Model of cytosine-, thymine-containing oligodeoxyribonucleotide protonation in solution

In the present study, the experimental data on the pH-induced formation of the i-motif structure in the nucleotide sequence 5′-CCTTTCCTTTTCCTTTCC-3′ (25°C, pH 3.3-8.9) obtained by spectroscopic techniques, such as UV molecular absorption and circular dichroism, has been analyzed using the chemometric soft modeling-based MCR-ALS approach and the hard modeling-based matrix method. Soft modeling using 2 or 3 spectral species correctly reproduced the spectral variations observed experimentally. The use of hard chemical modeling has allowed proposing an equilibrium model, which describes spectral changes as functions of solution acidity. Additionally, the intrinsic protonation constant K _in and the cooperativity parameter ω have been calculated from fitting of the circular dichroism as well as the molecular absorption spectra. The results indicated that folding was accompanied by a cooperative process, i.e. the enhancement of protonated structure stability upon protonation.     

Characterization of domain-specific interaction of synthesized dye with serum proteins by spectroscopic and docking approaches along with determination of in vitro cytotoxicity and antiviral activity

The interaction between a synthesized dye with proteins, bovine, and human serum albumin (BSA, HSA, respectively) under physiological conditions has been characterized in detail, by means of steady-state and time-resolved fluorescence, UV–vis absorption, and circular dichroism (CD) techniques. An extensive time-resolved fluorescence spectroscopic characterization of the quenching process has been undertaken in conjugation with temperature-dependent fluorescence quenching studies to divulge the actual quenching mechanism. From the thermodynamic observations, it is clear that the binding process is a spontaneous molecular interaction, in which van der Waals and hydrogen bonding interactions play the major roles. The UV–vis absorption and CD results confirm that the dye can induce conformational and micro-environmental changes of both the proteins. In addition, the dye binding provokes the functionality of the native proteins in terms of esterase-like activity. The average binding distance (r) between proteins and dye has been calculated using FRET. Cytotoxicity and antiviral effects of the dye have been found using Vero cell and HSV-1F virus by performing MTT assay. The AutoDock-based docking simulation reveals the probable binding location of dye within the sub-domain IIA of HSA and IB of BSA.     

Spectral changes induced in Cibacron Blue F3GA by salts,organic solvents,and polypeptides: Implications for Blue dye interaction with proteins

The interactions of Cibacron Blue F3GA with organic solvents, salts, oligopeptides, and polypeptides were studied by visible difference spectroscopy. The difference spectrum of the dye in an aqueous solution of NaCl (vs water) has a characteristic positive peak at 690 nm and negative double minima at 630 and 585 nm. Such a “salt-like” spectrum is also obtained for interaction of the dye with polycations such as oligolysines, polylysine, polyarginine, and protamine. In contrast, the difference spectrum of the dye in binary aqueous solvents containing dioxan or t-butyl alcohol at moderately high concentrations, measured against water, displays a positive peak and shoulder at 655 and 610 nm, respectively, with a small negative contribution below 550 nm. This spectrum is attributed to a nonpolar interaction of the dye with organic cosolvent molecules. The spectrum of the dye in 7 M urea is changed little from that in water, indicating similar interactions of the dye with water or urea molecules. The spectral characteristics described here for the interaction of the polyaromatic polysulfonate dye with positively charged groups, polar groups, and nonpolar moieties of neutral molecules provide a basis for describing the details of the interactions of Cibacron Blue F3GA with several proteins and for characterizing the dye binding environments in the proteins.     

Structural details of urea binding to barnase: a molecular dynamics analysis.

