Flipping a genetic switch by subunit exchange.

The bacteriophage T4 AsiA protein is a multifunctional protein that simultaneously acts as both a repressor and activator of gene expression during the phage life cycle. These dual roles with opposing transcriptional consequences are achieved by modification of the host RNA polymerase in which AsiA binds to conserved region 4 (SR4) of sigma(70), altering the pathway of promoter selection by the holoenzyme. The mechanism by which AsiA flips this genetic switch has now been revealed, in part, from the three-dimensional structure of AsiA and the elucidation of its interaction with SR4. The structure of AsiA is that of a novel homodimer in which each monomer is constructed as a seven-helix bundle arranged in four overlapping helix-loop-helix elements. Identification of the protein interfaces for both the AsiA homodimer and the AsiA-sigma(70) complex reveals that these interfaces are coincident. Thus, the AsiA interaction with sigma(70) necessitates that the AsiA homodimer dissociate to form an AsiA-SR4 heterodimer, exchanging one protein subunit for another to alter promoter choice by RNA polymerase.

Analytical sedimentation of the IIAChb and IIBChb proteins of the Escherichia coli N,N'-diacetylchitobiose phosphotransferase system. Demonstration of a model phosphotransfer transition state complex.

The phosphoenolpyruvate:glycose transferase system (PTS) is a prototypic signaling system responsible for the vectorial uptake and phosphorylation of carbohydrate substrates. The accompanying papers describe the proteins and product of the Escherichia coli N, N-diacetylchitobiose ((GlcNAc)(2)) PTS-mediated permease. Unlike most PTS transporters, the Chb system is composed of two soluble proteins, IIA(Chb) and IIB(Chb), and one transmembrane receptor (IIC(Chb)). The oligomeric states of PTS permease proteins and phosphoproteins have been difficult to determine. Using analytical ultracentrifugation, both dephospho and phosphorylated IIA(Chb) are shown to exist as stable dimers, whereas IIB(Chb), phospho-IIB(Chb) and the mutant Cys10SerIIB(Chb) are monomers. The mutant protein Cys10SerIIB(Chb) is unable to accept phosphate from phospho-IIA(Chb) but forms a stable higher order complex with phospho-IIA(Chb) (but not with dephospho-IIA(Chb)). The stoichiometry of proteins in the purified complex was determined to be 1:1, indicating that two molecules of Cys10SerIIB(Chb) are associated with one phospho-IIA(Chb) dimer in the complex. The complex appears to be a transition state analogue in the phosphotransfer reaction between the proteins. A model is presented that describes the concerted assembly and disassembly of IIA(Chb)-IIB(Chb) complexes contingent on phosphorylation-dependent conformational changes, especially of IIA(Chb).

X-ray crystallographic and analytical ultracentrifugation analyses of truncated and full-length yeast copper chaperones for SOD (LYS7): a dimer-dimer model of LYS7-SOD association and copper delivery.

Copper-zinc superoxide dismutase (CuZnSOD) acquires its catalytic copper ion through interaction with another polypeptide termed the copper chaperone for SOD. Here, we combine X-ray crystallographic and analytical ultracentrifugation methods to characterize rigorously both truncated and full-length forms of apo-LYS7, the yeast copper chaperone for SOD. The 1.55 A crystal structure of LYS7 domain 2 alone (L7D2) was determined by multiple-isomorphous replacement (MIR) methods. The monomeric structure reveals an eight-stranded Greek key beta-barrel similar to that found in yeast CuZnSOD, but it is substantially elongated at one end where the loop regions of the beta-barrel come together to bind a calcium ion. In agreement with the crystal structure, sedimentation velocity experiments indicate that L7D2 is monomeric in solution under all conditions and concentrations that were tested. In contrast, sedimentation velocity and sedimentation equilibrium experiments show that full-length apo-LYS7 exists in a monomer-dimer equilibrium under nonreducing conditions. This equilibrium is shifted toward the dimer by approximately 1 order of magnitude in the presence of phosphate anion. Although the basis for the specificity of the LYS7-SOD interaction as well as the exact mechanism of copper insertion into SOD is unknown, it has been suggested that a monomer of LYS7 and a monomer of SOD may associate to form a heterodimer via L7D2. The data presented here, however, taken together with previously published crystallographic and analytical gel filtration data on full-length LYS7, suggest an alternative model wherein a dimer of LYS7 interacts with a dimer of yeast CuZnSOD. The advantages of the dimer-dimer model over the heterodimer model are enumerated.

