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D T Dryden

Publications and source records attributed to D T Dryden.

31 records · Page 2Linked to original sources
PubMed1995

Mutational analysis of conserved amino-acid motifs in EcoKI adenine methyltransferase.

The EcoKI methyltransferase (M.EcoKI, MTase) contains the amino acid (aa) sequences AAGTA and NPPF believed to represent the two sequences that are strongly conserved in adenine MTases [Klimasauskas et al., Nucleic Acids Res. 17 (1989) 9823-9831]. We have analysed a mutation in the first sequence that abolishes cofactor binding and enzyme activity, and mutations in the second sequence that reduce or abolish activity without affecting cofactor and DNA binding.

Amino Acid Sequence↗
PubMed1995

Tyrosine 27 of the specificity polypeptide of EcoKI can be UV crosslinked to a bromodeoxyuridine-substituted DNA target sequence.

The specificity (S) subunit of the restriction enzyme EcoKI imparts specificity for the sequence AAC(N6)GTGC. Substitution of thymine with bromodeoxyuridine in a 25 bp DNA duplex containing this sequence stimulated UV light-induced covalent crosslinking to the S subunit. Crosslinking occurred only at the residue complementary to the first adenine in the AAC sequence, demonstrating a close contact between the major groove at this sequence and the S subunit. Peptide sequencing of a proteolytically-digested, crosslinked complex identified tyrosine 27 in the S subunit as the site of crosslinking. This is consistent with the role of the N-terminal domain of the S subunit in recognizing the AAC sequence. Tyrosine 27 is conserved in the S subunits of the three type I enzymes that share the sequence AA in the trinucleotide component of their target sequence. This suggests that tyrosine 27 may make a similar DNA contact in these other enzymes.

Amino Acid Sequence↗
PubMed1994

A mutational analysis of the two motifs common to adenine methyltransferases.

All methyltransferases that use S-adenosyl methionine as the methyl group donor contain a sequence similar to (D/E/S)XFXGXG which has been postulated to form part of the cofactor binding site. In N6-adenine DNA methyltransferases there is a second motif, (D/N)PP(Y/F), which has been proposed to play a role similar to the catalytically essential PC motif conserved in all C5-cytosine DNA methyltransferases. We have made a series of amino acid changes in these two motifs in the EcoKI N6-adenine DNA methyltransferase. The mutant enzymes have been purified to homogeneity and characterized by physical biochemical methods. The first G is the most conserved residue in motif I. Changing this G to D completely abolished S-adenosyl methionine binding, but left enzyme structure and DNA target recognition unaltered, thus documenting the S-adenosyl methionine binding function of motif I in N6-adenine methyltransferases. Substitution of the N with D, or F with either G or C, in motif II abolished enzyme activity, but left S-adenosyl methionine and DNA binding unaltered. Changes of F to Y or W resulted in partial enzyme activity, implying that an aromatic residue is important for methylation. The substitution of W for F greatly enhanced UV-induced cross-linking between the enzyme and S-adenosyl methionine, suggesting that the aromatic residue is close in space to the methyl-group donor.

Adenine↗
PubMed1994

The domains of a type I DNA methyltransferase. Interactions and role in recognition of DNA methylation.

The DNA methyltransferases of type I restriction-modification systems are trimeric enzymes composed of one DNA specificity (S) subunit and two modification (M) subunits. The S subunit contains two large regions, each of which recognizes one part of the split, asymmetrical DNA target sequence. Each M subunit contains an amino acid motif for binding the methyl group donor and cofactor, S-adenosyl methionine. The EcoKI methyltransferase has a strong preference for methylating a hemimethylated DNA target rather than an unmodified target. We have used partial proteolytic digestion of EcoKI methyltransferase to generate polypeptide domains that we have identified by amino acid sequencing. The S subunit was cut into two large, folded domains each containing one DNA binding region. Binding of DNA partially protected the S subunit from digestion. The M subunit was also cut into two large domains joined together by a short flexible loop, and a C-terminal tail region. The short loop contained part of the S-adenosyl methionine binding motif, and cofactor binding protected the loop and the two large domains from proteolysis. The C-terminal domain of M remained associated with the N-terminal domain of the S subunit even after the rest of the protein had been digested. The conformation of the tail region of the M subunit was sensitive to the methylation state of DNA in ternary complexes also containing S-adenosyl methionine, and could differentiate between unmethylated and hemimethylated DNA substrates.

Amino Acid Sequence↗
PubMed1993

DNA recognition by the EcoK methyltransferase. The influence of DNA methylation and the cofactor S-adenosyl-L-methionine.

