The application of protein-protein interaction (PPI) has been widely used in various industries, such as food, nutraceutical, and pharmaceutical. A deeper understanding of PPI is needed, and the molecular forces governing proteins and their interaction must be explained. The design of new structures with improved functional properties, e.g., solubility, emulsion, and gelation, has been fueled by the development of structural and colloidal building blocks. In this review, the molecular forces of protein structures are discussed, followed by the relationship between molecular force and structure, ways of a bind of proteins together in solution or at the interface, and functional properties. A more detailed look is thus taken at the relationship between the various influencing factors on molecular forces involved in PPI. These factors include protein properties, such as types, concentration, and mixing ratio, and solvent conditions, such as ionic strength and pH. This review also summarizes methods tha1t are capable of identifying molecular forces in protein and PPI, as well as characterizing protein structure.
Type of bond is vital to understand the mechanism of interaction between corresponds atoms. We used three kinds of method
to determine the type of bond between diatomic cluster of platinum and hydrogen: types of element, electronegativity
and electron distribution. In this work, we found that the results from these three methods are not unanimously agreed
with each other for bond type forming in platinum-hydrogen diatomic cluster. Thus, we conclude that the type of bond
is hybrid of both: mainly covalent and slightly ionic.
In the last few years we have seen a very rapid development on solving generalized geometric programming (GGP) problems, but so far less works has been devoted to MOGP due to the inherent difficulty which may arise in solving such problems. Our aim in this paper was to consider the problem of multi-objective geometric programming (MOGP) and solve the problem via two-level relaxed linear programming problem Yuelin et al. (2005) and that is due to simplicity which occurs through linearization i.e. transforming a GP to LP. In this approach each of the objective functions in multi-objective geometric programming is individually linearized using two-level linear relaxed bound method, which provides a lower bound for the optimal values. Finally our MOGP is transformed to a multi-objective linear programming problem (moLP) which is solved by reference point approach. In the end, a numerical example is given to investigate the feasibility and effectiveness of the proposed approach.
Two independent mol-ecules, A and B, comprise the asymmetric unit of the title compound, C20H21N3OSe. While the benzene ring directly bound to the central triazole ring is inclined to the same extent in both mol-ecules [dihedral angles = 40.41 (12) (mol-ecule A) and 44.14 (12)° (B)], greater differences are apparent in the dihedral angles between the Se-bound rings, i.e. 74.28 (12) (mol-ecule A) and 89.91 (11)° (B). Close intra-molecular Se⋯N inter-actions of 2.9311 (18) (mol-ecule A) and 2.9482 (18) Å (B) are noted. In the crystal, supra-molecular chains along the a axis are formed via O-H⋯N hydrogen bonding. These are connected into layers via C-H⋯O and C-H⋯N inter-actions; these stack along (01-1) without directional inter-molecular inter-actions between them.
This article presents the assessment of time-dependent national-level restrictions and control actions and their effects in fighting the COVID-19 pandemic. By analysing the transmission dynamics during the first wave of COVID-19 in the country, the effectiveness of the various levels of control actions taken to flatten the curve can be better quantified and understood. This in turn can help the relevant authorities to better plan for and control the subsequent waves of the pandemic. To achieve this, a deterministic population model for the pandemic is firstly developed to take into consideration the time-dependent characteristics of the model parameters, especially on the ever-evolving value of the reproduction number, which is one of the critical measures used to describe the transmission dynamics of this pandemic. The reproduction number alongside other key parameters of the model can then be estimated by fitting the model to real-world data using numerical optimisation techniques or by inducing ad-hoc control actions as recorded in the news platforms. In this article, the model is verified using a case study based on the data from the first wave of COVID-19 in the Republic of Kazakhstan. The model is fitted to provide estimates for two settings in simulations; time-invariant and time-varying (with bounded constraints) parameters. Finally, some forecasts are made using four scenarios with time-dependent control measures so as to determine which would reflect on the actual situations better.
In search of better α-glucosidase inhibitors, a series of bis-indolylmethane sulfonohydrazides derivatives (1-14) were synthesized and evaluated for their α-glucosidase inhibitory potential. All derivatives exhibited outstanding α-glucosidase inhibition with IC50 values ranging between 0.10 ± 0.05 to 5.1 ± 0.05 μM when compared with standard drug acarbose having IC50 value 856.28 ± 3.15 μM. Among the series, analog 7 (0.10 ± 0.05 μM) with tri-chloro substitution on phenyl ring was identified as the most potent inhibitor of α-glucosidase (∼ 8500 times). The structure activity relationship has been also established. Molecular docking studies were also performed to help understand the binding interaction of the most active analogs with receptors. From the docking studies, it was observed that all the active bis-indolylmethane sulfonohydrazides derivatives showed considerable binding interactions within the active site (acarbose inhibition site) of α-glucosidase. We also evaluated toxicity of all derivatives and found none of them are toxic.
