Single-molecule tracking for studying protein dynamics and target-search mechanism in live cells of S. cerevisiae

Single-molecule tracking (SMT) is a powerful approach to quantify the biophysical parameters of protein dynamics in live cells. Here, we describe a protocol for SMT in live cells of the budding yeast Saccharomyces cerevisiae. We detail how to genetically engineer yeast strains for SMT, how to set up image acquisition parameters, and how different software programs can be used to quantify a variety of biophysical parameters such as diffusion coefficient, residence time, bound fraction, jump angles, and target-search parameters. For complete details on the use and execution of this protocol, please refer to Mehta et al. ¹ and Ball et al..².

In-vivo Single-Molecule Imaging in Yeast: Applications and Challenges

Single-molecule imaging has gained momentum to quantify the dynamics of biomolecules in live cells, as it provides direct real-time measurements of various cellular activities under their physiological environment. Yeast, a simple and widely used eukaryote, serves as a good model system to quantify single-molecule dynamics of various cellular processes because of its low genomic and cellular complexities, as well as its facile ability to be genetically manipulated. In the past decade, significant developments have been made regarding the intracellular labeling of biomolecules (proteins, mRNA, fatty acids), the microscopy setups to visualize single-molecules and capture their fast dynamics, and the data analysis pipelines to interpret such dynamics. In this review, we summarize the current state of knowledge for the single-molecule imaging in live yeast cells to provide a ready reference for beginners. We provide a comprehensive table to demonstrate how various labs tailored the imaging regimes and data analysis pipelines to estimate various biophysical parameters for a variety of biological processes. Lastly, we present current challenges and future directions for developing better tools and resources for single-molecule imaging in live yeast cells.

Pharmacognostic, Phytochemical and Pharmacological Review of “Phog”- Calligonum polygonoides L

Calligonum polygonoides (Phog) belongs to family Polygonaceae. It is a geographically widely distributed shrub seen from the arctic to the tropics. This endangered plant (included in Red data book of IUCN) is morphologically having stem with nodes and internodes, white flowers in spike inflorescence and needle like leaves. It is traditionally used to stabilize sand dunes, as fuel, and in treatment of heat-stroke by mixing with curd or “Rayata”. It is also reported as antidote for opium poisoning. Various phyto-chemicals present include butanolides- calligonolides A and B, various flavanoids like kaempferol, quercetin and their derivatives. Various steroidal compounds are reported in roots. Pharmacologicallly, its cytotoxic, anti-inflammatory, antioxidant, antifungal and biosorbent potentials are reported by various researchers. Therefore, an attempt has been made to accumulate properties of this potential herb. Keywords: Calligonum, Phog, biosorbent, heat-stroke, calligonolides, kaempferol

In silico ligand based design of indolylpiperidinyl derivatives as novel histamine H(1) receptor antagonists

Histamine H(1) receptor antagonists play a vital role in the first line treatment of a broad range of allergic diseases. Frequent dosing of the antagonist results in side effects like sedation and cardiovascular toxicity. The present study highlights the important structural requirement and mechanistic interpretation of novel indolylpiperidinyl derivatives as H(1) receptor antagonists so as to facilitate the design of newer antihistaminics with increased duration of action and comparatively reduced side effects. The significance of the developed quantitative structure-activity relationship (QSAR) models were evaluated on the basis of statistical values of square of correlation coefficient (r(2)); (multiple linear regression (MLR), 0.86; and partial least squares (PLS), 0.85). The predictive ability of the resulting QSAR models was evaluated with cross-validated correlation coefficient (r(2)cv) values (MLR, 0.82; PLS, 0.82) generated for the training set and r(2) values (MLR, 0.763; PLS, 0.855) derived for test set. The final models comprised of multidimensional steric (verloop length, verloop B(3)), electronic (total dipole moment) and steric (KAlpha1 index) descriptors. The study indicates that antihistaminic activity is largely explained by steric and electronic parameters. In line with parameters entered in the model some indolylpiperidines derivatives were designed with good antihistaminic properties and pharmacokinetic profiles.

Entrapment of ketorolac tromethamine in polymeric vehicle for controlled drug delivery

The most common method for applying a drug in to the eye is to formulate the drug in the form of an eye drop, but this method is not considered ideal for ocular delivery of drug because of poor bioavailability arising from precorneal loss processes, this loss of drug from the precorneal area is a net effect of drainage, tear secretion and noncorneal absorption. Following the above lead we tried to improve the ocular bioavailability by increasing the corneal contact time and the feasible way was to formulate a drug with mucoadhesive/viscosity imparting agents. The adhesive strength of various polymers on corneal surface was studied with the help of self modified Franz diffusion cell and freshly excised goat/bovine cornea. The polymers hydroxypropylmethylcellulose, carboxymethylcellulose sodium, Eudragit type E/RL/RS, Carbopol ETD 2020 and Carbopol 934 National Formulary were formulated with drug, ketorolac tromethamine. The adhesive strength of polymers on corneal surface and permeation characteristics of drug through cornea were investigated by using above said formulations. Eudragit type E/RL/RS did not show any improvement in mucoadhesion, but the formulations containing Carbopol ETD 2020 and Carbopol 934 national formulary showed good mucoadhesion on corneal surface in the concentration as low as 0.75%. The mucoadhesive strength was also evaluated using the combination of Carbopol acrylates/C 10-30 alkylacrylate with allylpentaerithrital and preservative benzalkonium chloride, which also resulted in good mucoadhesion with improved corneal permeation. Observations made in this study indicate the potentiality of the ophthalmic formulations containing mucoadhesive/viscosity imparting agents.

