Michael G. Fried, Ph.D. - Publications

Molecular and Cellular Biochemisry University of Kentucky, Lexington, KY 
Protein-nucleic acid interactions

88 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2017 Melikishvili M, Fried MG. Quaternary interactions and supercoiling modulate the cooperative DNA binding of AGT. Nucleic Acids Research. PMID 28575445 DOI: 10.1093/Nar/Gkx223  0.72
2016 Chicka MC, Ren Q, Richards D, Hellman LM, Zhang J, Fried MG, Whiteheart SW. Role of Munc13-4 as a Ca2+-dependent tether during platelet secretion. The Biochemical Journal. 473: 627-39. PMID 26637270 DOI: 10.1042/Bj20151150  0.92
2015 Tessmer I, Fried MG. Characterization of Homogeneous, Cooperative Protein-DNA Clusters by Sedimentation Equilibrium Analytical Ultracentrifugation and Atomic Force Microscopy. Methods in Enzymology. 562: 331-48. PMID 26412659 DOI: 10.1016/Bs.Mie.2015.06.036  1
2015 Melikishvili M, Fried MG. Resolving the contributions of two cooperative mechanisms to the DNA Binding of AGT. Biopolymers. 103: 509-16. PMID 26017689 DOI: 10.1002/Bip.22684  0.72
2015 Melikishvili M, Fried MG. Resolving the contributions of two cooperative mechanisms to the DNA Binding of AGT Biopolymers. 103: 509-516. DOI: 10.1002/bip.22684  1
2014 Hines CS, Ray K, Schmidt JJ, Xiong F, Feenstra RW, Pras-Raves M, de Moes JP, Lange JH, Melikishvili M, Fried MG, Mortenson P, Charlton M, Patel Y, Courtney SM, Kruse CG, et al. Allosteric inhibition of the neuropeptidase neurolysin. The Journal of Biological Chemistry. 289: 35605-19. PMID 25378390 DOI: 10.1074/Jbc.M114.620930  1
2014 Hellman LM, Spear TJ, Koontz CJ, Melikishvili M, Fried MG. Repair of O6-methylguanine adducts in human telomeric G-quadruplex DNA by O6-alkylguanine-DNA alkyltransferase. Nucleic Acids Research. 42: 9781-91. PMID 25080506 DOI: 10.1093/Nar/Gku659  0.92
2014 Tessmer I, Fried MG. Insight into the cooperative DNA binding of the O⁶-alkylguanine DNA alkyltransferase. Dna Repair. 20: 14-22. PMID 24553127 DOI: 10.1016/J.Dnarep.2014.01.006  1
2013 Smith EC, Smith SE, Carter JR, Webb SR, Gibson KM, Hellman LM, Fried MG, Dutch RE. Trimeric transmembrane domain interactions in paramyxovirus fusion proteins: roles in protein folding, stability, and function. The Journal of Biological Chemistry. 288: 35726-35. PMID 24178297 DOI: 10.1074/Jbc.M113.514554  1
2012 Song ES, Melikishvili M, Fried MG, Juliano MA, Juliano L, Rodgers DW, Hersh LB. Cysteine 904 is required for maximal insulin degrading enzyme activity and polyanion activation. Plos One. 7: e46790. PMID 23077523 DOI: 10.1371/Journal.Pone.0046790  1
2012 Melikishvili M, Fried MG. Lesion-specific DNA-binding and repair activities of human O⁶-alkylguanine DNA alkyltransferase. Nucleic Acids Research. 40: 9060-72. PMID 22810209 DOI: 10.1093/Nar/Gks674  1
2012 Tessmer I, Melikishvili M, Fried MG. Cooperative cluster formation, DNA bending and base-flipping by O6-alkylguanine-DNA alkyltransferase. Nucleic Acids Research. 40: 8296-308. PMID 22730295 DOI: 10.1093/Nar/Gks574  1
2012 Alexander KS, Fried MG, Farrell DH. Role of electrostatic interactions in binding of thrombin to the fibrinogen γ' chain. Biochemistry. 51: 3445-50. PMID 22439748 DOI: 10.1021/Bi2016519  1
