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F W Dahlquist

Publications and source records attributed to F W Dahlquist.

At least 73 records · Page 4Linked to original sources
PubMed1991

Secondary structure of the homeo domain of yeast alpha 2 repressor determined by NMR spectroscopy.

The yeast alpha 2 protein is a regulator of cell type in Saccharomyces cerevisiae. It represses transcription of a set of target genes by binding to an operator located upstream of each of these genes. The alpha 2 protein shares weak sequence similarity with members of the homeo domain family; the homeo domain is a 60-amino-acid segment found in many eukaryotic transcriptional regulators. In this paper we address the question of whether alpha 2 is structurally related to prototypical members of the homeo domain family. We used solution 1H and 15N nuclear magnetic resonance [NMR] spectroscopy to determine the secondary structure of an 83-amino-acid residue fragment of alpha 2 that contains the homeo domain homology. We have obtained resonance assignments for the backbone protons and nitrogens of the entire 60-residue region of the putative homeo domain and for most of the remainder of the alpha 2 fragment. The secondary structure was determined by using NOE connectivities between backbone protons, 3JHN-H alpha coupling constants, and dynamical information from the hydrogen exchange kinetics of the backbone amides. Three helical segments exist in the alpha 2 fragment consisting of residues 11-23, 32-42, and 46-60 (corresponding to residues 138-150, 159-169, and 173-187 of the intact protein). The positions of these three helices correspond extremely well to those of the Drosophila Antennapedia (Antp) and engrailed (en) homeo domains, whose three-dimensional structures have recently been determined by NMR spectroscopy and X-ray crystallography, respectively.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acid Sequence↗
PubMed1990

Assignment of the backbone 1H and 15N NMR resonances of bacteriophage T4 lysozyme.

The proton and nitrogen (15NH-H alpha-H beta) resonances of bacteriophage T4 lysozyme were assigned by 15N-aided 1H NMR. The assignments were directed from the backbone amide 1H-15N nuclei, with the heteronuclear single-multiple-quantum coherence (HSMQC) spectrum of uniformly 15N enriched protein serving as the master template for this work. The main-chain amide 1H-15N resonances and H alpha resonances were resolved and classified into 18 amino acid types by using HMQC and 15N-edited COSY measurements, respectively, of T4 lysozymes selectively enriched with one or more of alpha-15N-labeled Ala, Arg, Asn, Asp, Gly, Gln, Glu, Ile, Leu, Lys, Met, Phe, Ser, Thr, Trp, Tyr, or Val. The heteronuclear spectra were complemented by proton DQF-COSY and TOCSY spectra of unlabeled protein in H2O and D2O buffers, from which the H beta resonances of many residues were identified. The NOE cross peaks to almost every amide proton were resolved in 15N-edited NOESY spectra of the selectively 15N enriched protein samples. Residue specific assignments were determined by using NOE connectivities between protons in the 15NH-H alpha-H beta spin systems of known amino acid type. Additional assignments of the aromatic proton resonances were obtained from 1H NMR spectra of unlabeled and selectively deuterated protein samples. The secondary structure of T4 lysozyme indicated from a qualitative analysis of the NOESY data is consistent with the crystallographic model of the protein.

Amino Acid Sequence↗
PubMed1990

Secondary structure of a leucine zipper determined by nuclear magnetic resonance spectroscopy.

Previous work has shown that a synthetic peptide corresponding to the leucine zipper region of the yeast transcriptional activator GCN4 forms a stable dimer of alpha-helices and that the helices are oriented in a parallel manner. Two-dimensional nuclear magnetic resonance spectroscopy (NMR) is used here to demonstrate that the helix is continuous for at least 32 of the 33 residues in the peptide. The results also indicate that the dimer is symmetric. It is therefore unlikely that the interdigitation model for the structure of leucine zippers is correct, since interdigitation of leucine residues in a parallel dimer would lead to an asymmetric structure. The data are consistent with a coiled-coil structure.

Amino Acid Sequence↗
PubMed1990

pH-induced denaturation of proteins: a single salt bridge contributes 3-5 kcal/mol to the free energy of folding of T4 lysozyme.

