The Distinctive Permutated Domain Structure of Periplasmic α-Amylase (MalS) from Glycoside Hydrolase Family 13 Subfamily 19

Periplasmic α-amylase MalS (EC. 3.2.1.1), which belongs to glycoside hydrolase (GH) family 13 subfamily 19, is an integral component of the maltose utilization pathway in Escherichia coli K12 and used among Ecnterobacteriaceae for the effective utilization of maltodextrin. We present the crystal structure of MalS from E. coli and reveal that it has unique structural features of circularly permutated domains and a possible CBM69. The conventional C-domain of amylase consists of amino acids 120-180 (N-terminal) and 646-676 (C-terminal) in MalS, and the whole domain architecture shows the complete circular permutation of C-A-B-A-C in domain order. Regarding substrate interaction, the enzyme has a 6-glucosyl unit pocket binding it to the non-reducing end of the cleavage site. Our study found that residues D385 and F367 play important roles in the preference of MalS for maltohexaose as an initial product. At the active site of MalS, β-CD binds more weakly than the linear substrate, possibly due to the positioning of A402. MalS has two Ca²⁺ binding sites that contribute significantly to the thermostability of the enzyme. Intriguingly, the study found that MalS exhibits a high binding affinity for polysaccharides such as glycogen and amylopectin. The N domain, of which the electron density map was not observed, was predicted to be CBM69 by AlphaFold2 and might have a binding site for the polysaccharides. Structural analysis of MalS provides new insight into the structure-evolution relationship in GH13 subfamily 19 enzymes and a molecular basis for understanding the details of catalytic function and substrate binding of MalS.

Impact of active and stable cancer on survival in patients undergoing percutaneous coronary intervention

Background

With advances in treatment of ischemic heart disease and cancer treatment, use of percutaneous coronary intervention (PCI) in cancer survivors and patients with active cancer (AC) is expanding.

Objectives

The purpose of this study was to determine the impact of cancer on survival and major cardiovascular events (MACE) in a long-term, single-center cohort of patients treated with PCI.

Methods

Patients treated with PCI between January 2010 and December 2017 were grouped as follows: controls (patients without cancer), stable cancer (SC), and AC. AC was included patients with cancer diagnosed within the past 6 months, patients who had cancer-related therapy within the past 6 months, active metastatic disease, or active recurrence of the cancer. The primary endpoints were 5-year survival and a secondary endpoint was 5-year MACE.

Results

A total of 6,743 patients (age 66±12 years, 68.4% men) treated with PCI were included: 6,404 (95.0%) controls, 245 (3.6%) SC, and 94 (1.4%) AC. Predominant malignancies were gastrointestinal (37.4%), lung (22.7%), and genitourinary cancer (14.7%). No differences were observed between patients with AC, SC and controls regarding 5-year MACE (total MACE, 33.2% vs. 28.1% vs. 17.5%, p=0.072; cardiac death, 13.6% vs. 9.1% vs. 6.7%, p=0.066; non-fatal myocardial infarction, 2.9% vs. 7.5% vs. 7.8%, p=0.820; revascularization, 17.9% vs. 17.6% vs. 11.6%, p=0.794, respectively). Patients with AC and SC had reduced 5-year survival compared with controls (62.0% vs. 81.5% vs. 89.8%, p<0.001) (Figure). AC was associated with a 1.76 (95% CI 1.22 to 2.54, p=0.002) fold increased risk of all-cause 5-year mortality in multivariable adjusted models.

Conclusions

Cumulative incidence of 5-year survival was discriminated by concurrent status of cancer following PCI. Individualized decision making is needed in the routine practice of PCI regarding concurrent cancer-specific treatment and prognosis.

Funding Acknowledgement

Type of funding sources: None.

Tetrameric architecture of an active phenol-bound form of the AAA+ transcriptional regulator DmpR

The Pseudomonas putida phenol-responsive regulator DmpR is a bacterial enhancer binding protein (bEBP) from the AAA⁺ ATPase family. Even though it was discovered more than two decades ago and has been widely used for aromatic hydrocarbon sensing, the activation mechanism of DmpR has remained elusive. Here, we show that phenol-bound DmpR forms a tetramer composed of two head-to-head dimers in a head-to-tail arrangement. The DmpR-phenol complex exhibits altered conformations within the C-termini of the sensory domains and shows an asymmetric orientation and angle in its coiled-coil linkers. The structural changes within the phenol binding sites and the downstream ATPase domains suggest that the effector binding signal is propagated through the coiled-coil helixes. The tetrameric DmpR-phenol complex interacts with the σ⁵⁴ subunit of RNA polymerase in presence of an ATP analogue, indicating that DmpR-like bEBPs tetramers utilize a mechanistic mode distinct from that of hexameric AAA⁺ ATPases to activate σ⁵⁴-dependent transcription.

