A novel technique for studying the effects of technologically processed antibodies by evaluating the rate of oxidation of ascorbic acid during the reduction of the green-blue ABTS + radical

Since the pharmaceutical market is developing, there is a need for novel techniques for determining the physical-chemical properties of drug solutions. Drugs based on technologically processed antibodies (TPA) are an example of compounds that require a methodology for studying their effects. It has been shown that the process of external impacts during the manufacture of TPA-based drugs can induce breaking of intermolecular and intramolecular bonds in the solvent molecules, providing the emergence of new bonds with the molecules of the substance used for the manufacture of an active pharmaceutical ingredient. This article focuses on the technique applied for assessing the mentioned effect of TPA and consists in spectrophotometric observation of the oxidation process of ascorbic acid (AA) in the solution. The amount of oxidized AA was detected using ABTS·+(2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) radical-cation, which, when interacting with AA, is reduced and changes the color from green-blue to colorless. This technique showed the reproducibility of statistically significant differences in the amount of oxidized AA in the presence of TPA compared to controls and can be used to detect the changes in the properties of solutions exposed to the effect of the TPA samples.

Large-scale study of the precision of the approximate number system: Differences between formats, heterogeneity and congruency effects

The study used a large sample of elementary schoolchildren in Russia (N = 3,448, 51.6% were girls, with a mean age of 8.70 years, ranging 6-11 years) to investigate the congruency, format and heterogeneity effects in a nonsymbolic comparison test and between-individual differences in these effects with generalized linear mixed effects models (GLMMs). The participants were asked to compare two arrays of figures of different colours in spatially separated or spatially intermixed formats. In addition, the figures could be similar or different for the two arrays. The results revealed that congruency (difference between congruent and incongruent items), format (difference between mixed and separated formats) and heterogeneity (difference between homogeneous and heterogeneous conditions) interacted. The heterogeneity effect was higher in the separated format, while the format effect was higher for the homogeneous condition. The separated format produced a greater congruency effect than the mixed format. In addition, the congruency effect was lower in the heterogeneous condition than in the homogeneous condition. Analysis of between-individual differences revealed that there was significant between-individual variance in the format and congruency effects. Analysis of between-grade differences revealed that accuracy improved from grade 1 to grade 4 only for congruent trials in separated formats. Consequently, the congruency effect increased in separated/homogeneous and separated/heterogeneous conditions. In general, the study demonstrated that the test format and heterogeneity affected accuracy and that this effect varied for congruent and incongruent items.

Multi-Qubit Bose-Einstein Condensate Trap for Atomic Boson Sampling

We propose a multi-qubit Bose-Einstein-condensate (BEC) trap as a platform for studies of quantum statistical phenomena in many-body interacting systems. In particular, it could facilitate testing atomic boson sampling of the excited-state occupations and its quantum advantage over classical computing in a full, controllable and clear way. Contrary to a linear interferometer enabling Gaussian boson sampling of non-interacting non-equilibrium photons, the BEC trap platform pertains to an interacting equilibrium many-body system of atoms. We discuss a basic model and the main features of such a multi-qubit BEC trap.

Electroactive Biofilms of Activated Sludge Microorganisms on a Nanostructured Surface as the Basis for a Highly Sensitive Biochemical Oxygen Demand Biosensor

The possibility of the developing a biochemical oxygen demand (BOD) biosensor based on electroactive biofilms of activated sludge grown on the surface of a graphite-paste electrode modified with carbon nanotubes was studied. A complex of microscopic methods controlled biofilm formation: optical microscopy with phase contrast, scanning electron microscopy, and laser confocal microscopy. The features of charge transfer in the obtained electroactive biofilms were studied using the methods of cyclic voltammetry and electrochemical impedance spectroscopy. The rate constant of the interaction of microorganisms with the extracellular electron carrier (0.79 ± 0.03 dm³(g s)^-1) and the heterogeneous rate constant of electron transfer (0.34 ± 0.02 cm s^-1) were determined using the cyclic voltammetry method. These results revealed that the modification of the carbon nanotubes' (CNT) electrode surface makes it possible to create electroactive biofilms. An analysis of the metrological and analytical characteristics of the created biosensors showed that the lower limit of the biosensor based on an electroactive biofilm of activated sludge is 0.41 mgO₂/dm³, which makes it possible to analyze almost any water sample. Analysis of 12 surface water samples showed a high correlation (R² = 0.99) with the results of the standard method for determining biochemical oxygen demand.