BACKGROUND: The molecular mechanism of urea-induced protein unfolding has not been established. It is generally thought that denaturation results from the stabilizing interactions of urea with portions of the protein that are buried in the native state and become exposed upon unfolding of the protein. RESULTS: We have performed molecular dynamics simulations of barnase (a 110 amino acid RNase from Bacillus amyloliquefaciens) with explicit water and urea molecules at 300 K and 360 K. The native conformation was unaffected in the 300 K simulations at neutral and low pH. Two of the three runs at 360 K and low pH showed some denaturation, with partial unfolding of the hydrophobic core 2. The first solvation shell has a much higher density of urea molecules (water/urea ratio ranging from 2.07 to 2.73) than the bulk (water/urea ratio of 4.56). About one half of the first-shell urea molecules are involved in hydrogen bonds with polar or charged groups on the barnase surface, and between 15% and 18% of the first-shell urea molecules participate in multiple hydrogen bonds with barnase. The more stably bound urea molecules tend to be in crevices or pockets on the barnase surface. CONCLUSIONS: The simulation results indicate that an aqueous urea solution solvates the surface of a polypeptide chain more favorably than pure water. Urea molecules interact more favorably with nonpolar groups of the protein than water does, and the presence of urea improves the interactions of water molecules with the hydrophilic groups of the protein. The results suggest that urea denaturation involves effects on both nonpolar and polar groups of proteins.     

Structure prediction and network analysis of chitinases from the Cape sundew,Drosera capensis

BackgroundCarnivorous plants possess diverse sets of enzymes with novel functionalities applicable to biotechnology, proteomics, and bioanalytical research. Chitinases constitute an important class of such enzymes, with future applications including human-safe antifungal agents and pesticides. Here, we compare chitinases from the genome of the carnivorous plant Drosera capensis to those from related carnivorous plants and model organisms.MethodsUsing comparative modeling, in silico maturation, and molecular dynamics simulation, we produce models of the mature enzymes in aqueous solution. We utilize network analytic techniques to identify similarities and differences in chitinase topology.ResultsHere, we report molecular models and functional predictions from protein structure networks for eleven new chitinases from D. capensis, including a novel class IV chitinase with two active domains. This architecture has previously been observed in microorganisms but not in plants. We use a combination of comparative and de novo structure prediction followed by molecular dynamics simulation to produce models of the mature forms of these proteins in aqueous solution. Protein structure network analysis of these and other plant chitinases reveal characteristic features of the two major chitinase families.General significanceThis work demonstrates how computational techniques can facilitate quickly moving from raw sequence data to refined structural models and comparative analysis, and to select promising candidates for subsequent biochemical characterization. This capability is increasingly important given the large and growing body of data from high-throughput genome sequencing, which makes experimental characterization of every target impractical.     

Calcium-ion-induced stabilization of the protease from Bacillus cereus WQ9-2 in aqueous hydrophilic solvents: effect of calcium ion binding on the hydration shell and intramolecular interactions

The neutral protease WQ from Bacillus cereus is stable in various aqueous organic mixtures, with the exception of those containing acetonitrile (ACN) and dimethylformamide (DMF). The stability of the enzyme in aqueous hydrophilic solvents was dramatically enhanced with the addition of calcium ions, with the degree of improvement in the half-life relative to different solutions ranging from fourfold to more than 70-fold. Studies of the kinetic constants showed that calcium ions induced slight conformational changes in the active site of the enzyme in aqueous ACN. We investigated the molecular mechanisms underlying this stabilizing effect by employing a combination of biophysical techniques and molecular dynamics simulation. In aqueous ACN, the intrinsic fluorescence and circular dichroism analysis demonstrated that the addition of calcium ions induced a relatively compact conformation and maintained both the native-like microenvironment near the tryptophan residues and the secondary structure. Alternatively, homology modeling confirmed the location of four calcium-ion-binding sites in the enzyme, and molecular dynamics simulation revealed that three other calcium ions were bound to the surface of the enzyme. Calcium ions, known as a type of kosmotrope, can strongly bond with water molecules, thus aiding in the formation of the regional hydration shell required for the maintenance of enzyme activity. In addition, the introduction of calcium ions resulted in the formation of additional ionic interactions, providing propitious means for protein stabilization. Thus, the stronger intramolecular interactions were also expected to contribute partially to the enhanced stability of the enzyme in an aqueous organic solvent.     

