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    Lynn Ten Eyck

    TitleRecall Non-faculty Academic
    SchoolUniversity of California, San Diego
    DepartmentChemistry and Biochemistry
    Address9500 Gilman Drive #0505
    CA La Jolla 92093
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      Collapse Research 
      Collapse Research Activities and Funding
      Computation and Mass Spec: Predicting Protein Complexes
      NIH/NIGMS R01GM070996May 1, 2004 - Apr 30, 2009
      Role: Principal Investigator
      Improved Macromolecular Refinement Methods
      NIH/NIGMS R01GM069758Feb 1, 2004 - Jan 31, 2009
      Role: Principal Investigator

      Collapse Bibliographic 
      Collapse Publications
      Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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      1. Fedosyuk S, Bezerra GA, Radakovics K, Smith TK, Sammito M, Bobik N, Round A, Ten Eyck L, Djinovic-Carugo K, Usón I, Skern T. Vaccinia Virus Immunomodulator A46: A Lipid and Protein-Binding Scaffold for Sequestering Host TIR-Domain Proteins. PLoS Pathog. 2016 Dec; 12(12):e1006079. PMID: 27973613.
        View in: PubMed
      2. Roberts VA, Pique ME, Ten Eyck L, Li S. Predicting protein-DNA interactions by full search computational docking. Proteins. 2013 Dec; 81(12):2106-18. PMID: 23966176.
        View in: PubMed
      3. Roberts VA, Thompson EE, Pique ME, Perez MS, Ten Eyck L. DOT2: Macromolecular docking with improved biophysical models. J Comput Chem. 2013 Jul 30; 34(20):1743-58. PMID: 23695987.
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      4. Roberts VA, Pique ME, Hsu S, Li S, Slupphaug G, Rambo RP, Jamison JW, Liu T, Lee JH, Tainer JA, Ten Eyck L, Woods VL. Combining H/D exchange mass spectroscopy and computational docking reveals extended DNA-binding surface on uracil-DNA glycosylase. Nucleic Acids Res. 2012 Jul; 40(13):6070-81. PMID: 22492624.
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      5. Levisson M, Han GW, Deller MC, Xu Q, Biely P, Hendriks S, Ten Eyck L, Flensburg C, Roversi P, Miller MD, McMullan D, von Delft F, Kreusch A, Deacon AM, van der Oost J, Lesley SA, Elsliger MA, Kengen SW, Wilson IA. Functional and structural characterization of a thermostable acetyl esterase from Thermotoga maritima. Proteins. 2012 Jun; 80(6):1545-59. PMID: 22411095.
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      6. Trinh MH, Odorico M, Pique ME, Teulon JM, Roberts VA, Ten Eyck L, Getzoff ED, Parot P, Chen SW, Pellequer JL. Computational reconstruction of multidomain proteins using atomic force microscopy data. Structure. 2012 Jan 11; 20(1):113-20. PMID: 22244760.
        View in: PubMed
      7. Thompson EE, Kornev AP, Kannan N, Kim C, Ten Eyck L, Taylor SS. Comparative surface geometry of the protein kinase family. Protein Sci. 2009 Oct; 18(10):2016-26. PMID: 19610074.
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      8. Kornev AP, Taylor SS, Ten Eyck L. A helix scaffold for the assembly of active protein kinases. Proc Natl Acad Sci U S A. 2008 Sep 23; 105(38):14377-82. PMID: 18787129.
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      9. Kornev AP, Taylor SS, Ten Eyck L. A generalized allosteric mechanism for cis-regulated cyclic nucleotide binding domains. PLoS Comput Biol. 2008 Apr; 4(4):e1000056. PMID: 18404204.
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      10. Ten Eyck L, Taylor SS, Kornev AP. Conserved spatial patterns across the protein kinase family. Biochim Biophys Acta. 2008 Jan; 1784(1):238-43. PMID: 18067871.
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      11. Anand GS, Hotchko M, Brown SH, Ten Eyck L, Komives EA, Taylor SS. R-subunit isoform specificity in protein kinase A: distinct features of protein interfaces in PKA types I and II by amide H/2H exchange mass spectrometry. J Mol Biol. 2007 Nov 23; 374(2):487-99. PMID: 17942118.