Crystal structure of the fungal nitroreductase Frm2 from Saccharomyces cerevisiae

Nitroreductases are flavoenzymes that catalyze nitrocompounds and are widely utilized in industrial applications due to their detoxification potential and activation of biomedicinal prodrugs. Type I nitroreductases are classified into subgroups depending on the use of NADPH or NADH as the electron donor. Here, we report the crystal structure of the fungal nitroreductase Frm2 from Saccharomyces cerevisiae, one of the uncharacterized subgroups of proteins, to reveal its minimal architecture previously observed in bacterial nitroreductases such as CinD and YdjA. The structure lacks protruding helical motifs that form part of the cofactor and substrate binding site, resulting in an open and wide active site geometry. Arg82 is uniquely conserved in proximity to the substrate binding site in Frm2 homologues and plays a crucial role in the activity of the active site. Frm2 primarily utilizes NADH to reduce 4-NQO. Because missing helical elements are involved in the direct binding to the NAD(P)H in group A or group B in Type I family, Frm2 and its homologues may represent a distinctive subgroup with an altered binding mode for the reducing compound. This result provides a structural basis for the rational design of novel prodrugs with the ability to reduce nitrogen-containing hazardous molecules.

Purification and characterization of Fab fragments with rapid reaction kinetics against myoglobin

Myoglobin is an early biomarker for acute myocardial infarction. Recently, we isolated the antibody IgG-Myo2-7ds, which exhibits unique rapid reaction kinetics toward human myoglobin antigen. Antibodies with rapid dissociation kinetics are thought to be premature IgG forms that are produced during the early stage of in vivo immunization. In the present study, we identified the epitope region of the IgG-Myo2-7ds antibody to be the C-terminal region of myoglobin, which corresponds to 144-154 aa. The Fab fragment was directly purified by papain cleavage and protein G affinity chromatography and demonstrated kinetics of an association constant of 4.02 × 10(4) M(-1) s(-1) and a dissociation constant of 2.28 × 10(-2) s(-1), which retained the unique reaction kinetics of intact IgG-Myo2-7ds antibodies. Because a rapid dissociation antibody can be utilized for antibody recycling, the results from this study would provide a platform for the development of antibody engineering in potential diagnostic areas such as a continuous monitoring system for heart disease.

Refolded scFv antibody fragment against myoglobin shows rapid reaction kinetics

Myoglobin is one of the early biomarkers for acute myocardial infarction. Recently, we have screened an antibody with unique rapid reaction kinetics toward human myoglobin antigen. Antibodies with rapid reaction kinetics are thought to be an early IgG form produced during early stage of in vivo immunization. We produced a recombinant scFv fragment for the premature antibody from Escherichia coli using refolding technology. The scFv gene was constructed by connection of the V(H)-V(L) sequence with a (Gly4Ser)3 linker. The scFv fragment without the pelB leader sequence was expressed at a high level, but the solubility was extremely low. A high concentration of 8 M urea was used for denaturation. The dilution refolding process in the presence of arginine and the redox reagents GSH and GSSH successfully produced a soluble scFv protein. The resultant refolded scFv protein showed association and dissociation values of 9.32 × 10⁻⁴ M⁻¹·s⁻¹ and 6.29 × 10⁻³ s⁻¹, respectively, with an affinity value exceeding 10⁷ M⁻¹ (k(on)/k(off)), maintaining the original rapid reaction kinetics of the premature antibody. The refolded scFv could provide a platform for protein engineering for the clinical application for diagnosis of heart disease and the development of a continuous biosensor.