Exact Recursive Calculation of Circulant Permanents: A Band of Different Diagonals inside a Uniform Matrix

We present a finite-order system of recurrence relations for the permanent of circulant matrices containing a band of k any-value diagonals on top of a uniform matrix (for k=1,2 and 3) and the method for deriving such recurrence relations, which is based on the permanents of the matrices with defects. The proposed system of linear recurrence equations with variable coefficients provides a powerful tool for the analysis of the circulant permanents, their fast, linear-time computing; and finding their asymptotics in a large-matrix-size limit. The latter problem is an open fundamental problem. Its solution would be tremendously important for a unified analysis of a wide range of the nature's ♯P-hard problems, including problems in the physics of many-body systems, critical phenomena, quantum computing, quantum field theory, theory of chaos, fractals, theory of graphs, number theory, combinatorics, cryptography, etc.

IVIG ameliorate inflammation in collagen-induced arthritis: projection for IVIG therapy in rheumatoid arthritis

Rheumatoid arthritis (RA) is a systemic inflammatory autoimmune disease that leads to joint destruction and disability. Despite a significant progress in administration of biological agents for RA patients, there is still a need for improved therapy. Intravenous immunoglobulins (IVIG), a pooled polyspecific immunoglobulin (Ig)G extracted from 5000 to 20 000 healthy subjects, showed beneficial therapeutic effect in patients with immune deficiency, sepsis and autoimmune diseases. The current study aimed to investigate the beneficial effect of treatment with IVIG in established collagen-induced arthritis in DBA/1j mice. Murine arthritis was induced in DBA/1j mice. Treatment with IVIG began when the disease was established. The clinical score was followed twice a week until day 48. The mice were bled for plasma and the paws were hematoxylin and eosin (H&E)-stained. Cytokine profile in the plasma was analyzed by Luminex technology and titers of circulating anti-collagen antibodies in the plasma was tested by enzyme-linked immunosorbent assay. Our results show that treatment with IVIG in murine significantly reduced the clinical arthritis score (P < 0·001). Moreover, mode of action showed that IVIG significantly reduced circulating levels of inflammatory cytokines [interferon (IFN)-γ, interleukin (IL)-1β, IL-17, IL-6, tumor necrosis factor (TNF)-α, P < 0·001], inhibiting anti-collagen antibodies (P < 0·001) in the plasma of collagen-induced arthritis mice. Importantly, histopathological examination revealed that IVIG treatment prevented the migration of inflammatory immune cells into the cartilage and synovium, reduced the extent of joint damage and preserved joint architecture. Our results proved for the first time the valuable anti-inflammatory treatment of IVIG in experimental RA. We propose IVIG therapy for a subgroup of patients with rheumatologically related diseases.

Influence of the anti-erosion complex on erosion-hydrological indicators and productivity of cultivated crops

An assessment of the impact of the anti-erosion complex on the productivity of cultivated crops has presented on the example of many years of experience in contour-ameliorative agriculture of the Kursk FARC located in the northern part of the Medvensky district of the Kursk region. Two subtypes of chernozem represent the soil of the experiment: typical and leached. As anti-erosion measures, narrow-row stock-regulating poplar forest belts, reinforced by a simple hydraulic structure (ditch and rampart along the lower edge), have designed and planted along the contour at a distance of 216 m. There are no anti-erosion measures in the control catchment. Analysis of long-term data showed a decrease in runoff and the absence of soil washout in the catchment area with a system of narrow-row forest belts 38 years after the experiment has laid in comparison with the control. For the control catchment, a maximum soil washing of 22 t/ha recorded which significantly exceeds the permissible standards of flush. A significant increase in crop productivity averaged 5.2 feed units. The profitability of growing crops in fields with forest belts exceeds the control by almost 50%. The anti-erosion complex performs the task of strengthening the soil-protective role of the farming system.

