1,211 research outputs found
Structural and Related Studies on Mycobacterial Lectins
No full textThis thesis is concerned with the first ever X-ray crystallographic and complimentary solution studies on mycobacterial lectins. Lectins, described as multivalent carbohydrate binding proteins of non-immune origin, are found in all kingdoms of life. As explained in the introductory chapter, those from plants and animals are the best characterized in terms of structure and function. Although not that extensive, important studies have been carried out on viral, fungal and parasite lectins as well. Bacterial lectins studied so far can be classified in to fimbrial, surface and secretory (or toxic). Applications of lectins include blood typing, cell separation and purification of glycoconjugates, mitogenic stimulation of lymphocytes, mapping of neuronal pathways and drug targeting and delivery. The work reported in the thesis lies at the intersection of two major long range programs in this laboratory, one on lectins and the other on mycobacterial proteins. Three putative lectins Rv1419 and Rv2813 from M. tuberculosis and MSMEG_3662 from M. smegmatis were chosen for exploratory studies on the basis of preliminary genomic searches.
Exploratory studies on Rv1419, Rv2813 and MSMEG_3662 are described in the second chapter. MSMEG_3662 contains two domains, a LysM domain and a lectin domain (MSL) connected by a long polypeptide chain. The two M. tuberculosis proteins, full length MSMEG_3662 and MSL were cloned, expressed, purified and characterized. Rv2813 did not show any appreciable agglutination activity. It showed ATPase activity. Clearly the protein was not a lectin. Rv1419, full length MSMEG_3662 and MSL exhibited lectin characteristics. Among them, Rv1419 and MSL could be crystallized. Preliminary X-ray diffraction studies on them were carried out.
Rv1419 could be successfully expressed only once. However, that was enough for the determination of crystal structure and the glycan array analysis of the lectin (Chapter 3). The monomeric lectin has a β-trefoil fold. It has high affinity for LacNAc and its Neu5Ac derivatives. Modeling studies using complexes of homologous structures, led to the identification of two carbohydrate binding sites on the lectins. Sequence comparisons of Rv1419 with homologous proteins with known structures and phylogenetic analysis involving them provide interesting insights into the relationship among trefoil lectins from different sources.
X-ray crystal structure analysis of MSL and its complexes with mannose and methyl-α-mannose, the first comprehensive effort of its kind on a mycobacterial lectin, reveals a structure very similar to β-prism II fold lectins from plant sources, but with extensive unprecedented domain swapping in dimer formation (Chapter 4). The two subunits in a dimer often show small differences in structure, but the two domains, not always related by 2-fold symmetry, have the same structure. Each domain carries three sugar-binding sites, similar to those in plant lectins, one on each Greek key motif. The occurrence of β-prism II fold lectins in bacteria, with characteristics similar to those from plants, indicates that this family of lectins is of ancient origin and had evolved into a mature system before bacteria and plants diverged. In plants, the number of binding sites per domain varies between one and three, whereas the number is two in the recently reported lectin domains from Pseudomonas putida and Pseudomonas aeruginosa. An analysis of the sequences of the lectins and the lectin domains shows that the level of sequence similarity among the three Greek keys in each domain has a correlation with the number of binding sites in it. Furthermore, sequence conservation among the lectins from different species is the highest for that Greek key which carries a binding site in all of them. Thus, it would appear that carbohydrate binding influences the course of the evolution of the lectin.
LysM domains have been recognized in bacteria and eukaryotes as carbohydrate-binding protein modules, but the mechanism of their binding to chitooligosaccharides is underexplored. Binding of a full length MSMEG_3662 containing LysM and lectin (MSL) domains to chitooligosaccharides has been studied using isothermal titration calorimetry and fluorescence titration (Chapter 5). This investigation demonstrates the presence of two binding sites of non-identical affinities per dimeric MSL-LysM molecule. Affinity of the molecule for chitooligosaccharides correlates with the length of the carbohydrate chain. Its binding to chitooligosaccharides is characterized by negative cooperativity in the interactions of the two domains. Apparently, the flexibility of the long linker that connects the LysM and MSL domains plays a facilitating role in this recognition. The LysM domain in MSL-LysM, like other bacterial domains but unlike plant LysM domains, recognizes equally well peptidoglycan fragments as well as chitin polymers. Interestingly, in the present case two LysM domains are enough for binding to peptidoglycan in contrast to the three reportedly required by the LysM domains of Bacillus subtilis and Lactococcus lactis. Also, the affinity of MSL-LysM for chitooligosaccharides is higher than that of LysM-chitooligosaccharide interactions reported so far.
