324 Outcomes of Prostate Artery Embolisation In Catheterised Patients: A Case Series

Aim

Prostate artery embolisation (PAE) is an approved treatment for men with lower urinary tract symptoms secondary to benign prostatic hyperplasia (BPH-LUTS). Evidence of efficacy for PAE in patients who are unable to void urine spontaneously is scant, however. Traditional treatments for BPH-LUTS have evidence in retention patients and this series aims to report outcomes for PAE in catheterised patients.

Method

The records of consecutive men with BPH-LUTS which required either an indwelling bladder catheter or clean intermittent self-catheterisation (CISC) who subsequently underwent PAE were retrospectively reviewed. Basic demographics were collected along with information on the prostate volume and PAE procedure specifics. The primary outcome was whether patients were catheter/CISC free at 3 months. Other outcomes include complications, use of medications and the need for other surgical treatments post-PAE.

Results

63 men underwent PAE for urinary retention and BPH-LUTS between 2013 and 2020. Of these, 7 underwent a unilateral embolisation for aberrant anatomy. The mean prostate volume was 128ml. 61% of men were free from a catheter/CISC post-treatment. 4 patients suffered post-PAE UTI, whilst 3 patients subsequently underwent Transurethral Resection of the Prostate following PAE for failure to become catheter free. 13 men were entirely free from BPH-LUTS medications.

Conclusions

PAE for catheterised men results in a similar catheter-free rate post procedure to several more invasive BPH treatments. It has a low side-effect profile and gives men with poor health an option to try to become catheter free. PAE should be discussed with men with catheters as a treatment option.

Resin Infiltration of Caries in Primary Molars in a Community Setting: 24-Month Randomized Controlled Trial Findings

This study aimed to assess whether resin infiltration of primary molar proximal lesions is more effective than noninvasive measures in radiographically controlling carious lesion progression into the dentin. A split-mouth randomized controlled trial included 90 children, each with 2 proximal lesions confined to the inner half of the enamel or ≤0.5 mm into the dentin. For each child, lesions were randomly allocated to test (infiltration: DMG Icon preproduct and fluoride varnish) or control (fluoride varnish) status. The primary outcome measure was 24-mo radiographic lesion progression. Placement of a restoration during the study period was counted as lesion progression. Proportions of teeth with progressed lesions were compared using the McNemar test. Children also reported on the treatment's acceptability to them. Children (46% female) ranged in age from 6 to 9 y. Their mean number of decayed, missing, and filled teeth (d₃mft) was 2.8 (SD 2.6). At baseline, 58% and 42% of children were at moderate and low risk, respectively. Test and control lesions presented with similar radiographic lesions at baseline. At the 24-mo follow-up, 6 children had moved and 30 teeth had exfoliated. In the test and control groups, 15 of 66 lesions (22.7%) and 30 of 69 lesions (43.5%) had progressed, respectively (P < 0.05). The 2-y therapeutic effect (based on pairwise radiographic readings) of infiltration over fluoride varnish was 20.8% (95% confidence interval, 10.6%-30.2%). Nearly all children (96.7%) had enjoyed their visit to the clinic, and more than two-thirds (72.2%) were not worried about returning for treatment. Infiltration is more efficacious than fluoride varnish for controlling carious lesion progression in proximal lesions in primary molars, and most children find the treatment acceptable (Australian New Zealand Clinical Trials Registry ANZCTR.org.au ACTRN12611000827932). Knowledge Transfer Statement: These study findings can help clinicians decide which caries management approach they wish to use to prevent progression of proximal lesions in primary molars. With consideration of cost and patient preference, this information could lead to more appropriate therapeutic decisions.

227 THE EFFECTS OF SEXED SEMEN ON EMBRYONIC DEVELOPMENT TO THE BLASTOCYST STAGE

Sexed semen (SS) exhibits approximately 80% of the fertilizing ability of conventional semen (CS), and studies have shown that this continues through the 8-cell stage of bovine embryo development. At the time of this study, no information could be found that, when used for IVF and intracytoplasmic sperm injection (ICSI) development, had been carried to the blastocyst stage. In addition, questions have arisen regarding which of the measured sperm parameters are responsible for the difference between the SS and CS and contribute to this decline in fertility. The goals of this project were to evaluate the effects of using sexed sperm as it relates to embryonic development and to determine if any of the differences in sperm parameters affect embryonic development. A preliminary project evaluated SS and CS from 5 bulls for IVF and ICSI. One bull was selected to provide the sperm (both SS and CS) for the trial, and 1752 oocytes were assigned to either IVF or ICSI. The SS and CS were divided among the available oocytes used for IVF and ICSI. Straws were thawed for 30 s at 37°C, and sperm were then evaluated for motility (provided by CASA, SpermVision, MiniTube of America, Verona, WI), morphology, acrosomal integrity (Coomassie and Pope stains), viability, and nuclear decondensation (SYBR Green and HALO). Results for SS v. CS were as follows: motility, 8 v. 26%; viability, 40.6 v. 30%; nuclear decondensation, 40 v. 30%; normal morphology and acrosomal integrity, no differences. Oocytes were obtained from Applied Reproductive Technologies, LLC (Madison, WI). The fertilization rate was consistently lower (Table 1) for both IVF and ICSI when SS were used (Z = 3.65; P = 0.0003), and there was no evidence that this decline in fertilization rate differed for the 2 methods (Z = 0.18; P = 0.86). Nor was there any evidence that the method affected the fertilization rate in general (Z = 0.75; P = 0.45). Thus, the difference was specific for fertilization rate and had no effect on Day 3 cells or Day 7 blastocysts. A higher fertility rate using ICSI would have indicated that a surface membrane factor may have been decreasing the fertility rate with SS because of the elimination of binding factors associated with ICSI. Thus, it may not be the sperm surface membrane that is distorted in the sexing procedure, but likely the integrity of the spermal DNA, as indicated by the increased nuclear decondensation of SS. Table 1.Comparison of sexed sperm with conventional sperm when used for IVF and intracytoplasmic sperm injection (ICSI) Partial funding for this project was made available by the California State University Agricultural Research Institute (ARI). Appreciation is extended to Sexing Technologies, Inc. (Navasota, TX) for donating the semen.

