Michael Gregory Fried | Molecular & Cellular Biochemistry

Michael Gregory Fried

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Michael.Fried@uky.edu
859-323-1205
BBSRB 259

Position(s):

Professor

Affiliation(s):

Molecular & Cellular Biochemistry

Bio / Education:

A.B. (Biology) Dartmouth College, 1976
Ph.D. (Molecular Biophysics) Yale University, 1982
Postdoctoral (Biochemistry) University of Minnesota, 1982-85

Research Description:

Protein-DNA and Protein-Protein Interactions
The assembly of macromolecular complexes is an essential step in many cellular processes. We are interested in the mechanisms that govern the assembly rates and the equilibrium stabilities of such complexes. We are currently exploring these issues for selected protein-DNA and protein-protein interactions.

1. Assembly of protein-DNA complexes.
Protein-DNA complexes play central roles in many of the transactions in which DNA is involved, including transcription, DNA replication, and chromosome structure. Our current work is focused on the DNA-repair protein O6-alkylguanine-DNA alkyltransferase (AGT). In humans this protein protects the integrity of the genome, but also contributes to the resistance of tumors to DNA-alkylating chemotherapeutic agents.

PubMed Publications:

Melikishvili, M.;Fried, M.G. "Quaternary interactions and supercoiling modulate the cooperative DNA binding of AGT." Nucleic acids research (2017): [PubMed Link] | [ Full text ]
Chicka, M.C.;Ren, Q.;Richards, D.;Hellman, L.M.;Zhang, J.;Fried, M.G.;Whiteheart, S.W. "Role of Munc13-4 as a Ca2+-dependent tether during platelet secretion." The Biochemical journal 473, 5 (2016): 627-39. [PubMed Link] | [ Full text ]
Melikishvili, M.;Fried, M.G. "Resolving the contributions of two cooperative mechanisms to the DNA binding of AGT." Biopolymers 103, 9 (2015): 509-16. [PubMed Link] | [ Full text ]
Tessmer, I.;Fried, M.G. "Characterization of Homogeneous, Cooperative Protein-DNA Clusters by Sedimentation Equilibrium Analytical Ultracentrifugation and Atomic Force Microscopy." Methods in enzymology 562, (2015): 331-48. [PubMed Link] | [ Full text ]
Hellman, L.M.;Spear, T.J.;Koontz, C.J.;Melikishvili, M.;Fried, M.G. "Repair of O6-methylguanine adducts in human telomeric G-quadruplex DNA by O6-alkylguanine-DNA alkyltransferase." Nucleic acids research 42, 15 (2014): 9781-91. [PubMed Link] | [ Full text ]
Hines, C.S.;Ray, K.;Schmidt, J.J.;Xiong, F.;Feenstra, R.W.;Pras-Raves, M.;Moes, J.P.;Lange, J.H.;Melikishvili, M.;Fried, M.G.;Mortenson, P.;Charlton, M.;Patel, Y.;Courtney, S.M.;Kruse, C.G.;Rodgers, D.W. "Allosteric inhibition of the neuropeptidase neurolysin." The Journal of biological chemistry 289, 51 (2014): 35605-19. [PubMed Link] | [ Full text ]
Tessmer, I.;Fried, M.G. "Insight into the cooperative DNA binding of the O⁶-alkylguanine DNA alkyltransferase." DNA repair 20, (2014): 14-22. [PubMed Link] | [ Full text ]
Smith, E.C.;Smith, S.E.;Carter, J.R.;Webb, S.R.;Gibson, K.M.;Hellman, L.M.;Fried, M.G.;Dutch, R.E. "Trimeric transmembrane domain interactions in paramyxovirus fusion proteins: roles in protein folding, stability, and function." The Journal of biological chemistry 288, 50 (2013): 35726-35. [PubMed Link] | [ Full text ]
