Electrophoretic mobility shift assay (EMSA) for detecting protein–nucleic acid interactions
- L. Hellman, M. Fried
- BiologyNature Protocols
- 1 August 2007
The most important factors that determine the stabilities and electrophoretic mobilities of complexes under assay conditions are identified and commonly used variants are discussed.
Equilibria and kinetics of lac repressor-operator interactions by polyacrylamide gel electrophoresis.
- M. Fried, D. Crothers
- Biology, ChemistryNucleic Acids Research
- 11 December 1981
Gel electrophoresis in studies of equilibrium binding, site distribution, and kinetics of protein-DNA interactions found that binding to the so-called third operator site (03) is 15-18 fold weaker than operator binding, and that the binding reactions with the first and third operators are uncoupled, implying that there is no communication between the sites.
A histone fold TAF octamer within the yeast TFIID transcriptional coactivator
- W. Selleck, Ryan Howley, Song Tan
- BiologyNature Structural Biology
- 1 August 2001
The results indicate that the TAF octamer is similar both in stoichiometry and histone fold interactions to the histone octamer component of chromatin.
Host-guest study of left-handed polyproline II helix formation.
- M. A. Kelly, B. W. Chellgren, T. Creamer
- Biology, ChemistryBiochemistry
- 4 December 2001
The formation of PPII helices by a short poly(proline) peptide is explored and it is postulated that propensities possessed by apolar residues are due in part to peptide-solvent interactions, and that the remarkably high propensity possessed by glutamine may be due to a side chain to backbone hydrogen bond.
Structure and nucleosome interaction of the yeast NuA4 and Piccolo-NuA4 histone acetyltransferase complexes
- J. Chittuluru, Y. Chaban, F. Asturias
- BiologyNature Structural &Molecular Biology
- 8 September 2011
EM and biochemistry are used to characterize the structure of NuA4, an essential yeast histone acetyltransferase (HAT) complex conserved throughout eukaryotes, and the interaction of Nu a4 with the nucleosome core particle (NCP) is determined.
Measurement of protein‐DNA interaction parameters by electrophoresis mobility shift assay
- M. Fried
- Biology, ChemistryElectrophoresis
How factors influence the acquisition of quantitative data from electrophoretic patterns and band intensities are discussed, and formulas for the estimation of equilibrium constants and rate constants for prototypical DNA‐protein interactions are presented.
Regulation, mechanisms and proposed function of ferritin translocation to cell nuclei.
- K. Thompson, M. Fried, Zheng Ye, Phillip Boyer, J. Connor
- BiologyJournal of Cell Science
- 15 May 2002
H-rich ferritin is present in the nucleus of human astrocytoma tumor cells and protected DNA from iron-induced oxidative damage in both in vitro and in cell culture models, suggesting a novel role for ferrit in nuclear protection.
Furin processing of semaphorin 3F determines its anti-angiogenic activity by regulating direct binding and competition for neuropilin.
- M. Parker, L. Hellman, P. Xu, M. Fried, C. V. Vander Kooi
- Biology, ChemistryBiochemistry
- 18 May 2010
This work demonstrates that furin activation of the C-terminus of Sema3F produces a species that potently inhibits the binding of VEGF to neuropilin, and provides a mechanistic basis for understanding the anti-angiogenic activity of semaphorin as well as the physical interaction and competition between neuro pilin ligands.
Characterization of nuclear ferritin and mechanism of translocation.
- N. Surguladze, S. Patton, A. Cozzi, M. Fried, J. Connor
- BiologyBiochemical Journal
- 15 June 2005
The results suggest that O-glycosylation accompanies the transfer of ferritin from the cytoplasm to the nucleus, but does not influence the reverse process, and the picture that emerges is one in whichferritin translocation between the cy toplasm and the nucleus is post-translationally regulated and responds to environmental and nutritional cues.
ATP Effects on Insulin-degrading Enzyme Are Mediated Primarily through Its Triphosphate Moiety*
- E. Song, M. Juliano, L. Juliano, M. Fried, S. Wagner, L. Hersh
- Biology, ChemistryJournal of Biological Chemistry
- 24 December 2004
It is reported here that with 2-aminobenzoyl-GGFLRKHGQ-ethylenediamine-2,4-dinitrophenyl as substrate, ATP and other nucleotides increase the rate >20-fold in Tris buffer, suggesting the presence of an allosteric regulatory site on insulysin that may shift its specificity toward small peptide substrates.