A part of the work presented in this thesis has been reported in the following publications:
• Patra D, Mishra P, Surolia A, Vijayan M. 2014. Structure, interactions and evolutionary implications of a domain-swapped lectin dimer from Mycobacterium smegmatis. Glycobiology, 24:956-965.
• Patra D, Sharma A, Chandran D, Vijayan M. 2011. Cloning, expression, purification, crystallization and preliminary X-ray studies of the mannose-binding lectin domain of MSMEG_3662 from Mycobacterium smegmatis. Acta Crystallogr Sect F Struct Biol Cryst Commun, 67:596-599.
• Patra D, Srikalaivani R, Misra A, Singh DD, Selvaraj M, Vijayan M. 2010. Cloning, expression, purification, crystallization and preliminary X-ray studies of a secreted lectin (Rv1419) from Mycobacterium tuberculosis. Acta Crystallogr Sect F Struct Biol Cryst Commun, 66:1662-1665
Analysis of the unstable behaviour of a single-phase natural circulation loop with one-dimensional and computational fluid-dynamic models
No full textThis paper discusses the results obtained using one-dimensional and three-dimensional computational fluid-dynamic codes for the prediction of the dynamic behaviour observed in experiments carried out in a single-phase natural circulation apparatus. The loop is made of glass and is equipped with vertical and horizontal heaters and coolers that can be separately operated, thus obtaining different working configurations.
An in-house program, capable of linear and non-linear stability analysis of one-dimensional loops, with arbitrary configurations of heat sources and sinks, and a transient thermal–hydraulics system code were adopted for the purpose of highlighting capabilities and limitations of one-dimensional models in predicting the involved phenomena. Both linear stability maps and transient flow evolutions have been calculated by the programs, obtaining information on both the linear and the non-linear dynamic behaviour of the addressed system, as predicted by one-dimensional, cross-section averaged balance equations.
A computational fluid-dynamics code has been also adopted for simulating the system dynamics in the different loop configurations. In particular, the CFD code was effective in showing the origin of pulsating instabilities observed with horizontal heater and cooler, which could in no way be predicted by the one-dimensional models.
Abbreviations: CFD, computational fluid-dynamics; HHHC, horizontal heater horizontal cooler; HHVC, horizontal heater vertical cooler; RNG, renormalised group theory; VHHC, vertical heater horizontal cooler; VHVC, vertical heater vertical cooler; 1D, one-dimensional; 3D, three-dimensional
FIGURE 4 in Two new species of Simulium (Gomphostilbia) (Diptera: Simuliidae) from South India
No full textFIGURE 4. Female of Simulium (Gomphostilbia) krishnani sp. nov. A, 3rd segment of right maxillary palp showing sensory vesicle (front view); B, cibarium (front view); C, basitarsus and 2nd tarsomere of left hind leg showing calcipala and pedisulcus (outer view); D, tarsal claw; E, 8th sternite, ovipositor valves (ventral view); F, genital fork (ventral view); G & H, right paraprocts and cerci (G, ventral view; H, lateral view); I, spermatheca (lateral view). Scale bars. 0.02 mm for (I); 0.01 mm for (A & B, D–H); 0.1 mm for (C).Published as part of Anbalagan, Sankarappan, Vijayan, Suruliyandi, Balachandran, Chellapandian, Thiyonila, Berchmans & Surya, Aathmanathan, 2020, Two new species of Simulium (Gomphostilbia) (Diptera: Simuliidae) from South India, pp. 57-72 in Zootaxa 4742 (1) on page 66, DOI: 10.11646/zootaxa.4742.1.3, http://zenodo.org/record/367446
FIGURE 1 in Two new species of Simulium (Gomphostilbia) (Diptera: Simuliidae) from South India