Tessmer, I.;Melikishvili, M.;Fried, M.G. "Cooperative cluster formation, DNA bending and base-flipping by O6-alkylguanine-DNA alkyltransferase." Nucleic acids research 40, 17 (2012): 8296-308. [PubMed Link] | [ Full text ]
Melikishvili, M.;Fried, M.G. "Lesion-specific DNA-binding and repair activities of human O⁶-alkylguanine DNA alkyltransferase." Nucleic acids research 40, 18 (2012): 9060-72. [PubMed Link] | [ Full text ]
Smith, E.C.;Culler, M.R.;Hellman, L.M.;Fried, M.G.;Creamer, T.P.;Dutch, R.E. "Beyond anchoring: the expanding role of the hendra virus fusion protein transmembrane domain in protein folding, stability, and function." Journal of virology 86, 6 (2012): 3003-13. [PubMed Link] | [ Full text ]
Popa, A.;Carter, J.R.;Smith, S.E.;Hellman, L.;Fried, M.G.;Dutch, R.E. "Residues in the hendra virus fusion protein transmembrane domain are critical for endocytic recycling." Journal of virology 86, 6 (2012): 3014-26. [PubMed Link] | [ Full text ]
Moeller, A.;Zhao, C.;Fried, M.G.;Wilson-Kubalek, E.M.;Carragher, B.;Whiteheart, S.W. "Nucleotide-dependent conformational changes in the N-Ethylmaleimide Sensitive Factor (NSF) and their potential role in SNARE complex disassembly." Journal of structural biology 177, 2 (2012): 335-43. [PubMed Link] | [ Full text ]
Alexander, K.S.;Fried, M.G.;Farrell, D.H. "Role of electrostatic interactions in binding of thrombin to the fibrinogen γ' chain." Biochemistry 51, 16 (2012): 3445-50. [PubMed Link] | [ Full text ]
Song, E.S.;Melikishvili, M.;Fried, M.G.;Juliano, M.A.;Juliano, L.;Rodgers, D.W.;Hersh, L.B. "Cysteine 904 is required for maximal insulin degrading enzyme activity and polyanion activation." PloS one 7, 10 (2012): e46790. [PubMed Link] | [ Full text ]
Chittuluru, J.R.;Chaban, Y.;Monnet-Saksouk, J.;Carrozza, M.J.;Sapountzi, V.;Selleck, W.;Huang, J.;Utley, R.T.;Cramet, M.;Allard, S.;Cai, G.;Workman, J.L.;Fried, M.G.;Tan, S.;Côté, J.;Asturias, F.J. "Structure and nucleosome interaction of the yeast NuA4 and Piccolo-NuA4 histone acetyltransferase complexes." Nature structural & molecular biology 18, 11 (2011): 1196-203. [PubMed Link] | [ Full text ]
Hellman, L.M.;Zhao, C.;Melikishvili, M.;Tao, X.;Hopper, J.E.;Whiteheart, S.W.;Fried, M.G. "Histidine-tag-directed chromophores for tracer analyses in the analytical ultracentrifuge." Methods (San Diego, Calif.) 54, 1 (2011): 31-8. [PubMed Link] | [ Full text ]
Adams, C.A.;Fried, M.G. "Mutations that probe the cooperative assembly of O⁶-alkylguanine-DNA alkyltransferase complexes." Biochemistry 50, 10 (2011): 1590-8. [PubMed Link] | [ Full text ]
Melikishvili, M.;Rodgers, D.W.;Fried, M.G. "6-Carboxyfluorescein and structurally similar molecules inhibit DNA binding and repair by O⁶-alkylguanine DNA alkyltransferase." DNA repair 10, 12 (2011): 1193-202. [PubMed Link] | [ Full text ]
Burns, L.H.;Adams, C.A.;Riley, S.P.;Jutras, B.L.;Bowman, A.;Chenail, A.M.;Cooley, A.E.;Haselhorst, L.A.;Moore, A.M.;Babb, K.;Fried, M.G.;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, 16 (2010): 5443-55. [PubMed Link] | [ Full text ]
Parker, M.W.;Hellman, L.M.;Xu, P.;Fried, M.G.;Vander Kooi, C.W. "Furin processing of semaphorin 3F determines its anti-angiogenic activity by regulating direct binding and competition for neuropilin." Biochemistry 49, 19 (2010): 4068-75. [PubMed Link] | [ Full text ]
