Gene V protein of fd bacteriophage. Dimer formation and the role of tyrosyl groups in DNA binding.

Pretorius, Harold T.; Klein, Michèle; Day, Loren A.

doi:10.1016/s0021-9258(19)40638-8

Cited by 81 publications

(27 citation statements)

References 36 publications

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“…In practical terms, this means that for in Vitro experiments carried out in the micromolar concentration range the gene V protein is always a dimer, and monomerdimer equilibria may safely be neglected. Although this conclusion is, as described in the introduction, at variance with some earlier work using equilibrium ultracentrifugation (Cavalieri et al, 1976;Oey et al, 1972;Porschke et al, 1983;Pretorius et al, 1975), it is in good agreement with more recent work on the properties of gene V protein in solutions containing guanidine hydrochloride (Liang et al, 1991). The concentration dependence of folding of the gene V protein in solutions containing 2.7 M guanidine hydrochloride demonstrates that the folded form of the protein is a dimer even at this high concentration of denaturant.…”

Section: Resultssupporting

confidence: 88%

“…Sucrose gradient sedimentation velocity experiments gave a somewhat different result, indicating that the protein was monomeric in 0.2 M KCl in the presence of sucrose (Oey et al, 1972). High concentrations of NaCl (0.68 M) were found in another equilibrium ultracentrifugation study to dissociate the gene V protein dimer (Pretorius et al, 1975).…”

mentioning

confidence: 96%

“…Despite the many biophysical studies carried out on the gene V protein, two of the important properties of the protein, the oligomeric state of the protein at micromolar concentrations and the cooperativity of binding to single-stranded nucleic acids, are still not precisely defined. The gene V protein is known to exist predominantly as a dimer when it is present at high concentrations (>10 -5 M) in solutions containing low to moderate concentrations of salt (0.15 M NaCl or lower) (Cavalieri et al, 1976;Oey & Knippers, 1972;Porschke & Rauh, 1983;Pretorius et al, 1975), and the crystal and NMR structures of the protein clearly show a dimer with extensive interactions between subunits (Skinner et al, 1994). The concentration of the gene V protein in ViVo inside an infected E. coli cell is high enough (10 -4 M) that the functional form of the protein is certainly the dimer (Alberts et al, 1972).…”

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confidence: 99%

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Gene V Protein Dimerization and Cooperativity of Binding to Poly(dA)

Terwilliger

1996

Biochemistry

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Gene V protein of bacteriophage f1 is a dimeric protein that binds cooperatively to single-stranded nucleic acids. In order to determine whether a monomer-dimer equilibrium has an appreciable effect upon the thermodynamics of gene V protein binding to nucleic acids, the dissociation constant for the protein dimer was investigated using size-exclusion chromatography. At concentrations ranging from 5 x 10(-10) to 1.2 x 10(-5) M, the Stokes radius of the protein was that expected of the dimer of the gene V protein. The Stokes radius of the protein was also independent of salt concentration from 0.2 to 1.0 M NaCl in a buffer containing 10 mM Tris-HCl, pH 7.4, and 1 mM EDTA. The binding of the dimeric gene V protein to poly(dA) was studied using a simplified lattice model for protein-protein interactions adapted for use with a dimeric protein that binds simultaneously to two strands of nucleic acid. Interpretation of the salt dependence, C = [d log(Kint omega)]/[d log(NaCl)], of binding of such a dimeric protein to nucleic acid using the theory of Record et al. (Record, M. T., et al. (1976) J. Mol. Biol. 107, 145-158) indicates that C is a function of the numbers of cations and anions released from protein and nucleic acid upon binding of the dimer, not of the monomer. Cooperativity of gene V protein binding to poly(dA) was studied with titration experiments that are sensitive to the degree of cooperativity of binding. The cooperativity factor omega, defined as the ratio of the binding constant for a site adjacent to a previously bound dimer to that for an isolated site, was found to be relatively insensitive to salt, with a value in the range of 2000-7000 for binding to poly(dA) at 3 degrees C and at 23 degrees C. This high cooperativity factor supports the suggestion that protein-protein contacts play a major role in the formation of the superhelical gene V protein-single-stranded nucleic acid complex.