Reduced-scale large-zone analytical gel-filtration chromatography for measurement of protein association equilibria

The proteasome plays a central role in eukaryotic cells since it is responsible for the degradation of specific proteins involved in a large range of cellular processes. Analysis of proteasome mechanisms of action, or in vitro reconstitution, or dissection of the complex biological pathways in which it partakes, requires a reliable source of pure active proteasome. Although the biologically relevant form of the proteasome is usually considered to be the 26S proteasome, this unit describes different methods for purification and study of both 26S and 20S proteasomes from Saccharomyces cerevisiae cells.

Non-infectious manifestations of stem cell transplantation

Stem cell transplantation (SCT) is now commonplace within medical practice. With growth in transplant activities, outcomes are likely to continue to improve. Increasing numbers of the population now face life after transplantation. The aetiology of post transplant complications is multifactorial. Background knowledge of SCT and common, radiographically detectable, non-infective complications are important in everyday clinical practice. A review of these complications using a variety of imaging modalities is presented and the process of SCT briefly described. Tumour recurrence is outside the remit of this review.

Competing protein:protein interactions are proposed to control the biological switch of the E coli biotin repressor

A model is suggested for the complex between the biotin repressor of Escherichia coli, BirA, and BCCP, the biotin carboxyl carrier protein to which BirA transfers biotin. The model is consistent with prior physical and biochemical studies. Measurement of transfer rates for variants of BirA with single-site mutations in the proposed BirA:BCCP interface region also provides support. The unique feature of the proposed interaction between BirA and BCCP is that it uses the same beta-sheet region on the surface of BirA that the protein uses for homodimerization into a form competent to bind DNA. The resulting mutually exclusive protein:protein interfaces explain the novel feature of the BirA regulatory system, namely, that transcription of the genes involved in biotin synthesis is not determined by the level of biotin, per se, but by the level of unmodified BCCP. The model also provides a role for the C-terminal domain of BirA that is structurally similar to an SH3 domain.

Regulated assembly of transcription factors and control of transcription initiation

Proteins that function in regulation of transcription initiation are typically homo or hetero-oligomeric. Results of recent biophysical studies of transcription regulators indicate that the assembly of these proteins is often subject to regulation. This regulation of assembly dictates the frequency of transcription initiation via its influence on the affinity of a transcription regulator for DNA and its affect on target site selection. Factors that modulate transcription factor assembly include binding of small molecules, post-translational modification, DNA binding and interactions with other proteins. Here, the results of recent structural and/or thermodynamic studies of a number of transcription regulators that are subject to regulated assembly are reviewed. The accumulated data indicate that this phenomenon is ubiquitous and that mechanisms utilized in eukaryotes and prokaryotes share common features.

Corepressor-induced organization and assembly of the biotin repressor: a model for allosteric activation of a transcriptional regulator

The Escherichia coli biotin repressor binds to the biotin operator to repress transcription of the biotin biosynthetic operon. In this work, a structure determined by x-ray crystallography of a complex of the repressor bound to biotin, which also functions as an activator of DNA binding by the biotin repressor (BirA), is described. In contrast to the monomeric aporepressor, the complex is dimeric with an interface composed in part of an extended beta-sheet. Model building, coupled with biochemical data, suggests that this is the dimeric form of BirA that binds DNA. Segments of three surface loops that are disordered in the aporepressor structure are located in the interface region of the dimer and exhibit greater order than was observed in the aporepressor structure. The results suggest that the corepressor of BirA causes a disorder-to-order transition that is a prerequisite to repressor dimerization and DNA binding.

Multiple disordered loops function in corepressor-induced dimerization of the biotin repressor

Cooperative association of the Escherichia coli biotin repressor with the biotin operator is allosterically activated by binding of the corepressor, bio-5'-AMP. The corepressor function of the adenylate is due, in part, to its ability to induce repressor dimerization. Since a high-resolution structure of only the apo or unliganded repressor is currently available, the location of the dimerization interface on the protein structure is not known. Here, five mutants in the corepressor-binding domain of the repressor have been analyzed with respect to their DNA-binding and self-assembly properties. Results of these studies reveal that four of the mutant proteins exhibit defects in DNA binding. These same proteins are compromised in self-assembly. Furthermore, in the three-dimensional structure of the apo protein the mutations all lie in partially disordered surface loops, one of which is known to participate directly in corepressor binding. These results suggest that multiple disordered surface loops function in the corepressor-induced dimerization required for sequence-specific DNA binding by the biotin repressor.