Detergent-solubilized Escherichia coli cytochrome bo3 ubiquinol oxidase: a monomeric, not a dimeric complex.

The protein molecular weight, M(r), and hydrodynamic radius, R(s), of Triton X-100-solubilized Escherichia coli cytochrome bo3 were evaluated by computer fitting of sedimentation velocity data with finite element solutions to the Lamm equation. Detergent-solubilized cytochrome bo3 sediments as a homogeneous species with an S20,w of 6.75 s and a D20,w of 3.71 x 10(-7) cm2/s, corresponding to a R(s) of 5.8 nm and a M(r) of 144,000 +/- 3500. The protein molecular weight agrees very well with the value of 143,929 calculated from the four known subunit sequences and the value of 143,025 measured by MALDI mass spectrometry for the histidine-tagged enzyme. We conclude that detergent-solubilized E. coli ubiquinol oxidase is a monomeric complex of the four known subunits.

Expression and characterization of a human mitochondrial phenylalanyl-tRNA synthetase.

Human mitochondrial phenylalanyl-tRNA synthetase (mtPheRS) has been identified from the human EST database. Using consensus sequences derived from conserved regions of the alpha and beta-subunits from bacterial PheRS, two partially sequenced cDNA clones were identified. Unexpectedly, sequence analysis indicated that one of these clones was a truncated form of the other. Detailed analysis indicates that unlike the (alphabeta)2 structure of the prokaryotic and eukaryotic cytoplasmic forms of PheRS, the human mtPheRS consists of a single polypeptide chain. This protein has been cloned and expressed in Escherichia coli. Gel filtration and analytical velocity sedimentation centrifugation indicate that the human mtPheRS is active in a monomeric form. The N-terminal 314 amino acid residues appear to be analogous to the alpha-subunit of the prokaryotic PheRS, while the C-terminal 100 amino acid residues correspond to a region of the beta-subunit known to interact with the anticodon of tRNAPhe. Comparisons with the sequences of PheRS from yeast and Drosophila mitochondria indicate they are 42 % and 51 % identical with the human mtPheRS, respectively. Sequence analysis confirms the presence of motifs characteristic of class II aminoacyl-tRNA synthetases. KM and kcat values for ATP:PPi exchange and for the aminoacylation reaction carried out by human mtPheRS have been determined. Evolutionary origins of this small monomeric human mtPheRS are unknown, however, implications are that this enzyme is a result of the simplification of the more complex (alphabeta)2 bacterial PheRS in which specific functional regions were retained.

Direct sedimentation analysis of interference optical data in analytical ultracentrifugation.

Sedimentation data acquired with the interference optical scanning system of the Optima XL-I analytical ultracentrifuge can exhibit time-invariant noise components, as well as small radial-invariant baseline offsets, both superimposed onto the radial fringe shift data resulting from the macromolecular solute distribution. A well-established method for the interpretation of such ultracentrifugation data is based on the analysis of time-differences of the measured fringe profiles, such as employed in the g(s*) method. We demonstrate how the technique of separation of linear and nonlinear parameters can be used in the modeling of interference data by unraveling the time-invariant and radial-invariant noise components. This allows the direct application of the recently developed approximate analytical and numerical solutions of the Lamm equation to the analysis of interference optical fringe profiles. The presented method is statistically advantageous since it does not require the differentiation of the data and the model functions. The method is demonstrated on experimental data and compared with the results of a g(s*) analysis. It is also demonstrated that the calculation of time-invariant noise components can be useful in the analysis of absorbance optical data. They can be extracted from data acquired during the approach to equilibrium, and can be used to increase the reliability of the results obtained from a sedimentation equilibrium analysis.

Domain structure of the Staphylococcus aureus collagen adhesin.

