Parasitic infections represent a significant health threat among recent immigrants in Chicago.

Parasitic infections are likely under-recognized among immigrant populations in the USA. We conducted a cross-sectional study to evaluate if such infections have health impacts among recent immigrants in Chicago and to identify predictive factors for parasitic infections. A total of 133 recent immigrants were enrolled, filling out a standardized medical questionnaire and providing blood and stool samples. Appriximately 12% of subjects (15/125) who provided a blood or stool sample for testing were found to have evidence of current or prior infection with a pathogenic parasite, of which Toxocara spp. (8 subjects, 6.4%) and Strongyloides stercoralis (5 subjects, 4%) were most commonly identified. Parasitic infection was more likely among subjects who had immigrated within the previous 2 years and those with a self-reported history of worms in the stool. The most useful surrogate markers identified for parasitic infections were an elevated immunoglobulin E level (seen in 46.7% (7/15) of subjects with parasitic infections and 20% (22/110) of uninfected individuals, p = 0.04) and the presence of Blastocystis hominis cysts on Ova & Parasite exam (detected in 38.5% (5/13) of subjects with parasitic infections who provided a stool sample and 5.1% (5/98) of uninfected subjects, p = 0.002). Our study found that parasitic infections may be common in recent US immigrants, which highlights an important health disparity among a vulnerable population that merits further study. Additionally, clinical risk factors, symptoms, and laboratory findings traditionally thought to be associated with parasites were commonly found but not predictive of infection in this study population.

Why are some amyloidoses systemic? Does hepatic "chaperoning at a distance" prevent cardiac deposition in a transgenic model of human senile systemic (transthyretin) amyloidosis?

In the human systemic amyloidoses caused by mutant or wild-type transthyretin (TTR), deposition occurs at a distance from the site of synthesis. The TTR synthesized and secreted by the hepatocyte circulates in plasma, then deposits in target tissues far from the producing cell, a pattern reproduced in mice transgenic for multiple copies of the human wild-type TTR gene. By 2 yr of age, half of the transgenic males show cardiac deposition resembling human senile systemic amyloidosis. However, as early as 3 mo of age, when there are no deposits, cardiac gene transcription differs from that of nontransgenic littermates, primarily in the expression of a large number of genes associated with inflammation and the immune response. At 24 mo, the hearts with histologically proven TTR deposits show expression of stress response genes, exuberant mitochondrial gene transcription, and increased expression of genes associated with apoptosis, relative to the hearts without TTR deposition. These 24-mo-old hearts with TTR deposits also show a decrease in transcription of inflammatory genes relative to that in the younger transgenic mice. After 2 yr of expressing large amounts of human TTR, the livers of the transgenic mice without cardiac deposition display chaperone gene expression and evidence of an activated unfolded protein response, while the livers of animals with cardiac TTR deposition display neither, showing increased transcription of interferon-responsive inflammatory genes and those encoding an antioxidant response. With time, in animals with cardiac deposition, it appears that hepatic proteostatic capacity is diminished, exposing the heart to a greater load of misfolded TTR with subsequent extracellular deposition. Hence systemic (cardiac) TTR deposition may be the direct result of the diminution in the distant chaperoning capacity of the liver related to age or long-standing exposure to misfolded TTR, or both.

Modeling the role of charged residues in thermophilic proteins by rotamer and dynamic cross correlation analysis.

Discerning the determinants of protein thermostability is very important both from the theoretical and applied perspective. Different lines of evidence seem to indicate that a dynamical network of salt bridges/charged residues plays a fundamental role in the thermostability of enzymes. In this work, we applied measures of dynamic variance, like the Gini coefficients, Kullback-Leibler (KL) divergence and dynamic cross correlation (DCC) coefficients to compare the behavior of 3 pairs of homologous proteins from the thermophilic bacterium Thermus thermophilus and mesophilic Escherichia coli. Molecular dynamic (MD) simulations of these proteins were performed at 303 K and 363 K. In the characterization of their side chain rotamer distributions, the corresponding Gini coefficients and KL-divergence both revealed significant correlations with temperature. Similarly, a DCC analysis revealed a higher trend to de-correlate the movement of charged residues at higher temperatures in the thermophilic proteins, when compared with their mesophilic homologues. These results highlight the importance of dynamic electrostatic network interactions for the thermostability of enzymes.