Operation of a multi-frequency parametric sidescan sonar in an ice waveguide

Hydroacoustic systems for mineral exploration, solving engineering problems and monitoring the ecological state of the world’s oceans are currently being intensively developed. However, the practical use of hydroacoustic systems for solving the problems under consideration, operating in the traditional mode, has some significant limitations. These restrictions are largely related to the state of the marine areas in which such work is carried out. Especially little is known about the patterns of propagation and interaction of acoustic waves in marine basins with ice cover. These areas are rich in minerals and intensive shipping is developing in them. Therefore, an important place in acoustic research is occupied by the study of the acoustic properties of the ice cover of the polar regions of the Earth. This is determined by the fact that the ice sheet is a unique constantly collapsing and renewable natural system. In this regard, the conditions for the propagation of acoustic waves are changing. More than 70% of the Arctic basin is covered with ice, the lower boundary of which has significant irregularities with a standard deviation of up to 3 m, so the scattering of acoustic waves at such a boundary is significant and different at different frequencies. The formation of the acoustic field of the hydroacoustic systems used in these conditions is quite complex. Therefore, the task of assessing changes in the characteristics of the field and the use of appropriate hydroacoustic systems for their effective use is urgent.

An approach to automation of a rational choice of adaptive agricultural technologies

The research was conducted at the premises of the agricultural systems laboratory on the basis of research findings and analysis and generalization of modern scientific literature on a rational choice of adaptive technologies for cultivation of 10 crops (wheat, barley, rye, peas, millet, etc.) for different conditions in Russia. The most effective conditions for technologies application facilitating the efficient use of available resources were determined. Criteria, standards and requirements for the efficiency of the most important technological techniques of modern agricultural technologies were posed, as well as approaches to automation and an algorithm for their rational choice. The scheme and structure of the database of the agricultural producer support system for a rational choice of highly profitable adaptive technologies for leading grain crops cultivation were developed. The structure of the database of the decision support system is represented in three units: initial information, regulatory and reference information and calculation algorithms. The implementation of the developments into the production process opens up opportunities for the most efficient use of the existing soil and climate potential of the territories and material and technical resources in order to ensure highly profitable sustainable crops yields.

The level of natural autoantibodies to IFN-gamma in varicella infection treated with antiviral drug Anaferon for children: A pilot study

Natural circulating antibodies (NAbs) to endogenous regulators have shown to be potential biomarkers in medicine. Due to the lack of reliable assays, only few of them have been well studied. To employ NAbs as biomarkers, an evaluation of changes over the course of a treatment is required. This paper describes our work to analyze the dynamics of NAbs titer to interferon-gamma (IFN-γ) among healthy children of different age and in patients with varicella infection receiving an antiviral drug Anaferon for children (AC, the API are highly diluted antibodies to IFN-γ) in comparison with placebo, and to correlate the findings with the treatment results. IFN-γ plays an essential role during varicella infection, and this fact causes the consequent increase of NAbs to IFN-γ level. The mean anti-IFN-γ NAbs level in the healthy volunteer group was 101 × 10³ U/ml (age: 0-15 years), which was significantly lower than the mean pre-treatment value in patients with varicella infection 167 × 10³ U/ml (age: 3-17 years). In the AC group, the NAbs level observed on days 5 and 10 decreased significantly to a level of 154 × 10³ U/ml, whereas in the placebo group it continued to rise in a time-dependent manner reaching 229 × 10³ U/ml on day 10. Our findings suggest that treatment with AC is characterized by "normalization" of the anti-IFN-γ NAbs levels in patients with varicella infection.