2012 Smith EC, Culler MR, Hellman LM, Fried MG, Creamer TP, Dutch RE. Beyond anchoring: the expanding role of the hendra virus fusion protein transmembrane domain in protein folding, stability, and function. Journal of Virology. 86: 3003-13. PMID 22238302 DOI: 10.1128/Jvi.05762-11  1
2012 Popa A, Carter JR, Smith SE, Hellman L, Fried MG, Dutch RE. Residues in the hendra virus fusion protein transmembrane domain are critical for endocytic recycling. Journal of Virology. 86: 3014-26. PMID 22238299 DOI: 10.1128/Jvi.05826-11  1
2012 Shen M, Fried MG. Detection of RNA-Protein Complexes by Electrophoretic Mobility Shift Assay Alternative Pre-Mrna Splicing: Theory and Protocols. 182-198. DOI: 10.1002/9783527636778.ch17  1
2011 Chittuluru JR, Chaban Y, Monnet-Saksouk J, Carrozza MJ, Sapountzi V, Selleck W, Huang J, Utley RT, Cramet M, Allard S, Cai G, Workman JL, Fried MG, Tan S, Côté J, et al. Structure and nucleosome interaction of the yeast NuA4 and Piccolo-NuA4 histone acetyltransferase complexes. Nature Structural & Molecular Biology. 18: 1196-203. PMID 21984211 DOI: 10.1038/Nsmb.2128  1
2011 Melikishvili M, Rodgers DW, Fried MG. 6-Carboxyfluorescein and structurally similar molecules inhibit DNA binding and repair by O⁶-alkylguanine DNA alkyltransferase. Dna Repair. 10: 1193-202. PMID 21982443 DOI: 10.1016/J.Dnarep.2011.09.007  1
2011 Adams CA, Fried MG. Mutations that probe the cooperative assembly of O⁶-alkylguanine-DNA alkyltransferase complexes. Biochemistry. 50: 1590-8. PMID 21226457 DOI: 10.1021/Bi101970D  1
2011 Hellman LM, Zhao C, Melikishvili M, Tao X, Hopper JE, Whiteheart SW, Fried MG. Histidine-tag-directed chromophores for tracer analyses in the analytical ultracentrifuge. Methods (San Diego, Calif.). 54: 31-8. PMID 21187151 DOI: 10.1016/J.Ymeth.2010.12.033  0.92
2010 Burns LH, Adams CA, Riley SP, Jutras BL, Bowman A, Chenail AM, Cooley AE, Haselhorst LA, Moore AM, Babb K, Fried MG, Stevenson B. BpaB, a novel protein encoded by the Lyme disease spirochete's cp32 prophages, binds to erp Operator 2 DNA. Nucleic Acids Research. 38: 5443-55. PMID 20421207 DOI: 10.1093/Nar/Gkq284  1
2010 Parker MW, Hellman LM, Xu P, Fried MG, Vander Kooi CW. Furin processing of semaphorin 3F determines its anti-angiogenic activity by regulating direct binding and competition for neuropilin. Biochemistry. 49: 4068-75. PMID 20387901 DOI: 10.1021/Bi100327R  1
2010 Zhao C, Hellman LM, Zhan X, Bowman WS, Whiteheart SW, Fried MG. Hexahistidine-tag-specific optical probes for analyses of proteins and their interactions. Analytical Biochemistry. 399: 237-45. PMID 20036207 DOI: 10.1016/J.Ab.2009.12.028  0.92
2010 Hellman LM, Rodgers DW, Fried MG. Phenomenological partial-specific volumes for G-quadruplex DNAs. European Biophysics Journal : Ebj. 39: 389-96. PMID 19238377 DOI: 10.1007/S00249-009-0411-7  1
2009 Melikishvili M, Hellman LM, Fried MG. Use of DNA length variation to detect periodicities in positively cooperative, nonspecific binding. Methods in Enzymology. 466: 65-81. PMID 21609858 DOI: 10.1016/S0076-6879(09)66004-3  1
2009 Cooley AE, Riley SP, Kral K, Miller MC, DeMoll E, Fried MG, Stevenson B. DNA-binding by Haemophilus influenzae and Escherichia coli YbaB, members of a widely-distributed bacterial protein family. Bmc Microbiology. 9: 137. PMID 19594923 DOI: 10.1186/1471-2180-9-137  1