Directed evolution of human heavy chain variable domain (VH) using in vivo protein fitness filter

Human immunoglobulin heavy chain variable domains (VH) are promising scaffolds for antigen binding. However, VH is an unstable and aggregation-prone protein, hindering its use for therapeutic purposes. To evolve the VH domain, we performed in vivo protein solubility selection that linked antibiotic resistance to the protein folding quality control mechanism of the twin-arginine translocation pathway of E. coli. After screening a human germ-line VH library, 95% of the VH proteins obtained were identified as VH3 family members; one VH protein, MG2x1, stood out among separate clones expressing individual VH variants. With further screening of combinatorial framework mutation library of MG2x1, we found a consistent bias toward substitution with tryptophan at the position of 50 and 58 in VH. Comparison of the crystal structures of the VH variants revealed that those substitutions with bulky side chain amino acids filled the cavity in the VH interface between heavy and light chains of the Fab arrangement along with the increased number of hydrogen bonds, decreased solvation energy, and increased negative charge. Accordingly, the engineered VH acquires an increased level of thermodynamic stability, reversible folding, and soluble expression. The library built with the VH variant as a scaffold was qualified as most of VH clones selected randomly were expressed as soluble form in E. coli regardless length of the combinatorial CDR. Furthermore, a non-aggregation feature of the selected VH conferred a free of humoral response in mice, even when administered together with adjuvant. As a result, this selection provides an alternative directed evolution pathway for unstable proteins, which are distinct from conventional methods based on the phage display.

Structural insight into the bifunctional mechanism of the glycogen-debranching enzyme TreX from the archaeon Sulfolobus solfataricus

TreX is an archaeal glycogen-debranching enzyme that exists in two oligomeric states in solution, as a dimer and tetramer. Unlike its homologs, TreX from Sulfolobus solfataricus shows dual activities for alpha-1,4-transferase and alpha-1,6-glucosidase. To understand this bifunctional mechanism, we determined the crystal structure of TreX in complex with an acarbose ligand. The acarbose intermediate was covalently bound to Asp363, occupying subsites -1 to -3. Although generally similar to the monomeric structure of isoamylase, TreX exhibits two different active-site configurations depending on its oligomeric state. The N terminus of one subunit is located at the active site of the other molecule, resulting in a reshaping of the active site in the tetramer. This is accompanied by a large shift in the "flexible loop" (amino acids 399-416), creating connected holes inside the tetramer. Mutations in the N-terminal region result in a sharp increase in alpha-1,4-transferase activity and a reduced level of alpha-1,6-glucosidase activity. On the basis of geometrical analysis of the active site and mutational study, we suggest that the structural lid (acids 99-97) at the active site generated by the tetramerization is closely associated with the bifunctionality and in particular with the alpha-1,4-transferase activity. These results provide a structural basis for the modulation of activities upon TreX oligomerization that may represent a common mode of action for other glycogen-debranching enzymes in higher organisms.

Novel headspace gas chromatographic method for determination of oxalate in oxygen delignification liquor

A novel headspace gas chromatographic (HS-GC) method is demonstrated for an indirect determination of oxalate in oxygen delignification liquors. A small volume (50-100 microL) of liquor sample is introduced into a sampling vial that contains 1.0 mL of 2 mol/L sulfuric acid. After removal of carbon dioxide (generated from carbonate in the acidic medium) by heating, the sample was mixed with a 0.5 mL of 0.02 mol/L potassium permanganate solution in a closed testing vial. At an elevated temperature (70 degrees C), the oxalate in the sample is rapidly converted to carbon dioxide by reacting with permanganate. The carbon dioxide in the headspace can be measured by gas chromatography with a thermal conductive detector. Using a multiple headspace extraction (MHE) measurement technique, the kinetics of formation of the carbon dioxide from the other organic species in the sample can be determined, and thus a correction can be made for minimizing the interferences. The present method is simple, accurate and can be easily automated.

Determination of microstickies in recycled whitewater by headspace gas chromatography

This study proposed a novel headspace gas chromatographic (HS-GC) method for determination of adhesive contaminants (microstickies) in recycled whitewater, a fiber containing process stream, in the paper mill. It is based on the adsorption behavior of toluene (as a tracer) on the hydrophobic surface of microstickies, which affects the apparent vapor-liquid equilibration partitioning of toluene. It was found that the equilibrium concentration of toluene in the vapor phase is inversely proportional to the apparent effective surface area of microstickies that remain in the corresponding solution. Thus, the amount of microsticky materials in the recycled whitewater can be quantified by HS-GC via indirect measurement of the toluene content in the vapor phase of the sample without any pretreatment. The presented method is simple, rapid and automated.