Function of a conserved sequence motif in biotin holoenzyme synthetases

The biotin holoenzyme synthetases (BHS) are essential enzymes in all organisms that catalyze post-translational linkage of biotin to biotin-dependent carboxylases. The primary sequences of a large number of these enzymes are now available and homologies are found among all. The glycine-rich sequence, GRGRXG, constitutes one of the homologous regions in these enzymes and, based on its similarity to sequences found in a number of mononucleotide binding enzymes, has been proposed to function in ATP binding in the BHSs. In the Escherichia coli enzyme, the only member of the family for which a three-dimensional structure has been determined, the conserved sequence is found in a partially disordered surface loop. Mutations in the sequence have previously been isolated and characterized in vivo. In this work these single-site mutants, G115S, R118G, and R119W, of the E. coli BHS have been purified and biochemically characterized with respect to binding of small molecule substrates and the intermediate in the biotinylation reaction. Results of this characterization indicate that, rather than functioning in ATP binding, this glycine-rich sequence is required for binding the substrate biotin and the intermediate in the biotinylation reaction, biotinyl-5'-AMP. These results are of general significance for understanding structure-function relationships in biotin holoenzyme synthetases.

Dimerization of the Escherichia coli biotin repressor: corepressor function in protein assembly

The repressor of biotin biosynthesis binds to the biotin operator sequence to repress transcription initiation at the biotin biosynthetic operon. Site-specific binding of BirA to the biotin operator is allosterically regulated by binding of the small molecule, biotinyl-5'-adenylate (bio-5'-AMP). The operator is a 40 base pair imperfect inverted palindrome and two holorepressor monomers bind cooperatively to the two operator half-sites. Results of previous detailed analyses of binding of holoBirA to bioO indicate that site-specific DNA binding and protein dimerization are obligatorily linked in the system. In the present work equilibrium sedimentation measurements have been used to examine the assembly properties of the aporepressor and its complexes with small ligands biotin and bio-5'-AMP. Results of these measurements indicate that while the free protein and the biotin complex exhibit no tendency to self-associate, the adenylate-bound protein assembles into dimers with an equilibrium constant of 11 microM. The results suggest that one mechanism by which the adenylate promotes binding of BirA to the biotin operator is by promoting repressor dimerization.

Ligand-linked structural changes in the Escherichia coli biotin repressor: the significance of surface loops for binding and allostery

The Escherichia coli repressor of biotin biosynthesis (BirA) is an allosteric site-specific DNA-binding protein. BirA catalyzes synthesis of biotinyl-5'-AMP from substrates biotin and ATP and the adenylate serves as the positive allosteric effector in binding of the repressor to the biotin operator sequence. Although a three-dimensional structure of the apo-repressor has been determined by X-ray crystallographic techniques, no structures of any ligand-bound forms of the repressor are yet available. Results of previously published solution studies are consistent with the occurrence of conformational changes in the protein concomitant with ligand binding. In this work the hydroxyl radical footprinting technique has been used to probe changes in reactivity of the peptide backbone of BirA that accompany ligand binding. Results of these studies indicate that binding of biotin to the protein results in protection of regions of the central domain in the vicinity of the active site and the C-terminal domain from chemical cleavage. Biotin-linked changes in reactivity constitute a subset of those linked to adenylate binding. Binding of both bio-5'-AMP and biotin operator DNA suppresses cleavage at additional sites in the amino and carboxy-terminal domains of the protein. Varying degrees of protection of the five surface loops on BirA from hydroxyl radical-mediated cleavage are observed in all complexes. These results implicate the C-terminal domain of BirA, for which no function has previously been known, in small ligand and site-specific DNA binding and highlight the significance of surface loops, some of which are disordered in the apoBirA structure, for ligand binding and transmission of allosteric information in the protein.

Potent anti-hepatitis B viral activity and inhibition of bacteriophage T7 RNA polymerase by a "fat" nucleoside and its 5'-triphosphate derivative: synthetic, biochemical, and biological studies of 4,8-diamino-6-imino-6H-1-beta-D-ribofuranosyl-imidazo[4,5-E] [1,3]diazepine-5'-triphosphate

The title nucleoside, 4,8-diamino-6-imino-6H-1-beta-d-ribofuranosylimidazo[4,5-e][1,3]-d iazepine, exhibited potent anti-hepatitis B viral activity with minimum toxicity in vitro, and its 5'-triphosphate derivative strongly inhibited the bacteriophage T7 RNA polymerase.