2009 Tubbs JL, Latypov V, Kanugula S, Butt A, Melikishvili M, Kraehenbuehl R, Fleck O, Marriott A, Watson AJ, Verbeek B, McGown G, Thorncroft M, Santibanez-Koref MF, Millington C, Arvai AS, ... ... Fried MG, et al. Flipping of alkylated DNA damage bridges base and nucleotide excision repair. Nature. 459: 808-13. PMID 19516334 DOI: 10.1038/Nature08076  1
2009 Adams CA, Melikishvili M, Rodgers DW, Rasimas JJ, Pegg AE, Fried MG. Topologies of complexes containing O6-alkylguanine-DNA alkyltransferase and DNA. Journal of Molecular Biology. 389: 248-63. PMID 19358853 DOI: 10.1016/J.Jmb.2009.03.067  1
2009 Riley SP, Bykowski T, Cooley AE, Burns LH, Babb K, Brissette CA, Bowman A, Rotondi M, Miller MC, DeMoll E, Lim K, Fried MG, Stevenson B. Borrelia burgdorferi EbfC defines a newly-identified, widespread family of bacterial DNA-binding proteins. Nucleic Acids Research. 37: 1973-83. PMID 19208644 DOI: 10.1093/Nar/Gkp027  1
2008 Melikishvili M, Rasimas JJ, Pegg AE, Fried MG. Interactions of human O(6)-alkylguanine-DNA alkyltransferase (AGT) with short double-stranded DNAs. Biochemistry. 47: 13754-63. PMID 19061338 DOI: 10.1021/Bi801666C  1
2008 Lu P, Rha GB, Melikishvili M, Wu G, Adkins BC, Fried MG, Chi YI. Structural basis of natural promoter recognition by a unique nuclear receptor, HNF4alpha. Diabetes gene product. The Journal of Biological Chemistry. 283: 33685-97. PMID 18829458 DOI: 10.1074/Jbc.M806213200  1
2008 Lu P, Liu J, Melikishvili M, Fried MG, Chi YI. Crystallization of hepatocyte nuclear factor 4 alpha (HNF4 alpha) in complex with the HNF1 alpha promoter element. Acta Crystallographica. Section F, Structural Biology and Crystallization Communications. 64: 313-7. PMID 18391435 DOI: 10.1107/S1744309108007136  1
2007 Hellman LM, Fried MG. Electrophoretic mobility shift assay (EMSA) for detecting protein-nucleic acid interactions. Nature Protocols. 2: 1849-61. PMID 17703195 DOI: 10.1038/Nprot.2007.249  1
2007 Rasimas JJ, Kar SR, Pegg AE, Fried MG. Interactions of human O6-alkylguanine-DNA alkyltransferase (AGT) with short single-stranded DNAs. The Journal of Biological Chemistry. 282: 3357-66. PMID 17138560 DOI: 10.1074/Jbc.M608876200  1
2007 Stickle DF, Fried MG. Cation binding linked to a sequence-specific CAP-DNA interaction. Biophysical Chemistry. 126: 106-16. PMID 16782261 DOI: 10.1016/J.Bpc.2006.05.016  1
2006 Song ES, Cady C, Fried MG, Hersh LB. Proteolytic fragments of insulysin (IDE) retain substrate binding but lose allosteric regulation. Biochemistry. 45: 15085-91. PMID 17154546 DOI: 10.1021/Bi061298U  1
2005 Song ES, Daily A, Fried MG, Juliano MA, Juliano L, Hersh LB. Mutation of active site residues of insulin-degrading enzyme alters allosteric interactions. The Journal of Biological Chemistry. 280: 17701-6. PMID 15749695 DOI: 10.1074/Jbc.M501896200  1
2005 Surguladze N, Patton S, Cozzi A, Fried MG, Connor JR. Characterization of nuclear ferritin and mechanism of translocation. The Biochemical Journal. 388: 731-40. PMID 15675895 DOI: 10.1042/Bj20041853  1
2004 Song ES, Juliano MA, Juliano L, Fried MG, Wagner SL, Hersh LB. ATP effects on insulin-degrading enzyme are mediated primarily through its triphosphate moiety. The Journal of Biological Chemistry. 279: 54216-20. PMID 15494400 DOI: 10.1074/Jbc.M411177200  1
