Publications

Recent Publications

  1. Computational and Experimental Characterization of Patient Derived Mutations Reveal an Unusual Mode of Regulatory Spine Assembly and Drug Sensitivity in EGFR Kinase
    Ruan Z, Katiyar S, Kannan N.
    Biochemistry 2016; 22:22-32

    PubMed DOI
  2. Tribbles in the 21st Century: The Evolving Roles of Tribbles Pseudokinases in Biology and Disease
    Eyers PA, Keeshan K, Kannan N.
    Trends Cell Biol. 2016

    PubMed DOI
  3. KinView: a visual comparative sequence analysis tool for integrated kinome research
    McSkimming DI, Dastgheib S, Baffi TR, Byrne DP, Ferries S, Scott ST, Newton AC, Eyers CE, Kochut KJ, Eyersd PA, Kannan N.
    Mol Biosyst. 2016; 12(12):3651-3665

    PubMed DOI
  4. Cerebellar Ataxia and Coenzyme Q Deficiency through Loss of Unorthodox Kinase Activity
    Stefely JA, Licitra F, Laredj L, Reidenbach AG, Kemmerer ZA, Grangeray A, Jaeg-Ehret T, Minogue CE, Ulbrich A, Hutchins PD, Wilkerson EM, Ruan Z, Aydin D, Hebert AS, Guo X, Freiberger EC, Reutenauer L, Jochem A, Chergova M, Johnson IE, Lohman DC, Rush MJ, Kwiecien NW, Singh PK, Schlagowski AI, Floyd BJ, Forsman U, Sindelar PJ, Westphall MS, Pierrel F, Zoll J, Dal Peraro M, Kannan N, Bingman CA, Coon JJ, Isope P, Puccio H, Pagliarini DJ.
    Mol Cell. 2016; 63(4):608-620

    PubMed DOI
  5. Hydrophobic Core Variations Provide a Structural Framework for Tyrosine Kinase Evolution and Functional Specialization
    Mohanty S, Oruganty K, Kwon A, Byrne DP, Ferries S, Ruan Z, Hanold LE, Katiyar S, Kennedy EJ, Eyers PA, Kannan N.
    PLoS Genet. 2016; 12(2):

    PubMed DOI
  6. Identification and classification of small molecule kinases: insights into substrate recognition and specificity
    Oruganty K, Talevich E, Neuwald AF, Kannan N.
    BMC Evolutionary Biology 2016; 16(7):

    PubMed DOI
  7. Creating Biomedical Ontologies Using mOntage
    Dastgheib S, McSkimming DI, Kannan N, Kochut K.
    Data Integration in the Life Sciences (Book Chapter) 2015; 9162:

    PubMed DOI
  8. The Ty1 Retrotransposon Restriction Factor p22 Targets Gag
    Tucker JM, Larango ME, Wachsmuth LP, Kannan N, Garfinkel DJ.
    PLoS Genetics 2015; 11(10):

    PubMed DOI
  9. Mechanistic Insights into R776H Mediated Activation of Epidermal Growth Factor Receptor (EGFR) Kinase
    Ruan Z, Kannan N.
    Biochemistry 2015; 54(27):4216-4225

    PubMed DOI
  10. Dialing in EGFR Signaling
    Kennedy EJ, Kannan N.
    Chem Biol. 2015; 22(6):687-688

    PubMed DOI
  11. Integration of signaling in the kinome: Architecture and regulation of the alphaC Helix
    Taylor SS, Shaw AS, Kannan N, Kornev AP.
    Biochim Biophys Acta. 2015; 1854:1567-1574

    PubMed DOI
  12. Structural and evolutionary divergence of cyclic nucleotide binding domains in eukaryotic pathogens: Implications for drug design
    Mohanty S, Kennedy EJ, Herberg FW, Hui R, Taylor SS, Langsley G, Kannan N.
    Biochim Biophys Acta. 2015; 1854:

    PubMed DOI
  13. Co-Conserved MAPK Features Couple D-Domain Docking Groove to Distal Allosteric Sites via the C-Terminal Flanking Tail
    Nguyen T, Ruan Z, Oruganty K, Kannan N.
    PLoS One 2015; 10(3):

    PubMed DOI
  14. Inhibiting EGFR Dimerization Using Triazolyl-Bridged Dimerization Arm Mimics
    Hanold LE, Oruganty K, Ton NT, Beedle AM, Kannan N, Kennedy EJ.
    PLoS One 2015; 10(3):

    PubMed DOI
  15. ProKinO: a unified resource for mining the cancer kinome
    McSkimming DI, Dastgheib S, Talevich E, Narayanan A, Katiyar S, Taylor SS, Kochut K, Kannan N.
    Hum Mutat. 2015; 36(2):175-186