The energetics of a salt bridge formed between the side chains of aspartic acid 70 (Asp70) and histidine 31 (His31) of T4 lysozyme have been examined by nuclear magnetic resonance techniques. The pKa values of the residues in the native state are perturbed from their values in the unfolded protein such that His31 has a pKa value of 9.1 in the native state and 6.8 in the unfolded state at 10 degrees C in moderate salt. Similarly, the aspartate pKa is shifted to a value of about 0.5 in the native state from its value of 3.5-4.0 in the unfolded state. These shifts in pKa show that the salt bridge is stabilized 3-5 kcal/mol. This implies that the salt bridge stabilizes the native state by 3-5 kcal/mol as compared to the unfolded state. This is reflected in the thermodynamic stability of mutants of the protein in which Asp70, His31, or both are replaced by asparagine. These observations and consideration of the thermodynamic coupling of protonation state to folding of proteins suggest a mechanism of acid denaturation in which the unfolded state is progressively stabilized by protonation of its acid residues as pH is lowered below pH 4. The unfolded state is stabilized only if acidic groups in the folded state have lower pKa values than in the unfolded state. When the pH is sufficiently low, the acid groups of both the native and unfolded states are fully protonated, and the apparent unfolding equilibrium constant becomes pH independent. Similar arguments apply to base-induced unfolding.(ABSTRACT TRUNCATED AT 250 WORDS)

Aspartic Acid↗
PubMed1990

Mutations that affect control of the methylesterase activity of CheB, a component of the chemotaxis adaptation system in Escherichia coli.

Sensory adaptation by the chemotaxis system of Escherichia coli requires adjustments of the extent of methyl esterification of the chemotaxis receptor proteins. One mechanism utilized by E. coli to make such adjustments is to control the activity of CheB, the enzyme responsible for removing receptor methyl ester groups. Previous work has established the existence of a multicomponent signal transduction pathway that enables the chemotaxis receptor proteins to control the methylesterase activity in response to chemotactic stimuli. We isolated and characterized CheB mutants that do not respond normally to this control mechanism. In intact cells these CheB variants could not be activated in response to negative chemotaxis stimuli. Further characterization indicated that these CheB variants could not be phosphorylated by the chemotaxis protein kinase CheA. Disruption of the mechanism responsible for regulating methylesterase activity was also observed in cells carrying chromosomal deletions of either cheA or cheW as well as in cells expressing mutant versions of CheA that lacked kinase activity. These results provide further support for recent proposals that activation of the methylesterase activity of CheB involves phosphorylation of CheB by CheA. Furthermore, our findings suggest that CheW plays an essential role in enabling the chemotaxis receptor proteins to control the methylesterase activity, possibly by controlling the CheA-CheB phosphotransfer reaction.

Adaptation, Physiological↗
PubMed1989

High-resolution structure of the temperature-sensitive mutant of phage lysozyme, Arg 96----His.

The structure of the temperature-sensitive mutant lysozyme of bacteriophage T4 in which arginine 96 is replaced by histidine has been determined crystallographically and refined to a residual of 17.6% at 1.9-A resolution. Overall, the three-dimensional structure of the mutant protein is extremely similar to that of wild type. There are local distortions in the mutant structure suggesting that the substituted His 96 residue is under strain. This appears to be one of the major reasons for the decreased thermostability. In wild-type lysozyme the guanidinium of Arg 96 is located at the carboxy terminus of alpha-helix 82-90 and makes a pair of hydrogen bonds to two of the carbonyl groups in the last turn of the helix. The loss of this "helix dipole" interaction also appears to contribute to the destabilization. The pKa* of His 96 in the mutant lysozyme has been determined by nuclear magnetic resonance and found to be 6.8 at 10 degrees C. This relatively normal value of the histidine pKa* suggests that the protonated and unprotonated forms of the imidazole ring are perturbed equally by the protein environment or, what is equivalent, the mutant lysozyme is equally stable with either histidine species.

Arginine↗
PubMed1989

Chromosomal transformation of Escherichia coli recD strains with linearized plasmids.

Wild-type Escherichia coli are resistant to genetic transformation by purified linear DNA, probably in part because of exonuclease activity. We demonstrate that E. coli containing a recD mutation could be easily transformed by linearized plasmids containing a selectable marker. The marker was transferred to the chromosome by homologous recombination, whereas plasmid markers not in the region of homology were lost.

Bacterial Proteins↗
PubMed1989

Exchange of chromosomal and plasmid alleles in Escherichia coli by selection for loss of a dominant antibiotic sensitivity marker.

Transfer of an allele from a donor DNA to a recipient DNA molecule was selected by the loss of a dominant conditional lethal mutation previously incorporated ito the gene of interest in the recipient DNA. Both the Escherichia coli chromosome and plasmids carrying E. coli genes were used successfully as donor molecules. Recipient molecules for these exchanges were constructed in vitro by using the rpsL gene, which confers sensitivity to streptomycin, to replace segments of specific E. coli genes located either on multicopy plasmids or in the E. coli chromosome. Plasmids carrying such replacements were capable of acquiring chromosomal alleles of the gene(s) of interest, and strains carrying rpsL replacements in the chromosome were capable of acquiring plasmid-encoded alleles at the sight of the rpsL replacement. In both situations, these allele transfers resulted in loss of the rpsL gene from the recipient DNA molecule. The desired transfer events constituted a large percentage of these events, which gave rise to viable colonies when appropriate donor-recipient pairs were subjected to streptomycin selection. Thus, this is a useful approach for transferring alleles of interest from plasmids to the E. coli chromosome and vice versa.