2004 Surguladze N, Thompson KM, Beard JL, Connor JR, Fried MG. Interactions and reactions of ferritin with DNA. The Journal of Biological Chemistry. 279: 14694-702. PMID 14734543 DOI: 10.1074/Jbc.M313348200  1
2004 Rasimas JJ, Dalessio PA, Ropson IJ, Pegg AE, Fried MG. Active-site alkylation destabilizes human O6-alkylguanine DNA alkyltransferase. Protein Science : a Publication of the Protein Society. 13: 301-5. PMID 14691244 DOI: 10.1110/Ps.03319404  1
2004 Adams CA, Kar SR, Hopper JE, Fried MG. Self-association of the amino-terminal domain of the yeast TATA-binding protein. The Journal of Biological Chemistry. 279: 1376-82. PMID 14534318 DOI: 10.1074/Jbc.M307867200  1
2003 Daugherty MA, Fried MG. Analysis of transcription factor interactions at sedimentation equilibrium. Methods in Enzymology. 370: 349-69. PMID 14712659 DOI: 10.1016/S0076-6879(03)70031-7  1
2003 Rasimas JJ, Kanugula S, Dalessio PM, Ropson IJ, Fried MG, Pegg AE. Effects of zinc occupancy on human O6-alkylguanine-DNA alkyltransferase. Biochemistry. 42: 980-90. PMID 12549918 DOI: 10.1021/Bi026970B  1
2003 Rasimas JJ, Pegg AE, Fried MG. DNA-binding mechanism of O6-alkylguanine-DNA alkyltransferase. Effects of protein and DNA alkylation on complex stability. The Journal of Biological Chemistry. 278: 7973-80. PMID 12496275 DOI: 10.1074/Jbc.M211854200  1
2002 Fried MG, Stickle DF, Smirnakis KV, Adams C, MacDonald D, Lu P. Role of hydration in the binding of lac repressor to DNA. The Journal of Biological Chemistry. 277: 50676-82. PMID 12379649 DOI: 10.1074/Jbc.M208540200  1
2002 Thompson KJ, Fried MG, Ye Z, Boyer P, Connor JR. Regulation, mechanisms and proposed function of ferritin translocation to cell nuclei. Journal of Cell Science. 115: 2165-77. PMID 11973357  1
2002 Dyckman D, Fried MG. The Escherichia coli cyclic AMP receptor protein forms a 2:2 complex with RNA polymerase holoenzyme, in vitro. The Journal of Biological Chemistry. 277: 19064-70. PMID 11904295 DOI: 10.1074/Jbc.M110554200  1
2001 Kelly MA, Chellgren BW, Rucker AL, Troutman JM, Fried MG, Miller AF, Creamer TP. Host-guest study of left-handed polyproline II helix formation. Biochemistry. 40: 14376-83. PMID 11724549 DOI: 10.1021/Bi011043A  1
2001 Selleck W, Howley R, Fang Q, Podolny V, Fried MG, Buratowski S, Tan S. A histone fold TAF octamer within the yeast TFIID transcriptional coactivator. Nature Structural Biology. 8: 695-700. PMID 11473260 DOI: 10.1038/90408  1
2001 Fried MG, Daugherty MA. In vitro interaction of the Escherichia coli cyclic AMP receptor protein with the lactose repressor. The Journal of Biological Chemistry. 276: 11226-9. PMID 11152685 DOI: 10.1074/Jbc.M009087200  1
2000 Moaddel M, Farrell DH, Daugherty MA, Fried MG. Interactions of human fibrinogens with factor XIII: roles of calcium and the gamma' peptide. Biochemistry. 39: 6698-705. PMID 10828988 DOI: 10.1021/Bi000098U  1
2000 Daugherty MA, Brenowitz M, Fried MG. Participation of the amino-terminal domain in the self-association of the full-length yeast TATA binding protein. Biochemistry. 39: 4869-80. PMID 10769145 DOI: 10.1021/Bi992423N  1
