Integrating Rigidity Analysis into the Exploration of Protein Conformational Pathways Using RRT* and MC

To understand how proteins function on a cellular level, it is of paramount importance to understand their structures and dynamics, including the conformational changes they undergo to carry out their function. For the aforementioned reasons, the study of large conformational changes in proteins has been an interest to researchers for years. However, since some proteins experience rapid and transient conformational changes, it is hard to experimentally capture the intermediate structures. Additionally, computational brute force methods are computationally intractable, which makes it impossible to find these pathways which require a search in a high-dimensional, complex space. In our previous work, we implemented a hybrid algorithm that combines Monte-Carlo (MC) sampling and RRT*, a version of the Rapidly Exploring Random Trees (RRT) robotics-based method, to make the conformational exploration more accurate and efficient, and produce smooth conformational pathways. In this work, we integrated the rigidity analysis of proteins into our algorithm to guide the search to explore flexible regions. We demonstrate that rigidity analysis dramatically reduces the run time and accelerates convergence.     

68Ga-5, 10, 15, 20-Tetrakis (2, 4, 6-trimethoxy phenyl) porphyrin: a novel radio-labeled porphyrin complex for positron emission tomography

Journal of Radioanalytical and Nuclear Chemistry - Porphyrins and 68Ga have emerged as novel synergic options for PET applications so the idea of preparation of a novel porphyrin complex using this...     

Nanofluid flow in a catheterized tapered artery

Journal of Thermal Analysis and Calorimetry - This study was conducted with the aim of investigating the Newtonian nanofluid flow in a catheterized tapered artery through using a completely...     

An enaminone-directed benzannulation/macrocyclization approach to cyclophane ring systems

A straightforward and modular preparative approach to 1,3,5-triaroylbenzene-based functionalized cyclophane ring systems has been developed. The key cyclophane-forming macrocyclization reaction was accomplished during the course of a regioselective cross-benzannulation between bis(aryl ethynyl) ketone and enaminone reactants. Macrocyclic products with ring sizes ranging from 18- to 22-membered were successfully constructed. The composition of the tether connecting the two aryl ethynyl ketone fragments can be easily varied; consequently, this method is suitable for construction of a diverse range of structurally distinct cyclophane products. To illustrate this feature, cyclophanes possessing xylyl, alkyl, di(ethylene triamine), and di(ethylene oxy) bridging units were synthesized in isolated yields of 11-46%. Three new cyclophanes (calixarene-like macrocyles 8 and 9, as well as crownophane 18) were structurally characterized by X-ray diffractometry.     

The extent of molecular orientation at liquid/vapor interface of pyridine and its alkyl derivatives by molecular dynamics simulation

In this paper, molecular dynamics simulation was performed to investigate the liquid∕vapor interfacial structure of neat polar liquids. Large-scale ensembles of liquid pyridine and its alkyl derivatives, 4-methylpyridine and 4-ethylpyridine, were simulated by classical molecular dynamics at 298 K. For the liquid system of low polarity, the surface density profile of the atoms meet exactly at the middle of interfacial region, and atoms of hydrophobic nature can be hardly discriminated from hydrophilic ones in either vapor or liquid sides. For a liquid system of high polarity, the density profile of atoms with different nature is highly discriminated all over the interfacial region, and as the polarity increases, a dense region of atomic density is clearly developed in the subsurface region. The recognized bivariate method was also used to study the molecular orientational distribution quantitatively. Orientational analysis of the three liquid systems indicates that the pyridine ring plane in the outmost surface tends to be vertical. Its tendency in the innermost interfacial region is parallel. The orientational states available to 4-ethylpyridine and pyridine are discriminated by predicting the possibility of a bisector-wise tumbling for the ring plane in pyridine and a side-wise tumbling in 4-ethylpyridine. The orientational distribution maps explain the trend of experimental surface tension and surface entropy. As the dipole moment of these liquids increases with the alkyl chain length, the surface structural profile changes from a regular definite one to a surface of complex atomic structure involving a dense phase near the interface. The development of dense region in alkyl derivatives is the result of segregation of molecules due to the alkyl group, which is captured and discriminated by molecular dynamics simulation even when the length of a short alkyl chain is increased by one carbon atom.     