Boophilin D1, a Kunitz type protease inhibitor, as a source of inhibitors for the ZIKA virus NS2B-NS3 protease.

Arboviruses are a global concern for a multitude of reasons, including their increased incidence and human mortality. Vectors associated with arboviruses include the mosquito Aedes sp., which is responsible for transmitting the Zika virus. Flaviviruses, like the Zika virus, present only one chymotrypsin-like serine protease (NS3) in their genome. Together with host enzymes, the NS2B co-factor NS3 protease complex are essential for the viral replication cycle by virus polyprotein processing. To search for Zika virus NS2B-NS3 protease (ZIKVPro) inhibitors, a phage display library was constructed using the Boophilin domain 1 (BoophD1), a thrombin inhibitor from the Kunitz family. A BoophilinD1 library mutated at positions P1-P4' was constructed, presenting a titer of 2.9x106 (cfu), and screened utilizing purified ZIKVPro. The results demonstrated at the P1-P4' positions the occurrence of 47% RALHA sequence (mut 12) and 11.8% RASWA sequence (mut14), SMRPT, or KALIP (wt) sequence. BoophD1-wt and mutants 12 and 14 were expressed and purified. The purified BoophD1 wt, mut 12 and 14, presented Ki values for ZIKVPro of 0.103, 0.116, and 0.101 µM, respectively. The BoophD1 mutant inhibitors inhibit the Dengue virus 2 protease (DENV2) with Ki values of 0.298, 0.271, and 0.379 µM, respectively. In conclusion, BoophD1 mut 12 and 14 selected for ZIKVPro demonstrated inhibitory activity like BoophD1-wt, suggesting that these are the strongest Zika inhibitors present in the BoophD1 mutated phage display library. Furthermore, BoophD1 mutants selected for ZIKVPro inhibit both Zika and Dengue 2 proteases making them potential pan-flavivirus inhibitors.

Biochemical Screening of Potent Zika Virus Protease Inhibitors.

As the Zika virus protease is an essential and well-established target for the development of antiviral agents, we biochemically screened for inhibitors using a purified recombinantly expressed form of this enzyme. As a result, we were able to identify 10 new Zika virus protease inhibitors. These compounds are natural products and showed strong inhibition in the biochemical assays. Inhibitory constants values for the compounds ranged from 5 nM to 8 µM. Among the most potent inhibitors are flavonoids like irigenol hexa-acetate (Ki =0.28 µM), katacine (Ki =0.26 µM), theaflavin gallate (Ki =0.40 µM) and hematein (Ki =0.33 µM). Inhibitors from other groups of natural products include sennoside A (Ki =0.19 µM) and gossypol (Ki =0.70 µM). Several of the obtained compounds are known for their beneficial health effects and have acceptable pharmacokinetic characteristics. Thus, they could be of interest as lead compounds for the development of important and essential Zika antiviral drugs.

A proteomics-MM/PBSA dual approach for the analysis of SARS-CoV-2 main protease substrate peptide specificity.

The main protease Mpro of SARS-CoV-2 is a well-studied major drug target. Additionally, it has been linked to this virus' pathogenicity, possibly through off-target effects. It is also an interesting diagnostic target. To obtain more data on possible substrates as well as to assess the enzyme's primary specificity a two-step approach was introduced. First, Terminal Amine Isobaric Labeling of Substrates (TAILS) was employed to identify novel Mpro cleavage sites in a mouse lung proteome library. In a second step, using a structural homology model, the MM/PBSA variant MM/GBSA (Molecular Mechanics Poisson-Boltzmann/Generalized Born Surface Area) free binding energy calculations were carried out to determine relevant interacting amino acids. As a result, 58 unique cleavage sites were detected, including six that displayed glutamine at the P1 position. Furthermore, modeling results indicated that Mpro has a far higher potential promiscuity towards substrates than expected. The combination of proteomics and MM/PBSA modeling analysis can thus be useful for elucidating the specificity of Mpro, and thus open novel perspectives for the development of future peptidomimetic drugs against COVID-19, as well as diagnostic tools.