1999 Daugherty MA, Brenowitz M, Fried MG. The TATA-binding protein from Saccharomyces cerevisiae oligomerizes in solution at micromolar concentrations to form tetramers and octamers. Journal of Molecular Biology. 285: 1389-99. PMID 9917384 DOI: 10.1006/Jmbi.1998.2427  1
1998 Fried MG, Daugherty MA. Electrophoretic analysis of multiple protein-DNA interactions. Electrophoresis. 19: 1247-53. PMID 9694259 DOI: 10.1002/Elps.1150190804  1
1998 Thompson K, Ye Z, Fried M, Connor J. H-ferritin binds to DNA and protects DNA from iron-induced oxidative damage Faseb Journal. 12: A1482.  1
1998 Fried MG, Bromberg JL. Changes in protein hydration during thermal denaturation of rnase A Faseb Journal. 12: A1436.  1
1997 Vossen KM, Wolz R, Daugherty MA, Fried MG. Role of macromolecular hydration in the binding of the Escherichia coli cyclic AMP receptor to DNA. Biochemistry. 36: 11640-7. PMID 9305953 DOI: 10.1021/Bi971193E  1
1997 Fried MG, Bromberg JL. Factors that affect the stability of protein-DNA complexes during gel electrophoresis. Electrophoresis. 18: 6-11. PMID 9059813 DOI: 10.1002/Elps.1150180103  1
1997 Vossen KM, Fried MG. Sequestration stabilizes lac repressor-DNA complexes during gel electrophoresis. Analytical Biochemistry. 245: 85-92. PMID 9025972 DOI: 10.1006/Abio.1996.9944  1
1997 Fried MG, Vossen KM. The role of water in CAP-DNA interactions Faseb Journal. 11: A1206.  1
1997 Farrell H, Fried MG, Falls LA. Characterization of factor xiii-γ/γ fibrinogen complexesd Faseb Journal. 11: A1264.  1
1997 Daugherty MA, Brenowitz M, Fried MG. Analytical ultracentrifugation studies on the self-association of yeast TBP Faseb Journal. 11: A1206.  1
1996 Fried MG, Hudson JM. DNA looping and lac repressor-CAP interaction. Science (New York, N.Y.). 274: 1930-1; author reply. PMID 8984648  1
1996 Perros M, Steitz TA. DNA looping and lac repressor-CAP interaction. Science (New York, N.Y.). 274: 1929-30; author repl. PMID 8984647 DOI: 10.1126/Science.274.5294.1929  1
1996 Fried MG, Kanugula S, Bromberg JL, Pegg AE. DNA binding mechanism of O6-alkylguanine-DNA alkyltransferase: stoichiometry and effects of DNA base composition and secondary structure on complex stability. Biochemistry. 35: 15295-301. PMID 8952480 DOI: 10.1021/Bi960971K  1
1996 Vossen KM, Stickle DF, Fried MG. The mechanism of CAP-lac repressor binding cooperativity at the E. coli lactose promoter. Journal of Molecular Biology. 255: 44-54. PMID 8568874 DOI: 10.1006/Jmbi.1996.0005  1
1995 Vossen KM, Fried MG. Stability of lac repressor-operator complexes in a new agarose-based gel matrix. Nucleic Acids Research. 23: 2346-7. PMID 7610068 DOI: 10.1093/Nar/23.12.2346  1
1994 Stickle DF, Vossen KM, Riley DA, Fried MG. Free DNA concentration in E. coli estimated by an analysis of competition for DNA binding proteins. Journal of Theoretical Biology. 168: 1-12. PMID 8022188 DOI: 10.1006/Jtbi.1994.1082  1
1994 Stickle DF, Liu G, Fried MG. Analysis of the thermodynamic linkage of DNA binding and ion binding for dimeric and tetrameric forms of the lac repressor. European Journal of Biochemistry / Febs. 226: 869-76. PMID 7813477 DOI: 10.1111/J.1432-1033.1994.00869.X  1
1994 Fried MG, Liu G. Molecular sequestration stabilizes CAP-DNA complexes during polyacrylamide gel electrophoresis. Nucleic Acids Research. 22: 5054-9. PMID 7800499 DOI: 10.1093/Nar/22.23.5054  1
