Aromatic 19F-13C TROSY: a background-free approach to probe biomolecular structure, function, and dynamics.

Atomic-level information about the structure and dynamics of biomolecules is critical for an understanding of their function. Nuclear magnetic resonance (NMR) spectroscopy provides unique insights into the dynamic nature of biomolecules and their interactions, capturing transient conformers and their features. However, relaxation-induced line broadening and signal overlap make it challenging to apply NMR spectroscopy to large biological systems. Here we took advantage of the high sensitivity and broad chemical shift range of 19F nuclei and leveraged the remarkable relaxation properties of the aromatic 19F-13C spin pair to disperse 19F resonances in a two-dimensional transverse relaxation-optimized spectroscopy spectrum. We demonstrate the application of 19F-13C transverse relaxation-optimized spectroscopy to investigate proteins and nucleic acids. This experiment expands the scope of 19F NMR in the study of the structure, dynamics, and function of large and complex biological systems and provides a powerful background-free NMR probe.

Various Factors that are Causing Difference in Prevalence of Coronary Risk Factors among Siblings.

BACKGROUND AND AIM: Coronary artery disease (CAD) is one of the predominant types of cardiovascular disease (CVD). The aim of present study was to study various factors that are causing difference in prevalence of coronary risk factors among siblings. MATERIALS AND METHODS: This cross-sectional study was conducted in Dayanand Medical College and Hospital, among the healthy individuals (not known CAD) attending regular health care outpatient department (OPD) and their siblings over a period of 1½ years. All individuals coming for regular health checkup (not known CAD) of age more than 30 years or above and their siblings (with or without known CAD). RESULTS: This was a cross-sectional study, conducted among 100 pairs of healthy siblings (not known cases of CAD) who came for health checkup at health center of Dayanand Medical College and Hospital, a tertiary care hospital in North India. Prevalence of obesity was more in siblings living in urban area than their counter siblings living in rural area, but it was statistically insignificant. Six had impaired fasting blood sugar (FBS) and two were diabetic. Among their siblings living in urban area, 21 were nondiabetic, 10 had impaired FBS, and seven were diabetic. This correlation was statistically significant with p-value of 0.02. Among the CAD negative, out of 23 subjects, two subjects (9.0%) had heavy stress level, while remaining four subjects (17.0%) and 17 subjects (74.0%) had light and moderate stress levels, respectively. Among the CAD negative, out of 23 subjects, 10 subjects (43.0%) had high stress level, while remaining zero subject (0%) and 13 subjects (57.0%) had light and moderate stress levels, respectively. Significant results were obtained while comparing the CAD findings of subjects divided on the basis of stress level. CONCLUSION: In our study, among siblings (CAD positive and CAD negative), significant results were obtained for residence, socioeconomic class, physical activity, stress levels, smoking, waist-to-hip ratio (WHR), and diabetes, that is, all these factors have correlation in increasing CAD among siblings.

15N detection harnesses the slow relaxation property of nitrogen: Delivering enhanced resolution for intrinsically disordered proteins.

Studies over the past decade have highlighted the functional significance of intrinsically disordered proteins (IDPs). Due to conformational heterogeneity and inherent dynamics, structural studies of IDPs have relied mostly on NMR spectroscopy, despite IDPs having characteristics that make them challenging to study using traditional 1H-detected biomolecular NMR techniques. Here, we develop a suite of 3D 15N-detected experiments that take advantage of the slower transverse relaxation property of 15N nuclei, the associated narrower linewidth, and the greater chemical shift dispersion compared with those of 1H and 13C resonances. The six 3D experiments described here start with aliphatic 1H magnetization to take advantage of its higher initial polarization, and are broadly applicable for backbone assignment of proteins that are disordered, dynamic, or have unfavorable amide proton exchange rates. Using these experiments, backbone resonance assignments were completed for the unstructured regulatory domain (residues 131-294) of the human transcription factor nuclear factor of activated T cells (NFATC2), which includes 28 proline residues located in functionally important serine-proline (SP) repeats. The complete assignment of the NFATC2 regulatory domain enabled us to study phosphorylation of NFAT by kinase PKA and phosphorylation-dependent binding of chaperone protein 14-3-3 to NFAT, providing mechanistic insight on how 14-3-3 regulates NFAT nuclear translocation.