Distribution and antibiotic resistance profile of key Gram-negative bacteria that cause community-onset urinary tract infections in the Russian Federation: RESOURCE multicentre surveillance 2017 study

BACKGROUND

Urinary tract infections (UTIs) are among the most common bacterial infections in clinical practice. This RESOURCE (pathogen distribution and antibiotic RESistance prOfile of key Gram-negative bacteria caUsing community-onsEt URinary traCt) study aimed to determine the antimicrobial resistance profile of Gram-negative bacteria isolated from outpatient urine samples collected across the Russian Federation.

METHODS

A total of 96 781 urine samples were collected from 520 cities in the Russian Federation between 01 January 1 and 31 December 2017. Antibiotic susceptibility was performed using semi-automated analysers. The mean age of the study population was 40.9 years; 80.2% were female and 19.8% were male.

RESULTS

Of the uropathogens that were isolated, 64.2% were Gram-negative bacteria. Among these, Escherichia coli (E. coli) was the most common (49.1%) followed by Klebsiella pneumoniae (9.5%), Proteus mirabilis (2.9%), Pseudomonas aeruginosa (1.7%), and Enterobacter spp. (1.0%). Of the antibiotics that were tested, 50% of the isolated E. coli strains were resistant to ampicillin, 30.3% to co-trimoxazole, 26.2% to aztreonam, 28.8% to levofloxacin, and 21% to cefuroxime. Conversely, E. coli was highly susceptible to imipenem (0.7% resistant strains isolated), amikacin (0.9%), nitrofurantoin (4.5%), and fosfomycin (1.2%). The most active antimicrobials against Klebsiella pneumoniae were imipenem (6.8% resistant strains) and colistin (0.5%), while piperacillin/tazobactam (4.2%), cefoperazone/sulbactam (3.1%) and imipenem (0%) were the most active agents against Proteus mirabilis. The antimicrobials showing the highest activity against Pseudomonas aeruginosa were colistin (10.7% resistant strains) and aztreonam (0%), while piperacillin/tazobactam (7.1%) and cefoperazone/sulbactam (2.3%) showed the highest activity against Enterobacter spp.

CONCLUSION

The prevalence of fluoroquinolone and cephalosporin resistance among common UTI-causing Gram-negative bacteria highlights the growing challenge of successfully treating community-onset UTIs.

Efficacy and safety of Subetta add-on therapy in type 1 diabetes mellitus: The results of a multicenter, double-blind, placebo-controlled, randomized clinical trial

BACKGROUND

To examine efficacy of Subetta as an add-on to insulin therapy in patients with type 1 diabetes mellitus (T1DM) a multicenter, double-blind, placebo-controlled, randomized clinical trial was performed. Derived by technological treatment of antibodies to insulin receptor β-subunit and endothelial NO synthase Subetta was previously proved to activate insulin signaling pathway.

METHODS

A total of 144 randomized patients with poor glycemic control in basal-bolus insulin regime were included in intention-to-treat analysis in Subetta add-on therapy or placebo (n = 72 in both groups). Hemoglobin A1c (HbA1c), fasting plasma glucose (FPG), basal and prandial insulin doses, number of hypoglycemia episodes confirmed by self-monitoring of blood glucose were recorded for 36 weeks.

RESULTS

The baseline characteristics of subjects did not differ between the two groups. HbA1c mean (±standard deviation) change was -0.59 ± 0.99% (95% CI -0.84 to -0.37) after 36 weeks in Subetta (vs. -0.20 ± 1.14%; 95% CI -0.44 to 0.11 in placebo; p = 0.028). The rate of overall hypoglycemia events was 7.9 per patient year (95% CI 7.1-8.6) in Subetta group and 7.6 (95% CI 6.9-8.4) in Placebo group (p = 0.63). The basal and total insulin doses did not change at the end of 36 weeks in both groups.

CONCLUSIONS

Subetta add-on therapy boosting insulin activity and improving glycemic control in patients with T1DM is proved to be beneficial.

CLINICAL TRIAL REGISTRATION

ClinicalTrials.gov identifier: NCT01868594.

