Predicting the melting point of human C-type lysozyme mutants

A complete understanding of the relationships between protein structure and stability remains an open problem. Much of our insight comes from laborious experimental analyses that perturb structure via directed mutation. The glycolytic enzyme lysozyme is among the most well characterized proteins under this paradigm, due to its abundance and ease of manipulation. To speed up such analyses, efficient computational models that can accurately predict mutation effects are needed. We employ a minimal Distance Constraint Model (mDCM) to predict the stability of a series of lysozyme mutants (specifically, human wild-type C-type lysozyme and 14 point mutations). With three phenomenological parameters that characterize microscopic interactions, the mDCM parameters are determined by obtaining the least squares error between predicted and experimental heat capacity curves. The mutants are chemically and structurally diverse, but have been experimentally characterized under nearly identical thermodynamic conditions (pH, ionic strength, etc.). The parameters found from best fits to heat capacity curves for one or more lysozyme structures are subsequently used to predict the heat capacity on the remaining. We simulate a typical experimental situation, where prediction of relative stabilities in an untested mutated structure is based on known results as they accumulate. From the statistical significance of these simulations, we establish that the mDCM is a viable predictor for relative stability of protein mutants. Remarkably, using parameters from any single fitting yields an average percent error of 4.3%. Across the dataset, the mDCM reproduces experimental trends sufficiently well (R = 0.64) to be of practical value to experimentalists when making decisions about which mutations to invest time and funds for characterization.     

Forces mediating protein–protein interactions: a computational study of p53 “approaching” MDM2

The protein MDM2 forms a complex with the tumor suppressing protein p53 and targets it for proteolysis in order to down-regulate p53 in normal cells. Inhibition of this interaction is of therapeutic importance. Molecular dynamics simulations of the association between p53 and MDM2 have revealed mutual modulation of the two surfaces. Analysis of the simulations of the two species approaching each other in solution shows how long range electrostatics steers these two proteins together. The net electrostatics is controlled largely by a few cationic residues that surround the MDM2 binding site. There is an overall separation in electrostatics of MDM2 and p53 that are mutually complementary and drive association. Upon close approach, there is significant energetic strain as the charges are occluded from water (desolvated). However, the complexation is driven by packing interactions that lead to highly favorable van der Waals interactions. Although the complementarity of the electrostatics of the two surfaces is essential for the two partners to form a complex, steric collisions of Y100 and short ranged van der Waals interactions of F19, W23, L26 of p53 determine the final steps of native complex formation. The electrostatics seem to be evolutionarily conserved, including variations in both partners.     

Chemical investigation of the essential oil of Thymus linearis (Benth. ex Benth) from western Himalaya, India

Thymus linearis (Benth. ex Benth) was collected from five distinct locations of western Himalaya (India) during the summer season. The hydro-distilled essential oil (yield 0.84-0.95%) was analysed by gas chromatography (GC) and gas chromatography-mass spectrometry (GC-MS). A total of 56 constituents, representing 81.55% to 98.11% of the total oil composition, were identified. Thymol (52.28-66.65%), p-cymene (1.81-21.60%) and γ-terpinene (1.94-12.48%) were the major constituents in all populations. Other constituents identified in significant amounts were carvacrol, p-cymen-8-ol, borneol, terpinen-4-ol and thymol methyl ether. The presence of high phenol and essential oil contents in this species make it a suitable substitute for common thyme oil.     

