed Central PMCID: PMC2578805.

  • Madan LL, Gopal B. Addition of a polypeptide stretch at the N-terminus improves the expression, stability and solubility of recombinant protein tyrosine phosphatases from Drosophila melanogaster. Protein Expr Purif. 2008 Feb;57(2):234-43. doi: 10.1016/j.pep.2007.10.002. Epub 2007 Oct 13. PubMed PMID: 18023205.

  • Gopal B, Madan LL, Betz SF, Kossiakoff AA. The crystal structure of a quercetin 2,3-dioxygenase from Bacillus subtilis suggests modulation of enzyme activity by a change in the metal ion at the active site(s). Biochemistry. 2005 Jan 11;44(1):193-201. doi: 10.1021/bi0484421. PubMed PMID: 15628860.

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Scientific  Monograghs 

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Protein Tyrosine Phosphatases   Structure, Signaling and Drug Discovery

Lalima  G. Ahuja. De Gruyter, 2018.                            ISBN 978-3-11-042643-4

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Ask your library to buy this:

https://www.degruyter.com/view/product/456363

https://www.amazon.com/Protein-Tyrosine-Phosphatases-Structure-Signaling-ebook/dp/B06Y6G6X98​

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Book Review in Acta Crystallographica Section D STRUCTURAL BIOLOGY 

http://journals.iucr.org/d/issues/2019/05/00/xo0134/

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