No full textFIGURE 1. Female of Simulium (Gomphostilbia) dinakarani sp. nov. A, 3rd segment of right maxillary palp showing sensory vesicle (front view); B, cibarium (front view); C, left hind tibia (outer view); D, basitarsus and 2nd tarsomere of left hind leg showing calcipala and pedisulcus (outer view); E, tarsal claw; F, 8th sternite, ovipositor valves (ventral view); G, genital fork (ventral view); H & I, right paraprocts and cerci (H, ventral view; I, lateral view); J, spermatheca (lateral view). Scale bars. 0.02 mm for (G) and (J); 0.01 mm for (A, B, E, F, H and I); 0.1 mm for (C) and (D).Published as part of Anbalagan, Sankarappan, Vijayan, Suruliyandi, Balachandran, Chellapandian, Thiyonila, Berchmans & Surya, Aathmanathan, 2020, Two new species of Simulium (Gomphostilbia) (Diptera: Simuliidae) from South India, pp. 57-72 in Zootaxa 4742 (1) on page 61, DOI: 10.11646/zootaxa.4742.1.3, http://zenodo.org/record/367446
FIGURE 3 in A new species of Simulium (Gomphostilbia) (Diptera: Simuliidae) from South India
No full textFIGURE 3. Male of Simulium (Simulium) kumbakkaraiense sp.n. A, 3rd segment of left maxillary palp showing small sensory vesicle (frontal view); B, basitarsus and 2nd tarsomere of left hind leg showing calcipala and pedisulcus (outer view); C, coxites, styles, ventral plate and median sclerite (ventral view); D left styles (ventrolateral view); E, ventral plate and median sclerite; F, ventral plate (end view); G, left paramere and aedeagal membrane (end view); H, 10th abdominal segment and cercus (right side and lateral view). Scale bars. 0.02 mm for A and E–H; 0.05 mm for C and D; 0.1 mm for B.Published as part of Anbalagan, Sankarappan, Vijayan, Suruliyandi, Dinakaran, Sundaram & Krishnan, Muthukalingan, 2019, A new species of Simulium (Gomphostilbia) (Diptera: Simuliidae) from South India, pp. 479-486 in Zootaxa 4551 (4) on page 483, DOI: 10.11646/zootaxa.4551.4.8, http://zenodo.org/record/262313
FIGURE 2 in A new species of Simulium (Gomphostilbia) (Diptera: Simuliidae) from South India
No full textFIGURE 2. Female of Simulium (Simulium) kumbakkaraiense sp.n. A, 3rd segment of right maxillary palp showing sensory vesicle (frontal view); B, cibarium (frontal view); C, basitarsus and 2nd tarsomere of left hind leg showing calcipala and pedisulcus (frontal view); D, tarsal claw; E, 8th sternite, ovipositor valves (ventral view); F, genital fork (ventral view); G & H, right paraprocts and cerci (G, ventral view; H, lateral view); I, spermatheca (lateral view). Scale bars. 0.02 mm for D–I; 0.05 mm for A and B; 0.1 mm for C.Published as part of Anbalagan, Sankarappan, Vijayan, Suruliyandi, Dinakaran, Sundaram & Krishnan, Muthukalingan, 2019, A new species of Simulium (Gomphostilbia) (Diptera: Simuliidae) from South India, pp. 479-486 in Zootaxa 4551 (4) on page 482, DOI: 10.11646/zootaxa.4551.4.8, http://zenodo.org/record/262313
Acetogenins from Annona muricata as potential inhibitors of antiapoptotic proteins: a molecular modeling study
No full textPriya Antony, Ranjit Vijayan Department of Biology, College of Science, United Arab Emirates University, Al Ain, Abu Dhabi, United Arab Emirates Abstract: Apoptosis is a highly regulated process crucial for maintaining cellular homeostasis and development. The B-cell lymphoma 2 (Bcl-2) family of proteins play a crucial role in regulating apoptosis. Overexpressed Bcl-2 proteins are associated with the development and progression of several human cancers. Annona muricata is a tropical plant that belongs to the Annonaceae family and is well known for its anticancer properties. In this study, molecular docking and simulations were performed to investigate the inhibitory potential of phytochemicals present in A. muricata against antiapoptotic proteins of the Bcl-2 family including Bcl-2, B-cell lymphoma extra-large (Bcl-Xl), and Mcl-1. Docking results revealed that the acetogenins, such as annomuricin A, annohexocin, muricatocin A, annomuricin-D-one, and muricatetrocin A/B, exhibited strong binding interactions with Bcl-Xl when compared to Bcl-2 and Mcl-1. Binding score and interactions of these acetogenins were notably better than those of currently available synthetic and natural inhibitors. Molecular dynamics simulations of the top-scoring lead molecules established that these molecules could bind strongly and consistently in the active site of Bcl-Xl. These results suggest that acetogenins could be explored as selective natural inhibitors of Bcl-Xl that could assist in promoting the intrinsic pathway of apoptosis. Keywords: apoptosis, molecular docking, molecular dynamics, phytocompounds, drug discover