Model of cytosine-, thymine-containing olygodeoxyribonucleotide protonation in solution

In the present study, the experimental data on the pH-induced formation of the i-motif structure in the nucleotide sequence 5'-CCTTTCCTTTTCCTTTCC-3' (25oC, pH 3.3-8.9) obtained by spectroscopic techniques, such as UV molecular absorption and circular dichroism, has been analysed using the chemometric soft modelling-based MCR-ALS approach and the hard modelling-based matrix method. Soft modelling using 2 or 3 spectral species correctly reproduced spectral variations observed experimentally. The use of hard chemical modelling enabled us to propose the equilibrium model, which describes spectral changes as functions of solution acidity. Additionally, the intrinsic protonation constant Kin, and the cooperativity parameter w have been calculated from the fitting procedure of the circular dichroism as well as molecular absorption spectra. The results indicated that folding was accompanied by a cooperative process, i.e. the enhancement of protonated structure stability upon protonation.     

Homology modeling,molecular dynamic simulation and docking studies of cyclin dependent kinase 1

In order to develop promising cyclin dependent kinase 1 inhibitors, homology modeling, docking and molecular dynamic simulation techniques were applied to get insight into the functional and structural properties of cyclin dependent kinase 1 (CDK1). Since there is no reported CDK1 crystal structural data, the three dimensional structure of CDK1 was constructed based on homology modeling. An extensive dynamic simulation was also performed on a Flavopiridol-CDK1 complex for probing the binding pattern of Flavopiridol in the active site of CDK1. The binding modes of other inhibitors to CDK1 were also proposed by molecular docking. The structural requirement for developing more potent CDK1 inhibitors was obtained by the above-mentioned molecular simulations and pharmacophore modeling.     

Mathematical Modeling of the Reduction of Safranin onto Chemically Modified Rice Husks in Stirred Tank Reactor Using Response Surface Methodology and Artificial Neural Network

ABSTRACT

The effluents coming from the dye industries are colored and polluted, and the disposal of these wastes into receiving waters causes damage to the water as well as the environment. The use of rice husk for the removal of dye from wastewater has been explored in a stir tank reactor. The effects of operation variables such as adsorbent dosage, contact time, dye concentration, initial pH, and agitation on the removal of safranin were investigated in a stirred tank reactor. The combined effect of various process parameters on dye removal were analyzed using response surface methodology (RSM), and the modeling of the process parameter had been done using the artificial neural network simulation method. It was observed that response surface methodology can determine the optimization of the process parameters and the model derived from the simulation of the artificial neural network (ANN) (deviation from experimental results was ～0.09%) described the process variable efficiently. It was observed that at the initial solution pH of 6.28 and adsorbent dosage of 15.63 g L^?1, dye removal of safranin was 97%.     

Use of the fluorescent weak acid dansylglycine to measure transmembrane proton concentration gradients

The amphiphilic fluorescent dye N-[(5-dimethylamino)naphth-1-ylsulfonyl]glycine (dansylglycine) can be used to monitor the magnitude and stability of transmembrane proton gradients. Although freely soluble in aqueous media, the dye readily adsorbs to the surfaces of lipid vesicles. Because membrane-bound dye fluoresces at a higher frequency, and with greater efficiency, than dye in aqueous solution, it is easy to isolate the fluorescence emission from those dye molecules adsorbed to the lipid surface. When dansylglycine is mixed with phospholipid vesicles, the dye molecules attain a partition equilibrium between buffer and the outer, proximal surface of the vesicles. This is a rapid, diffusion-limited process that is indicated by a fast phase of fluorescence intensity increase monitored at 510 nm. In a second step, the inner, distal surface of each vesicle becomes populated with dye, a process that involves permeation through the lipid bilayer and that is generally much slower than the original adsorption step. Dansylglycine is a weak acid that permeates as an electrically neutral species; the flux of dye across the bilayer is thus strongly dependent on the degree of protonation of the dye's carboxylate moiety. When the external pH is lower than that of the vesicle lumen, the inward flux of dye is greater than that in the opposite direction, and dye accumulates in the lumen. This leads to a local elevation of dansylglycine concentration in the inner membrane monolayer, which in turn results in an elevated fluorescence intensity proportional to the membrane pH gradient.     