Local Deuteration Enables NMR Observation of Methyl Groups in Proteins from Eukaryotic and Cell-Free Expression Systems.

Therapeutically relevant proteins such as GPCRs, antibodies and kinases face clear limitations in NMR studies due to the challenges in site-specific isotope labeling and deuteration in eukaryotic expression systems. Here we describe an efficient and simple method to observe the methyl groups of leucine residues in proteins expressed in bacterial, eukaryotic or cell-free expression systems without modification of the expression protocol. The method relies on simple stereo-selective 13 C-labeling and deuteration of leucine that alleviates the need for additional deuteration of the protein. The spectroscopic benefits of "local" deuteration are examined in detail through Forbidden Coherence Transfer (FCT) experiments and simulations. The utility of this labeling method is demonstrated in the cell-free synthesis of bacteriorhodopsin and in the insect-cell expression of the RRM2 domain of human RBM39.

Reinvestigation of the biological activity of d-allo-ShK protein.

ShK toxin from the sea anemone Stichodactyla helianthus is a 35-residue protein that binds to the Kv1.3 ion channel with high affinity. Recently we determined the X-ray structure of ShK toxin by racemic crystallography, in the course of which we discovered that d-ShK has a near-background IC50 value ∼50,000 times lower than that of the l-ShK toxin. This lack of activity was at odds with previously reported results for an ShK diastereomer designated d-allo-ShK, for which significant biological activity had been observed in a similar receptor-blocking assay. As reported, d-allo-ShK was made up of d-amino acids, but with retention of the natural stereochemistry of the chiral side chains of the Ile and Thr residues, i.e. containing d-allo-Ile and d-allo-Thr along with d-amino acids and glycine. To understand its apparent biological activity, we set out to chemically synthesize d-allo-ShK and determine its X-ray structure by racemic crystallography. Using validated allo-Thr and allo-Ile, both l-allo-ShK and d-allo-ShK polypeptide chains were prepared by total chemical synthesis. Neither the l-allo-ShK nor the d-allo-ShK polypeptides folded, whereas both l-ShK and d-ShK folded smoothly under the same conditions. Re-examination of NMR spectra of the previously reported d-allo-ShK protein revealed that diagnostic Thr and Ile signals were the same as for authentic d-ShK. On the basis of these results, we conclude that the previously reported d-allo-ShK was in fact d-ShK, the true enantiomer of natural l-ShK toxin, and that the apparent biological activity may have arisen from inadvertent contamination with trace amounts of l-ShK toxin.

8-Mercaptoguanine Derivatives as Inhibitors of Dihydropteroate Synthase.

Dihydropteroate synthase (DHPS) is an enzyme of the folate biosynthesis pathway, which catalyzes the formation of 7,8-dihydropteroate (DHPt) from 6-hydroxymethyl-7,8-dihydropterin pyrophosphate (DHPPP) and para-aminobenzoic acid (pABA). DHPS is the long-standing target of the sulfonamide class of antibiotics that compete with pABA. In the wake of sulfa drug resistance, targeting the structurally rigid (and more conserved) pterin site has been proposed as an alternate strategy to inhibit DHPS in wild-type and sulfa drug resistant strains. Following the work on developing pterin-site inhibitors of the adjacent enzyme 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK), we now present derivatives of 8-mercaptoguanine, a fragment that binds weakly within both enzymes, and quantify sub-µm binding using surface plasmon resonance (SPR) to Escherichia coli DHPS (EcDHPS). Eleven ligand-bound EcDHPS crystal structures delineate the structure-activity relationship observed providing a structural framework for the rational development of novel, substrate-envelope-compliant DHPS inhibitors.

Hypocalcemia Presenting as Life Threatening Torsades de Pointes with Prolongation of QTc Interval.

Torsades de pointes with prolonged QTc interval is a form of ventricular tachycardia. Many predisposing factors have been identified and hypocalcemia is among the rare ones. Our case illustrates that though rare, hypocalcemia might manifest as torsades de pointes with prolongation of QTc interval. Early diagnosis and management of dyselectrolytemia can prevent these patients from catastrophic torsades de pointes.

Structural Basis for the Inhibition of Voltage-gated Sodium Channels by Conotoxin µO§-GVIIJ.