Outliers in the X-direction or high leverage points are the latest known source of multicollinearity. Multicollinearity is a nonorthogonality of two or more explanatory variables in multiple regression models, which may have important influential impacts on interpreting a fitted regression model. In this paper, we performed Monte Carlo simulation studies to achieve two main objectives. The first objective was to study the effect of certain magnitude and percentage of high leverage points, which are two important issues in tending the high leverage points to be collinearity-enhancing observations, on the multicollinarity pattern of the data. The second objective was to investigate in which situations these points do make different degrees of multicollinearity, such as moderate or severe. According to the simulation results, high leverage points should be in large magnitude for at least two explanatory variables to guarantee that they are the cause of multicollinearity problems. We also proposed some practical Lower Bound (LB) and Upper Bound (UB) for High Leverage Collinearity Influential Measure (HLCIM) which is an essential measure in detecting the degree of multicollinearity. A well-known example is used to confirm the simulation results.
A mutation is ultimately essential for adaptive evolution in all populations. It arises all the time, but is mostly fixed by enzymes. Further, most do consider that the evolution mechanism is by a natural assortment of variations in organisms in line for random variations in their DNA, and the suggestions for this are overwhelming. The altering of the construction of a gene, causing a different form that may be communicated to succeeding generations, produced by the modification of single base units in DNA, or the deletion, insertion, or rearrangement of larger units of chromosomes or genes. This altering is called a mutation. In this paper, a mathematical model is introduced to this reality. The model describes the time and space for the evolution. The tool is based on a complex domain for the space. We show that the evolution is distributed with the hypergeometric function. The Boundedness of the evolution is imposed by utilizing the Koebe function.
Clinacanthus nutans has been reported to have many medicinal properties and it is traditionally used in treating viral lesions. This study aims to determine the molecular docking of C. nutans compounds detected by Gas Chromatography-Mass Spectrometry (GC-MS) with the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2 main protease) protein and its host receptor angiotensin-converting enzyme 2 (ACE2) protein using the AutoDock 4.2 tool. The drug-likeness and molecular docking analyses showed that fourteen compounds of C. nutans satisfied the Lipinski's rule of five and they exhibited good inhibitory effects against the SARS-Cov-2 main protease and ACE2 proteins. In addition, the glyceryl 2-linolenate compound was found to have the most potent binding affinities with both proteins. The results provide useful insights into the molecular inhibitory interactions of C. nutans compounds detected by GC-MS analysis with the targeted SARS-CoV-2 main protease and ACE2 protein.
The title compound, C17H15N3O2, is a monoclinic polymorph (P21/c with Z' = 1) of the previously reported triclinic (P-1 with Z' = 2) form [Gajera et al. (2013 ▸). Acta Cryst. E69, o736-o737]. The mol-ecule in the monoclinic polymorph features a central pyrazolyl ring with an N-bound p-tolyl group and a C-bound 1,3-benzodioxolyl fused-ring system on either side of the C atom bearing the amino group. The dihedral angles between the central ring and the N- and C-bound rings are 50.06 (5) and 27.27 (5)°, respectively. The angle between the pendent rings is 77.31 (4)°, indicating the mol-ecule has a twisted conformation. The five-membered dioxolyl ring has an envelope conformation with the methyl-ene C atom being the flap. The relative disposition of the amino and dioxolyl substituents is syn. One of the independent mol-ecules in the triclinic form has a similar syn disposition but the other has an anti arrangement of these substituents. In the crystal structure of the monoclinic form, mol-ecules assemble into supra-molecular helical chains via amino-pyrazolyl N-H⋯N hydrogen bonds. These are linked into layers via C-H⋯π inter-actions, and layers stack along the a axis with no specific inter-actions between them.