Biochemical characterization of a protein tyrosine phosphatase from Trypanosoma cruzi involved in metacyclogenesis and cell invasion.

Protein tyrosine phosphatases (PTPs) form a large family of enzymes involved in the regulation of numerous cellular functions in eukaryotes. Several protein tyrosine phosphatases have been recently identified in trypanosomatides. Here we report the purification and biochemical characterization of TcPTP1, a protein tyrosine phosphatase from Trypanosoma cruzi, the causing agent of Chagas' disease. The enzyme was cloned and expressed recombinantly in Escherichia coli and purified by Ni-affinity chromatography. Biochemical characterization of recombinant TcPTP1 with the PTP pseudo-substrate pNPP allowed the estimation of a Michaelis-Menten constant K(m) of 4.5mM and a k(cat) of 2.8s(-1). We were able to demonstrate inhibition of the enzyme by the PTP1b inhibitor BZ3, which on its turn was able to accelerate the differentiation of epimastigotes into metacyclic forms of T. cruzi induced by nutritional stress. Additionally, this compound was able to inhibit by 50% the infectivity of T. cruzi trypomastigotes in a separate cellular assay. In conclusion our results indicate that TcPTP1 is of importance for cellular differentiation and invasivity of this parasite and thus is a valid target for the rational drug design of potential antibiotics directed against T. cruzi.

Dynamic cross correlation analysis of Thermus thermophilus alkaline phosphatase and determinants of thermostability.

BACKGROUND: Understanding the determinants of protein thermostability is very important both from the theoretical and applied perspective. One emerging view in thermostable enzymes seems to indicate that a salt bridge/charged residue network plays a fundamental role in their thermostability. METHODS: The structure of alkaline phosphatase (AP) from Thermus thermophilus HB8 was solved by X-ray crystallography at 2.1 Å resolution. The obtained structure was further analyzed by molecular dynamics studies at different temperatures (303 K, 333 K and 363 K) and compared to homologous proteins from the cold-adapted organisms Shewanella sp. and Vibrio strain G15-21. To analyze differences in measures of dynamic variation, several data reduction techniques like principal component analysis (PCA), residue interaction network (RIN) analysis and rotamer analysis were used. Using hierarchical clustering, the obtained results were combined to determine residues showing high degree dynamical variations due to temperature jumps. Furthermore, dynamic cross correlation (DCC) analysis was carried out to characterize networks of charged residues. RESULTS: Top clustered residues showed a higher propensity for thermostabilizing mutations, indicating evolutionary pressure acting on thermophilic organisms. The description of rotamer distributions by Gini coefficients and Kullback-Leibler (KL) divergence both revealed significant correlations with temperature. DCC analysis revealed a significant trend to de-correlation of the movement of charged residues at higher temperatures. SIGNIFICANCE: The de-correlation of charged residues detected in Thermus thermophilus AP, highlights the importance of dynamic electrostatic network interactions for the thermostability of this enzyme.

Biochemical screening for SARS-CoV-2 main protease inhibitors.

The Severe Acute Respiratory Syndrome Corona Virus 2 (SARS-CoV-2) pandemic represents a global challenge. SARS-CoV-2's ability to replicate in host cells relies on the action of its non-structural proteins, like its main protease (Mpro). This cysteine protease acts by processing the viruses' precursor polyproteins. As proteases, together with polymerases, are main targets of antiviral drug design, we here have performed biochemical high throughput screening (HTS) with recombinantly expressed SARS-CoV-2 Mpro. A fluorescent assay was used to identify inhibitors in a compound library containing known drugs, bioactive molecules and natural products. These screens led to the identification of 13 inhibitors with IC50 values ranging from 0.2 µM to 23 µM. The screens confirmed several known SARS-CoV Mpro inhibitors as inhibitors of SARS-CoV-2 Mpro, such as the organo-mercuric compounds thimerosal and phenylmercuric acetate. Benzophenone derivatives could also be identified among the most potent screening hits. Additionally, Evans blue, a sulfonic acid-containing dye, could be identified as an Mpro inhibitor. The obtained compounds could be of interest as lead compounds for the development of future SARS-CoV-2 drugs.