The methyltransferase of the EcoK type I restriction/modification system is trimeric, M2S1, where the S subunit determines the sequence specificity of the enzyme. The methyltransferase has a strong preference for hemimethylated substrate DNA and, therefore, we have investigated the effect of the methylation state of DNA on binding by the enzyme, together with the effects on binding of the cofactor S-adenosyl-L-methionine. Our results indicate that the methyltransferase has two non-interacting S-adenosyl-L-methionine binding sites, each with a dissociation constant of 3.60 (+/- 0.42) microM determined by equilibrium dialysis, or 2.21 (+/- 0.29) microM determined by the displacement of a fluorescent probe. Ultraviolet light-induced crosslinking showed that S-adenosyl-L-methionine binds strongly only to the modification (M) subunits. Changes in the sedimentation velocity of the methyltransferase imply a protein conformational change due to S-adenosyl-L-methionine binding. Gel retardation results show that the binding of S-adenosyl-L-methionine to the methyltransferase enhances binding to both specific and non-specific DNAs, but the enhancement is greater for the specific DNA. Differences in binding affinities contribute to the recognition of the specific nucleotide sequence AAC(N)6GTGC by the methyltransferase in preference to a non-specific sequence. In contrast, although the complexes of unmodified and hemimethylated DNAs with the methyltransferase have different mobilities in non-denaturing gels, there appears to be no contribution of binding affinity to the distinction between these two substrates. Therefore, the preference for a hemimethylated substrate must be due to a difference in catalysis.

Allosteric Regulation↗
PubMed1993

Purification and characterization of the methyltransferase from the type 1 restriction and modification system of Escherichia coli K12.

The DNA methyltransferase component of the type I restriction and modification enzyme of Escherichia coli K12 has been purified. The active component, a trimer of molecular mass 170 kDa consisting of one DNA recognition subunit (S) and two modification subunits (M), showed the expected preference for modifying a hemimethylated substrate rather than an unmethylated one. Small amounts of the dimers M2 and M1S1 were also isolated. Subunit rearrangements of the three protein species occurred on ion exchange and heparin-agarose chromatography. Denaturation of the trimer gave folding intermediates, and these and the dimer forms isolated during purification may reflect the assembly of the protein in vivo. Enzyme activity was recovered on refolding the denatured protein by dilution of the denaturant. A comparison of the predicted isoelectric points of all known S subunits of type I restriction and modification enzymes revealed values that correlated with the arrangement of type I systems in several families. Electrostatic interactions may explain the different subunit stoichiometries observed during purification of type I enzymes and the differing preferences for hemimethylated DNA displayed by the three type I families.

Base Sequence↗
PubMed1992

A study of the hinge-bending mechanism of yeast 3-phosphoglycerate kinase.

The hinge-bending mechanism proposed as part of the catalytic mechanism for phosphoglycerate kinase (PGK) has been investigated using yeast PGK and the site-directed mutant [H388Q]PGK, where His388 is replaced by Gln. The emission and quenching of fluorescence, supported by the aromatic CD band, show that the mutation in the waist region affects the tryptophan environment in the C-terminal domain. The mutant is also less stable to guanidine denaturation and less cooperative in its unfolding. The effect of substrates on the conformation of PGK was studied using 8-anilino-1-naphthalenesulphonic acid (ANS), a competitive inhibitor of ATP binding to the C-terminal domain, and 8-(2-[(iodoacetyl)ethyl]amino)naphthalene (I-AEDANS), attached to Cys197 on the N-terminal domain. Under the influence of substrates the novel anisotropy decay curves for ANS indicate a 1-5 degrees change in the orientation of the probe, interpreted as a small reorientation of the domains about the waist region. The experimental data are interpreted as a small swivelling of the domains about the waist region under the influence of substrate. The results with AEDANS anisotropy decay are consistent with those for ANS. The enzyme activity of PGK shows a break in the Arrhenius plot at 20 degrees C mirrored by a break in the temperature dependence of tryptophan ellipticity. This is interpreted as a change in protein dynamics associated with destabilisation of the waist region. This destabilisation is shown to have already taken place in the mutant enzyme and in the wild type at pH 5.6, both of which exhibit linear Arrhenius plots. NMR titration curves show that the pH effect must be due to a group other than histidine. The results give further support to the permissive model of hinge bending previously proposed by one of the authors, in which binding of substrate destabilises the waist region. This loosens the hinge which can then swing slightly to bring the domains closer together to make favourable interactions between the domains and the substrates, with the exclusion of water.

Acrylamide↗
PubMed1992

Characterization of the structure and conformation of platelet-derived growth factor-BB (PDGF-BB) and proteinase-resistant mutants of PDGF-BB expressed in Saccharomyces cerevisiae.