A minimal peptide substrate in biotin holoenzyme synthetase-catalyzed biotinylation

The Escherichia coli biotin holoenzyme synthetase, BirA, catalyzes transfer of biotin to the epsilon amino group of a specific lysine residue of the biotin carboxyl carrier protein (BCCP) subunit of acetyl-CoA carboxylase. Sequences of naturally biotinylated substrates are highly conserved across evolutionary boundaries, and cross-species biotinylation has been demonstrated in several systems. To define the minimal substrate requirements in BirA-catalyzed biotinylation, we have measured the kinetics of modification of a 23-residue peptide previously identified by combinatorial methods. Although the sequence of the peptide bears little resemblance to the biotinylated sequence in BCCP, it is enzymatically biotinylated in vivo. Rates of biotin transfer to the 23-residue peptide are similar to those determined for BCCP. To further elucidate the sequence requirements for biotinylation, transient kinetic measurements were performed on a series of amino- and carboxy-terminal truncations of the 23-mer. The results, determined by stopped-flow fluorescence, allowed identification of a 14-residue peptide as the minimum required sequence. Additional support was obtained using matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometric analysis of peptides that had been incubated with an excess of biotinyl-5'-adenylate intermediate and catalytic amounts of BirA. Results of these measurements indicate that while kinetically inactive truncations showed no significant shift in molecular mass to the values expected for biotinylated species, kinetically active truncations exhibited 100% biotinylation. The specificity constant (k(cat)/Km) governing BirA-catalyzed biotinylation of the 14-mer minimal substrate is similar to that determined for the natural substrate, BCCP. We conclude that the 14-mer peptide efficiently mimics the biotin acceptor function of the much larger protein domain normally recognized by BirA.

Comparison of the backbone dynamics of the apo- and holo-carboxy-terminal domain of the biotin carboxyl carrier subunit of Escherichia coli acetyl-CoA carboxylase

The biotin carboxyl carrier protein (BCCP) is a subunit of acetyl-CoA carboxylase, a biotin-dependent enzyme that catalyzes the first committed step of fatty acid biosynthesis. In its functional cycle, this protein engages in heterologous protein-protein interactions with three distinct partners, depending on its state of post-translational modification. Apo-BCCP interacts specifically with the biotin holoenzyme synthetase, BirA, which results in the post-translational attachment of biotin to a single lysine residue on BCCP. Holo-BCCP then interacts with the biotin carboxylase subunit of acetyl-CoA carboxylase, which leads to the addition of the carboxylate group of bicarbonate to biotin. Finally, the carboxy-biotinylated form of BCCP interacts with transcarboxylase in the transfer of the carboxylate to acetyl-CoA to form malonyl-CoA. The determinants of protein-protein interaction specificity in this system are unknown. The NMR solution structure of the unbiotinylated form of an 87 residue C-terminal domain fragment (residue 70-156) of BCCP (holoBCCP87) and the crystal structure of the biotinylated form of a C-terminal fragment (residue 77-156) of BCCP from Escherichia coli acetyl-CoA carboxylase have previously been determined. Comparative analysis of these structures provided evidence for small, localized conformational changes in the biotin-binding region upon biotinylation of the protein. These structural changes may be important for regulating specific protein-protein interactions. Since the dynamic properties of proteins are correlated with local structural environments, we have determined the relaxation parameters of the backbone 15N nuclear spins of holoBCCP87, and compared these with the data obtained for the apo protein. The results indicate that upon biotinylation, the inherent mobility of the biotin-binding region and the protruding thumb, with which the biotin group interacts in the holo protein, are significantly reduced.

Energetic methods to study bifunctional biotin operon repressor

Application of a broad range of approaches and techniques to analysis of the functional energetics of the biotin regulatory system has enabled dissection of each of the steps in the assembly of this transcriptional repression complex. Although the molecular details of the interactions are not yet completely understood, the studies described in this article have laid a solid foundation for future studies of the system. The application of kinetic and equilibrium methods to studies of binding of the allosteric effector has allow determination of the kinetic parameters governing the interaction of the protein and ligand. The kinetic parameters have, furthermore, been utilized to calculate the equilibrium parameters associated with the binding. The great advantage of using kinetic methods to study the binding process is the additional information provide about the mechanism of allosteric activation of the protein. Based on the initial observation of a kinetic time course that is consistent with the occurrence of a structural change concomitant with effector binding, additional measurements have been performed that have allowed formulation of a testable hypothesis concerning the nature and location of one locus: the structural change in the three-dimensional structure of BirA. Studies of assembly of the protein indicate the bio-5-AMP is an allosteric activator of dimerization of the protein. The dimerization is, however, weak. These results have been critical in analyzing site-specific DNA binding measurements. Application of the DNase I footprinting technique has allowed formulation of a model for association of holoBirA with bioO. Results of studies of binding of the protein to mutant operator templates, although not yielding the anticipated results, provide further insight into the mechanism of association of the protein and DNA. Two models for binding, the validity of which can be tested via the application of kinetic techniques, have been derived from these measurements. The results of quantitative studies of the biotin regulatory system can be interpreted in the context of the biological function of the system. The biotin holoenzyme ligases are a class of enzymes found across the evolutionary spectrum. Only a subset of these enzymes, including BirA, also function as transcriptional repressors. The tight binding of the allosteric effector may be understood in light of the bifunctional nature of the BirA-bio-5'-AMP complex. It is possible that the unusually high thermodynamic and kinetic stability of the complex ensures that the most probable state of the protein in vivo is the adenylate-bound form. This complex, not the unliganded protein, is active in both enzymatic transfer of biotin and site-specific DNA binding. This ensures that on depletion of the intracellular pool of apoBCCP, BirA-bio-5'-AMP accumulates and binds to bioO to repress transcription of the biotin biosynthesis operon. The intracellular demand for and synthesis of biotin are, consequently, tightly coupled in the system. The dimerization that accompanies adenylate binding to BirA appears to be significant for site-specific binding of the protein to bioO. Functionally, the simultaneous binding of the two monomers to the two operator half-sites, regardless of the kinetic mechanism by which it occurs, ensures coordinate regulation of transcription initiation from both biotin operon promoters. The multifaceted approach utilized in studies of the biotin regulatory system can serve as a model for studies of any complex transcriptional regulatory system. It is critical in elucidating the functional energetics of any of these systems that the assembly first be dissected into the constituent interactions and that each of these interactions be studied in isolation. This is not only critical for understanding the physicochemical properties of each individual contributing interaction, but is also a necessary precursor to studies of thermodynamic linkage in the system. (AB

