SH3-like fold proteins are structurally conserved and functionally divergent

The folding space for all the protein sequences is limited. Therefore it was observed that many proteins, whose sequences are not related, have similar fold characteristics. The fold databases like SCOP and CATH have classified various protein folds. However, in-depth analysis of the functional features of these folds was not done. We analyzed about twenty unique SH3-like folded proteins in their structural environment and functional characteristics. From our analysis it is apparent that the SH3-like folds could carry out various functions by modulation of loops and the functional region is restricted to one side of a particular sheet helped by two or three loops. The functions vary from oligonucleotide-binding to peptide-binding and other ligand binding. Although certain degree of sequence similarity was observed among the SH3-fold proteins, the similarity was restricted to the beta-strand regions of the proteins.     

Modular forms and ellipsoidal T-designs

The Ramanujan Journal - In recent work, Miezaki introduced the notion of a spherical T-design in $$\mathbb {R}^2$$ , where T is a potentially infinite set. As an example, he offered the $$\mathbb...     

DNA as a bioligand supported on magnetite for grafting palladium nanoparticles for cross-coupling reaction

The utilization of deoxyribonucleic acid (DNA) in nanotechnology is a promising area of research wherein the distinct properties of DNA are exploited for the design and development of new materials and applications. The biodegradability and natural profusion of DNA makes it highly suitable for use in various fields. In this report, we have treated DNA as a bioligand, supported on functionalized magnetite for the grafting of palladium (Pd) nanoparticles to make Pd-DNA bio-nanocatalyst. The Pd-DNA was subjected to Fourier-transform infrared spectroscopy, field-emission scanning electron microscopy, transmission electron microscopy, X-ray powder diffraction, Brunauer–Emmett–Teller, energy dispersive X-ray spectroscopy, vibrating sample magnetometry, X-ray photoelectron spectroscopy, and inductively coupled plasma optical emission spectrometry analysis. The prepared Pd-DNA was found to be highly efficient in catalyzing Suzuki–Miyaura cross-coupling reaction with excellent yields when compared with commercially available palladium-based catalysts. Also, the Pd-DNA could be easily recovered from the reaction mass using an external magnet and recycled up to six times without substantial loss of activity. Furthermore, Felbinac, a non-inflammatory drug, was synthesized in quantitative yields using the Pd-DNA bio-nanocatalyst.     

Homologation and alkylation of boronic esters and boranes by 1,2‐metallate rearrangement of boron ate complexes

Organoboranes and boronic esters readily undergo nucleophilic addition, and if the nucleophile also bears an α‐leaving group, 1,2‐metallate rearrangement of the ate complex results. Through such a process a carbon chain can be extended, usually with high stereocontrol and this is the focus of this review. A chiral boronic ester (substrate control) can be used for stereocontrolled homologations with (dichloromethyl)lithium in the presence of ZnCl₂. Subsequent alkylation by an organometallic reagent also occurs with high levels of stereocontrol. Chiral lithiated carbanions (reagent control) can also be used for the reaction sequence with achiral boronic esters and boranes. Aryl‐stabilized sulfur ylide derived chiral carbanions can be homologated with a range of boranes including vinyl boranes in good yield and high diastereo‐ and enantioselectivity. Lithiated alkyl chlorides react with boronic esters, again with high stereocontrol, but both sets of reactions are limited in scope. Chiral lithiated carbamates show the greatest substrate scope and react with both boronic esters and boranes with excellent enantioselectivity. Furthermore, iterative homologation with chiral lithiated carbamates allows carbon chains to be “grown” with control over relative and absolute stereochemistry. The factors responsible for stereocontrol are discussed. © 2009 The Japan Chemical Journal Forum and Wiley Periodicals, Inc. Chem Rec 9: 24–39; 2009: Published online in Wiley InterScience ( www.interscience.wiley.com ) DOI 10.1002/tcr.20168     

Using massively parallel simulation and Markovian models to study protein folding: examining the dynamics of the villin headpiece

We report on the use of large-scale distributed computing simulation and novel analysis techniques for examining the dynamics of a small protein. Matters addressed include folding rate, very long time scale kinetics, ensemble properties, and interaction with water. The target system for the study, the villin headpiece, has been of great interest to experimentalists and theorists both. Sampling totaled nearly 500 mus-the most extensive published to date for a system of villin's size in explicit solvent with all atom detail-and was in the form of tens of thousands of independent molecular dynamics trajectories, each several tens of nanoseconds in length. We report on kinetics sensitivity analyses that, using a set of short simulations, probed the role of water in villin's folding and sensitivity to the simulation's electrostatics treatment. By constructing Markovian state models (MSMs) from the collected data, we were able to propagate dynamics to times far beyond those directly simulated and to rapidly compute mean first passage times, long time kinetics (tens of microseconds), and evolution of ensemble property distributions over long times, otherwise currently impossible. We also tested our MSM by using it to predict the structure of villin de novo.     

Total synthesis and initial biological evaluation of new B-ring-modified bryostatin analogs

[Structure: see text] The total synthesis and preliminary biological evaluation of the first bryostatin analogs (bryologs) to incorporate B-ring substitution are reported. Asymmetric syntheses of two new polyketide "spacer" domains are described, one exploiting the pseudosymmetry of the C1-C13 region. These fragments are convergently joined to the "recognition" domain through a remarkably versatile macrotransacetalization process. The resulting new analogs exhibit potent nanomolar or picomolar affinity to protein kinase C (PKC), comparable to or better than that found for bryostatin.     

Anticancer Properties of Highly Purified l-Asparaginase from Withania somnifera L. against Acute Lymphoblastic Leukemia

Withania somnifera L. has been traditionally used as a sedative and hypnotic. The present study was carried out for the purification, characterization, and in vitro cytotoxicity of l-asparaginase from W. somnifera L. l-Asparaginase was purified from the fruits of W. somnifera L. up to 95% through chromatography. The purified l-asparaginase was characterized by size exclusion chromatography, polyacrylamide gel electrophoresis (PAGE), and 2D PAGE. The antitumor and growth inhibition effect of the l-asparaginase was assessed using [3-(4, 5-dimethyl-thiazol-2yl)-2, 5-diphenyl-tetrazolium bromide] (MTT) colorimetric dye reduction method. The purified enzyme is a homodimer, with a molecular mass of 72 ± 0.5 kDa, and the pI value of the enzyme was around 5.1. This is the first report of the plant containing l-asparaginase with antitumor activity. Data obtained from the MTT assay showed a LD₅₀ value of 1.45 ± 0.05 IU/ml. W. somnifera L. proved to be an effective and a novel source of l-asparaginase. Furthermore, it shows a lot of similarity with bacterial l-asparaginases EC-2.