Crystal structure of Thermus thermophilus methylenetetrahydrofolate dehydrogenase and determinants of thermostability.

The elucidation of mechanisms behind the thermostability of proteins is extremely important both from the theoretical and applied perspective. Here we report the crystal structure of methylenetetrahydrofolate dehydrogenase (MTHFD) from Thermus thermophilus HB8, a thermophilic model organism. Molecular dynamics trajectory analysis of this protein at different temperatures (303 K, 333 K and 363 K) was compared with homologous proteins from the less temperature resistant organism Thermoplasma acidophilum and the mesophilic organism Acinetobacter baumannii using several data reduction techniques like principal component analysis (PCA), residue interaction network (RIN) analysis and rotamer analysis. These methods enabled the determination of important residues for the thermostability of this enzyme. The description of rotamer distributions by Gini coefficients and Kullback-Leibler (KL) divergence both revealed significant correlations with temperature. The emerging view seems to indicate that a static salt bridge/charged residue network plays a fundamental role in the temperature resistance of Thermus thermophilus MTHFD by enhancing both electrostatic interactions and entropic energy dispersion. Furthermore, this analysis uncovered a relationship between residue mutations and evolutionary pressure acting on thermophilic organisms and thus could be of use for the design of future thermostable enzymes.

Free light chains in plasma of patients with light chain amyloidosis and non-amyloid light chain deposition disease. High proportion and heterogeneity of disulfide-linked monoclonal free light chains as pathogenic features of amyloid disease.

Immunoglobulin light chain amyloidosis (AL) and non-amyloid light chain deposition disease (NALCDD) are different forms of protein aggregation disorders accompanied by a monoclonal gammopathy. Monoclonal free light chains (FLCs) are precursors of the pathological light chain tissue deposits that are fibrillar in AL and granular in NALCDD. However, direct biochemical examination of plasma FLC precursors, which would allow comparison and better understanding of these two diseases, is still lacking. In this study, we examined FLCs in plasma of patients with AL and NALCDD by employing separation on Sep-PaK C18 cartridges, micro-preparative electrophoresis, Western blotting and mass spectrometry. Comparative analysis of AL versus NALCDD and control plasma samples showed new evidence of increased level and heterogeneity of circulating disulfide-bound FLC species in AL. In addition to full length monomers comprising the disulfide-linked FLCs, the monoclonal disulfide-bound FLC fragments were typically revealed in AL plasma. We hypothesized that enhanced disulfide binding of FLCs in AL interferes with their normal clearance and metabolism, which in turn might play a role in amyloid formation. The applied methods might be useful to diagnose or predict the pathological form of the disease and shed light on the mechanisms involved in light chain aggregation in tissues.

In vivo stabilization of mutant human transthyretin in transgenic mice.

Transthyretin (TTR) is a 55 kD homotetrameric serum protein transporter of retinol binding protein charged with retinol and thyroxine (T4). The highly amyloidogenic human TTR variant in which leucine at position 55 is replaced by proline (L55P TTR) is responsible for aggressive fatal amyloidosis with peripheral and autonomic neuropathy, cardiomyopathy and nephropathy. Mice bearing one or two copies of a 19.2 kB human genomic fragment containing the entire coding sequence and the known control regions of the L55P TTR transgene, failed to develop TTR amyloidosis even though their sera contained mutant human TTR. The frequency of TTR tissue deposition was increased when the L55P TTR transgene was bred onto a murine TTR-null background. Denaturation of sera from the transgenic animals and murine TTR-knockouts expressing the human L55P TTR transgene revealed that the TTR tetramer was much more stable in the presence of the murine protein because the TTR circulates as hybrid human/murine heterotetramers. Intraperitoneal administration of diflunisal, a non-steroidal anti-inflammatory drug that binds to TTR in its T4-binding site and inhibits fibril formation in vitro, to human L55P TTR transgenic animals in which the murine TTR gene had been silenced, also stabilizes the circulating mutant protein to in vitro urea denaturation.