A map of the biotin repressor-biotin operator interface: binding of a winged helix-turn-helix protein dimer to a forty base-pair site

The Escherichia coli biotin repressor is a member of the "winged helix-turn-helix" class of site-specific DNA binding proteins. The protein binds as a dimer to the 40 bp biotin operator sequence. Although the structure of the aporepressor has been solved by X-ray crystallographic techniques, no structure of the holorepressor-DNA complex is yet available. In order to characterize the structural features of the biotin repressor-biotin operator interface we have applied a number of solution techniques including DNase I, hydroxyl radical and dimethyl sulfate footprinting and the circular permutation or "bending" assay. Results of these combined studies indicate that each repressor monomer forms a bipartite interface with each half-site of the biotin operator sequence. The results imply that, in addition to the helix-turn-helix module of each monomer, a second structural element participates in the protein-DNA interface. The two bipartite protein-DNA interfaces appear, moreover, to primarily involve the two 12 bp termini of the operator site. Results of combined DNase I footprinting and circular permutation analysis indicate, furthermore, that the central 16 bp region that links the two termini becomes distorted concomitant with binding of holoBirA.

Coupling of site-specific DNA binding to protein dimerization in assembly of the biotin repressor-biotin operator complex

The Escherichia coli repressor of biotin biosynthesis, BirA, binds site-specifically to the biotin operator, a 40 base pair imperfect inverted palindrome. Two repressor monomers have been shown to bind to the two operator half-sites. Analysis of results of quantitative DNase I footprint titrations performed on the wild-type biotin operator template indicate that binding is well described by a cooperative mechanism. The data obtained from these studies were, however, insufficient to independently resolve all of the energetic parameters associated with cooperative binding of the two repressor monomers to the operator site. In this work, to further dissect the energetics of assembly of the biotin repressor-biotin operator complex, measurements of binding of BirA to four bioO variants designed to reduce the valency of repressor binding from 2 to 1 have been performed. Results of these measurements indicate, as was found with the wild-type biotin operator template, that two repressor monomers bind simultaneously to the two half-sites of all variant operators. Protein dimerization and DNA binding are thus obligatorily coupled in the biotin repressor system. Furthermore, the results suggest that, in the context of a cooperative binding mechanism, the cooperative free energy associated with the biotin repressor-biotin operator interaction is significantly more favorable than the previously estimated -2 kcal/mol.

Structure of the carboxy-terminal fragment of the apo-biotin carboxyl carrier subunit of Escherichia coli acetyl-CoA carboxylase

The biotin carboxyl carrier protein (BCCP) is a subunit of acetyl-CoA carboxylase, a biotin-dependent enzyme that catalyzes the first committed step of fatty acid biosynthesis. In its functional cycle the biotin carboxyl carrier protein engages in heterologous protein-protein interactions with three distinct partners, depending on its state of posttranslational modification. Apo-BCCP interacts specifically with the biotin holoenzyme synthetase, BirA, which results in the posttranslational attachment of biotin to an essential lysine residue on BCCP. Holo-BCCP then interacts with the biotin carboxylase subunit, which leads to the addition of the carboxylate group of bicarbonate to biotin. Finally, the carboxybiotinylated form of BCCP interacts with transcarboxylase in the conversion of acetyl-CoA to malonyl-CoA. The determinants of protein-protein interaction specificity in this system are unknown. One hypothesis is that posttranslational modification of BCCP may result in conformational changes that regulate specific protein-protein interactions. To test this hypothesis, we have determined the NMR solution structure of the unbiotinylated form of an 87 residue C-terminal domain fragment of BCCP (apoBCCP87) from Escherichia coli acetyl-CoA carboxylase and compared this structure with the high-resolution structure of the biotinylated form that was recently solved by X-ray crystallographic techniques. Although the overall folding of the two proteins is highly similar, small structural differences are apparent for residues of the biotin-binding loop that may be important for mediating specific protein-protein interactions.

Oligomerization state of S100B at nanomolar concentration determined by large-zone analytical gel filtration chromatography

S100B is a Ca(2+)-binding protein known to be a non-covalently associated dimer, S100B(beta beta), at high concentrations (0.2-3.0 mM) under reducing conditions. The solution structure of apo-S100B (beta beta) shows that the subunits associate in an antiparallel manner to form a tightly packed hydrophobic core at the dimer interface involving six of eight helices and the C-terminal loop (Drohat AC, Amburgey JC, Abildgaard F, Starich MR, Baldisseri D, Weber DJ. 1996. Solution structure of rat apo-S100B (beta beta) as determined by NMR spectroscopy. Biochemistry 35:11577-11588). The C-terminal loop, however, is also known to participate in the binding of S100B to target proteins, so its participation in the dimer interface raises questions as to the physiological relevance of dimeric S100B (beta beta). Therefore, we investigated the oligomerization state of S100B at low concentrations (1-10,000 nM) using large-zone analytical gel filtration chromatography with 35S-labeled S100B. We found that S100B exists (> 99%) as a non-covalently associated dimer, S100B (beta beta), at 1 nM subunit concentration (500 pM dimer) in the presence or absence of saturating levels of Ca2+, which implies a dissociation constant in the picomolar range or lower. These results demonstrate for the first time that in reducing environments and at physiological concentrations, S100B exists as dimeric S100B (beta beta) in the presence or absence of Ca2+, and that the non-covalent dimer is most likely the form of S100B presented to target proteins.