Interaction of an anticancer drug, vandetanib (VDB) with a ligand transporter, lysozyme (LYZ) was explored using multispectroscopic techniques, such as fluorescence, absorption and circular dichroism along with computational analysis. Fluorescence data and absorption results confirmed VDB-LYZ complexation. VDB-induced quenching was characterized as static quenching based on inverse correlation of KSV with temperature as well as kq values. The complex was characterized by the weak binding constant (Ka=4.96-3.14×103M-1). Thermodynamic data (ΔS=+12.82Jmol-1K-1; ΔH=-16.73kJmol-1) of VDB-LYZ interaction revealed participation of hydrophobic and van der Waals forces along with hydrogen bonds in VDB-LYZ complexation. Microenvironmental perturbations around tryptophan and tyrosine residues as well as secondary and tertiary structural alterations in LYZ upon addition of VDB were evident from the 3-D fluorescence, far- and near-UV CD spectral analyses, respectively. Interestingly, addition of VDB to LYZ significantly increased protein's thermostability. Molecular docking results suggested the location of VDB binding site near the LYZ active site while molecular dynamics simulation results suggested stability of VDB-LYZ complex. Presence of Mg2+, Ba2+ and Zn2+ was found to interfere with VDB-LYZ interaction.
Tyrphostin 9 (Tyr 9) is a potent platelet-derived growth factor receptor (PDGFR) inhibitor, which induces apoptosis in various cancer cell types. The binding of Tyr 9 to the major transport protein, human serum albumin (HSA) was investigated using several spectroscopic techniques and molecular docking method. Fluorescence quenching titration results showed progressive decrease in the protein fluorescence with increasing drug concentrations. A decreasing trend of the Stern-Volmer constant, Ksv with increasing temperature characterized the drug-induced quenching as static quenching, thus pointed towards the formation of Tyr 9-HSA complex. The binding constant of Tyr 9-HSA interaction was found to lie within the range 3.48-1.69 × 105 M-1 at three different temperatures, i.e. 15 °C, 25 °C and 35 °C, respectively and suggested intermediate binding affinity between Tyr 9 and HSA. The drug-HSA complex seems to be stabilized by hydrophobic forces, van der Waals forces and hydrogen bonds, as suggested from the thermodynamic data as well as molecular docking results. The far-UV and the near-UV CD spectral results showed slight alteration in the secondary and tertiary structures, respectively, of the protein upon Tyr 9 binding. Interaction of Tyr 9 with HSA also produced microenvironmental perturbations around protein fluorophores, as evident from the three-dimensional fluorescence spectral results but increased protein's thermal stability. Both competitive drug binding results and molecular docking analysis suggested Sudlow's Site I of HSA as the preferred Tyr 9 binding site. Communicated by Ramaswamy H. Sarma.
A study of vector boson scattering in pp collisions at a center-of-mass energy of 8 TeV is presented. The data sample corresponds to an integrated luminosity of 19.4 fb(-1) collected with the CMS detector. Candidate events are selected with exactly two leptons of the same charge, two jets with large rapidity separation and high dijet mass, and moderate missing transverse energy. The signal region is expected to be dominated by electroweak same-sign W-boson pair production. The observation agrees with the standard model prediction. The observed significance is 2.0 standard deviations, where a significance of 3.1 standard deviations is expected based on the standard model. Cross section measurements for W(±)W(±) and WZ processes in the fiducial region are reported. Bounds on the structure of quartic vector-boson interactions are given in the framework of dimension-eight effective field theory operators, as well as limits on the production of doubly charged Higgs bosons.
A third order Nakashima type implicit Pseudo Runge-Kutta method is presented. The free parameter was determined by minimizing the error bound. The stability region of the method was presented. Some problems on delay differential equations are tested to compare the accuracy of the proposed method with third order RADAU I.
We report on the assembly of three-fold axially compressed icosahedral arrays of the bowl shaped p-sulfonatocalix[4]arene molecules in the solid-state, intricately bound to dipicolinate and yttrium(iii) ions, with the compression reflected in Hirshfeld surface analyses. Solution studies show dissolution of the icosahedra intact, but with a geometrical rearrangement to regular icosahedra.
The crystal and mol-ecular structures of two di-phenyl-tin bis-(di-thio-carbamate)s, [Sn(C6H5)2(C5H10NOS2)2], (I), and [Sn(C6H5)2(C7H14NO2S2)2], (II), are described. In (I), in which the metal atom lies on a twofold rotation axis, the di-thio-carbamate ligand coordinates with approximately equal Sn-S bond lengths and the ipso-C atoms of the Sn-bound phenyl groups occupy cis-positions in the resulting octa-hedral C2S4 donor set. A quite distinct coordination geometry is noted in (II), arising as a result of quite disparate Sn-S bond lengths. Here, the four S-donors define a trapezoidal plane with the ipso-C atoms lying over the weaker of the Sn-S bonds so that the C2S4 donor set defines a skewed trapezoidal bipyramid. The packing of (I) features supra-molecular layers in the ab plane sustained by methyl-ene-C-H⋯π(Sn-ar-yl) inter-actions; these stack along the c-axis direction with no specific inter-actions between them. In (II), supra-molecular chains along the b-axis direction are formed by methyl-ene-C-O(ether) inter-actions; these pack with no directional inter-actions between them. A Hirshfeld surface analysis was conducted on both (I) and (II) and revealed the dominance of H⋯H inter-actions contributing to the respective surfaces, i.e. >60% in each case, and other features consistent with the description of the mol-ecular packing above.