Abstract LB-075: Structural stabilization of protein fragments by membrane anchoring for generation of cell-permeable protein mimetics

Targeting protein-protein interactions can provide plentiful opportunities for the discovery of novel drug candidates and powerful chemical biology tools. However, the majority of these interactions are ‘undruggable”, and we still know very little about the structural mechanisms and functions for the vast majority of them. We have developed a rational approach that allows for the straightforward development of cell-permeable metabolically stable inhibitors of protein-protein interactions. The approach is based on structural stabilization of peptides by membrane anchoring. Biophysical data suggests that proximity to the membrane facilitates interactions of hydrophobic side chains of amphiphilic peptides with the bilayer and stabilizes natural fold of not only helical but also stretched and hairpin-type peptides. Membrane tethering is achieved through straightforward derivatization of peptides with fatty acids of appropriate length that depends on peptide's hydrophobicity. Lipidation facilitates cell entry and allows intracellular delivery of peptides up to 14-16 residues long. Negative charges can interfere with the entry, while positive charges generally have little effect. Wide applicability of this method was confirmed by generation of selective and highly potent dominant negative inhibitors of RAS oncogenes, β-catenin, STAT1, STAT3 and STAT5 N-domains, Il10R1, IFNGR1 and other non-druggable targets. Rational design of inhibitors can be accomplished even in the absence of the target tertiary structure by using conservation of certain sequence parts during the evolution. High throughput generation of selective chemical biology tools allows for effective interrogation of protein-protein interactions leading to discovery of mechanistic details of molecular signaling that could not be obtained with the help of genetic approaches.

Citation Format: Nadya Tarasova, Karen Stefanisko, Lyuba Khavrutskii, Sergey Tarasov. Structural stabilization of protein fragments by membrane anchoring for generation of cell-permeable protein mimetics [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr LB-075.

Anomalous Statistics of Bose-Einstein Condensate in an Interacting Gas: An Effect of the Trap's Form and Boundary Conditions in the Thermodynamic Limit

We analytically calculate the statistics of Bose-Einstein condensate (BEC) fluctuations in an interacting gas trapped in a three-dimensional cubic or rectangular box with the Dirichlet, fused or periodic boundary conditions within the mean-field Bogoliubov and Thomas-Fermi approximations. We study a mesoscopic system of a finite number of trapped particles and its thermodynamic limit. We find that the BEC fluctuations, first, are anomalously large and non-Gaussian and, second, depend on the trap's form and boundary conditions. Remarkably, these effects persist with increasing interparticle interaction and even in the thermodynamic limit-only the mean BEC occupation, not BEC fluctuations, becomes independent on the trap's form and boundary conditions.

Structure and dynamics of the insulin receptor: implications for receptor activation and drug discovery

Recently, major progress has been made in uncovering the mechanisms of how insulin engages its receptor and modulates downstream signal transduction. Here, we present in detail the current structural knowledge surrounding the individual components of the complex, binding sites, and dynamics during the activation process. A novel kinase triggering mechanism, the 'bow-arrow model', is proposed based on current knowledge and computational simulations of this system, in which insulin, after its initial interaction with binding site 1, engages with site 2 between the fibronectin type III (FnIII)-1 and -2 domains, which changes the conformation of FnIII-3 and eventually translates into structural changes across the membrane. This model provides a new perspective on the process of insulin binding to its receptor and, thus, could lead to future novel drug discovery efforts.

Use of Piezoelectric Immunosensors for Detection of Interferon-Gamma Interaction with Specific Antibodies in the Presence of Released-Active Forms of Antibodies to Interferon-Gamma

In preliminary ELISA studies where released-active forms (RAF) of antibodies (Abs) to interferon-gamma (IFNg) were added to the antigen-antibody system, a statistically significant difference in absorbance signals obtained in their presence in comparison to placebo was observed. A piezoelectric immunosensor assay was developed to support these data and investigate the effects of RAF Abs to IFNg on the specific interaction between Abs to IFNg and IFNg. The experimental conditions were designed and optimal electrode coating, detection circumstances and suitable chaotropic agents for electrode regeneration were selected. The developed technique was found to provide high repeatability, intermediate precision and specificity. The difference between the analytical signals of RAF Ab samples and those of the placebo was up to 50.8%, whereas the difference between non-specific controls and the placebo was within 5%–6%. Thus, the piezoelectric immunosensor as well as ELISA has the potential to be used for detecting the effects of RAF Abs to IFNg on the antigen-antibody interaction, which might be the result of RAF’s ability to modify the affinity of IFNg to specific/related Abs.