Thermodynamic analysis of small ligand binding to the Escherichia coli repressor of biotin biosynthesis

BirA is the transcriptional repressor of biotin biosynthesis and a biotin holoenzyme synthetase. It catalyzes synthesis of biotinyl-5'-AMP from the substrates biotin and ATP. The adenylate is the activated intermediate in the biotin transfer reaction as well as the positive allosteric effector for site-specific DNA binding. The affinity of BirA for the adenylate is considerably greater than its affinity for biotin, and both binding reactions are coupled to changes in the conformation of the protein. The temperature dependencies of the two binding interactions have been determined using kinetic techniques. Van't Hoff analysis of the equilibrium dissociation constants derived from the kinetic data indicate that while the two binding processes are characterized by large negative enthalpies, the entropic contributions are small for both. Binding enthalpies have also been determined by isothermal titration calorimetry. Consistent with the results of the van't Hoff analyses, the calorimetric enthalpies are large and negative. The greater precision of the calorimetric measurements allowed more accurate estimation of the entropic contributions to the binding processes, which are of opposite sign for the two ligands. In addition, the heat capacity changes associated with the two binding reactions are small. The measured thermodynamic parameters for binding of biotin and bio-5'-AMP to BirA have been utilized to dissect out structural contributions to the binding energetics. Results of these calculations indicate equivalent contributions of burial of polar and apolar surface area to both binding processes. The total loss of solvent accessible surface area is, however, greater for biotin binding. The analysis indicates furthermore that although both binding reactions are coupled to losses in configurational entropy, the magnitude of the conformational change is significantly larger for biotin binding.

Purification and characterization of intact and truncated forms of the Escherichia coli biotin carboxyl carrier subunit of acetyl-CoA carboxylase

Biotin biosynthesis and retention in Escherichia coli is regulated by the multifunctional protein, BirA. The protein acts as both the transcriptional repressor of the biotin biosynthetic operon and as a ligase for covalent attachment of biotin to a unique lysine residue of the acetyl-CoA carboxylase. Biotinyl-5'-AMP is the activated intermediate for the ligase reaction and the allosteric effector for DNA binding. We have purified and characterized apoBCCP and a truncated form containing the COOH-terminal 87 residues (apoBCCP87). Molecular masses of the proteins measured using matrix-assisted laser desorption ionization time-of-flight mass spectrometry conformed to the expected values. The assembly states of apoBCCP and apoBCCP87 were determined using sedimentation equilibrium ultracentrifugation. Nearly quantitative enzymatic transfer of biotin from BirA-biotinyl-5'-AMP to the apoBCCP forms was assessed using two methods, mass spectrometric analysis of acceptor proteins after incubation with BirA-bio-5'-AMP and a steady state fluorescence assay. The BirA catalyzed rates of transfer of biotin from bio-5'-AMP to apoBCCP and apoBCCP87 were measured by stopped-flow fluorescence. Kinetic parameters estimated from these measurements indicate that the intact and truncated forms of the acceptor protein are functionally identical.

Evidence for interdomain interaction in the Escherichia coli repressor of biotin biosynthesis from studies of an N-terminal domain deletion mutant

The Escherichia coli repressor of biotin biosynthesis (BirA) is an allosteric site-specific DNA binding protein. The protein is composed of three structural domains. Contact with the biotin operator (bioO) in the transcriptional repression complex is made by the N-terminal domain which contains a helix-turn-helix structural module. The central domain is required for the catalytic functions of BirA including synthesis of biotinyl-5'-AMP from substrates ATP and transfer of biotin from the adenylate to a lysine residue of the biotin carboxyl carrier protein (BCCP) of acetyl CoA carboxylase. The adenylate serves not only as the activated intermediate in the biotin transfer reaction but also as the positive allosteric effector for site-specific DNA binding. Little interaction between the N-terminal and central domains is observed in the apo-repressor structure (Wilson et al., 1992). In this work, we have engineered an N-terminal deletion mutant of BirA, BirA65-321. Biochemical analysis of the purified truncated repressor indicates that, as expected, it does not bind to biotin operator DNA. BirA65-321 is, moreover, identical to intact BirA in catalysis of synthesis of bio-5'-AMP and in transfer of biotin from the adenylate to BCCP. Deletion of the DNA binding domain severely compromises the ability of BirA to bind to biotin or bio-5'-AMP. The affinity of BirA65-321 for biotin is decreased 100-fold while that for bio-5'-AMP is decreased 1000-fold, relative to intact BirA. The significant functional role of the DNA binding domain in tight binding of the two ligands to the central domain may be indicative of formation of extensive interdomain contacts in the holorepressor structure.