This paper presents parameters analysis for the estimated modal damping ratio using a new version of the automated enhanced frequency domain decomposition (AEFDD). The purpose of this study is to provide a better choice of a maximum number of points of time segments and modal assurance criterion (MAC) index number regarding to the variable level of system damping (low and high damped structure) and degree of freedom of the system. According current literature, frequency domain (FD) methods seem to have the problem with providing a correct identification of the modal damping ratio, since the correct estimate of modal damping is still an open problem and often leads to biased estimates. This technique is capable of providing consistent modal parameters estimation, particularly for modal frequencies and mode shapes. As a necessary fundamental condition, the algorithm has been assessed first from computed numerical responses according to random white noise, acting on different shear-type frame structures and corrupted with noise. Results indicate that reducing the value of natural frequencies and modal damping ratios of the modes under analysis demands longer time segments and a high value of the maximum number of points for adequate information on the decaying correlation functions when computing a modal damping ratio. In addition, the results also prove that the MAC index does not significantly affect the results for the low damped system. However, the use of a high MAC index value for the high damped system significantly introduces large error bound and it becomes worse, particularly for the higher modes, as the standard deviation of percentage error increases gradually. Furthermore, the use of a MAC index for a high number of points of time segments significantly increases the standard deviation of the percentage error.
A series of novel α-furfuryl-2-alkylaminophosphonates have been efficiently synthesized from the one-pot three-component classical Kabachnik-Fields reaction in a green chemical approach by addition of an in situ generated dialkylphosphite to Schiff's base of aldehydes and amines by using environmental and eco-friendly silica gel supported iodine as a catalyst by microwave irradiation. The advantage of this protocol is simplicity in experimental procedures and products were resulted in high isolated yields. The synthesized α-furfuryl-2-alkylaminophosphonates were screened to in vitro antioxidant and plant growth regulatory activities and some are found to be potent with antioxidant and plant growth regulatory activities. These in vitro studies have been further supported by ADMET (absorption, distribution, metabolism, excretion, and toxicity), quantitative structure-activity relationship, molecular docking, and bioactivity studies and identified that they were potentially bound to the GLN340 amino acid residue in chain C of 1DNU protein and TYR597 amino acid residue in chain A of 4M7E protein, causing potential exhibition of antioxidant and plant growth regulatory activities. Eventually, title compounds are identified as good blood-brain barrier (BBB)-penetrable compounds and are considered as proficient central nervous system active and neuroprotective antioxidant agents as the neuroprotective property is determined with BBB penetration thresholds.
In this work, a chitosan-modified nanofiber membrane was fabricated and used to examine the permeation characteristics of C-phycocyanin (CPC) obtained from Spirulina platensis. The effects of NaCl concentration (0.1-1.0 M), chitosan coupling pH (6-8), chitosan coupling concentration (0.1-3.0%), algal solution pH (6-8), algal mass concentration (0.1-1.0% dw/v), and membrane flux (4.08 × 10-2-2.04 × 10-1 mL/min·cm2) on the penetration performance of the membrane for CPC were investigated. The results show that the order of binding selectivity of the membrane for these proteins is contaminating proteins (TP) > allophycocyanin (APC) > CPC. TP and APC molecules were more easily adsorbed by the chitosan-modified membrane, and the CPC molecules most easily penetrated the membrane without being adsorbed, enhancing CPC purity. The purification factor and total mass flux were 3.3 fold and 66%, respectively, in a single step.
Surface functionalization of multi-walled carbon nanotubes (MWCNTs) was carried out using a gas phase treatment in a Universal Temperature Program (UTP) reactor by flowing SO3 gas onto the CNTs while being heated at different temperatures. The functionalized nanotubes were characterized using X-ray Fluorescence (XRF), Fourier Transform Infrared Spectroscopy (FT-IR) and Raman spectroscopy. The amount of oxyen and sulfur containing groups was determined by acid-base titration. The titration results were in good agreement with elemental analysis using x-ray fluorescence. FTIRanalysis showed the presence of oxygen and sulfur containing groups, S=O, C-S, C=O and -COOH. Raman spectroscopy confirmed that oxygen and sulfur containing acidic groups covalently attached to the sidewall of the MWCNTs.