1993 Gerstle JT, Fried MG. Measurement of binding kinetics using the gel electrophoresis mobility shift assay. Electrophoresis. 14: 725-31. PMID 8404816 DOI: 10.1002/Elps.11501401115  1
1993 Hudson JM, Crowe M, Fried MG. Effects of anions on the binding of the cAMP receptor protein to the lactose promoter. European Journal of Biochemistry / Febs. 212: 539-48. PMID 8383049 DOI: 10.1111/J.1432-1033.1993.Tb17691.X  1
1993 Fried MG, Stickle DF. Ion-exchange reactions of proteins during DNA binding. European Journal of Biochemistry / Febs. 218: 469-75. PMID 8269936 DOI: 10.1111/J.1432-1033.1993.Tb18398.X  1
1991 Hudson JM, Fried MG. The binding of cyclic AMP receptor protein to two lactose promoter sites is not cooperative in vitro. Journal of Bacteriology. 173: 59-66. PMID 1987134 DOI: 10.1128/Jb.173.1.59-66.1991  1
1990 Hudson JM, Crowe LG, Fried MG. A new DNA binding mode for CAP. The Journal of Biological Chemistry. 265: 3219-25. PMID 2406249  1
1990 Hudson JM, Fried MG. Co-operative interactions between the catabolite gene activator protein and the lac repressor at the lactose promoter. Journal of Molecular Biology. 214: 381-96. PMID 2166165 DOI: 10.1016/0022-2836(90)90188-R  1
1990 Fried MG. Cooperative interactions in transcriptional regulation. Saas Bulletin, Biochemistry and Biotechnology. 3: 1-7. PMID 1366505  1
1989 Hudson JM, Fried MG. A streamlined, low ionic strength DNase I footprinting reaction. Biotechniques. 7: 812-5. PMID 2698657  1
1989 Fried MG. Measurement of protein-DNA interaction parameters by electrophoresis mobility shift assay. Electrophoresis. 10: 366-76. PMID 2670548 DOI: 10.1002/Elps.1150100515  1
1984 Fried MG, Bloomfield VA. DNA gelation in concentrated solutions. Biopolymers. 23: 2141-55. PMID 6498295 DOI: 10.1002/Bip.360231104  1
1984 Fried MG, Crothers DM. Kinetics and mechanism in the reaction of gene regulatory proteins with DNA. Journal of Molecular Biology. 172: 263-82. PMID 6319716 DOI: 10.1016/S0022-2836(84)80026-1  1
1984 Fried MG, Crothers DM. Equilibrium studies of the cyclic AMP receptor protein-DNA interaction. Journal of Molecular Biology. 172: 241-62. PMID 6319715 DOI: 10.1016/S0022-2836(84)80025-X  1
1983 Fried MG, Wu HM, Crothers DM. CAP binding to B and Z forms of DNA. Nucleic Acids Research. 11: 2479-94. PMID 6344018 DOI: 10.1093/Nar/11.8.2479  1
1983 Fried MG, Crothers DM. CAP and RNA polymerase interactions with the lac promoter: binding stoichiometry and long range effects. Nucleic Acids Research. 11: 141-58. PMID 6306561 DOI: 10.1093/Nar/11.1.141  1
1982 Crothers DM, Fried M. Transmission of long-range effects in DNA Cold Spring Harbor Symposia On Quantitative Biology. 47: 263-269. PMID 6345058  1
1981 Fried M, Crothers DM. Equilibria and kinetics of lac repressor-operator interactions by polyacrylamide gel electrophoresis Nucleic Acids Research. 9: 6505-6525. DOI: 10.1093/Nar/9.23.6505  1
1980 McKay DB, Fried MG. Crystallization and preliminary X-ray diffraction data for the cyclic AMP receptor protein of Escherichia coli. Journal of Molecular Biology. 139: 95-6. PMID 7021851 DOI: 10.1016/0022-2836(80)90118-7  1
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