Alleles↗
PubMed1989

Control of transducer methylation levels in Escherichia coli: investigation of components essential for modulation of methylation and demethylation reactions.

During bacterial chemotaxis in Escherichia coli, adaptation is accomplished by reversible methylation of the transmembrane signal transducers. Methyl groups are added by the CheR protein in a slow response to attractants and removed by the CheB protein in response to repellents. The methylesterase activity of the CheB protein is modulated by a factor that is controlled in a global fashion throughout the cell. By controlling the level of expression of the cheR, cheB, and transducer genes with exogenous promoters on multicopy plasmids, we demonstrate that the modulating factor exists in stoichiometric concentrations relative to CheB protein and that the generation or efficacy of this factor requires the cheA and/or cheW gene products, suggesting that phosphorylation of the methylesterase by CheA may be involved in its global activation. We show that in the absence of any modulation of the CheB activity, the CheR methyltransferase activity is modulated in a local fashion at the transducers, most likely as a result of a conformational change in the transducer protein brought about by the binding of ligand, and does not require CheA or CheW.

Carboxylic Ester Hydrolases↗
PubMed1989

Use of 13C and 15N isotope labels for proton nuclear magnetic resonance and nuclear Overhauser effect. Structural and dynamic studies of larger proteins and nucleic acids.

This article reviews methods based on direct observation of proton NMR in macromolecules containing 13C or 15N labels. The resonances and Overhauser effects of protons attached to the labels can be edited or filtered from the remaining overlapping resonances. This leads to simplification of the spectra when labels are incorporated selectively. In 2D and related methods the label's chemical shift provides a second dimension which is useful for spectral differentiation and identification. The methods are useful for larger proteins and we describe our progress on studies of T4 lysozyme, mass 18.7 kD, in which we have already identified a large number of resonances.

Carbon Isotopes↗
PubMed1988

N-terminal half of CheB is involved in methylesterase response to negative chemotactic stimuli in Escherichia coli.

The chemotactic receptor-transducer proteins of Escherichia coli are responsible for directing the swimming behavior of cells by signaling for either straight swimming or tumbling in response to chemostimuli. The signaling states of these proteins are affected not only by the concentrations of various stimuli but also by the extent to which they have been methylated at specific glutamyl residues. The activities of a chemotaxis-specific methyltransferase (CheR) and a chemotaxis-specific methylesterase (CheB) are regulated in response to chemotactic stimuli to enable sensory adaptation to unchanging levels of stimuli by appropriately shifting the signaling states of the transducer proteins. For CheB this regulation involves a feedback loop that requires some of the components making up the chemotactic signal transduction machinery of the cell. This feedback loop causes the methylesterase activity of CheB to decrease transiently in response to attractant stimuli and to increase transiently in response to negative stimuli (repellent addition or attractant removal). In this report we demonstrate that the methylesterase response to negative stimuli involves the N-terminal half of the CheB protein, whereas the response to positive stimuli does not require this segment of the protein. Both aspects of the methylesterase response to positive stimuli does not require this segment of the protein. Both aspects of the methylesterase response require CheA. In addition, we demonstrate that mutant forms of CheB lacking methylesterase activity can adversely affect the swimming behavior and chemotactic ability of cells and can markedly diminish modulation of the wild-type methylesterase activity in response to negative stimuli. The significance of these results is discussed in relation to the recent demonstration of phosphoryl transfer from CheA to CheB (J. F. Hess, K. Oosawa, N. Kaplan, and M. I. Simon, Cell 53:79-87, 1988) and the discovery of sequence homology between the N-terminal half of CheB and CheY (A. Stock, D. E. Koshland, Jr., and J. Stock, Proc. Natl. Acad. Sci. USA 82:7989-7993, 1985).

Carboxylic Ester Hydrolases↗
PubMed1987

Proton NMR measurements of bacteriophage T4 lysozyme aided by 15N isotopic labeling: structural and dynamic studies of larger proteins.