FIGURE 5 in Two new species of Simulium (Gomphostilbia) (Diptera: Simuliidae) from South India
No full textFIGURE 5. Male of Simulium (Gomphostilbia) krishnani sp. nov. (A) 3rd segment of left maxillary palp showing small sensory vesicle (frontal view); (B) basitarsus and 2nd tarsomere of left hind leg showing calcipala and pedisulcus (outer view); (C) coxites, styles, ventral plate and median sclerite (ventral view); (D) left style (ventrolateral view); (E & F) ventral plate (E) ventral view; (F) end view; (G) left paramere and aedeagal membrane (end view); (H) 10th abdominal segment and cercus (right side and lateral view). Scale bars. 0.02 mm for (C–H); 0.01 mm for (A); 0.1 mm for (B).Published as part of Anbalagan, Sankarappan, Vijayan, Suruliyandi, Balachandran, Chellapandian, Thiyonila, Berchmans & Surya, Aathmanathan, 2020, Two new species of Simulium (Gomphostilbia) (Diptera: Simuliidae) from South India, pp. 57-72 in Zootaxa 4742 (1) on page 67, DOI: 10.11646/zootaxa.4742.1.3, http://zenodo.org/record/367446
Effect of organically modified nanoclay on the miscibility, rheology, morphology and physical properties of diglycidyl ether of bisphenol-A epoxy/ carboxyl-terminated (butadiene-co-acrylonitrile) blend
No full textCarboxyl-terminated (butadiene-co-acrylonitrile) (CTBN) modified epoxy/clay nanocomposites (epoxy/clay/CTBN ternary nanocomposites) were synthesized using nadic methyl anhydride as curing agent. Effect of nanoclay on the phase behavior (UCST) of epoxy oligomer/CTBN blend has been studied in detail. The phase diagram was shifted to a higher temperature with increase in clay loading due to the easy penetration of low molecular weight CTBN into the clay galleries. The XRD studies confirmed the penetration of CTBN into the clay galleries, as the ‘ d ’ spacing increased with increase in CTBN content in the epoxy/clay/CTBN ternary nanocomposite. The interaction of organically modified clay with epoxy and CTBN were studied using frequency sweep rheological analysis. The individual and combined effect of nanoclay and CTBN on the cure reaction was followed by isothermal rheological analysis. It was found that complex viscosity profiles during cure reaction follow an exponential growth. The characteristic relaxation time of viscosity growth was described by the WLF equation. Moreover the dynamics of phase separation during cure was followed using optical microscopy. The scanning electron microscopic (SEM) images revealed that the domain size of phase separated CTBN in epoxy/clay/CTBN ternary nanocomposite was smaller than in epoxy/CTBN binary blend. The kinetic factor in epoxy-anhydride cure reaction and the presence of clay at epoxy–CTBN interface was used to explain this size reduction. The high resolution transmission electron microscopic (HRTEM) image of epoxy/3 phr clay nanocomposite showed that the clay platelets were mostly intercalated. Epoxy/3 phr clay/15 phr CTBN nanocomposite has an intercalated with occasional exfoliated microstructure with slightly distorted clay orientation. Low magnification TEM images showed that most of the clay platelets located near the phase separated CTBN and the presence of clay at the epoxy–CTBN interface. The viscoelastic properties of epoxy/clay/CTBN nanocomposite was studied and compared with that of epoxy/clay nanocomposite and epoxy/CTBN blend. A quantitative measurement of constrained region (macromolecular chains immobilized by the clay platelets) was carried out for epoxy/clay and epoxy/clay/CTBN nanocomposites. Finally thermal degradation studies were performed to evaluate the thermal stability of the ternary nanocomposites
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