Hellman, L.M.;Rodgers, D.W.;Fried, M.G. "Phenomenological partial-specific volumes for G-quadruplex DNAs." European biophysics journal : EBJ 39, 3 (2010): 389-96. [PubMed Link] | [ Full text ]
Zhao, C.;Hellman, L.M.;Zhan, X.;Bowman, W.S.;Whiteheart, S.W.;Fried, M.G. "Hexahistidine-tag-specific optical probes for analyses of proteins and their interactions." Analytical biochemistry 399, 2 (2010): 237-45. [PubMed Link] | [ Full text ]
Adams, C.A.;Melikishvili, M.;Rodgers, D.W.;Rasimas, J.J.;Pegg, A.E.;Fried, M.G. "Topologies of complexes containing O6-alkylguanine-DNA alkyltransferase and DNA." Journal of molecular biology 389, 2 (2009): 248-63. [PubMed Link] | [ Full text ]
Tubbs, J.L.;Latypov, V.;Kanugula, S.;Butt, A.;Melikishvili, M.;Kraehenbuehl, R.;Fleck, O.;Marriott, A.;Watson, A.J.;Verbeek, B.;McGown, G.;Thorncroft, M.;Santibanez-Koref, M.F.;Millington, C.;Arvai, A.S.;Kroeger, M.D.;Peterson, L.A.;Williams, D.M.;Fried, M.G.;Margison, G.P.;Pegg, A.E.;Tainer, J.A. "Flipping of alkylated DNA damage bridges base and nucleotide excision repair." Nature 459, 7248 (2009): 808-13. [PubMed Link] | [ Full text ]
Cooley, A.E.;Riley, S.P.;Kral, K.;Miller, M.C.;DeMoll, E.;Fried, M.G.;Stevenson, B. "DNA-binding by Haemophilus influenzae and Escherichia coli YbaB, members of a widely-distributed bacterial protein family." BMC microbiology 9, (2009): 137. [PubMed Link] | [ Full text ]
Riley, S.P.;Bykowski, T.;Cooley, A.E.;Burns, L.H.;Babb, K.;Brissette, C.A.;Bowman, A.;Rotondi, M.;Miller, M.C.;DeMoll, E.;Lim, K.;Fried, M.G.;Stevenson, B. "Borrelia burgdorferi EbfC defines a newly-identified, widespread family of bacterial DNA-binding proteins." Nucleic acids research 37, 6 (2009): 1973-83. [PubMed Link] | [ Full text ]
Melikishvili, M.;Hellman, L.M.;Fried, M.G. "Use of DNA length variation to detect periodicities in positively cooperative, nonspecific binding." Methods in enzymology 466, (2009): 65-81. [PubMed Link] | [ Full text ]
Lu, P.;Rha, G.B.;Melikishvili, M.;Wu, G.;Adkins, B.C.;Fried, M.G.;Chi, Y.I. "Structural basis of natural promoter recognition by a unique nuclear receptor, HNF4alpha. Diabetes gene product." The Journal of biological chemistry 283, 48 (2008): 33685-97. [PubMed Link] | [ Full text ]
Melikishvili, M.;Rasimas, J.J.;Pegg, A.E.;Fried, M.G. "Interactions of human O(6)-alkylguanine-DNA alkyltransferase (AGT) with short double-stranded DNAs." Biochemistry 47, 52 (2008): 13754-63. [PubMed Link] | [ Full text ]
Lu, P.;Liu, J.;Melikishvili, M.;Fried, M.G.;Chi, Y.I. "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, Pt 4 (2008): 313-7. [PubMed Link] | [ Full text ]
Stickle, D.F.;Fried, M.G. "Cation binding linked to a sequence-specific CAP-DNA interaction." Biophysical chemistry 126, 1-3 (2007): 106-16. [PubMed Link] | [ Full text ]
Rasimas, J.J.;Kar, S.R.;Pegg, A.E.;Fried, M.G. "Interactions of human O6-alkylguanine-DNA alkyltransferase (AGT) with short single-stranded DNAs." The Journal of biological chemistry 282, 5 (2007): 3357-66. [PubMed Link] | [ Full text ]