A strategy for resolution and assignment of single proton resonances in proteins of molecular mass up to at least 40 kDa is presented. This approach is based on 15N (or 13C) labeling of selected residues in a protein. The resonances from protons directly bonded to labeled atoms are detected in a two-dimensional 1H-15N (or 13C) spectrum. The nuclear Overhauser effects from isotopically tagged protons are selectively observed in one-dimensional isotope-directed measurements. Using this approach, we have observed approximately 160 resonances from 15N-bonded protons in the backbone and sidechains of uniformly 15N-labeled T4 lysozyme (molecular mass = 18.7 kDa). Partial proton-deuterium exchange can be used to simplify the 1H-15N spectrum of this protein. These resonances are identified by amino acid class using selective incorporation of 15N-labeled amino acids and are assigned to specific residues by mutational substitution, multiple 15N and 13C labeling, and isotope-directed nuclear Overhauser effect measurements. For example, using a phenyl[15N]alanine-labeled lysozyme variant containing two consecutive phenylalanine residues in an alpha-helical region, we observe an isotope-directed nuclear Overhauser effect from the amide proton of Phe-66 to that of Phe-67.

Deuterium↗
PubMed1987

Proton NMR and NOE structural and dynamic studies of larger proteins and nucleic acids aided by isotope labels: T4 lysozyme.

This article reviews methods based on direct observation of proton NMR in macromolecules containing 13C or 15N labels. The resonances and Overhauser effects of protons attached to the labels can be edited or filtered from the remaining overlapping resonances. This leads to simplification of the spectra when labels are incorporated selectively. In 2D and related methods the label's chemical shift provides a second dimension which is useful for spectral differentiation and identification. The methods are useful for larger proteins and we describe our progress on studies of T4 lysozyme, mass 18.7 kD, in which we have already identified a large number of resonances.

Carbon Isotopes↗
PubMed1985

Simultaneous observation of order and dynamics at several defined positions in a single acyl chain using 2H NMR of single acyl chain perdeuterated phosphatidylcholines.

Deuterium nuclear magnetic resonance (2H NMR) spectra from aqueous dispersions of phosphatidylcholines in which perdeuterated palmitic acid is esterified at the sn-1 position have several very useful features. The powder spectra show six well-resolved 90 degree edges which correspond to the six positions closest to the methyl end of the acyl chain. The spectral overlap inherent in the multiple powder pattern line shape of these dispersions can be removed by using a "dePaking" procedure [Bloom, M., Davis, J.H., & Mackay, A. (1981) Chem. Phys. Lett. 80, 198-202] which calculates the spectra that would result if the lipid bilayers were oriented in the magnetic field. This procedure produces six well-resolved doublets whose NMR properties can be observed without interference from the resonances of other labeled positions. The presence of a single double bond in the sn-2 chain increases the order of the saturated 16:0 sn-1 chain at every position in the bilayer compared with a saturated sn-2 chain at the same reduced temperature. Surprisingly, addition of five more double bonds to the sn-2 chain only slightly reduces the order of the 16:0 sn-1 chain at many positions in the bilayer compared with the single double bond. Calculating oriented spectra from a spin-lattice (T1) relaxation series of powder spectra allows one to obtain the T1 relaxation times of six positions on the acyl chain simultaneously. As an example of the utility of these molecules, we demonstrate that the dependence of the spin-lattice (T1) relaxation rate as a function of orientational order for two unsaturated phospholipids differs significantly from the corresponding fully saturated analogue. Interpreting this difference using current models of acyl chain dynamics suggests that the bilayers containing either of the two unsaturated phospholipids are significantly more deformable than bilayers made from the fully saturated phospholipid.

Acylation↗
PubMed1985

Membrane protein conformational change dependent on the hydrophobic environment.

Two conformational states of the coat protein of the filamentous bacteriophage M13 have been detected in detergent solution by using magnetic resonance techniques. When 3-fluorotyrosine is incorporated in place of the two tyrosine residues in the protein, four 19F nuclear magnetic resonance signals are observed, two for each conformer of the protein. The equilibrium between the two forms can be modulated by pH, temperature, and detergent structure. The rate of interconversion of the isomers is rapid on the minutes time scale but is slow relative to the T1 relaxation time of the fluorine resonances of approximately 50 ms. The conformational change between the conformers results in the perturbation of a basic residue in the protein such that this group has a pKa of approximately 9.5 in one state which shifts to 10.5 or more in the other conformational state. The temperature dependence of the equilibrium suggests an enthalpy difference of about 10 kcal/mol which is offset by entropy to give nearly zero free energy difference between the states at pH 8.3 in deoxycholate solution at room temperature. This suggests a substantial reorganization of the noncovalent interactions defining the two conformational states. The conformational equilibrium is strongly dependent on detergent structure and the presence of phospholipid in the detergent micelle. The results are not consistent with a strong, specific lipid binding to the protein but appear to be consistent with a more general effect of the overall micelle structure on the conformational state of the protein.

Coliphages↗