The novel oral drug Subetta exerts an antidiabetic effect in the diabetic Goto-Kakizaki rat: comparison with rosiglitazone

The aim of the present study was to evaluate the potential antidiabetic effects of two-component drug Subetta and its components (release-active dilutions of antibodies to β -subunit insulin receptor (RAD of Abs to β -InsR) and to endothelial nitric oxide synthase (RAD of Abs to eNOS)) in Goto-Kakizaki (Paris colony) (GK/Par) diabetic rats. Subetta was administered orally for 28 days once daily (5 mL/kg) and compared to its two components (2.5 mL/kg), Rosiglitazone (5 mg/kg), and vehicle (5 mL water/kg). At day 28, fasting plasma glucose levels were significantly decreased only in Subetta and Rosiglitazone groups as compared to vehicle (P < 0.01): 147 ± 4 mg/dL and 145 ± 4 mg/dL and 165 ± 4 mg/dL, respectively. The data of glucose tolerance test showed that Subetta and RAD of Abs to β -InsR (similar to Rosiglitazone) prevented significantly (P < 0.01) the age-related spontaneous deterioration of glucose tolerance as seen in the control group. Subetta and RAD of Abs to β -InsR did not significantly modify the glucose-induced insulin secretion. Chronic administration of Subetta and RAD of Abs to β -InsR improves glucose control, to an extent similar to that of Rosiglitazone. We hypothesize that Subetta and RAD of Abs to β -InsR mostly act via an insulin-sensitizing effect upon target tissues.

Promiscuous interactions of gp78 E3 ligase CUE domain with polyubiquitin chains

Recognition of ubiquitin and polyubiquitin chains by ubiquitin-binding domains (UBDs) is vital for ubiquitin-mediated signaling pathways. The endoplasmic reticulum resident RING finger ubiquitin ligase (E3) gp78 regulates critical proteins via the ubiquitin-proteasome system to maintain cellular homeostasis and includes a UBD known as the CUE domain, which is essential for function. A probable role of this domain is to recognize ubiquitin-modified substrates, enabling gp78 to assemble polyubiquitin chains on these substrates and mark them for degradation. Here, we report the molecular details of the interaction of gp78CUE domain with ubiquitin and diubiquitin. The gp78CUE domain exhibits a well-defined set of interactions with ubiquitin and a dynamic, promiscuous interaction with diubiquitin chains. This leads to a model in which the CUE domain functions to both facilitate substrate binding and enable switching between adjacent ubiquitin molecules of a growing chain to enable processivity in ubiquitination.

Parachorius semsanganus sp. n. (Coleoptera, Scarabaeidae, Scarabaeinae) from Laos and its significance in the phylogeny of Oriental Deltochilini

The new species Parachorius semsanganussp. n. is described from Laos. This enigmatic Oriental deltochiline represents a “morphological link” between Parachorius and Cassolus by sharing characters of the two genera. The fact that Parachorius semsanganus cannot be unequivocally placed in either of these two genera stresses some more general problems of the current classification of Parachorius and Cassolus. Such problems can be solved only in the course of phylogenetic analysis, the need of which is briefly outlined.