Hellman, L.M.;Fried, M.G. "Electrophoretic mobility shift assay (EMSA) for detecting protein-nucleic acid interactions." Nature protocols 2, 8 (2007): 1849-61. [PubMed Link] | [ Full text ]
Song, E.S.;Cady, C.;Fried, M.G.;Hersh, L.B. "Proteolytic fragments of insulysin (IDE) retain substrate binding but lose allosteric regulation." Biochemistry 45, 50 (2006): 15085-91. [PubMed Link] | [ Full text ]
Song, E.S.;Daily, A.;Fried, M.G.;Juliano, M.A.;Juliano, L.;Hersh, L.B. "Mutation of active site residues of insulin-degrading enzyme alters allosteric interactions." The Journal of biological chemistry 280, 18 (2005): 17701-6. [PubMed Link] | [ Full text ]
Surguladze, N.;Patton, S.;Cozzi, A.;Fried, M.G.;Connor, J.R. "Characterization of nuclear ferritin and mechanism of translocation." The Biochemical journal 388, Pt 3 (2005): 731-40. [PubMed Link] | [ Full text ]
Adams, C.A.;Kar, S.R.;Hopper, J.E.;Fried, M.G. "Self-association of the amino-terminal domain of the yeast TATA-binding protein." The Journal of biological chemistry 279, 2 (2004): 1376-82. [PubMed Link] | [ Full text ]
Rasimas, J.J.;Dalessio, P.A.;Ropson, I.J.;Pegg, A.E.;Fried, M.G. "Active-site alkylation destabilizes human O6-alkylguanine DNA alkyltransferase." Protein science : a publication of the Protein Society 13, 1 (2004): 301-5. [PubMed Link] | [ Full text ]
Song, E.S.;Juliano, M.A.;Juliano, L.;Fried, M.G.;Wagner, S.L.;Hersh, L.B. "ATP effects on insulin-degrading enzyme are mediated primarily through its triphosphate moiety." The Journal of biological chemistry 279, 52 (2004): 54216-20. [PubMed Link] | [ Full text ]
Surguladze, N.;Thompson, K.M.;Beard, J.L.;Connor, J.R.;Fried, M.G. "Interactions and reactions of ferritin with DNA." The Journal of biological chemistry 279, 15 (2004): 14694-702. [PubMed Link] | [ Full text ]
Rasimas, J.J.;Pegg, A.E.;Fried, M.G. "DNA-binding mechanism of O6-alkylguanine-DNA alkyltransferase. Effects of protein and DNA alkylation on complex stability." The Journal of biological chemistry 278, 10 (2003): 7973-80. [PubMed Link] | [ Full text ]
Rasimas, J.J.;Kanugula, S.;Dalessio, P.M.;Ropson, I.J.;Fried, M.G.;Pegg, A.E. "Effects of zinc occupancy on human O6-alkylguanine-DNA alkyltransferase." Biochemistry 42, 4 (2003): 980-90. [PubMed Link] | [ Full text ]
Daugherty, M.A.;Fried, M.G. "Analysis of transcription factor interactions at sedimentation equilibrium." Methods in enzymology 370, (2003): 349-69. [PubMed Link] | [ Full text ]
Dyckman, D.;Fried, M.G. "The Escherichia coli cyclic AMP receptor protein forms a 2:2 complex with RNA polymerase holoenzyme, in vitro." The Journal of biological chemistry 277, 21 (2002): 19064-70. [PubMed Link] | [ Full text ]
Thompson, K.J.;Fried, M.G.;Ye, Z.;Boyer, P.;Connor, J.R. "Regulation, mechanisms and proposed function of ferritin translocation to cell nuclei." Journal of cell science 115, Pt 10 (2002): 2165-77. [PubMed Link] | [ Full text ]
Fried, M.G.;Stickle, D.F.;Smirnakis, K.V.;Adams, C.;MacDonald, D.;Lu, P. "Role of hydration in the binding of lac repressor to DNA." The Journal of biological chemistry 277, 52 (2002): 50676-82. [PubMed Link] | [ Full text ]
Kelly, M.A.;Chellgren, B.W.;Rucker, A.L.;Troutman, J.M.;Fried, M.G.;Miller, A.F.;Creamer, T.P. "Host-guest study of left-handed polyproline II helix formation." Biochemistry 40, 48 (2001): 14376-83. [PubMed Link] | [ Full text ]