Sequence analysis of surface proteins from Gram-positive bacteria indicates a composite organization consisting of unique and repeated segments. Thus, these proteins may contain discrete domains that could fold independently. In this paper, we have used a panel of biophysical methods, including gel permeation chromatography, analytical ultracentrifugation, circular dichroism, and fluorescence spectroscopy, to analyze the structural organization of the Staphylococcus aureus collagen adhesin, CNA. Our results indicate that the structure, function, and folding of the ligand-binding domain (A) are not affected by the presence or absence of the other major domain (B). In addition, little or no interaction is observed between the nearly identical repeat units within the B domain. We propose that CNA is indeed a mosaic protein in which the different domains previously indicated by sequence analysis operate independently.

Mechanism of Rab geranylgeranylation: formation of the catalytic ternary complex.

Rab proteins are geranylgeranylated on one or two C-terminal cysteines by Rab geranylgeranyl transferase (RabGGTase). The reaction is dependent on a Rab-binding protein, termed Rab escort protein (REP). Here, we studied the role of REP in the geranylgeranylation reaction. We first characterized the interaction between REP and ungeranylgeranylated Rab using analytical ultracentrifugation and a fluorescence-based assay. We measured an equilibrium dissociation constant of 0.2 microM for the formation of a 1:1 REP-Rab complex and showed that this interaction relies mostly on ionic bonds and does not involve the two C-terminal cysteine residues. Second, we show that REP is required for recognition of Rab by RabGGTase and therefore that the REP-Rab complex is the true substrate for RabGGTase. Third, we show that free REP inhibits the geranylgeranylation reaction, suggesting that the complex is recognized by RabGGTase primarily via a REP-binding site. Our data suggest a model whereby REP behaves kinetically as an essential activator of the reaction.

Determination of molecular parameters by fitting sedimentation data to finite-element solutions of the Lamm equation.

A method for fitting experimental sedimentation velocity data to finite-element solutions of various models based on the Lamm equation is presented. The method provides initial parameter estimates and guides the user in choosing an appropriate model for the analysis by preprocessing the data with the G(s) method by van Holde and Weischet. For a mixture of multiple solutes in a sample, the method returns the concentrations, the sedimentation (s) and diffusion coefficients (D), and thus the molecular weights (MW) for all solutes, provided the partial specific volumes (v) are known. For nonideal samples displaying concentration-dependent solution behavior, concentration dependency parameters for s(sigma) and D(delta) can be determined. The finite-element solution of the Lamm equation used for this study provides a numerical solution to the differential equation, and does not require empirically adjusted correction terms or any assumptions such as infinitely long cells. Consequently, experimental data from samples that neither clear the meniscus nor exhibit clearly defined plateau absorbances, as well as data from approach-to-equilibrium experiments, can be analyzed with this method with enhanced accuracy when compared to other available methods. The nonlinear least-squares fitting process was accomplished by the use of an adapted version of the "Doesn't Use Derivatives" nonlinear least-squares fitting routine. The effectiveness of the approach is illustrated with experimental data obtained from protein and DNA samples. Where applicable, results are compared to methods utilizing analytical solutions of approximated Lamm equations.

Preformed GroES oligomers are not required as functional cochaperonins.

We have previously shown that the C-terminal sequence of GroES is required for oligomerization [Seale and Horowitz (1995), J. Biol. Chem. 270, 30268-30270]. In this report, we have generated a C-terminal deletion mutant of GroES with a significantly destabilized oligomer and have investigated its function in the chaperonin-assisted protein folding cycle. Removal of the two C-terminal residues of GroES results in a cochaperonin [GroESD(96-97)] that is monomeric at concentrations where GroES function is assessed. Using equilibrium ultracentrifugation, we measured the dissociation constant for the oligomer-monomer equilibrium to be 7.3 x 10(-34)M6. The GroESD(96-97) is fully active as a cochaperonin. This mutant is able to inhibit the ATPase activity of GroEL to levels comparable to wild-type GroES. It is also able to assist the refolding of urea-denatured rhodanese by GroEL. While GroESD(96-97) can function at levels comparable to wild-type GroES, higher concentrations of mutant are required to produce the same effect. These results support the idea that the performed GroES heptamer is not required for function, but they suggest that the oligomeric cochaperonin is most efficient.

