Predicting the Impact of Deleterious Mutations in the Protein Kinase Domain of FGFR2 in the Context of Function, Structure, and Pathogenesis—a Bioinformatics Approach

Fibroblast growth factor receptor 2 (FGFR2) controls a wide range of biological functions by regulating the cellular proliferation, survival, migration and differentiation. A growing body of preclinical data demonstrated that deregulation of the FGFR signalling through genetic modification was observed in various types of cancers. However, the extent to which genetic modifications interfere with gene regulation and their involvement in cancer susceptibility remains largely unknown. In this work, we performed in silico profiling of harmful non-synonymous single nucleotide polymorphisms (SNPs) in the protein kinase domain of FGFR2. Tolerance index, position-specific independent count score, change in free energy score (ΔΔG), Eris and FoldX indicated that seven mutations were found to be deleterious and may alter the protein function and structure. Furthermore, based on physico-chemical properties, two mutations K659N and R747H were found to be most deleterious in protein kinase domain and taken for further structural analysis. Docking study showed a complete loss of binding affinity followed by interference in hydrogen bonding and surrounding residues due to K659N and R747H mutations. In order to elucidate the mechanism behind the impact of mutation that can generate a ripple effect throughout the protein structure and ultimately affect the function, in-depth molecular dynamics simulation and principal component analysis were performed. The obtained results indicate that K659N and R747H mutations have a distinct effect on the dynamic behaviour of FGFR2 protein. Our strategy may be helpful for understanding SNP effects on proteins with function and their role in human genetic diseases and for the development of novel pharmacological strategies.     

Electric field induced switching of poly(ethylene glycol) terminated self-assembled monolayers: a parallel molecular dynamics simulation

Effects of electric field on the structure of poly(ethylene glycol) (PEG) terminated alkanethiol self-assembled monolayer (SAM) on gold have been studied using parallel molecular dynamics method. An applied electric field triggers a conformational transition from all-trans to a mostly gauche conformation. The polarity of the electric field has a significant effect on the surface structure of PEG leading to a profound effect on the hydrophilicity of the surface. The electric field applied antiparallel to the surface normal causes a reversible transition to an ordered state in which the oxygen atoms are exposed. On the other hand, an electric field applied in a direction parallel to the surface normal introduces considerable disorder in the system and the oxygen atoms are buried inside. The parallel field affects the overall tilt structure of SAMs more adversely than the antiparallel field.     

Isolation,Purification and Characterisation of an Organic Solvent-Tolerant Ca2+-Dependent Protease from Bacillus megaterium AU02

A new organic solvent-tolerant strain Bacillus megaterium AU02 which secretes an organic solvent-tolerant protease was isolated from milk industry waste. Statistical methods were employed to achieve optimum protease production of 43.6 U/ml in shake flask cultures. The productivity of the protease was increased to 53 U/ml when cultivated under controlled conditions in a 7-L fermentor. The protease was purified to homogeneity by a three-step process with 24 % yield and specific activity of 5,375 U/mg. The molecular mass of the protease was found to be 59 kDa. The enzyme was active over a wide range of pH (6.0–9.0), with an optimum activity at pH 7.0 and temperature from 40 to 70 °C having an optimum activity at 50 °C. The thermal stability of the enzyme increased significantly in the presence of CaCl₂, and it retained 90 % activity at 50 °C for 3 h. The K _m and V _max values were determined as 0.722 mg/ml and 0.018 U/mg respectively. The metalloprotease exhibited significant stability in the presence of organic solvents with log P values more than 2.5, nonionic detergents and oxidising agent. An attempt was made to test the synthesis of aspartame precursor (Cbz-Asp-Phe-NH₂) which was catalysed by AU02 protease in the presence of 50 % DMSO. These properties of AU02 protease make it an ideal choice for enzymatic peptide synthesis in organic media.     

Isolation and Identification of α-Glucosidase and Protein Glycation Inhibitors from Stereospermum colais

Stereospermum colais (family Bignoniaceae) is a well-known pharmacologically potent medicinal plant reported in traditional systems of medicine. Phytochemical investigation of the roots of S. colais resulted in the isolation of seven compounds, and the metabolites were screened for its α-glucosidase enzyme inhibition and anti-glycation property. The compounds identified were β-sitosterol (1), 2-(4′-hydroxyphenyl) ethyl undecanoate (2), 2-(4′-hydroxyphenyl)ethyl pentadecanoate (3), 5α-ergosta-7,22-dien-3β-ol (4), ursolic acid (5), lapachol (6), and pinoresinol (7). Ursolic acid, lapachol, and pinoresinol possessed IC₅₀ values of 119.01, 130.29, and 125.62 nM, respectively, compared to standard ascorbic acid with an IC₅₀ value of 201.01 nM. The other compounds failed to show the activity. Results of the current study showcased the possible exploration of this medicinal plant for the treatment of type 2 diabetes in line with the development of phytopharmaceutical industry.     