Molecular-imprinted polymer extraction combined with dispersive liquid-liquid micro-extractionfor ultra-preconcentration of mononitrotoluene

Molecular-imprinted polymer (MIP) combined with dispersive liquid-liquid micro-extraction (DLLME) were developed for ultra-preconcentration and determination of mononitrotoluenes in wastewater samples using gas chromatography-flame ionization detector. MIP was synthesized by copolymerization of methacrylic acid-ethylene glycole dimethacrylate-2,2-azobisisobutyronitrile as the initiator that imprinted with 3-nitrotoluene as the template molecule. Effects of several factors, such as type and volume of eluent, adsorption, and desorption times of the analyte on the polymer, and breakthrough volume were investigated. Optimization of 3-nitrotoluene extraction from MIP was studied forward followed by DLLME. Preconcentration factor of MIP-DLLME method was about 2800 under the optimum conditions. The LOD of the proposed method was 0.02?μg/L and a linear dynamic range in the range of 0.04-20?μg/L was obtained. The performance of the present method was evaluated for extraction and determination of nitrotoluene compounds in wastewater samples in the range of microgram per liter and satisfactory results were achieved (RSD<13%).     

Determination of k 0-factors and validation of k 0-INAA for short-lived nuclides

For standardization of k ₀-based instrumental neutron activation analysis, k ₀-factors for short-lived nuclides (half-lives—11 s to 37 min) of elements F, Se, Sc, Al, V, Ti, Cu, Ca, Mg, I, and Cl with respect to gold (¹⁹⁷Au) were determined using pneumatic carrier facility (PCF) at CIRUS reactor of BARC, Mumbai. Characterization of PCF was carried out by cadmium-ratio method using Au and Zr. The experimental k ₀-factors of the isotopes were found to be in good agreement with the recommended k ₀-factors in most of the cases, as evident from the values of % error and U-score at 95% confidence level. The method was validated by determining concentrations of elements through their short-lived nuclides in one type of the synthetic multielement standards (SMELS-I) obtained from SCK-CEN, Belgium. The method was also applied for determination of concentrations of some of the elements in two reference materials of IAEA, SL-3, and SL-1.     

Luminescent Quantum Clusters of Gold in Bulk by Albumin‐Induced Core Etching of Nanoparticles: Metal Ion Sensing,Metal‐Enhanced Luminescence,and Biolabeling

The synthesis of a luminescent quantum cluster (QC) of gold with a quantum yield of ～4 % is reported. It was synthesized in gram quantities by the core etching of mercaptosuccinic acid protected gold nanoparticles by bovine serum albumin (BSA), abbreviated as Au_QC@BSA. The cluster was characterized and a core of Au₃₈ was assigned tentatively from mass spectrometric analysis. Luminescence of the QC is exploited as a “turn‐off” sensor for Cu²⁺ ions and a “turn‐on” sensor for glutathione detection. Metal‐enhanced luminescence (MEL) of this QC in the presence of silver nanoparticles is demonstrated and a ninefold maximum enhancement is seen. This is the first report of the observation of MEL from QCs. Folic acid conjugated Au_QC@BSA was found to be internalized to a significant extent by oral carcinoma KB cells through folic acid mediated endocytosis. The inherent luminescence of the internalized Au_QC@BSA was used in cell imaging.     

The Effect of Heavy Atoms on Photoinduced Electron Injection from Nonthermalized and Thermalized Donor States of MII–Polypyridyl (M=Ru/Os) Complexes to Nanoparticulate TiO2 Surfaces: An Ultrafast Time‐Resolved Absorption Study

We have synthesized ruthenium(II)– and osmium(II)–polypyridyl complexes ([M(bpy)₂ L ]²⁺, in which M=Os^II or Ru^II, bpy=2,2′‐bipyridyl, and L =4‐(2,2′‐bipyridinyl‐4‐yl)benzene‐1,2‐diol) and studied the interfacial electron‐transfer process on a TiO₂ nanoparticle surface using femtosecond transient‐absorption spectroscopy. Ruthenium(II)‐ and osmium(II)‐based dyes have a similar molecular structure; nevertheless, we have observed quite different interfacial electron‐transfer dynamics (both forward and backward). In the case of the Ru^II/TiO₂ system, single‐exponential electron injection takes place from photoexcited nonthermalized metal‐to‐ligand charge transfer (MLCT) states. However, in the case of the Os^II/TiO₂ system, electron injection takes place biexponentially from both nonthermalized and thermalized MLCT states (mainly ³MLCT states). Larger spin–orbit coupling for the heavier transition‐metal osmium, relative to that of ruthenium, accounts for the more efficient population of the ³MLCT states in the Os^II‐based dye during the electron‐injection process that yields biexponential dynamics. Our results tend to suggest that appropriately designed Os^II–polypyridyl dye can be a better sensitizer molecule relative to its Ru^II analogue not only due to much broader absorption in the visible region of the solar‐emission spectrum, but also on account of slower charge recombination.     