Orientation specific positioning of organophosphorus hydrolase on solid interfaces for biosensor applications

Protein immobilization on solid interfaces is a crucial aspect of their successful application in technologies such as biosensing, purification, separation, decontamination, etc. Although immobilization can improve the long-term and operational stability of proteins, this is often at the cost of significant losses in the catalytic activity of the tethered enzyme. Covalent attachment methods take advantage of reactive groups on the amino acid side chains. The distribution of the solvent exposed side chains on an enzyme's molecular surface often results in an ensemble of orientations when the protein is immobilized on a surface or in a matrix through these side chain linkages. Depending on the attachment mechanism and resulting orientation, access to and from the active site could be restricted. This study describes a methodology for the design and implementation of an orientation specific attachment of an enzyme to a surface plasmon resonance sensor surface. The enzyme, organophosphorus hydrolase, was structurally analyzed to identify surface resides as candidates for modification to optimize active site accessibility and, thus, sensitivity of detection. A single surface lysine on the active site face of the enzyme dimer was selected for elimination, thus allowing for the immobilization of the catalyst in the preferred orientation. Kinetic evaluation of the enzymes determined that the surface lysine-to-alanine variant retained 80% of the wild-type activity with the neurotoxin substrates, paraoxon and demeton-S. After immobilization, surfaces bearing the variant were determined to be more active even though the enzyme coverage on the sensor surface was reduced by 17%.

Fluorescence-based sensing of p-nitrophenol and p-nitrophenyl substituent organophosphates

A novel detection method for organophosphate neurotoxins has been described, based on the fluorescence quenching of a Coumarin derivative. These dyes are similar in structure to some organophosphates (OPs), and they fluoresce in the blue-green region of the spectra. This methodology has been utilized for the detection of organophosphates whose hydrolysis product is p-nitrophenol by using an enzyme, organophosphorus hydrolase (OPH). Coumarin1 in the presence of p-nitrophenol results in a quenching of fluorescence, providing a direct measure of the concentration of p-nitrophenol present in the sample. The decrease in fluorescence intensity is proportional to the paraoxon concentration in the range of 7.0x10(-7)-1.7x10(-4) M. The specificity of this sensing application for p-nitrophenyl substituent OPs has also been demonstrated. OPs are a class of synthetic organic pesticides which generally have a short residual life and can cause numerous acute and chronic health effects. They have been an integral part of the agricultural industry for the past several decades due to their target specificities and selectable toxicities. The toxic nature of these compounds can be attributed to the species-specific inhibition of acetylcholinesterase (AChE), an important enzyme responsible for the regeneration of neural synaptic function. In addition to their wide agricultural and urban usage, they have also been exploited for the development of neurological chemical warfare agents. Currently available technologies for OP detection include sol-gel thin films, screen printed electrodes, acoustic patterning, gas chromatography-mass spectrometry, and various other intricate techniques that have limited field applicabilities. This optically-based approach promises much simpler and more direct detection capabilities.

Enzyme-encapsulated silica monolayers for rapid functionalization of a gold surface

We report a simple and rapid method for the deposition of amorphous silica onto a gold surface. The method is based on the ability of lysozyme to mediate the formation of silica nanoparticles. A monolayer of lysozyme is deposited via non-specific binding to gold. The lysozyme then mediates the self-assembled formation of a silica monolayer. The silica formation described herein occurs on a surface plasmon resonance (SPR) gold surface and is characterized by SPR spectroscopy. The silica layer significantly increases the surface area compared to the gold substrate and is directly compatible with a detection system. The maximum surface concentration of lysozyme was found to be a monolayer of 2.6 ng/mm(2) which allowed the deposition of a silica layer of a further 2 ng/mm(2). For additional surface functionalization, the silica was also demonstrated to be a suitable matrix for immobilization of biomolecules. The encapsulation of organophosphate hydrolase (OPH) was demonstrated as a model system. The silica forms at ambient conditions in a reaction that allows the encapsulation of enzymes directly during silica formation. OPH was successfully encapsulated within the silica particles and a detection limit for the substrate, paraoxon, using the surface-encapsulated enzyme was found to be 20 microM.