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      12. Weis DD, Wales TE, Engen JR, Hotchko M, Ten Eyck L. Identification and characterization of EX1 kinetics in H/D exchange mass spectrometry by peak width analysis. J Am Soc Mass Spectrom. 2006 Nov; 17(11):1498-509. PMID: 16875839.
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      13. Hotchko M, Anand GS, Komives EA, Ten Eyck L. Automated extraction of backbone deuteration levels from amide H/2H mass spectrometry experiments. Protein Sci. 2006 Mar; 15(3):583-601. PMID: 16501228.
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      14. Wu J, Yang J, Kannan N. Crystal structure of the E230Q mutant of cAMP-dependent protein kinase reveals an unexpected apoenzyme conformation and an extended N-terminal A helix. Protein Sci. 2005 Nov; 14(11):2871-9. PMID: 16253959.
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      15. Law D, Hotchko M, Ten Eyck L. Progress in computation and amide hydrogen exchange for prediction of protein-protein complexes. Proteins. 2005 Aug 1; 60(2):302-7. PMID: 15981246.
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      16. Cerutti DS, Ten Eyck L, McCammon JA. Rapid Estimation of Solvation Energy for Simulations of Protein-Protein Association. J Chem Theory Comput. 2005 Jan; 1(1):143-52. PMID: 26641125.
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      17. Berman HM, Ten Eyck L, Goodsell DS, Haste NM, Kornev A, Taylor SS. The cAMP binding domain: an ancient signaling module. Proc Natl Acad Sci U S A. 2005 Jan 4; 102(1):45-50. PMID: 15618393.
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      18. Wu J, Jones JM, Nguyen-Huu X, Ten Eyck L, Taylor SS. Crystal structures of RIalpha subunit of cyclic adenosine 5'-monophosphate (cAMP)-dependent protein kinase complexed with (Rp)-adenosine 3',5'-cyclic monophosphothioate and (Sp)-adenosine 3',5'-cyclic monophosphothioate, the phosphothioate analogues of cAMP. Biochemistry. 2004 Jun 1; 43(21):6620-9. PMID: 15157095.
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      19. Yang J, Ten Eyck L, Xuong NH, Taylor SS. Crystal structure of a cAMP-dependent protein kinase mutant at 1.26A: new insights into the catalytic mechanism. J Mol Biol. 2004 Feb 13; 336(2):473-87. PMID: 14757059.
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      20. Anand GS, Law D, Mandell JG, Snead AN, Tsigelny I, Taylor SS, Ten Eyck L, Komives EA. Identification of the protein kinase A regulatory RIalpha-catalytic subunit interface by amide H/2H exchange and protein docking. Proc Natl Acad Sci U S A. 2003 Nov 11; 100(23):13264-9. PMID: 14583592.
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      21. Kotlovyi V, Nichols WL, Ten Eyck L. Protein structural alignment for detection of maximally conserved regions. Biophys Chem. 2003 Sep; 105(2-3):595-608. PMID: 14499921.
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      22. Law DS, Ten Eyck L, Katzenelson O, Tsigelny I, Roberts VA, Pique ME, Mitchell JC. Finding needles in haystacks: Reranking DOT results by using shape complementarity, cluster analysis, and biological information. Proteins. 2003 Jul 1; 52(1):33-40. PMID: 12784365.
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      23. Akamine P. Dynamic features of cAMP-dependent protein kinase revealed by apoenzyme crystal structure. J Mol Biol. 2003 Mar 14; 327(1):159-71. PMID: 12614615.
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      24. Ten Eyck L. Full matrix refinement as a tool to discover the quality of a refined structure. Methods Enzymol. 2003; 374:345-69. PMID: 14696381.
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      25. Tsigelny I, Sharikov Y, Ten Eyck L. Hidden Markov models-based system (HMMSPECTR) for detecting structural homologies on the basis of sequential information. Protein Eng. 2002 May; 15(5):347-52. PMID: 12034853.
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      26. Emrick MA, Hoofnagle AN, Miller AS, Ten Eyck L, Ahn NG. Constitutive activation of extracellular signal-regulated kinase 2 by synergistic point mutations. J Biol Chem. 2001 Dec 7; 276(49):46469-79. PMID: 11591711.