A proteomics-MM/PBSA dual approach for the analysis of SARS-CoV-2 main protease substrate peptide specificity

The main protease Mpro of SARS-CoV-2 is a well-studied major drug target. Additionally, it has been linked to this virus’ pathogenicity, possibly through off-target effects. It is also an interesting diagnostic target. To obtain more data on possible substrates as well as to assess the enzyme’s primary specificity a two-step approach was introduced. First, Terminal Amine Isobaric Labeling of Substrates (TAILS) was employed to identify novel Mpro cleavage sites in a mouse lung proteome library. In a second step, using a structural homology model, the MM/PBSA variant MM/GBSA (Molecular Mechanics Poisson-Boltzmann/Generalized Born Surface Area) free binding energy calculations were carried out to determine relevant interacting amino acids. As a result, 58 unique cleavage sites were detected, including six that displayed glutamine at the P1 position. Furthermore, modeling results indicated that Mpro has a far higher potential promiscuity towards substrates than expected. The combination of proteomics and MM/PBSA modeling analysis can thus be useful for elucidating the specificity of Mpro, and thus open novel perspectives for the development of future peptidomimetic drugs against COVID-19, as well as diagnostic tools.

Structural basis for dimer formation of the CRISPR-associated protein Csm2 of Thermotoga maritima.

UNLABELLED: The clusters of regularly interspaced short palindromic repeats (CRISPR) and the Cas (CRISPR-associated) proteins form an adaptive immune system in bacteria and archaea that evolved as an RNA-guided interference mechanism to target and degrade foreign genetic elements. In the so-called type IIIA CRISPR-Cas systems, Cas proteins from the Csm family form a complex of RNPs that are involved in surveillance and targeting tasks. In the present study, we report the crystal structure of Thermotoga maritima Csm2. This protein is considered to assemble into the helically shaped Csm RNP complex in a site opposite to the CRISPR RNA binding backbone. Csm2 was solved via cadmium single wavelength anomalous diffraction phasing at 2.4 Å resolution. The structure reveals that Csm2 is composed of a large 42 amino-acid long α-helix flanked by three shorter α-helices. The structure also shows that the protein is capable of forming dimers mainly via an extensive contact surface conferred by its long α-helix. This interaction is further stabilized by the N-terminal helix, which is inserted into the C-terminal helical portion of the adjacent subunit. The dimerization of Csm2 was additionally confirmed by size exclusion chromatography of the pure recombinant protein followed by MS analysis of the eluted fractions. Because of its role in the assembly and functioning of the Csm CRISPR RNP complex, the crystal structure of Csm2 is of great importance for clarifying the mechanism of action of the subtype IIIA CRISPR-Cas system, as well as the similarities and diversities between the different CRISPR-Cas system. DATABASE: The structure of Thermotoga maritima Csm2 has been deposited in the Protein Data Bank under accession code 5AN6.

Extraction and chemical characterization of tissue-deposited proteins from minute diagnostic biopsy specimens.

The compelling need for early detection and chemical characterization of protein deposits in conformational disorders has always relied on immunohistochemical techniques performed on diagnostic biopsy specimens. Although the identity of the culprit can be assessed, the molecular nature of the defect still requires the analysis of the extracted material. The purpose of this chapter is to provide investigators with a method to extract and analyze-from minute residual diagnostic tissue biopsies-the deposited proteins. If done successfully, the technique will allow further investigation by molecular studies, while the patient is still being evaluated.

Binding of polymeric IgG to fibronectin in extracellular matrices: an in vitro paradigm for immune-complex deposition.