Cone snail toxins are well known blockers of voltage-gated sodium channels, a property that is of broad interest in biology and therapeutically in treating neuropathic pain and neurological disorders. Although most conotoxin channel blockers function by direct binding to a channel and disrupting its normal ion movement, conotoxin µO§-GVIIJ channel blocking is unique, using both favorable binding interactions with the channel and a direct tether via an intermolecular disulfide bond. Disulfide exchange is possible because conotoxin µO§-GVIIJ contains anS-cysteinylated Cys-24 residue that is capable of exchanging with a free cysteine thiol on the channel surface. Here, we present the solution structure of an analog of µO§-GVIIJ (GVIIJ[C24S]) and the results of structure-activity studies with synthetic µO§-GVIIJ variants. GVIIJ[C24S] adopts an inhibitor cystine knot structure, with two antiparallel ß-strands stabilized by three disulfide bridges. The loop region linking the ß-strands (loop 4) presents residue 24 in a configuration where it could bind to the proposed free cysteine of the channel (Cys-910, rat NaV1.2 numbering; at site 8). The structure-activity study shows that three residues (Lys-12, Arg-14, and Tyr-16) located in loop 2 and spatially close to residue 24 were also important for functional activity. We propose that the interaction of µO§-GVIIJ with the channel depends on not only disulfide tethering via Cys-24 to a free cysteine at site 8 on the channel but also the participation of key residues of µO§-GVIIJ on a distinct surface of the peptide.

Installation of a Rigid EDTA-Like Motif into a Protein α-Helix for Paramagnetic NMR Spectroscopy with Cobalt(II) Ions.

Coupling two copies of an iminodiacetic acid-cysteine hybrid ligand to a pair of cysteine residues positioned in an i, i+4 arrangement within a protein α-helix leads to generation of an EDTA-like metal ion-binding motif. Rigid binding of a Co(II) ion by this motif produces pseudo-contact shifts suitable for paramagnetic NMR structural studies.

Kv1.3 channel-blocking immunomodulatory peptides from parasitic worms: implications for autoimmune diseases.

The voltage-gated potassium (Kv) 1.3 channel is widely regarded as a therapeutic target for immunomodulation in autoimmune diseases. ShK-186, a selective inhibitor of Kv1.3 channels, ameliorates autoimmune diseases in rodent models, and human phase 1 trials of this agent in healthy volunteers have been completed. In this study, we identified and characterized a large family of Stichodactyla helianthus toxin (ShK)-related peptides in parasitic worms. Based on phylogenetic analysis, 2 worm peptides were selected for study: AcK1, a 51-residue peptide expressed in the anterior secretory glands of the dog-infecting hookworm Ancylostoma caninum and the human-infecting hookworm Ancylostoma ceylanicum, and BmK1, the C-terminal domain of a metalloprotease from the filarial worm Brugia malayi. These peptides in solution adopt helical structures closely resembling that of ShK. At doses in the nanomolar-micromolar range, they block native Kv1.3 in human T cells and cloned Kv1.3 stably expressed in L929 mouse fibroblasts. They preferentially suppress the proliferation of rat CCR7(-) effector memory T cells without affecting naive and central memory subsets and inhibit the delayed-type hypersensitivity (DTH) response caused by skin-homing effector memory T cells in rats. Further, they suppress IFNγ production by human T lymphocytes. ShK-related peptides in parasitic worms may contribute to the potential beneficial effects of probiotic parasitic worm therapy in human autoimmune diseases.

Development of highly selective Kv1.3-blocking peptides based on the sea anemone peptide ShK.