Analytical ultracentrifugation and agarose gel electrophoresis as tools for studying chromatin folding in solution.

Analytical ultracentrifugation and agarose gel electrophoresis each can be used to accurately quantify changes in structure that accompany chromatin folding in solution. Analytical ultracentrifugation directly measures the extent of compaction of each species present in a chromatin sample under a wide range of solution conditions. Agarose gel electrophoresis yields information about changes in the average surface charge density, size and/or shape, and conformational flexibility during chromatin folding. When used together, these methodologies are particularly powerful. Protocols for the characterization of chromatin folding by analytical ultracentrifugation and agarose gel electrophoresis are described. Discussion focuses on analysis and interpretation of experimental chromatin folding data.

Human coproporphyrinogen oxidase. Biochemical characterization of recombinant normal and R231W mutated enzymes expressed in E. coli as soluble, catalytically active homodimers.

To obtain recombinant human coproporphyrinogen oxidase (CPX), a cDNA for the coding region of mature human CPX has been expressed in E. coli. CPX was produced as a fusion protein with glutathione S-transferase followed by the hexapeptide recognition site for thrombin cleavage just preceding first amino acid of the CPX protein. The human CPX was found to be in the soluble fraction. This previously unobtainable human heme synthetic enzyme was purified to electrophoretic homogeneity with a specific activity of 4200 nmol/hr./mg of protein using a Glutathione Sepharose 4B column and gel filtration. Recombinant human CPX exhibits homogeneous behavior during high performance liquid chromatography (HPLC) and the N-terminal sequence, confirmed by protein sequencing, revealed a single polypeptide chain. In its active form, human CPX is a homodimer. According to the hydrodynamic properties derived from analytical ultracentrifugation, dimeric CPX has a nearly globular shape. Additionally, naturally occurring Arg to Trp (R231W)-mutated CPX has been also expressed in E. coli and further characterized. The mutated enzyme has a Km value of 0.55 microM as compared to 0.30 microM for the wild type. The catalytic efficiency (specificity constant, kcat/Km) of the mutated CPX was four fold lower than wild-type enzyme. The activity measurement of the mutated enzyme showed higher thermal sensitivity as compared with wild type CPX. The measured pI for mutated CPX is 5.65, compared to 6.40 for wild type. The pH optima for the mutated and wild-type protein are 6.6 and 6.8, respectively. The R231W mutation of CPX does not affect dimer formation and both normal and mutated CPX exhibit identical sedimentation properties. The thermal denaturation of both wild type and mutant CPX was found to be irreversible. The mutated CPX contained a significant amount of tightly bound porphyrin coproporphyrin. No metal association was found either in wild type or in mutated CPX. The availability of the recombinant human CPX will aid in structural and mechanistic studies.

Identification and interpretation of complexity in sedimentation velocity boundaries.

Synthetic sedimentation velocity boundaries were generated using finite-element solutions to the original and modified forms of the Lamm equation. Situations modeled included ideal single- and multicomponent samples, concentration-dependent samples, noninteracting multicomponent samples, and reversibly self-associating samples. Synthetic boundaries subsequently were analyzed using the method of van Holde and Weischet, and results were compared against known input parameters. Results indicate that this analytical method provides rigorous diagnostics for virtually every type of sample complexity encountered experimentally. Accordingly, both the power and utility of sedimentation velocity experiments have been significantly expanded.

Pyruvate dehydrogenase multienzyme complex. Characterization of assembly intermediates by sedimentation velocity analysis.