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      27. Mandell JG, Roberts VA, Pique ME, Kotlovyi V, Mitchell JC, Nelson E, Tsigelny I, Ten Eyck L. Protein docking using continuum electrostatics and geometric fit. Protein Eng. 2001 Feb; 14(2):105-13. PMID: 11297668.
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      28. Mitchell JC, Kerr R, Ten Eyck L. Rapid atomic density methods for molecular shape characterization. J Mol Graph Model. 2001; 19(3-4):325-30, 388-90. PMID: 11449571.
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      29. Cowtan K, Ten Eyck L. Eigensystem analysis of the refinement of a small metalloprotein. Acta Crystallogr D Biol Crystallogr. 2000 Jul; 56(Pt 7):842-56. PMID: 10930831.
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      30. Tsigelny I, Greenberg JP, Cox S, Nichols WL, Taylor SS, Ten Eyck L. 600 ps molecular dynamics reveals stable substructures and flexible hinge points in cAMP dependent protein kinase. Biopolymers. 1999 Oct 15; 50(5):513-24. PMID: 10479734.
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      31. Taylor SS, Radzio-Andzelm E. Catalytic subunit of cyclic AMP-dependent protein kinase: structure and dynamics of the active site cleft. Pharmacol Ther. 1999 May-Jun; 82(2-3):133-41. PMID: 10454192.
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      32. Narayana N, Diller TC, Koide K, Bunnage ME, Nicolaou KC, Brunton LL, Xuong NH, Ten Eyck L, Taylor SS. Crystal structure of the potent natural product inhibitor balanol in complex with the catalytic subunit of cAMP-dependent protein kinase. Biochemistry. 1999 Feb 23; 38(8):2367-76. PMID: 10029530.
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      33. de las Alas MM, de Bruin RA, Ten Eyck L, Los G, Howell SB. Prediction-based threading of the hMSH2 DNA mismatch repair protein. FASEB J. 1998 Jun; 12(9):653-63. PMID: 9619444.
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      34. Smith CM, Shindyalov IN, Veretnik S, Gribskov M, Taylor SS, Ten Eyck L, Bourne PE. The protein kinase resource. Trends Biochem Sci. 1997 Nov; 22(11):444-6. PMID: 9397688.
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      35. Nichols WL, Zimm BH, Ten Eyck L. Conformation-invariant structures of the alpha1beta1 human hemoglobin dimer. J Mol Biol. 1997 Jul 25; 270(4):598-615. PMID: 9245590.
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      36. Tsigelny I, Grant BD, Taylor SS, Ten Eyck L. Catalytic subunit of cAMP-dependent protein kinase: electrostatic features and peptide recognition. Biopolymers. 1996 Sep; 39(3):353-65. PMID: 8756515.
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      37. Ten Eyck L. Gro-ing pains. Nat Struct Biol. 1995 Dec; 2(12):1038-42. PMID: 8846212.
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      38. Nichols WL, Rose GD, Ten Eyck L, Zimm BH. Rigid domains in proteins: an algorithmic approach to their identification. Proteins. 1995 Sep; 23(1):38-48. PMID: 8539249.
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      39. Su Y, Dostmann WR, Herberg FW, Durick K, Xuong NH, Ten Eyck L, Taylor SS, Varughese KI. Regulatory subunit of protein kinase A: structure of deletion mutant with cAMP binding domains. Science. 1995 Aug 11; 269(5225):807-13. PMID: 7638597.
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      40. cAMP-dependent protein kinase: crystallographic insights into substrate recognition and phosphotransfer. Protein Sci. 1994 Feb; 3(2):176-87. PMID: 8003955.
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      41. Veron M, Radzio-Andzelm E, Tsigelny I, Ten Eyck L, Taylor SS. A conserved helix motif complements the protein kinase core. Proc Natl Acad Sci U S A. 1993 Nov 15; 90(22):10618-22. PMID: 7504272.
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      42. Zheng J, Knighton DR, Xuong NH, Taylor SS, Sowadski JM, Ten Eyck L. Crystal structures of the myristylated catalytic subunit of cAMP-dependent protein kinase reveal open and closed conformations. Protein Sci. 1993 Oct; 2(10):1559-73. PMID: 8251932.