ShK, from the sea anemone Stichodactyla helianthus, is a 35-residue disulfide-rich peptide that blocks the voltage-gated potassium channel Kv1.3 at ca. 10 pM and the related channel Kv1.1 at ca. 16 pM. We developed an analog of this peptide, ShK-186, which is currently in Phase 1b-2a clinical trials for the treatment of autoimmune diseases such as multiple sclerosis and rheumatoid arthritis. While ShK-186 displays a >100-fold improvement in selectivity for Kv1.3 over Kv1.1 compared with ShK, there is considerable interest in developing peptides with an even greater selectivity ratio. In this report, we describe several variants of ShK that incorporate p-phophono-phenylalanine at the N-terminus coupled with internal substitutions at Gln16 and Met21. In addition, we also explored the combinatorial effects of these internal substitutions with an alanine extension at the C-terminus. Their selectivity was determined by patch-clamp electrophysiology on Kv1.3 and Kv1.1 channels stably expressed in mouse fibroblasts. The peptides with an alanine extension blocked Kv1.3 at low pM concentrations and exhibited up to 2250-fold selectivity for Kv1.3 over Kv1.1. Analogs that incorporates p-phosphono-phenylalanine at the N-terminus blocked Kv1.3 with IC50s in the low pM range and did not affect Kv1.1 at concentrations up to 100 nM, displaying a selectivity enhancement of >10,000-fold for Kv1.3 over Kv1.1. Other potentially important Kv channels such as Kv1.4 and Kv1.6 were only partially blocked at 100 nM concentrations of each of the ShK analogs.

Conformational flexibility in the binding surface of the potassium channel blocker ShK.

ShK is a 35-residue peptide that binds with high affinity to human voltage-gated potassium channels through a conserved K-Y dyad. Here we have employed NMR measurements of backbone-amide (15)N spin-relaxation rates to investigate motions of the ShK backbone. Although ShK is rigid on the ps to ns timescale, increased linewidths observed for 11 backbone-amide (15)N resonances identify chemical or conformational exchange contributions to the spin relaxation. Relaxation dispersion profiles indicate that exchange between major and minor conformers occurs on the sub-millisecond timescale. Affected residues are mostly clustered around the central helix-kink-helix structure and the critical K22-Y23 motif. We suggest that the less structured minor conformer increases the exposure of Y23, known to contribute to binding affinity and selectivity, thereby facilitating its interaction with potassium channels. These findings have potential implications for the design of new channel blockers based on ShK.

Kikuchi's disease--a rare cause of lymphadenopathy and fever.

Kikuchi's disease is a rare, benign, self-limited disorder, characterised clinically by fever and tender regional lymphadenopathy. It has been reported worldwide and is particularly common in people of Asian descent. The cause of Kikuchi's disease is unknown. It predominantly affects young females and can closely mimic several infectious and immunological conditions. Histopathologic features of lymph nodes in Kikuchi's disease are characteristic and permit differentiation of this benign condition from lymphomas, systemic lupus erythematosus and infectious lymphadenopathies. We report a female patient presenting with fever and tender cervical lymphadenopathy. She was being treated for tubercular lymphadenitis and was referred after she developed a transient hepatitis and a skin rash following treatment with anti-tubercular drugs. An excisional biopsy of the lymph node revealed histiocytic necrotising lymphadenitis, consistent with Kikuchi's disease. A brief review of the pathogenesis and differential diagnosis of Kikuchi's disease is presented.

Microfluidic viscometer by acoustic streaming transducers.

Measurement of fluid viscosity represents a huge need for many biomedical and materials processing applications. Sample fluids containing DNA, antibodies, protein-based drugs, and even cells have become important therapeutic options. The physical properties, including viscosity, of these biologics are critical factors in the optimization of the biomanufacturing processes and delivery of therapeutics to patients. Here we demonstrate an acoustic microstreaming platform termed as microfluidic viscometer by acoustic streaming transducers (µVAST) that induces fluid transport from second-order microstreaming to measure viscosity. Validation of our platform is achieved with different glycerol content mixtures to reflect different viscosities and shows that viscosity can be estimated based on the maximum speed of the second-order acoustic microstreaming. The µVAST platform requires only a small volume of fluid sample (∼1.2 µL), which is 16-30 times smaller than that of commercial viscometers. In addition, µVAST can be scaled up for ultra-high throughput measurements of viscosity. Here we demonstrate 16 samples within 3 seconds, which is an attractive feature for automating the process flows in drug development and materials manufacturing and production.

Diabetes Mellitus Increases the Risk of Significant Hepatic Fibrosis in Patients With Non-alcoholic Fatty Liver Disease.