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Section: Resultssupporting

confidence: 88%

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confidence: 96%

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Gene V Protein Dimerization and Cooperativity of Binding to Poly(dA)

Terwilliger

1996

Biochemistry

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“…While neither the tyrosine fluorescence nor the circular dichroism spectrum is affected by the monomer-dimer equilibrium, both optical signals are perturbed upon binding of the protein to fd-DNA or to poly(dT). Pretorius et al (109) interpreted the quenching of the gene V protein tyrosine fluorescence as being consistent with reports in the literature that tyrosine is totally quenched on stacking with DNA. They concluded that three of the five tyrosines per gene V monomer were involved in stacking interactions with bases.…”

Section: Nucleic Acid-binding Proteinssupporting

confidence: 84%

“…The gene V protein of fd bacteriophage is required for replication of viral DNA in infected Escherichia coli cells. Pretorius et al (109) have shown that the gene V protein exists principally as a dimer at neutral pH and physiological salt concentrations (0.15 M). Higher concentrations of NaCl or disrupt the dimer.…”

Section: Nucleic Acid-binding Proteinsmentioning

confidence: 99%

Tyrosine Fluorescence and Phosphorescence from Proteins and Polypeptides

Ross

Laws

Rousslang

et al.

Topics in Fluorescence Spectroscopy

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The fluorescence and phosphorescence of proteins and polypeptides is the sum of the contributions from the three aromatic amino acids tryptophan, tyrosine, and phenylalanine. The work on protein and polypeptide luminescence prior to 1971 has been reviewed in detail by Longworth. (1) Another fine account of the early work, emphasizing tryptophan and tyrosine, is the monograph by Konev. (2) An excellent review on tyrosine fluorescence in proteins and model peptides, for the period up to 1975, is given by Cowgill. (3) In 1984, Creed (4) reviewed the photophysics and photochemistry of tyrosine and its simple derivatives, including a thorough coverage of steady-state fluorescence and a brief discussion of triplet-state properties, but did not include any work on proteins or polypeptides.The first quantitative studies of the excited-state properties of the three aromatic amino acids were carried out in the 1950s. The low-temperature phosphorescence of the aromatic amino acids was initially observed by Debye and Edwards (5) in 1952, and phosphorescence emission spectra were reported by Steele and Szent-Gyorgyi (6) in 1957. In 1953, Weber (7) postulated that the fluorescence of the aromatic amino acids should occur in the near-ultraviolet region of the electromagnetic spectrum. In 1956, independently and almost simultaneously, Duggan and Udenfriend (8) and Shore and Pardee (9) reported the results of their investigations of protein fluorescence. At the same time,

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Structure of the dna binding cleft of the gene 5 protein from bacteriophage fd

et al. 1979

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The structure of the gene 5 DNA unwinding protein from bacteriophage fd has been solved to 2.3-A resolution by X-ray diffraction techniques. The molecule contains an extensive cleft region that we have identified as the DNA binding site on the basis of the residues that comprise its surface. The interior of the groove has a rather large number of basic amino acid residues that serve to draw the polynucleotide backbone into the cleft. Arrayed along the external edges of the groove are a number of aromatic amino acid side groups that are in position to stack upon the bases of the DNA and fix it in place. The structure and binding mechanism as we visualize it appear to be fully consistent with evidence provided by physical-chemical studies of the protein in solution.

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Gene V protein of fd bacteriophage. Dimer formation and the role of tyrosyl groups in DNA binding.

Cited by 81 publications

References 36 publications

Gene V Protein Dimerization and Cooperativity of Binding to Poly(dA)

Gene V Protein Dimerization and Cooperativity of Binding to Poly(dA)

Tyrosine Fluorescence and Phosphorescence from Proteins and Polypeptides

Structure of the dna binding cleft of the gene 5 protein from bacteriophage fd

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