We have previously shown a biochemical interaction between fibronectin (Fn) and polymeric immunoglobulins (Igs), that we localized to the fourth and fifth N-terminal type I repeats (4F1.5F1) in Fn and the Fc portion of IgG. Therefore, we hypothesized that Fn, as a constituent of the extracellular matrix (ECM) may directly bind circulating immune complexes (ICs) causing their deposition, thereby contributing to the pathogenesis of IC diseases. As an in vitro paradigm to test this idea, we have generated Fn-containing ECMs from varied cells in culture and demonstrated a saturable dose-dependent binding of aggregated (agg) IgG, as a prototype of ICs, as well as the binding of both heat and cold aggregated purified type I cryoglobulins (CGs) to these ECMs. No binding was observed to ECMs (Matrigel) that do not contain Fn. Characteristic of our previous findings, polymeric but not monomeric IgG bound to the acellular Fn-containing ECMs. To further demonstrate the specificity of the interaction and implicate matrix Fn in the binding of aggIgG, complete inhibition of binding of aggIgG to Fn was achieved by blocking Fn on the ECMs with anti-Fn antiserum and by preincubation of the Ig aggregates with anti-human IgG antibodies. By competing the binding interaction with fluid phase Fn and the Ig-binding site on Fn, 4F(1).5F(1), 70% inhibition was obtained. Additional experiments performed with purified CGs show that an identical dose-dependent increase in Fn binding occurred using both preformed and forming cryoprecipitates suggesting that Fn does not confer cryoprecipitation of CGs and that the specific association of Fn with cryoprecipitates probably results from their polymeric configuration. Our results support the notion that Fn, as it exits in expanding ECMs characteristic of glomerulonephropathies and rheumatoid synovial disease, specifically interacts with complexed/polymeric Igs, thereby perpetuating IC deposition and playing a role in the pathogenesis of IC diseases.

Purification, crystallization, crystallographic analysis and phasing of the CRISPR-associated protein Csm2 from Thermotoga maritima.

The clusters of regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated proteins (Cas) system consists of an intriguing machinery of proteins that confer bacteria and archaea with immunity against phages and plasmids via an RNA-guided interference mechanism. Here, the cloning, recombinant expression in Escherichia coli BL21 (DE3), purification, crystallization and preliminary X-ray diffraction analysis of Csm2 from Thermotoga maritima are reported. Csm2 is thought to be a component of an important protein complex of the type IIIA CRISPR-Cas system, which is involved in the CRISPR-Cas RNA-guided interference pathway. The structure of Csm2 was solved via cadmium single-wavelength anomalous diffraction (Cd-SAD) phasing. Owing to its involvement in the CRISPR-Cas system, the crystal structure of this protein could be of importance in elucidating the mechanism of type IIIA CRISPR-Cas systems in bacteria and archaea.

Biochemical subtyping of amyloid in formalin-fixed tissue samples confirms and supplements immunohistologic data.

The systemic amyloidoses are a heterogeneous group of congophilic fibrillar protein deposition diseases that should be subtyped chemically by immunohistologic methods. Biochemical methods sometimes are required to confirm or identify the amyloid type in unfixed or informalin-fixed tissue samples. We report the results of formic acid extraction and immunochemical and biochemical characterization of deposits informalin-fixed tissue samples from 10 cases of amyloidosis and 3 from nonamyloid monoclonal immunoglobulin light chain deposition disease. The results in 11 of 13 cases demonstrated concordance with the previous immunohistochemical and/or biochemical data obtained in unfixed tissue samples from the same specimens, and in 2 of 13, the protein deposits that previously could not be classified by standard immunohistochemical methods were identified by amino acid sequence. An additional new finding of constant-region rather than variable-region fragments as the major constituent protein in 1 case of lambda light chain amyloidosis demonstrated the value of the method and its importance for future applications.

Amyloidogenesis is neither accelerated nor enhanced by injections of preformed fibrils in mice transgenic for wild-type human transthyretin: the question of infectivity.

It is possible to accelerate amyloid formation in both the Senescence Accelerated Mouse, where ApoAIIC is the precursor, and in murine Amyloid A (AA) by the injection of preformed fibrils in the former and amyloid enhancing factor, which appears to consist of AA fibril fragments, in the latter. These two observations have raised the question of whether murine amyloids, like scrapie, are infectious. Injection of preformed fibrils into mice transgenic for many copies of the human wild-type transthyretin gene do not result in acceleration or enhancement of the process of deposition or the conversion of non-Congophilic deposits to fibrils.

Mice transgenic for human TTR have the same frequency of renal TTR deposition whether maintained in conventional or specific pathogen free environments.

Mice transgenic for many copies of the human wild type transthyretin gene were bred and maintained in a specific pathogen free environment until twelve months of age. At that time, half the animals were moved to a conventional animal facility. The incidence of both transthyretin and AA amyloid was the same in both groups at two years of age, indicating that in this model, the frequency, extent or nature of TTR-amyloid deposition did not differ significantly between conventional and specific pathogen-free environments.