    PubMed DOI
  16. Going for broke: Targeting the human cancer pseudokinome
    MBailey FP, Byrne DP, McSkimming D, Kannan N, Eyers PA.
    Biochem J. 2015; 467(2):195-211

    PubMed DOI
  17. The Tribbles 2 (TRB2) pseudokinase binds to ATP and autophosphorylates in a metal-independent manner
    Bailey FP, Byrne DP, Oruganty K, Eyers CE, Novotny CJ, Shokat KM, Kannan N, Eyers PA.
    Biochem J. 2015; 467(1):

    PubMed DOI
  18. Mitochondrial ADCK3 Employs an Atypical Protein Kinase-like Fold to Enable Coenzyme Q Biosynthesis
    Stefely JA, Reidenbach AG, Ulbrich A, Oruganty K, Floyd BJ, Jochem A, Saunders JM, Johnson IE, Minogue CE, Wrobel RL, Barber GE, Lee D, Li S, Kannan N, Coon JJ, Bingman CA, Pagliarini DJ.
    Mol Cell. 2014; 57(1):

    PubMed DOI
  19. Kinase Regulation by Hydrophobic Spine Assembly in Cancer
    Hu J, Ahuja LG, Meharena HS, Kannan N, Kornev AP, Taylor SS, Shaw AS.
    Mol Cell Biol. 2014; 35(1):

    PubMed DOI
  20. Prediction and Prioritization of Rare Oncogenic Mutations in the Cancer Kinome Using Novel Features and Multiple Classifiers
    U M, Talevich E, Katiyar S, Rasheed K, Kannan N.
    PLoS Comput Biol. 2014; 10(4):

    PubMed DOI
  21. Deciphering the Structural Basis of Eukaryotic Protein Kinase Regulation
    Meharena HS, Chang P, Keshwani MM, Oruganty K, Nene AK, Kannan N, Taylor SS, Kornev AP.
    PLoS Biol 2013; 11(10):

    PubMed DOI
  22. Global Analysis of Protein Expression and Phosphorylation of Three Stages of Plasmodium falciparum Intraerythrocytic Development
    Pease BN, Huttlin EL, Jedrychowski MP, Talevich E, Harmon J, Dillman T, Kannan N, Doerig C, Chakrabarti R, Gygi SP, Chakrabarti D.
    J Proteome Res. 2013; 12(9):4028-4045

    PubMed DOI
  23. Structural and evolutionary adaptation of rhoptry kinases and pseudokinases, a family of coccidian virulence factors
    Talevich E, Kannan N.
    BMC Evol. Biol. 2013; 13:117

    PubMed DOI
  24. Evolutionary variation and adaptation in a conserved protein kinase allosteric network: Implications for inhibitor design
    Oruganty K, Kannan N.
    Biochim. Biophys. Acta 2013; 1834(7):1322-1329

    PubMed DOI
  25. Identification of a hidden strain switch provides clues to an ancient structural mechanism in protein kinases
    Oruganty K, Talathi NS, Wood ZA, Kannan N.
    PNAS 2012; 110(3):924-929

    PubMed DOI
  26. Design principles underpinning the regulatory diversity of protein kinases
    Oruganty K, Kannan N.
    Philos. Trans. B 2012; 367(1602):2517-28

    PubMed DOI
  27. An evolutionary perspective on the kinome of malaria parasites
    Talevich E, Tobin AB, Kannan N, Doerig C.
    Philos. Trans. B 2012; 367(1602):2607-18

    PubMed DOI
  28. ProKinO: An Ontology for Integrative Analysis of Protein Kinases in Cancer
    Gosal G, Kochut KJ, Kannan N.
    PLoS One 2011; 6(12):e28782

    PubMed DOI
  29. Structural and evolutionary divergence of eukaryotic protein kinases in Apicomplexa
    Talevich E, Mirza A, Kannan N.
    BMC Evol. Biol. 2011; 11:321

    PubMed DOI
  30. Conformational regulation of the EGFR kinase core by the juxtamembrane and C-terminal tail: A molecular dynamics study
    Mustafa M, Mirza A, Kannan N.
    Proteins 2011; 79(1):99-114

    PubMed DOI
  31. Co-conserved features associated with cis regulation of ErbB tyrosine kinases
    Mirza A, Mustafa M, Talevich E, Kannan N.
    PLoS One 2010; 5(12):e14310

    PubMed DOI
  32. Comparative surface geometry of the protein kinase family
    Thompson EE, Kornev AP, Kannan N, Kim C, Ten Eyck LF, Taylor SS.
    Protein Sci. 2009; 18(10):2016-26

    PubMed
  33. A chimeric mechanism for polyvalent trans-phosphorylation of PKA by PDK1
    Romano RA, Kannan N, Kornev AP, Allison CJ, Taylor SS.
    Protein Sci. 2009; 18(7):1486-97

