Computational Design of Novel Allosteric Inhibitors for Plasmodium falciparum DegP

The serine protease, DegP exhibits proteolytic and chaperone activities, essential for cellular protein quality control and normal cell development in eukaryotes. The P. falciparum DegP is essential for the parasite survival and required to combat the oscillating thermal stress conditions during the infection, protein quality checks and protein homeostasis in the extra-cytoplasmic compartments, thereby establishing it as a potential target for drug development against malaria. Previous studies have shown that diisopropyl fluorophosphate (DFP) and the peptide SPMFKGV inhibit E. coli DegP protease activity. To identify novel potential inhibitors specific to PfDegP allosteric and the catalytic binding sites, we performed a high throughput in silico screening using Malaria Box, Pathogen Box, Maybridge library, ChEMBL library and the library of FDA approved compounds. The screening helped identify five best binders that showed high affinity to PfDegP allosteric (T0873, T2823, T2801, {"type":"entrez-protein","attrs":{"text":"RJC02337","term_id":"1480409465","term_text":"RJC02337"}}RJC02337, CD00811) and the catalytic binding site (T0078L, T1524, T2328, BTB11534 and 552691). Further, molecular dynamics simulation analysis revealed {"type":"entrez-protein","attrs":{"text":"RJC02337","term_id":"1480409465","term_text":"RJC02337"}}RJC02337, BTB11534 as the best hits forming a stable complex. WaterMap and electrostatic complementarity were used to evaluate the novel bio-isosteric chemotypes of {"type":"entrez-protein","attrs":{"text":"RJC02337","term_id":"1480409465","term_text":"RJC02337"}}RJC02337, that led to the identification of 231 chemotypes that exhibited better binding affinity. Further analysis of the top 5 chemotypes, based on better binding affinity, revealed that the addition of electron donors like nitrogen and sulphur to the side chains of butanoate group are more favoured than the backbone of butanoate group. In a nutshell, the present study helps identify novel, potent and Plasmodium specific inhibitors, using high throughput in silico screening and bio-isosteric replacement, which may be experimentally validated.     

Investigation of annealing effects on the structural, magnetic and transport properties of Co/GaAs(0 0 1) thin films

Present paper deals with the structural, magnetic and transport studies of as-deposited as well as annealed Co/GaAs(0 0 1) thin film at different temperatures. The X-ray diffraction measurements show oriented growth of as-deposited Co film in the hcp (0 0 2) direction. However, the sample annealed at higher temperatures shows formation of ternary Co₂GaAs phase at the interface. Corresponding magnetic and transport measurements show decrement in magnetization and resistivity with annealing temperatures. The observed reductions in magnetization and resistivity values are mainly attributed to the formation of ternary Co₂GaAs phase at the interface.     

High temperature annealing effect on structural and magnetic properties of Ti/Ni multilayers

High temperature annealing effect on structural and magnetic properties of Ti/Ni multilayer (ML) up to 600 °C have been studied and reported in this paper. Ti/Ni multilayer samples having constant layer thicknesses of 50 Å each are deposited on float glass and Si(1 1 1) substrates using electron-beam evaporation technique under ultra-high vacuum (UHV) conditions at room temperatures. The micro-structural parameters and their evolution with temperature for as-deposited as well as annealed multilayer samples up to 600 °C in a step of 100 °C for 1 h are determined by using X-ray diffraction (XRD) and grazing incidence X-ray reflectivity techniques. The X-ray diffraction pattern recorded at 300 °C annealed multilayer sample shows interesting structural transformation (from crystalline to amorphous) because of the solid-state reaction (SSR) and subsequent re-crystallization at higher temperatures of annealing, particularly at ≥400 °C due to the formation of TiNi₃ and Ti₂Ni alloy phases. Sample quality and surface morphology are examined by using atomic force microscopy (AFM) technique for both as-deposited as well as annealed multilayer samples. In addition to this, a temperature dependent dc resistivity measurement is also used to study the structural transformation and subsequent alloy phase formation due to annealing treatment. The corresponding magnetization behavior of multilayer samples after each stage of annealing has been investigated by using Magneto-Optical Kerr Effect (MOKE) technique and results are interpreted in terms of observed micro-structural changes.     

An automated laboratory EXAFS spectrometer of Johansson type: indigenous development and testing

An automated linear laboratory EXAFS spectrometer of the Johansson type has been indigenously developed. Only two translational motions are required to achieve the necessary Rowland circle configuration for the (fixed) X-ray source, the dispersing and focusing bent crystal and the receiving slit. With the available crystals the spectral region from 5 to 25 keV can be scanned. The linear motions of the crystal and receiving slit including the detector assembly are achieved by employing software-controlled DC motors and utilizing optical encoders for position sensing. The appropriate rotation of the crystal is achieved by the geometry of the instrument. There is a facility to place the sample alternately in the path of the X-ray beam and out of the path to record both the incident X-ray intensityI ₀ and the transmitted intensityI employing the scintillation detector. An arrangement with a two-window proportional detector before the sample to measureI ₀ and the scintillation detector to recordI is also developed; in this case it is not necessary to oscillate the sample. Fast electronic circuits are employed to minimize counting errors. The instrument is user-friendly and it is operated through a menu-driven IBM compatible PC. EXAFS spectra of high resolution have been recorded using the spectrometer and employing the Si(111) reflecting planes; the X-ray source being a Rigaku 12 kW rotating anode with Cu target. We describe the spectrometer and discuss its performance with a few representative spectra.     

Deformations of complex structures on Γ/SL 2(C)

LetG be a connected complex semisimple Lie group. Let Γ be a cocompact lattice inG. In this paper, we show that whenG isSL ₂(C), nontrivial deformations of the canonical complex structure onX exist if and only if the first Betti number of the lattice Γ is non-zero. It may be remarked that for a wide class of arithmetic groups Γ, one can find a subgroup Γ′ of finite index in Γ, such that Γ′/[Γ′,Γ′] is finite (it is a conjecture of Thurston that this is true for all cocompact lattices inSL(2, C)). We also show thatG acts trivially on the coherent cohomology groupsH ⁱ(Γ/G, O) for anyi≥0.     

Cyclic networks with general blocking and starvation

We introducegeneral starvation and consider cyclic networks withgeneral blocking and starvation (GBS). The mechanism of general blocking allows the server to process a limited number of jobs when the buffer downstream is full, and that of general starvation allows the server to perform a limited number of services in anticipation of jobs that are yet to arrive. The two main goals of this paper are to investigate how the throughput of cyclic GBS networks is affected by varying (1) the total number of jobsJ, and (2) the buffer allocationk=(k₁..., k_m) subject to a fixed total buffer capacityK=k ₁ +... + k_m. In particular, we obtain sufficient conditions for the throughput to be symmetric inJ and to be maximized whenJ=K/2. We also show that the equal buffer allocation is optimal under the two regimes of light or heavy usage. In order to establish these results, we obtain several intermediate structural properties of the throughput, using duality, reversibility, and concavity, which are of independent interest.Research supported in part by NSF Grant No. ECS-8919818.