Evidence for distinct ligand-bound conformational states of the multifunctional Escherichia coli repressor of biotin biosynthesis

The Escherichia coli repressor of biotin biosynthesis (BirA) is a unique transcriptional repressor which catalyzes synthesis of its own corepressor and catalyzes attachment of a cofactor to an essential metabolic enzyme. BirA both catalyzes synthesis of biotinyl-5'-AMP from the substrates ATP and biotin and transfer of the biotin moiety from the adenylate to a lysine residue of a subunit of the acetyl-CoA carboxylase. BirA-bio-5'-AMP, moreover, binds sequence specifically to the biotin operator to repress transcription of the biotin biosynthetic genes. Using a combination of kinetic measurements of binding of the two ligands, biotin and bio-5'-AMP, to BirA as well as proteolytic digestion experiments, we have found evidence for at least three discrete conformational states of BirA. Results of stopped-flow fluorescence measurements of association of both ligands with BirA indicate that the process involves initial formation of a collision complex followed by a slow conformational change. The kinetics of the conformational change are distinct for the two ligands and are the basis for the difference in the thermodynamic stabilities of the two protein-ligand complexes. Different rates of proteolytic digestion of apoBirA and complexes of BirA with the two ligands were also observed. Results of the combined approaches indicate that apoBirA, and the BirA-bio-5'-AMP and BirA-biotin complexes are conformationally distinct.

Reduced-scale large-zone analytical gel filtration chromatography for measurement of protein association equilibria

The method of large-zone analytical gel filtration chromatography (AGFC) for determination of the energetics and stoichiometries of protein association processes was adapted for use with a semicompressible hydrophilic sieving resin and high-performance liquid chromatography (HPLC) instrumentation. Chromatography was performed using a 2.3-ml glass column, providing a 10-fold reduction in column volume over the conventional AGFC low-pressure chromatography format. Equipment consisted of a Teflon injection valve, HPLC pump, and uv-vis spectrophotometric detector. Method validation included preparation of calibration curves using data obtained from small- and large-zone chromatography of monomeric protein standards. Following confirmation of the agreement of small- and large-zona data obtained for monomeric proteins, the method was further tested by measurement of the dimer-tetramer equilibrium constant for the well-characterized oxygenated human hemoglobin system. Excellent agreement between the experimentally determined equilibrium association constant and the literature value was obtained, as well as a dramatic savings in material and time required to perform the experiment.

Self-assembly of bacteriophage lambda cI repressor: effects of single-site mutations on the monomer-dimer equilibrium

Dimerization of lambda cI repressor monomers is required for high-affinity binding to bacteriophage lambda operator DNA and is known to involve protein-protein contacts between C-terminal domains of the repressor monomers. In order to address the importance of the C-terminal domain in mediating the oligomeric properties of dimerization and cooperative binding to operator DNA, eight single-site mutant repressors were screened for possible deficiencies in cooperative interactions; all but one of the amino acid substitutions are located within the C-terminal domain. As a prelude to binding studies and the complete characterization of cooperativity mutants of lambda cI repressor (Burz, D. S., & Ackers, G. K. (1994) Biochemistry 33, 8406-8416), the thermodynamics of self-assembly of seven of these mutants was examined from 10(-11) to 10(-5) M total repressor using analytical gel chromatography. Results show that the structural perturbation accompanying single amino acid replacement does not significantly affect the monomer-dimer equilibrium with the exception of that accompanying replacements of serine 228; mutations at that site weaken, by 2-4 kcal/mol, the protein-protein interactions responsible for self-association. An additional mutant repressor, Pro158-->Thr, was also examined and found to associate reversibly from monomers to a species with stoichiometry greater than 2. All mutations increase the apparent Stokes radius of the monomeric form by 2-4.5 A and that of dimers by 1 or 3 A.

Kinetics of biotinyl-5'-adenylate synthesis catalyzed by the Escherichia coli repressor of biotin biosynthesis and the stability of the enzyme-product complex

The Escherichia coli repressor of biotin biosynthesis is both a biotin ligase and the repressor of transcriptional initiation at the biotin biosynthetic operon. The small molecule, biotinyl-5'-adenylate (bio-5'-AMP), is the intermediate in the biotin ligation reaction and the positive allosteric effector for sequence-specific DNA binding by BirA. Synthesis of the adenylate from the substrates biotin and ATP is catalyzed by BirA. Although BirA and other biotin holoenzyme synthetases have been the subject of biochemical studies, no direct measurements of the bio-5'-AMP synthesis reaction have been reported. No information relating to the mechanism and kinetic parameters governing adenylate synthesis is available. In addition to this lack of kinetic information, the thermodynamic stability of the BirA-bio-5'-AMP complex is not known. Since the BirA-adenylate complex plays a pivotal role in the biotin regulatory system, both the kinetic and thermodynamic information are essential to a quantitative understanding of the system. We have developed a method for measuring the time course of bio-5'-AMP synthesis. The results of these measurements indicate that the time course is characterized by an initial burst followed by a slow linear phase. The burst corresponds to the rapid synthesis of 1 mol of product per mole of enzyme, and the rate of the slow linear phase is limited by the release of product from the enzyme.(ABSTRACT TRUNCATED AT 250 WORDS)

Cooperative binding of the Escherichia coli repressor of biotin biosynthesis to the biotin operator sequence