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      43. Taylor SS, Zheng J, Radzio-Andzelm E, Knighton DR, Ten Eyck L, Sowadski JM, Herberg FW, Yonemoto WM. cAMP-dependent protein kinase defines a family of enzymes. Philos Trans R Soc Lond B Biol Sci. 1993 Jun 29; 340(1293):315-24. PMID: 8103934.
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      44. Knighton DR, Cadena DL, Zheng J, Ten Eyck L, Taylor SS, Sowadski JM, Gill GN. Structural features that specify tyrosine kinase activity deduced from homology modeling of the epidermal growth factor receptor. Proc Natl Acad Sci U S A. 1993 Jun 1; 90(11):5001-5. PMID: 8389462.
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      45. Knighton DR, Bell SM, Zheng J, Ten Eyck L, Xuong NH, Taylor SS, Sowadski JM. 2.0 A refined crystal structure of the catalytic subunit of cAMP-dependent protein kinase complexed with a peptide inhibitor and detergent. Acta Crystallogr D Biol Crystallogr. 1993 May 1; 49(Pt 3):357-61. PMID: 15299526.
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      46. Zheng J, Trafny EA, Knighton DR, Xuong NH, Taylor SS, Ten Eyck L, Sowadski JM. 2.2 A refined crystal structure of the catalytic subunit of cAMP-dependent protein kinase complexed with MnATP and a peptide inhibitor. Acta Crystallogr D Biol Crystallogr. 1993 May 1; 49(Pt 3):362-5. PMID: 15299527.
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      47. Zheng J, Knighton DR, ten Eyck LF, Karlsson R, Xuong N, Taylor SS, Sowadski JM. Crystal structure of the catalytic subunit of cAMP-dependent protein kinase complexed with MgATP and peptide inhibitor. Biochemistry. 1993 Mar 9; 32(9):2154-61. PMID: 8443157.
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      48. Taylor SS, Radzio-Andzelm E, Knighton DR, Ten Eyck L, Sowadski JM, Herberg FW, Yonemoto W, Zheng J. Crystal structures of the catalytic subunit of cAMP-dependent protein kinase reveal general features of the protein kinase family. Receptor. 1993; 3(3):165-72. PMID: 8167567.
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      49. Knighton DR, Pearson RB, Sowadski JM, Means AR, Ten Eyck L, Taylor SS, Kemp BE. Structural basis of the intrasteric regulation of myosin light chain kinases. Science. 1992 Oct 2; 258(5079):130-5. PMID: 1439761.
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      50. Taylor SS, Knighton DR, Zheng J, Ten Eyck L, Sowadski JM. cAMP-dependent protein kinase and the protein kinase family. Faraday Discuss. 1992; (93):143-52. PMID: 1290929.
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      51. Taylor SS, Knighton DR, Zheng J, Ten Eyck L, Sowadski JM. Structural framework for the protein kinase family. Annu Rev Cell Biol. 1992; 8:429-62. PMID: 1335745.
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      52. Knighton DR, Zheng JH, Ten Eyck L, Ashford VA, Xuong NH, Taylor SS, Sowadski JM. Crystal structure of the catalytic subunit of cyclic adenosine monophosphate-dependent protein kinase. Science. 1991 Jul 26; 253(5018):407-14. PMID: 1862342.
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      53. Knighton DR, Zheng JH, Ten Eyck L, Xuong NH, Taylor SS, Sowadski JM. Structure of a peptide inhibitor bound to the catalytic subunit of cyclic adenosine monophosphate-dependent protein kinase. Science. 1991 Jul 26; 253(5018):414-20. PMID: 1862343.
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      54. Ten Eyck L. Fast Fourier transform calculation of electron density maps. Methods Enzymol. 1985; 115:324-37. PMID: 3841183.
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      55. Remington SJ, Anderson WF, Owen J, Ten Eyck L, Grainger CT, Matthews BW. Structure of the lysozyme from bacteriophage T4: an electron density map at 2.4 A resolution. J Mol Biol. 1978 Jan 5; 118(1):81-98. PMID: 625058.
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      56. Weaver LH, Kester WR, Ten Eyck L, Matthews BW. The structure and stability of thermolysin. Experientia Suppl. 1976; 26:31-9. PMID: 820566.
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