A detailed biophysical study of the secondary and tertiary structures of recombinant platelet-derived growth factor (PDGF)-BB produced in yeast has been carried out. The secondary structure of the molecule is composed of 54% beta-sheet with less than 5% ordered helix. The single tryptophan residue has been shown to be solvent-accessible; however, the ability of the side chain to rotate is severely restricted. The fluorescence emission is quenched at pH 7.0 and in the presence of high salt, but dequenched by titration to lower pH with a pK of 5.8. Two proteinase-resistant mutants of PDGF [( Ser28]- and [Pro32]-PDGF-BB) have also been characterized and shown to have secondary and tertiary structures indistinguishable from wild-type PDGF-BB. These are, therefore, suitable stable background molecules in which to carry out structure-activity-relationship studies on PDGF-BB.

Mutagenesis, Site-Directed↗
PubMed1991

Resolution of the fluorescence of the buried tryptophan in yeast 3-phosphoglycerate kinase using succinimide.

The heterogeneous fluorescence of yeast 3-phosphoglycerate kinase, a hinge-bending enzyme with two tryptophans, has been resolved into two approximately equal components, one accessible and one inaccessible to the relatively inefficient quencher succinimide. The inaccessible component is blue-shifted and exhibits a heterogeneous fluorescence decay which has a temperature-dependence and steady-state acrylamide quenching properties typical of a single tryptophan in a buried environment. This component is therefore assigned to the buried tryptophan W333. The presence of succinimide greatly simplifies the fluorescence allowing the conformational dynamics of the buried tryptophan and its environment to be studied without interference from the other tryptophan.

Calorimetry↗
PubMed1989

Assignment of the heterogeneous static and time-resolved tryptophan fluorescence of 3-phosphoglycerate kinase.

The heterogeneous fluorescence of yeast 3-phosphoglycerate kinase, a hinge-bending enzyme with two tryptophan residues, has been resolved into three emission components using steady-state and time-resolved studies of the fluorescence quenching by acrylamide, iodide and caesium ions at different emission wavelengths. The buried Trp-333 has a blue-shifted heterogeneous emission spectrum characterised by three fluorescence lifetimes, and is inaccessible to quenchers. The surface Trp-308 also has a heterogeneous emission with multiple lifetimes. The emission of Trp-308 can be separated into a blue-shifted emission accessible to acrylamide and caesium only, and a red-shifted emission accessible to all three quenchers.

Kinetics↗
PubMed1989

Proton permeability and lipid dynamics of gastric and duodenal apical membrane vesicles.

The passive proton permeability (Pnet) of apical membrane vesicles from rabbit parietal cells (gastric) and duodenal and renal cortical brush-border membranes (BBM) was determined by acridine orange fluorescence quenching. Values of Pnet were found to be gastric (4 x 10(-4) cm/s) less than duodenal (10(-3) cm/s) much less than renal (10(-2) cm/s). Arrhenius plots of the temperature profile of proton permeation of gastric vesicles was linear, whereas that of duodenal BBM displayed a discontinuity at 30-33 degrees C. Alcohols (octyl, benzyl, ethyl) increased Pnet in a concentration-dependent manner, with efficacy related to their oil-water partition coefficients. In a parallel series of experiments, structural parameters of the vesicle membrane lipids (fluidity) were monitored from both the steady-state and time-resolved fluorescence anisotropy of diphenylhexatriene. Fluidity of the membranes was unrelated to Pnet (renal congruent to duodenal less than gastric). Gastric vesicles demonstrated a linear Arrhenius plot of temperature dependence for fluidity, whereas duodenal BBM demonstrated a discontinuity. Membrane fluidity of gastric and duodenal vesicles was increased by alcohols, with the same potency as for Pnet, and these two variables were significantly correlated after perturbation with alcohols. Thus the fluidity of the lipid bilayer is not the major determinant of Pnet, but alteration of its structural parameters, as reflected by fluidity, produces parallel changes in Pnet.

Animals↗
PubMed1984

Allostery without conformational change. A plausible model.

A general model is presented whereby ligand-induced changes in protein dynamics could produce allosteric communication between distinct binding sites, even in the absence of a macromolecular conformational change. Theoretical analysis, based on the statistical thermodynamics of ligand binding, shows that cooperative interaction free energies amounting to several kJ . mol-1 may be generated by this means. The effect arises out of the possible changes in frequencies and amplitudes of macromolecular thermal fluctuations in response to ligand attachment, and can involve all forms of dynamic behaviour, ranging from highly correlated, low-frequency normal mode vibrations to random local anharmonic motions of individual atoms or groups. Dynamic allostery of this form is primarily an entropy effect, and we derive approximate expressions which might allow the magnitude of the interaction in real systems to be calculated directly from experimental observations such as changes in normal mode frequencies and mean-square atomic displacements. Long-range influence of kinetic processes at different sites might also be mediated by a similar mechanism. We suggest that proteins and other biological macromolecules may have evolved to take functional advantage not only of mean conformational states but also of the inevitable thermal fluctuations about the mean.

Allosteric Regulation↗