Selleck, W.;Howley, R.;Fang, Q.;Podolny, V.;Fried, M.G.;Buratowski, S.;Tan, S. "A histone fold TAF octamer within the yeast TFIID transcriptional coactivator." Nature structural biology 8, 8 (2001): 695-700. [PubMed Link] | [ Full text ]
Fried, M.G.;Daugherty, M.A. "In vitro interaction of the Escherichia coli cyclic AMP receptor protein with the lactose repressor." The Journal of biological chemistry 276, 14 (2001): 11226-9. [PubMed Link] | [ Full text ]
Moaddel, M.;Farrell, D.H.;Daugherty, M.A.;Fried, M.G. "Interactions of human fibrinogens with factor XIII: roles of calcium and the gamma' peptide." Biochemistry 39, 22 (2000): 6698-705. [PubMed Link] | [ Full text ]
Daugherty, M.A.;Brenowitz, M.;Fried, M.G. "Participation of the amino-terminal domain in the self-association of the full-length yeast TATA binding protein." Biochemistry 39, 16 (2000): 4869-80. [PubMed Link] | [ Full text ]
Daugherty, M.A.;Brenowitz, M.;Fried, M.G. "The TATA-binding protein from Saccharomyces cerevisiae oligomerizes in solution at micromolar concentrations to form tetramers and octamers." Journal of molecular biology 285, 4 (1999): 1389-99. [PubMed Link] | [ Full text ]
Fried, M.G.;Daugherty, M.A. "Electrophoretic analysis of multiple protein-DNA interactions." Electrophoresis 19, 8-9 (1998): 1247-53. [PubMed Link] |
Vossen, K.M.;Wolz, R.;Daugherty, M.A.;Fried, M.G. "Role of macromolecular hydration in the binding of the Escherichia coli cyclic AMP receptor to DNA." Biochemistry 36, 39 (1997): 11640-7. [PubMed Link] | [ Full text ]
Fried, M.G.;Bromberg, J.L. "Factors that affect the stability of protein-DNA complexes during gel electrophoresis." Electrophoresis 18, 1 (1997): 6-11. [PubMed Link] |
Vossen, K.M.;Fried, M.G. "Sequestration stabilizes lac repressor-DNA complexes during gel electrophoresis." Analytical biochemistry 245, 1 (1997): 85-92. [PubMed Link] | [ Full text ]
Vossen, K.M.;Stickle, D.F.;Fried, M.G. "The mechanism of CAP-lac repressor binding cooperativity at the E. coli lactose promoter." Journal of molecular biology 255, 1 (1996): 44-54. [PubMed Link] | [ Full text ]
Fried, M.G.;Kanugula, S.;Bromberg, J.L.;Pegg, A.E. "DNA binding mechanism of O6-alkylguanine-DNA alkyltransferase: stoichiometry and effects of DNA base composition and secondary structure on complex stability." Biochemistry 35, 48 (1996): 15295-301. [PubMed Link] | [ Full text ]
Fried, M.G.;Hudson, J.M. "DNA looping and lac repressor-CAP interaction." Science (New York, N.Y.) 274, 5294 (1996): 1930-1; author reply 1931-2. [PubMed Link] | [ Full text ]
Vossen, K.M.;Fried, M.G. "Stability of lac repressor-operator complexes in a new agarose-based gel matrix." Nucleic acids research 23, 12 (1995): 2346-7. [PubMed Link] |
Fried, M.G.;Liu, G. "Molecular sequestration stabilizes CAP-DNA complexes during polyacrylamide gel electrophoresis." Nucleic acids research 22, 23 (1994): 5054-9. [PubMed Link] |
Stickle, D.F.;Vossen, K.M.;Riley, D.A.;Fried, M.G. "Free DNA concentration in E. coli estimated by an analysis of competition for DNA binding proteins." Journal of theoretical biology 168, 1 (1994): 1-12. [PubMed Link] | [ Full text ]