Background: Diabetes mellitus is associated with an increased risk of development of non-alcoholic fatty liver disease (NAFLD). However, the risk posed by diabetes mellitus in progression of liver disease is uncertain. This study compared the severity of hepatic fibrosis in patients with NAFLD with and without diabetes mellitus. Methods: Consecutive adult patients with NAFLD undergoing transient elastography [FibroScan Touch 502 (Echosens, Paris, France)] at a tertiary care center in north India were analyzed for severity of hepatic fibrosis. The aspartate aminotransferase (AST) to platelet ratio index (APRI), fibrosis index based on 4 factors (FIB-4), and NAFLD Fibrosis Score (NFS) were calculated. The degree of hepatic fibrosis as determined by FibroScan and non-invasive serum fibrosis models in patients with and without diabetes mellitus were compared. Results: A total of two hundred patients [118 (59%) males, mean age 50.30 ± 11.13 years] were enrolled. Significant hepatic fibrosis was present in 86 (43%) patients [mean age 50.66 ± 10.96 years, 56 (65.11%) males]. The mean FibroScan, APRI, FIB-4, and NFS scores were 9.86 ± 2.97, 0.75 ± 0.47, 2.41 ± 1.41 and -0.24 ± 1.43 in patients with diabetes compared to 5.31 ± 1.09, 0.49 ± 0.27, 1.55 ± 0.85, and -2.12 ± 1.88 in patients without diabetes, respectively (P=<0.0001). There was a fair correlation between FibroScan and non-invasive serum fibrosis models (P=<0.0001). Conclusion: Presence of diabetes increases the risk of significant hepatic fibrosis in patients with NAFLD. FIB-4 correlates fairly with FibroScan in patients with diabetes and can be used as a screening tool to detect significant hepatic fibrosis.

Clinical Profile of Coronavirus Disease 2019 Comparing the First and Second Waves: A Single-Center Study from North India.

Background and Objectives: Severe acute respiratory syndrome coronavirus 2, caused by the novel coronavirus disease 2019 (COVID-19), led to a devastating pandemic that hit majority of the countries globally in a wave-like pattern. The characteristics of the disease varied in different geographical areas and different populations. This study highlights the epidemiological and clinical characteristics of COVID-19 during two major waves in North India. Materials and Methods: Clinical characteristics and outcomes of all COVID-19-reverse transcription-polymerase chain reaction-positive patients, admitted from March 2020 to June 2021, to a tertiary care center in North India, were studied retrospectively. Results: During this period, total of 5652 patients were diagnosed having COVID. Patients who were incidentally diagnosed as COVID-positive (n=667) with other unrelated comorbid conditions and patients admitted under level 1 facility (n=1655; 1219 from first and 436 from second wave) were excluded from final analysis. Males were most commonly affected in both waves, with male to female ratio 4:1 in first and 3:1 in second wave. First wave had significantly more people with co-morbidities like diabetes mellitus and hypertension (P=0.001), whereas younger age group (age <40 years) were significantly more affected in second wave (P= 0.000). Fever was the most common presenting complaint in both waves, followed by cough and breathlessness. Patients during first wave had more severe disease at presentation and high mortality compared to the second wave. Conclusion: Majority of the patients with COVID-19 infection presenting to our hospital were young during the second wave. Fever was noted as presenting manifestation. Mortality was low during the second wave as compared to the first wave, likely to be due to proper protocol-based treatment resulting in better outcomes.

15N-Detected TROSY NMR experiments to study large disordered proteins in high-field magnets.

Intrinsically disordered regions (IDRs) of proteins are critical in the regulation of biological processes but difficult to study structurally. Nuclear magnetic resonance (NMR) is uniquely equipped to provide structural information on IDRs at atomic resolution; however, existing NMR methods often pose a challenge for large molecular weight IDRs. Resonance assignment of IDRs using 15ND-detection was previously demonstrated and shown to overcome some of these limitations. Here, we improve the methodology by overcoming the need for deuterated buffers and provide better sensitivity and resolution at higher magnetic fields and physiological salt concentrations using transverse relaxation optimized spectroscopy (TROSY). Finally, large disordered regions with low sequence complexity can be assigned efficiently using these new methods as demonstrated by achieving near complete assignment of the 398-residue N-terminal IDR of the transcription factor NFAT1 harboring 18% prolines.

DOTA-amide lanthanide tag for reliable generation of pseudocontact shifts in protein NMR spectra.