Determination of the effective atomic and mass numbers for mixture and compound materials in high energy photon interactions

In consideration the radiological properties of materials and studying the scattering processes in atomic and nuclear physics, the effective atomic and mass numbers is widely employed. These numbers have been calculated for any mixed or composite materials in interaction with high energy photons (Linac in radiation therapy). A pair equation in terms of these numbers is obtained. The first equation has been derived from the conservation of mass energy law and the second by minimizing the binding energy from the semiempirical mass formula (Myers and Swiatecki formula) that gives a relation between atomic and mass numbers for stable nuclei approximately. By these equations one can obtain the effective atomic and mass numbers for any compound or mixed materials uniquely. These numbers are calculated for some materials and compared with the other studies.     

Electrochemical determinations of 6-mercaptopurine on the surface of a carbon nanotube-paste electrode modified with a cobalt salophen complex

A mixture of multi-walled carbon nanotube/graphite paste electrode modified with a salophen complex of cobalt was prepared and was applied for the study of the electrochemical behavior of 6-mercaptopurine (MP) using cyclic and differential pulse voltammetry (DPV). An excellent electrocatalytic activity toward the oxidation of MP was achieved, which led to a considerable lowering in the anodic overpotential and remarkable increase in the response sensitivity in comparison with unmodified electrode. Utilizing DPV method, a linear dynamic range of 1–100 μM with detection limit of 0.1 μM was obtained in phosphate buffer of pH 3.0. The electrochemical detection system was very stable, and the reproducibility of the electrode response, based on the six measurements during 1 month, was less than 3.0% for the slope of the calibration curves of MP. The electrochemical method as a simple, sensitive, and selective method was developed for the determination of MP in pharmaceutical dosage form and human plasma without any treatments.     

Solvothermal Synthesis and Characterization of PbSe Nanostructures with the Aid of Schiff-base Ligand

In this work, Pb(II)N,N-bis(salicylidene)-ethylenediamine; [Pb(salen)]; was applied as lead precursor to synthesis PbSe nanostructures. Besides [Pb(salen)], SeCl₄ and reducing agents like N₂H₄·H₂O have been employed for the production of PbSe nanostructures via a solvothermal route at 180 °C for 3 h in propylene glycol. The effect of preparation factors such as temperature, reaction time, and surfactant on the morphology of PbSe nanostructures was investigated. The experimental results indicated that PbSe synthesized at 150 and 210 °C was composed of agglomerated particles. On the other hand, the use of KBH₄ as reducing agent led to produce PbSe with higher particle size and agglomeration. The as-prepared PbSe nanostructures were characterized by XRD, SEM, TEM, EDS, and FT-IR.     

Carbon nanotube-ionic liquid nanocomposite modified carbon-ceramic electrode for determination of dopamine in real samples

Room temperature 1-butyl-3-methylimidazolium tetraflouroborate ([BMIM][BF₄]) ionic liquid was employed for dispersion of multi walled carbon nanotubes (MWCNTs) and the formation of nanocomposite on the surface of a carbon-ceramic electrode. The surface of the modified electrode was characterized using scanning electron microscopy and electrochemical impedance spectroscopy. The modified electrode exhibited excellent electrochemical activity to oxidation of dopamine (DA); whereas electro oxidation of ascorbic acid (AA) was not seen and electro oxidation of uric acid (UA) appeared at a more positive potential than DA. The multi walled carbon nanotube-ionic liquid nanocomposite modified carbon-ceramic electrode was used for the selective determination of DA in the presence of high levels of AA and UA using differential pulse voltammetry. The calibration curve for DA was linear in the range of 3.00 to 130 µM with the detection limit (S/N=3) of 0.87 µM. The present electrode was successfully applied to the determination of DA in some commercial pharmaceutical samples and human blood serum.