Stickle, D.F.;Liu, G.;Fried, M.G. "Analysis of the thermodynamic linkage of DNA binding and ion binding for dimeric and tetrameric forms of the lac repressor." European journal of biochemistry 226, 3 (1994): 869-76. [PubMed Link] | [ Full text ]
Hudson, J.M.;Crowe, M.;Fried, M.G. "Effects of anions on the binding of the cAMP receptor protein to the lactose promoter." European journal of biochemistry 212, 2 (1993): 539-48. [PubMed Link] | [ Full text ]
Fried, M.G.;Stickle, D.F. "Ion-exchange reactions of proteins during DNA binding." European journal of biochemistry 218, 2 (1993): 469-75. [PubMed Link] | [ Full text ]
Gerstle, J.T.;Fried, M.G. "Measurement of binding kinetics using the gel electrophoresis mobility shift assay." Electrophoresis 14, 8 (1993): 725-31. [PubMed Link] |
Erickson, D.R.;Hlavinka, T.C.;Rockwood, A.P.;Metter, J.D.;Novicki, D.E.;Fried, M.G. "Prostatic acid phosphatase, beta-glucuronidase and prostate specific antigen assays in fine needle aspirates from benign and malignant prostates." The Journal of urology 146, 5 (1991): 1402-7. [PubMed Link] |
Hudson, J.M.;Fried, M.G. "The binding of cyclic AMP receptor protein to two lactose promoter sites is not cooperative in vitro." Journal of bacteriology 173, 1 (1991): 59-66. [PubMed Link] | [ Full text ]
Hudson, J.M.;Fried, M.G. "Co-operative interactions between the catabolite gene activator protein and the lac repressor at the lactose promoter." Journal of molecular biology 214, 2 (1990): 381-96. [PubMed Link] | [ Full text ]
Fried, M.G. "Cooperative interactions in transcriptional regulation." SAAS bulletin, biochemistry and biotechnology 3, (1990): 1-7. [PubMed Link] |
Hudson, J.M.;Crowe, L.G.;Fried, M.G. "A new DNA binding mode for CAP." The Journal of biological chemistry 265, 6 (1990): 3219-25. [PubMed Link] | [ Full text ]
Hudson, J.M.;Fried, M.G. "A streamlined, low ionic strength DNase I footprinting reaction." BioTechniques 7, 8 (1989): 812-5. [PubMed Link] |
Fried, M.G.;Bloomfield, V.A. "DNA gelation in concentrated solutions." Biopolymers 23, 11 Pt 1 (1984): 2141-55. [PubMed Link] | [ Full text ]
Fried, M.G.;Crothers, D.M. "Kinetics and mechanism in the reaction of gene regulatory proteins with DNA." Journal of molecular biology 172, 3 (1984): 263-82. [PubMed Link] |
Fried, M.G.;Crothers, D.M. "Equilibrium studies of the cyclic AMP receptor protein-DNA interaction." Journal of molecular biology 172, 3 (1984): 241-62. [PubMed Link] |
Fried, M.G.;Crothers, D.M. "CAP and RNA polymerase interactions with the lac promoter: binding stoichiometry and long range effects." Nucleic acids research 11, 1 (1983): 141-58. [PubMed Link] |
Fried, M.G.;Wu, H.M.;Crothers, D.M. "CAP binding to B and Z forms of DNA." Nucleic acids research 11, 8 (1983): 2479-94. [PubMed Link] |
McKay, D.B.;Fried, M.G. "Crystallization and preliminary X-ray diffraction data for the cyclic AMP receptor protein of Escherichia coli." Journal of molecular biology 139, 1 (1980): 95-6. [PubMed Link] | [ Full text ]
Cohen, R.J.;Fried, M.G.;Atkinson, M.M. "Olfactory responses of Phycomyces blakesleeanus." Biochemical and biophysical research communications 86, 3 (1979): 877-84. [PubMed Link] | [ Full text ]