Structural studies of proteins and protein-ligand complexes by nuclear magnetic resonance (NMR) spectroscopy can be greatly enhanced by site-specific attachment of lanthanide ions to create paramagnetic centers. In particular, pseudocontact shifts (PCS) generated by paramagnetic lanthanides contain important and unique long-range structure information. Here, we present a high-affinity lanthanide binding tag that can be attached to single cysteine residues of proteins. The new tag has many advantageous features that are not available in this combination from previously published tags: (i) it binds lanthanide ions very tightly, minimizing the generation of nonspecific effects, (ii) it produces PCSs with high reliability as its bulkiness prevents complete motional averaging of PCSs, (iii) it can be attached to single cysteine residues, alleviating the need of detailed prior knowledge of the 3D structure of the target protein, and (iv) it does not display conformational exchange phenomena that would increase the number of signals in the NMR spectrum. The performance of the tag is demonstrated with the N-terminal domain of the E. coli arginine repressor and the A28C mutant of human ubiquitin.

Anemia and Nutritional Status in Tuberculosis Patients.

INTRODUCTION: Anemia is a common complication of pulmonary tuberculosis (TB). Nutritional deficiency and malabsorption syndrome can deepen the severity of anemia. The aim of the present study was to study anemia and nutritional status in patients with TB at a tertiary care center. MATERIALS AND METHODS: All patients diagnosed with TB (pulmonary and extrapulmonary), registered withRevised National TB Control Programme (RNTCP), taking DOTS regimen, attending the outpatient department as well as those admitted in the medicine and chest units of a tertiary care hospital, were enrolled in the present study. RESULTS: Anemia was more common between the age groups of 51 and 60 years, with distribution of males (87 [58%]), patients with diabetes (49 [32%]), and hypertensive patients (29 [19.3%]). In our study, 48 (85.7%) out of 56 patients diagnosed with extrapulmonary TB were found to have anemia; similarly, 77 (88.5%) out of 87 patients diagnosed to have pulmonary TB were anemic. Anemia of chronic disease (128 [97.17%]) was higher when compared to that of those with iron-deficiency anemia (3 [2.29%]). According to body mass index (BMI), 135 (90%) patients were underweight; according to mid-arm circumference (MAC), 131 (87.3%) patients had severe malnutrition; and according to waist-hip ratio [WHR], 96 (64%) patients were underweight. CONCLUSION: Anemia was common in males and alcoholics, and there was a high prevalence of anemia of chronic disease. In addition, anemia was associated with high erythrocyte sedimentation rate and C-reactive protein. High proportions of TB patients (pulmonary and extrapulmonary) were classified as underweight and malnourished on the basis of different parameters (BMI, MAC, and WHR); in addition, the degree of malnutrition was higher in patients with anemia than in those without.

Chemoradiation in locally advanced Ca Cx: Effect on NGAL levels.

INTRODUCTION: Neutrophil gelatinase-associated lipocalin (NGAL) has been reported to be unregulated in many cancers and to suppress tumor suppressor genes like p53 leading to cell proliferation. Studies to report its relationship with carcinoma cervix (Ca Cx) are still scant. MATERIALS AND METHODS: Serum NGAL levels were analyzed in 30 patients of histopathologically proven locally advanced Ca Cx at the time of diagnosis and 3 weeks after standard chemoradiation by enzyme-linked immunosorbent assay. These patients underwent either brachytherapy or supplementary external beam radiotherapy (EBRT) depending on the response of treatment. The results were analyzed statistically by applying Student's paired t-test. RESULTS: No statistically significant difference (P > 0.05) was observed in patients of Ca Cx before and after treatment or when compared stage wise, histopathological grade wise, or response wise. But the levels were found to increase when duration of treatment was ≥8 weeks (P = 0.040) and to decrease significantly when duration of treatment was <8 weeks (P = 0.0052). The NGAL levels also increased significantly after treatment in patients who received EBRT and supplementary radiotherapy (P = 0.019) while the pre- and post-treatment difference in NGAL levels was not statistically significant in patients who received EBRT + intracavitary brachytherapy (P > 0.05). CONCLUSION: As the duration as well as modality of treatment is quite important in Ca Cx, shorter duration associated with better results and lower NGAL levels, NGAL might prove to be a useful biomarker although further studies are needed to support the claim.