DESIGN OF LIPOSOMES CONTAINING PHOTOPOLYMERIZABLE PHOSPHOLIPIDS FOR TRIGGERED RELEASE OF CONTENTS

We describe a novel class of light-triggerable liposomes prepared from a photo-polymerizable phospholipid DC(8,9)PC (1,2- bis (tricosa-10,12-diynoyl)-sn-glycero-3-phosphocholine) and DPPC (1,2-Dipalmitoyl-sn-Glycero-3-Phosphocholine). Exposure to UV (254 nm) radiation for 0-45 minutes at 25 degrees C resulted in photo-polymerization of DC(8,9)PC in these liposomes and the release of an encapsulated fluorescent dye (calcein). Kinetics and extents of calcein release correlated with mol% of DC(8,9)PC in the liposomes. Photopolymerization and calcein release occurred only from DPPC/DC(8,9)PC but not from Egg PC/DC(8,9)PC liposomes. Our data indicate that phase separation and packing of polymerizable lipids in the liposome bilayer are major determinants of photo-activation and triggered contents release.

Light chain somatic mutations change thermodynamics of binding and water coordination in the HyHEL-10 family of antibodies

Thermodynamic and structural studies addressed the increased affinity due to L-chain somatic mutations in the HyHEL-10 family of affinity matured IgG antibodies, using ITC, SPR with van't Hoff analysis, and X-ray crystallography. When compared to the parental antibody H26L26, the H26L10 and H26L8 chimeras binding to lysozyme showed an increase in favorable DeltaG(o) of -1.2+/-0.1 kcal mol(-1) and -1.3+/-0.1 kcal mol(-1), respectively. Increase in affinity of the H26L10 chimera was due to a net increase in favorable enthalpy change with little difference in change in entropy compared to H26L26. The H26L8 chimera exhibited the greatest increase in favorable enthalpy but also showed an increase in unfavorable entropy change, with the result being that the affinities of both chimeras were essentially equivalent. Site-directed L-chain mutants identified the shared somatic mutation S30G as the dominant contributor to increasing affinity to lysozyme. This mutation was not influenced by H-chain somatic mutations. Residue 30L is at the periphery of the binding interface and S30G effects an increase in hydrophobicity and decrease in H-bonding ability and size, but does not make any new energetically important antigen contacts. A new 1.2-A structure of the H10L10-HEL complex showed changes in the pattern of both inter- and intra-molecular water bridging with no other significant structural alterations near the binding interface compared to the H26L26-HEL complex. These results highlight the necessity for investigating both the structure and the thermodynamics associated with introduced mutations, in order to better assess and understand their impact on binding. Furthermore, it provides an important example of how backbone flexibility and water-bridging may favorably influence the thermodynamics of an antibody-antigen interaction.

Structural biophysics of the NusB:NusE antitermination complex

In prokaryotic transcription regulation, several host factors form a complex with RNA polymerase and the nascent mRNA. As part of a process known as antitermination, two of these host factors, NusB and NusE, bind to form a heterodimer, which interacts with a specific boxA site on the RNA. The NusB/NusE/boxA RNA ternary complex interacts with the RNA polymerase transcription complex, stabilizing it and allowing transcription past premature termination points. The NusB protein also binds boxA RNA individually and retains all specificity for boxA. However, NusE increases the affinity of RNA to NusB in the ternary complex, which contributes to efficient antitermination. To understand the molecular mechanism of the process, we have determined the structure of NusB from the thermophilic bacterium Aquifex aeolicus and studied the interaction of NusB and NusE. We characterize this binding interaction using NMR, isothermal titration calorimetry, gel filtration, and analytical ultracentrifugation. The binding site of NusE on NusB was determined using NMR chemical shift perturbation studies. We have also determined the NusE binding site in the ternary Escherichia coli NusB/NusE/boxA RNA complex and show that it is very similar to that in the NusB/NusE complex. There is one loop of residues (from 113 to 118 in NusB) affected by NusE binding in the ternary complex but not in the binary complex. This difference may be correlated to an increase in binding affinity of RNA for the NusB/NusE complex.

