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Lynn Ten Eyck

TitleRecall Non-faculty Academic
InstitutionUniversity of California San Diego
DepartmentChemistry and Biochemistry
Address9500 Gilman Drive #0505
La Jolla CA 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; PMCID: PMC4045845.
    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; PMCID: PMC4370774.
    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; PMCID: PMC3401472.
    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; PMCID: PMC3348966.
    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; PMCID: PMC3264848.
    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; PMCID: PMC2786965.
    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; PMCID: PMC2533684.
    9. Kornev AP, Taylor SS, Ten Eyck L. A generalized allosteric mechanism for cis-regulated cyclic nucleotide binding domains. PLoS Comput Biol. 2008 Apr 11; 4(4):e1000056. PMID: 18404204; PMCID: PMC2275311.
    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.
      View in: PubMed
    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; PMCID: PMC3419600.
    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):1498-1509. PMID: 16875839.
      View in: PubMed
    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; PMCID: PMC2249778.
    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; PMCID: PMC2253214.
    15. Law D, Hotchko M, Ten Eyck L. Progress in computation and amide hydrogen exchange for prediction of protein-protein complexes. Proteins. 2005 Aug 01; 60(2):302-7. PMID: 15981246.
      View in: PubMed
    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.
      View in: PubMed
    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 04; 102(1):45-50. PMID: 15618393; PMCID: PMC544069.
    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 01; 43(21):6620-9. PMID: 15157095.
      View in: PubMed
    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.
      View in: PubMed
    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; PMCID: PMC263775.
    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.
      View in: PubMed
    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 01; 52(1):33-40. PMID: 12784365.
      View in: PubMed
    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.
      View in: PubMed
    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.
      View in: PubMed
    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.
      View in: PubMed
    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 07; 276(49):46469-79. PMID: 11591711.
      View in: PubMed
    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.
      View in: PubMed
    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. 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.
      View in: PubMed
    30. 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.
      View in: PubMed
    31. 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.
      View in: PubMed
    32. 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.
      View in: PubMed
    33. Narayana N, Cox S, Nguyen-huu X, Ten Eyck L, Taylor SS. A binary complex of the catalytic subunit of cAMP-dependent protein kinase and adenosine further defines conformational flexibility. Structure. 1997 Jul 15; 5(7):921-35. PMID: 9261084.
      View in: PubMed
    34. 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.
      View in: PubMed
    35. 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.
      View in: PubMed
    36. cAMP-dependent protein kinase: crystallographic insights into substrate recognition and phosphotransfer. Protein Sci. 1994 Feb; 3(2):176-87. PMID: 8003955; PMCID: PMC2142788.
    37. 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; PMCID: PMC47828.
    38. 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; PMCID: PMC2142252.
    39. 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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    40. 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 01; 90(11):5001-5. PMID: 8389462; PMCID: PMC46641.
    41. 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 01; 49(Pt 3):357-61. PMID: 15299526.
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    42. 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 01; 49(Pt 3):362-5. PMID: 15299527.
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    43. 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 09; 32(9):2154-61. PMID: 8443157.
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    44. 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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    45. 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 02; 258(5079):130-5. PMID: 1439761.
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    46. 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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    47. 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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    48. 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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    49. 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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    50. 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 05; 118(1):81-98. PMID: 625058.
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