TDCR measurements of 3H, 63Ni and 55Fe using Hidex 300SL LSC device

The commercial Hidex LSC system has been used to measure triple to double coincidence ratio (TDCR), experimental counting efficiency (CE) and the absolute activity for radioactive standards of pure beta emitters viz. ³H, ⁶³Ni and ⁵⁵Fe, an electron capture nuclide. Colour and chemical quench measurements of ⁶³Ni and ⁵⁵Fe have been done. An excellent match between TDCR and CE has been obtained for beta emitters, while very large deviations have been observed for ⁵⁵Fe. The deviation between TDCR and experimental efficiency has been found to be nearly uniform. Based on this, an empirical correction factor for TDCR which gives the correct efficiency has been evaluated, to enable efficient application of this commercial instrument for ⁵⁵Fe estimation. These TDCR correction factors were further validated by applying for ⁵⁵Fe activity measurements in ASTM standard steel samples irradiated to a fixed neutron flux in research reactor CIRUS. Finally, ⁵⁵Fe activity in steel sample from APSARA reactor decommissioning waste was successfully estimated using this modified TDCR.     

Growth of gold nanoparticles in human cells

Gold nanoparticles of 20-100 nm diameter were synthesized within HEK-293 (human embryonic kidney), HeLa (human cervical cancer), SiHa (human cervical cancer), and SKNSH (human neuroblastoma) cells. Incubation of 1 mM tetrachloroaurate solution, prepared in phosphate buffered saline (PBS), pH 7.4, with human cells grown to approximately 80% confluency yielded systematic growth of nanoparticles over a period of 96 h. The cells, stained due to nanoparticle growth, were adherent to the bottom of the wells of the tissue culture plates, with their morphology preserved, indicating that the cell membrane was intact. Transmission electron microscopy of ultrathin sections showed the presence of nanoparticles within the cytoplasm and in the nucleus, the latter being much smaller in dimension. Scanning near field microscopic images confirmed the growth of large particles within the cytoplasm. Normal cells gave UV-visible signatures of higher intensity than the cancer cells. Differences in the cellular metabolism of cancer and noncancer cells were manifested, presumably in their ability to carry out the reduction process.     

Asymmetric Modulation of Protein Order–Disorder Transitions by Phosphorylation and Partner Binding

As for many intrinsically disordered proteins, order–disorder transitions in the N‐terminal oligomerization domain of the multifunctional nucleolar protein nucleophosmin (Npm‐N) are central to its function, with phosphorylation and partner binding acting as regulatory switches. However, the mechanism of this transition and its regulation remain poorly understood. In this study, single‐molecule and ensemble experiments revealed pathways with alternative sequences of folding and assembly steps for Npm‐N. Pathways could be switched by altering the ionic strength. Phosphorylation resulted in pathway‐specific effects, and decoupled folding and assembly steps to facilitate disorder. Conversely, binding to a physiological partner locked Npm‐N in ordered pentamers and counteracted the effects of phosphorylation. The mechanistic plasticity found in the Npm‐N order–disorder transition enabled a complex interplay of phosphorylation and partner‐binding steps to modulate its folding landscape.     

Unsteady state mathematical model of chemically reactive pollutants from an instantaneous line source into a stable atmospheric boundary layer

A time dependent atmospheric model represented for chemically reactive primary pollutants emitted from an elevated line source into a stable atmospheric boundary layer over a surface terrain. The model obtained from an analytical solution of the atmospheric diffusion equation with the quadratic diffusion coefficient (exchange coefficient) and the variable wind velocity taken to be of three different types’ viz. constant, constant shear and parabolic functions of vertical height. The pollutants considered to be of chemically reactive primary pollutants emitted from a time-dependent line source of Instantaneous type. In order to facilitate the application of the model the results for the general situation that includes chemical reaction rate & time dependent source incorporated in the model.     

Modulation of Kinetic Pathways of Enzyme–Substrate Interaction in a Microfluidic Channel: Nanoscopic Water Dynamics as a Switch

Enzyme-mediated catalysis is attributed to enzyme–substrate interactions, with models such as “induced fit” and “conformational selection” emphasizing the role of protein conformational transitions. The dynamic nature of the protein structure, thus, plays a crucial role in molecular recognition and substrate binding. As large-scale protein motions are coupled to water motions, hydration dynamics play a key role in protein dynamics, and hence, in enzyme catalysis. Here, microfluidic techniques and time-dependent fluorescence Stokes shift (TDFSS) measurements are employed to elucidate the role of nanoscopic water dynamics in the interaction of an enzyme, α-Chymotrypsin (CHT), with a substrate, Ala-Ala-Phe-7-amido-4-methylcoumarin (AMC) in the cationic reverse micelles of benzylhexadecyldimethylammonium chloride (BHDC/benzene) and anionic reverse micelles of sodium bis(2-ethylhexyl)sulfosuccinate (AOT/benzene). The kinetic pathways unraveled from the microfluidic setup are consistent with the “conformational selection” fit for the interaction of CHT with AMC in the cationic reverse micelles, whereas an “induced fit” mechanism is indicated for the anionic reverse micelles. In the cationic reverse micelles of BHDC, faster hydration dynamics (≈550 ps) aid the pathway of “conformational selection”, whereas in the anionic reverse micelles of AOT, the significantly slower dynamics of hydration (≈1600 ps) facilitate an “induced fit” mechanism for the formation of the final enzyme–substrate complex. The role of water dynamics in dictating the mechanism of enzyme–substrate interaction becomes further manifest in the neutral reverse micelles of Brij-30 and Triton X-100. In the former, the faster water dynamics aid the “conformational selection” pathway, whereas the significantly slower dynamics of water molecules in the latter are conducive to the “induced fit” mechanism in the enzyme–substrate interaction. Thus, nanoscopic water dynamics act as a switch in modulating the pathway of recognition of an enzyme (CHT) by the substrate (AMC) in reverse micelles.