Interactions between HIV-1 Gag molecules in solution: an inositol phosphate-mediated switch

Retrovirus particle assembly is mediated by the Gag protein. Gag is a multi-domain protein containing discrete domains connected by flexible linkers. When recombinant HIV-1 Gag protein (lacking myristate at its N terminus and the p6 domain at its C terminus) is mixed with nucleic acid, it assembles into virus-like particles (VLPs) in a fully defined system in vitro. However, this assembly is defective in that the radius of curvature of the VLPs is far smaller than that of authentic immature virions. This defect can be corrected to varying degrees by addition of inositol phosphates to the assembly reaction. We have now explored the binding of inositol hexakisphosphate (IP6) to Gag and its effects upon the interactions between Gag protein molecules in solution. Our data indicate that basic regions at both ends of the protein contribute to IP6 binding. Gag is in monomer-dimer equilibrium in solution, and mutation of the previously described dimer interface within its capsid domain drastically reduces Gag dimerization. In contrast, when IP6 is added, Gag is in monomer-trimer rather than monomer-dimer equilibrium. The Gag protein with a mutation at the dimer interface also remains almost exclusively monomeric in IP6; thus the "dimer interface" is essential for the trimeric interaction in IP6. We discuss possible explanations for these results, including a change in conformation within the capsid domain induced by the binding of IP6 to other domains within the protein. The participation of both ends of Gag in IP6 interaction suggests that Gag is folded over in solution, with its ends near each other in three-dimensional space; direct support for this conclusion is provided in a companion manuscript. As Gag is an extended rod in immature virions, this apparent proximity of the ends in solution implies that it undergoes a major conformational change during particle assembly.

Codon-optimized cloning, expression and characertization of the C-terminal region of human apoptotic protein GADD34 in Escherichia coli

The human GADD34 (Growth Arrest and DNA Damage-inducible 34) is the product of an apoptosis- and DNA-damage-inducible gene. The C-terminus domain of GADD34 is highly homologous to HSV-1 gamma-1 34.5, HSV-2 and the African swine fever virus virulence-associated factor NL-S. Among these viral proteins, HSV-1 gamma 34.5 protein is known to prevent apoptosis of viral-infected cells. Because of the difficulty in expressing GADD34 protein or any of its fragments, including the C-terminus (amino acids 533-632) in E. coli, partially due to sub-optimal expression of eukaryotic codons in prokaryotic E. coli, we used a codon-optimized cloning scheme to construct the eukaryotic gene that codes for GADD34(533-632). We derived a novel PCR protocol to assemble 20 oligonucleotides into the synthetic GADD34(533-632) gene. The clear advantage of using this protocol is that the assembled gene is without the mutation and deletion that are usually of a major problem in constructing synthetic genes. The synthetic GADD34(533-632) gene was cloned, expressed, and purified in large quantity. We obtained approximately 50 mg of GADD34(533-632) protein per liter minimum-medium culture. To our knowledge, this is the first report of a large-scale production of the C-terminus of GADD34. The production and purification of GADD34(533-632) in large quantity are essential for structure determination as well as for understanding its interactions with other proteins such as phosphatase 1-alpha using NMR spectroscopy and other biophysical methods.

Biophysical characterization of cyclic nucleotide phosphodiesterases

We have compared selected biophysical properties of three phosphodiesterases, from Arabidopsis thaliana, Saccharomyces cerevisiae, and Escherichia coli. All of them belong to a recently identified family of cyclic nucleotide phosphodiesterases. Experiments elucidating folding stability, protein fluorescence, oligomerization behavior, and the effects of substrates were conducted, revealing differences between the plant and the yeast protein. According to CD spectroscopy, the latter protein exhibits an (alpha + beta) fold rather than an (alpha/beta) fold as found with CPDase (A. thaliana). The redox-dependent structural reorganization recently found for the plant protein by X-ray crystallography could not be detected by CD spectroscopy due to its only marginal effect on the total percentage of helical content. However, in the present study a redox-dependent effect was also observed for the yeast CPDase. The enzymatic activity of wild type CPDase (A. thaliana) as well as of four mutants were characterized by isothermal titration calorimetry and the results prove the requirement of all four residues of the previously identified tandem signature motif for the catalytic function. Within the comparison of the three proteins in this study, the PDase Homolog/RNA ligase (E. coli) shares more similarities with the plant than with the yeast protein.