Induction of cancer-specific cytotoxicity towards human prostate and skin cells using quercetin and ultrasound

Bioflavonoids, such as quercetin, have recently emerged as a new class of chemotherapeutic drugs for the treatment of various cancer types, but are marred by their low potency and poor selectivity. We report that a short application of low-frequency ultrasound selectively sensitises prostate and skin cancer cells against quercetin. Pretreatment of cells with ultrasound (20 kHz, 2 W cm⁻², 60 s) selectively induced cytotoxicity in skin and prostate cancer cells, while having minimal effect on corresponding normal cell lines. About 90% of the viable skin cancer cell population was lost within 48 h after ultrasound-quercetin (50 μM) treatment. Ultrasound reduced the LC₅₀ of quercetin for skin cancer cells by almost 80-fold, while showing no effect on LC₅₀ for nonmalignant skin cells.

A novel 70-kDa Triton X-114-soluble antigen of Plasmodium falciparum that contains interspecies-conserved epitopes

In order to identify novel conserved integral membrane and other membrane-associated proteins of Plasmodium falciparum, lambda gt11-P. falciparum DNA library phages were immunoscreened with convalescent-phase mouse sera and rabbit antiserum against Triton X-114-soluble proteins of P. falciparum. One recombinant phage clone, L857, reacted with both of the antibody probes. Insert DNA (857 bp long) in L857 was 69% dA+dT rich and hybridized to a fragment of 1800 bp from mung bean nuclease-digested P. falciparum genomic DNA. The cloned parasite DNA did not show notable sequence homology with any known protein gene. The L857-encoded polypeptide, p34 (M(r) 34 kDa) was expressed in bacteria, fused to glutathione S-transferase (GST). The fusion peptide, GST-p34 (M(r) 62 kDa), was recognized by immune serum against Triton X-114-soluble antigens of P. falciparum and was reactive with anti-P. falciparum, anti-Plasmodium yoelii, and anti-GST sera. Rabbit antiserum raised against the fusion peptide recognized a 70-kDa protein from lysates of P. falciparum cells and a putative homologous 100-kDa protein from lysates of P. yoelii. The rabbit serum anti-fusion peptide antibodies bound to acetone-fixed P. falciparum-infected erythrocytes and, in immunofluorescent antibody tests, produced a punctate pattern of fluorescence suggesting that the 70-kDa native protein is associated with an apical organelle of the parasite.

Disulfide bond assignments and secondary structure analysis of human and murine interleukin 10

Interleukin 10 (IL-10), which was first discovered by its ability to inhibit the synthesis of various cytokines, most notably gamma interferon, from Th1 helper cells, displays pleiotropic immunoregulatory properties. Human and murine IL-10 have a high amino acid sequence identity (ca. 73%) which includes the conservation of all four cysteine residues in human IL-10 and the first four out of five cysteine residues for murine IL-10. Chemical analysis was used to determine that both recombinant human and recombinant murine IL-10 contain two disulfide bonds. The disulfide pairs for each were determined by mass spectrometric and reversed-phase HPLC analysis of trypsin-derived polypeptide fragments. The disulfide bond assignments for both species were similar in that the first cysteine residue in the sequence paired with the third and the second paired with the fourth. The fifth cysteine in murine IL-10 was determined by chemical modification to be unpaired. Far-UV circular dichroism analysis indicated that the secondary structure of recombinant human and murine IL-10 are composed of ca. 60% alpha-helix. Reduction of the disulfide bonds structurally destabilized the protein and led to a structure containing only 53% alpha-helix. The reduced protein displayed no in vitro biological activity in a mast cell proliferation assay. These studies indicate that IL-10 is a highly alpha-helical protein containing two disulfide bonds, either one or both of which are critical for its structure and function. In addition, these properties suggest that this interesting cytokine may belong to the alpha helical cytokine class of hematopoietic ligands.

A simple and sensitive spectrophotometric method for the quantitative determination of solid supported amino groups

A simple and sensitive method for the quantitative determination of free amino groups on solid support is described. This approach is a modification of Ngo's [(1986) J. Biochem. Biophys. Methods 12, 349-354] method reported earlier. The method is based on the reaction of the solid support with an excess of 5'-O-(4,4'-dimethoxytrityl)-thymidine-3'-O-(2,4-dinitrophenyl) succinate (DTDS) in the presence of a catalytic amount of 4-dimethylaminopyridine. After removing the excess reagent, solid support is treated with perchloric acid to release 4,4'-dimethoxytrityl cation into the solution. The released 4,4'-dimethoxytrityl cation, which has a strong absorption at 498 nm (epsilon 498 = 70,000), is then determined spectrophotometrically. A comparative study of DTDS, N-succinimidyl-3-(2-pyridyldithio)propionate and 4,4-dimethoxytrityl chloride is also included. The method was found to be very useful to determine those amino groups which are available for functionalization of solid supports, especially, monitoring the functionalization of solid supports for affinity chromatography and synthesis of biopolymers.