A Physiologically Regulated Multidomain Cystatin of Wheat Shows Stage-Dependent Immunity Against Karnal Bunt (Tilletia indica)

To identify novel components of basal resistance against the Tellitia indica of wheat, breeding for disease resistance was carried out on resistant and susceptible genotype of Karnal Bunt. The different members of wheat cystatin gene families were cloned, and their role in triggering differential resistance through co-expression was analyzed in our lab. The multidomain wheat cystatin (WCM) is a proteinase inhibitor characterized by cloning the gene from susceptible (WH542) and resistant genotype (HD 29). A WCM cDNA was isolated from both genotypes and sequenced. The WCM had a highly conserved N-terminal cystatin domain and a long C-terminal extension containing a second region, which exhibited similarity to the cystatin domain. The expression level was significantly (P?>?0.001) higher in resistant compared to susceptible genotype at all the physiological stages of wheat spikes. In order to characterize the biochemical properties of WCM, the coding sequence was expressed in Escherichia coli using pET expression vector. The recombinant WCM was purified from soluble fraction of the cell extract by using affinity chromatography. WCM, with 23 KDa molecular mass, showed cysteine proteinase inhibitory activity against papain (Ki 3.039?×?10^?7?M) as determined by using BAPNA as substrate. Furthermore, it was able to arrest the fungal mycelial growth of T. indica. Hyphae growth was inhibited, and morphological changes such as swelling and fragmentation of the fungus were observed. Overall, these observations suggest an endogenous high expression of cystatin, possibly associated with the resistance of wheat against Karnal bunt.     

High pressure studies on the electrical resistivity of As–Te–bond Si glasses and the effect of network topological thresholds

The variation of resistivity in an amorphous As₃₀Te_70?x Si _x system of glasses with high pressure has been studied for pressures up to 8 GPa. It is found that the electrical resistivity and the conduction activation energy decrease continuously with increase in pressure, and samples become metallic in the pressure range 1.0–2.0 GPa. Temperature variation studies carried out at a pressure of 0.92 GPa show that the activation energies lie in the range 0.16–0.18 eV. Studies on the composition/average co-ordination number ? r? dependence of normalized electrical resistivity at different pressures indicate that rigidity percolation is extended, the onset of the intermediate phase is around ? r?=2.44, and completion at ? r?=2.56, respectively, while the chemical threshold is at ? r?=2.67. These results compare favorably with those obtained from electrical switching and differential scanning calorimetric studies.     

Hybrid inexact proximal point algorithms based on RMM frameworks with applications to variational inclusion problems

A new application-oriented notion of relatively A-maximal monotonicity (RMM) framework is introduced, and then it is applied to the approximation solvability of a general class of inclusion problems, while generalizing other existing results on linear convergence, including Rockafellar’s theorem (1976) on linear convergence using the proximal point algorithm in a real Hilbert space setting. The obtained results not only generalize most of the existing investigations, but also reduce smoothly to the case of the results on maximal monotone mappings and corresponding classical resolvent operators. Furthermore, our proof approach differs significantly to that of Rockafellar’s celebrated work, where the Lipschitz continuity of M ^?1, the inverse of M:X→2 ^X , at zero is assumed to achieve a linear convergence of the proximal point algorithm. Note that the notion of relatively A-maximal monotonicity framework seems to be used to generalize the classical Yosida approximation (which is applied and studied mostly based on the classical resolvent operator in the literature) that in turn can be applied to first-order evolution equations as well as evolution inclusions.