Regulation of biotin biosynthesis and retention in Escherichia coli depends on a complex set of coupled protein-protein, protein-nucleic acid, and protein-small molecule interactions. The complexity of the biotin system is analogous to that found in gene regulatory systems from other prokaryotes and from eukaryotes. Quantitative understanding of these systems requires thermodynamic studies of the individual contributing interactions. We have initiated such studies of the biotin regulatory interactions. The assembly states of the biotin operon repressor (BirA) and its complex with the allosteric effector, bio-5'-AMP, have been determined by analytical gel filtration chromatography. Both the apo- and holo-repressors are monomeric at protein concentrations several orders of magnitude higher than those required for DNA binding. Results of stoichiometric DNA binding measurements indicate that the BirA-biotin operator (bioO) complex consists of two holo-repressor monomers per operator site. Equilibrium binding of BirA to bioO has been measured using the quantitative DNase footprint technique. Analysis of the data indicates that the binding process is best described by a cooperative model. An upper limit for the cooperative free energy is estimated to be between -2.0 and -3.0 kcal/mol.

Isolation of lambda repressor mutants with defects in cooperative operator binding

A hybrid operator-promoter region was designed to aid in a screen for cooperativity mutants of the lambda repressor. In this system, lambda repressor mutants with defects in pairwise cooperative binding are unable to act as efficient transcriptional repressors. Four single amino acid substitutions in the C-terminal domain of the repressor were isolated. Studies of the DNA binding properties of the purified mutant proteins show that a repressor bearing the Gly147-->Asp mutation binds with normal affinity to single operator sites but is defective in pairwise cooperative site binding. Quantitative footprinting studies show that the free energy of interaction between repressor dimers bound at operator sites OR1 and OR2 is reduced from -2.4 kcal/mol for the wild-type repressor to 0 kcal/mol for the GD147 mutant.

Quantitative study of protein association at picomolar concentrations: the lambda phage cl repressor

A method has been developed for radiolabeling the lambda cl repressor to a specific activity sufficiently high to permit accurate quantitation of the protein in the picomolar range of concentration. Procedures are described whereby the labeled protein can be used for accurate quantitative study of the energetics of repressor assembly by large zone analytical gel chromatography. This methodology is applicable to other systems in which the stoichiometry and energetics of tightly associating DNA binding proteins are currently difficult to measure.

Ribonucleoprotein complexes of R17 coat protein and a translational operator analog

The coat protein of the simple spherical (triangulation no. T = 3) RNA coliphage R17 protects the genomic RNA in the virus particle and acts as a translational repressor of the phage-encoded replicase gene. It has been suggested that these two functions are related and that the translational repression complex serves as a nucleation complex for subsequent assembly of the bacteriophage. We have used a translational operation fragment to examine the relationship between formation of the translational repression complex and the assembly of the protein into T = 3 capsids. In vitro analysis of the aggregation properties of R17 coat protein reveals that binding of the translational operator fragment to the protein dimer triggers polymerization of the protein into T = 3 capsids of well-defined composition. The data further implicate the translational operator in nucleation of assembly and suggest a possible physical-chemical basis of the nucleation step.

Roles of operator and non-operator RNA sequences in bacteriophage R17 capsid assembly

In order to understand the role of sequences other than the translational operator on bacteriophage R17 assembly, in vitro capsid assembly was studied with R17 coat protein and a variety of RNAs. For a series of RNA oligomers of the same chain length, sequences that bind coat protein dimer with a lower affinity require higher concentrations of RNA and protein for assembly. Among a series of non-specific RNA molecules of differing lengths, lower protein and RNA concentrations are required for assembly of capsids containing longer RNAs. For RNA molecules of any length, the presence of a single high-affinity translational operator sequence lowered the concentration requirements for capsid assembly. However, the advantage for encapsidation provided by the operator sequence is small for large RNA molecules. The experiments indicate that in the overall assembly process the interaction of coat protein with non-specific sequences is at least as important as its interaction with the specific translational operator sequence. In light of the data, a mechanism of achieving selective packaging of the R17 genomic RNA in vivo is discussed.

Interaction of R17 coat protein with its RNA binding site for translational repression

The interaction between bacteriophage R17 coat protein and its RNA binding site for translational repression was studied as an example of a sequence-specific RNA-protein interaction. A nitrocellulose filter retention assay is used to demonstrate equimolar binding between the coat protein and a synthetic 21 nucleotide RNA fragment. The Kd at 2 degrees C in a buffer containing 0.19 M salt is about 1 nM. The relatively weak ionic strength dependence of Ka and a delta H = -19 kcal/mole indicates that most of the binding free energy is due to non-electrostatic interactions. Since a variety of RNAs failed to compete with the 21 nucleotide fragment for coat protein binding, the interaction appears highly sequence specific. We have synthesized more than 30 different variants of the binding site sequence in order to identify the portions of the RNA molecule which are important for protein binding. Out of the five single stranded residues examined, four were essential for protein binding whereas the fifth could be replaced by any nucleotide. One variant was found to bind better than the wild type sequence. Substitution of nucleotides which disrupted the secondary structure of the binding fragment resulted in very poor binding to the protein. These data indicated that there are several points of contact between the RNA and the protein and the correct hairpin secondary structure of the RNA is essential for protein binding.