    PubMed
  34. The chaperones Hsp90 and Cdc37 mediate the maturation and stabilization of protein kinase C through a conserved PXXP motif in the C-terminal tail
    Gould CM, Kannan N, Taylor SS, Newton AC.
    J. Biol Chem. 2009; 284:4921-4935

    PubMed
  35. Congenital disease SNPs target lineage specific structural elements in protein kinases
    Torkamani A, Kannan N, Taylor SS, Schork NJ.
    PNAS 2008; 105(26):9011-6

    PubMed DOI
  36. Rethinking pseudokinases
    Kannan N, Taylor SS..
    Cell 2008; 133(2):204-5

    PubMed
  37. Analogous regulatory sites in ZAP-70 tyrosine kinase and AGC kinases
    Kannan N, Neuwald AF, Taylor SS.
    Biochemica Biophysica Acta 2008; 1784(1):27-32

    PubMed
  38. Signaling through cAMP and cAMP-dependent protein kinase: Diverse strategies for Drug Design
    Taylor SS, Kim C, Cheng CY, Brown SH, Wu J, Kannan N.
    Biochemica Biophysica Acta 2008; 1784(1):16-26

    PubMed
  39. Evolution of allostery in the cyclic nucleotide binding module
    Kannan N, Wu J, Anand G, Shibu Y, Venter C, Taylor SS.
    Genome Biol. 2007; 8(12):R264

    PubMed
  40. Structural and functional diversity of the microbial kinome
    Kannan N, Taylor SS, Yufeng Z, Venter C, Manning G.
    PLoS Biol. 2007; 5(3):e83

    PubMed
  41. The hallmark of AGC kinase functional divergence is its C-terminal tail, a cis-acting regulatory module
    Kannan N, Haste N, Taylor SS, Neuwald AF.
    PNAS 2007; 104(4):1272-7

    PubMed
  42. Did protein kinase regulatory mechanisms evolve through elaboration of a simple structural component?
    Kannan N, Neuwald AF.
    J. Mol. Biol. 2005; 351:956-972

    PubMed
  43. Structural features associated with functional specificity of CMGC protein kinases MAPK, CDK, GSK, SRPK, DYRK and CK2alpha
    Kannan N, Neuwald AF.
    Protein Sci. 2004; 13(8):100-128

    PubMed
  44. Crystal structure of the E230Q mutant of cAMP-dependent protein kinase reveals an unexpected apoenzyme conformation and an extended N-terminal A helix
    Wu J, Yang J, Kannan N, Madhusudhan, Xuong NH, Ten Eyck LF, Taylor SS.
    Protein Sci. 2005; 14(11):2871-9

    PubMed
  45. Computational analysis of protein tyrosine phosphatases: practical guide to bioinformatics and data resources
    Andersen JN, Kannan N, Gergel J, Neuwald AF, Tonks NK.
    Methods 2005; 35(1):90-114

    PubMed
  46. Ran's C-terminal basic patch and nucleotide exchange mechanisms in light of a canonical structure for Rab, Rho, Ras and Ran GTPases
    Neuwald AF, Kannan N, Poleksic A, Hata N, Lu J.
    Genome Res. 2002; 13(4):673-692

    PubMed
  47. Protein structure: Insights from graph theory
    Vishveshwara S, Brinda KV, Kannan N.
    J. of Theor. and Comp. Chemistry 2002; 1(1):187-212

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  48. Analysis of homodimeric protein interfaces using graph spectral method
    Brinda KV, Kannan N, Vishveshwara S.
    Protein Eng. 2002; 15(4):265-77

    PubMed
  49. Clusters in alpha/beta barrel proteins: implications for protein structure and folding: a graph theoretical approach
    Kannan N, Selvaraj S, Gromiha MM, Vishveshwara S.
    Proteins 2001; 43(2):103-12

    PubMed
  50. Stabilizing interactions in the dimer interface of alpha-subunit in E. coli RNA polymerase: A graph spectral and point mutation study
    Kannan N, Chander P, Ghosh P, Vishveshwara S, Chatterji D.
    Protein Sci. 2001; 10(1):46-54

    PubMed
  51. Logos for amino-acid preferences in different backbone packing density regions of protein structural classes
    Kannan N, Schneider TD, Vishveshwara S.
    Acta Crystallog. D 2000; 59(9):1156-65

    PubMed
  52. Aromatic clusters: a determinant of thermal stability in thermophilic proteins
    Kannan N, Vishveshwara S.
    Protein Eng. 2000; 13(11):753-61

    PubMed
  53. Identification of side-chain clusters in protein structures by a graph spectral method
    Kannan N, Vishveshwara S.
    J. Mol. Biol. 1999; 292(2):441-64

    PubMed