The pyruvate dehydrogenase complex is a large, highly organized assembly of several different catalytic and regulatory component enzymes. The structural core of the complex is the E2-X subcomplex, consisting of 60 dihydrolipoamide transacetylase (E2) subunits arranged in a pentagonal dodecahedron; 6 protein X and 2 pyruvate dehydrogenase kinase molecules are tightly associated with this E2 60-mer. The native E2-X subcomplex exhibits a sedimentation coefficient of 32 S. The effects of several chaotropes (guanidinium chloride, potassium thiocyanide, and urea) on the E2-X subcomplex were assessed. Treatment of the E2-X subcomplex with 4 M guanidinium chloride caused a complete loss of enzymatic activity and the dissociation of the subcomplex into monomeric 1.5-3 S species. Removal of the chaotrope by dialysis for 18 h resulted in complete restoration of E2 enzymatic activity and reassembly of a 32 S subcomplex; this reassembled subcomplex contained less protein X than the native subcomplex. Sedimentation velocity analysis of reassembled E2-X subcomplex demonstrated the presence of an 8 S assembly intermediate; this sedimentation coefficient is characteristic of globular proteins of molecular weights similar to that expected for a trimer of E2. Shorter periods of dialysis also gave rise to the 8 S species; the amount of this intermediate decreased with increasing times of dialysis. The 8 S species associated non-cooperatively to yield additional assembly intermediates exhibiting sedimentation coefficients of 10-32 S.

Alteration of the quaternary structure of cpn60 modulates chaperonin-assisted folding. Implications for the mechanism of chaperonin action.

Chaperonin-mediated, in vitro folding of rhodanese by the intact protein cpn60 has previously been shown to require cpn10 and ATP hydrolysis (Martin, J., Langer, T., Boteva, R., Schramel, A., Horwich, A. L., and Hartl, F.-U. (1991) Nature 352, 36-42; Mendoza, J. A., Rogers, E., Lorimer, G. H., and Horowitz, P. M. (1991) J. Biol. Chem. 266, 13044-13049). The present work demonstrates that the rhodanese-cpn60 complex can be dissociated by urea to allow folding to proceed, thus removing the obligatory requirement for cpn10 and ATP. Analytical ultracentrifugation and circular dichroism show that tetradecameric cpn60 can be disassembled into monomers that retain substantial secondary structure. Unfolded rhodanese induces the reassembly of tetradecameric cpn60 from monomers, and binding of rhodanese stabilizes cpn60 quaternary structure. Intermediate cpn60 species, possibly heptamers, are detected at intermediate urea concentrations after addition of unfolded rhodanese. The use of urea has demonstrated a functionally related loosening of subunit interactions in cpn60 that is not detectable under usual solution conditions. Our data suggest a highly dynamic role for the quaternary structure of cpn60 in chaperonin-mediated protein folding.

Binding of the RNA polymerase I transcription complex to its promoter can modify positioning of downstream nucleosomes assembled in vitro.

We have studied the reconstitution of chromatin-like structures in vitro, using purified RNA polymerase I transcription complexes and histone octamers. The plasmid construct used in these studies is a pUC8 derivative in which we have inserted an RNA polymerase I core promoter region of Acanthamoeba castellanii upstream of four repeats of the 5 S rDNA nucleosome positioning sequence (208 base pairs) from Lytechinus variegatus. When histone octamers were reconstituted onto the naked DNA template, the expected nucleosome positioning previously observed using tandem repeats of the same 208-base pair fragment was not obtained (as assayed by restriction enzyme digestion mapping of the inserted region of the plasmid). We show that the location of the RNA polymerase I core promoter region with regard to the tandemly repeated 208-base pair positioning sequence is a major determinant in the positioning of the histone octamers. Reconstituting first with the stalled transcription complex excluded octamers from the promoter region and recovered the expected nucleosome positioning downstream on the four repeats of the 5 S positioning sequence. The observed competition between histone octamers and the transcription complex for the promoter region suggests a great similarity with what has been reported from in vitro studies of RNA polymerase II and III transcription systems. We may be looking at a mechanism of regulation of transcription for the RNA polymerase I.

Neural network optimization for E. coli promoter prediction.

Methods for optimizing the prediction of Escherichia coli RNA polymerase promoter sequences by neural networks are presented. A neural network was trained on a set of 80 known promoter sequences combined with different numbers of random sequences. The conserved -10 region and -35 region of the promoter sequences and a combination of these regions were used in three independent training sets. The prediction accuracy of the resulting weight matrix was tested against a separate set of 30 known promoter sequences and 1500 random sequences. The effects of the network's topology, the extent of training, the number of random sequences in the training set and the effects of different data representations were examined and optimized. Accuracies of 100% on the promoter test set and 98.4% on the random test set were achieved with the optimal parameters.