Experimental and computational studies on the binding of diazinon to human serum albumin

In the present research, the binding properties of diazinon (DZN), as an organophosphorus herbicide, to human serum albumin (HSA) were investigated using combination of spectroscopic, electrochemistry, and molecular modeling techniques. Changes in the UV–Vis and FT-IR spectra were observed upon ligand binding along with a significant degree of tryptophan fluorescence quenching on complex formation. The obtained results from spectroscopic and electrochemistry experiments along with the computational studies suggest that DZN binds to residues located in subdomains IIA of HSA with binding constant about 1410.9 M^?1 at 300 K. From the thermodynamic parameters calculated according to the van’t Hoff equation, the enthalpy change ΔH° and entropy change ΔS° were found to be ?16.695 and 0.116 KJ/mol K, respectively. The primary binding pattern is determined by hydrophobic interaction and hydrogen binding occurring in so-called site I of HSA. DZN could slightly alter the secondary structure of HSA. All of experimental results are supported by computational techniques such as docking and molecular dynamics simulation using a HSA crystal model.     

Urea Impedes the Hydrophobic Collapse of Partially Unfolded Proteins

Proteins are denatured in aqueous urea solution. The nature of the molecular driving forces has received substantial attention in the past, whereas the question how urea acts at different phases of unfolding is not yet well understood at the atomic level. In particular, it is unclear whether urea actively attacks folded proteins or instead stabilizes unfolded conformations. Here we investigated the effect of urea at different phases of unfolding by molecular dynamics simulations, and the behavior of partially unfolded states in both aqueous urea solution and in pure water was compared. Whereas the partially unfolded protein in water exhibited hydrophobic collapses as primary refolding events, it remained stable or even underwent further unfolding steps in aqueous urea solution. Further, initial unfolding steps of the folded protein were found not to be triggered by urea, but instead, stabilized. The underlying mechanism of this stabilization is a favorable interaction of urea with transiently exposed, less-polar residues and the protein backbone, thereby impeding back-reactions. Taken together, these results suggest that, quite generally, urea-induced protein unfolding proceeds primarily not by active attack. Rather, thermal fluctuations toward the unfolded state are stabilized and the hydrophobic collapse of partially unfolded proteins toward the native state is impeded. As a result, the equilibrium is shifted toward the unfolded state.     

Effect of urea, dimethylurea, and tetramethylurea on the phase behavior of dioleoylphosphatidylethanolamine

The phase behavior of dioleoylphosphatidylethanolamine in aqueous solutions of urea, N,N'-dimethylurea (DMU), and N,N,N',N'-tetramethylurea (TMU) has been characterized by synchrotron X-ray diffraction and differential scanning calorimetry. All three solutes stabilize the lamellar liquid-crystalline phase at the expense of lamellar-gel phase and inverted hexagonal phase of the phospholipid when present in concentrations up to 3 M. X-ray diffraction data demonstrated that the repeat spacing of DOPE increased with increasing urea concentration, but decreased as the DMU and TMU concentrations increased. The repeat spacing of DOPE in the liquid-crystal phase dispersed in the three solutes is d(urea)>d(DMU)>d(TMU). The molecular mechanisms underlying these observations are discussed in terms of either membrane Hofmeister effect, where urea acts as a water structure breaker, or a direct insertion effect of the amphiphilic DMU and TMU molecules into the lipid head groups in the interfacial region of the phospholipid bilayer.     

Interactions between lignin and urea researched by molecular simulation

Molecular simulations of interactions between urea molecules and lignin polymer have been carried out with the aim of understanding the mechanism of urea slow-release behaviours in lignin–urea materials. It has been found, by docking technology and natural bond orbital analysis, that H-bonds and π-electronic conjugation effect are the main driving forces to keep urea molecules adsorbed on the lignin. In the NPT (isothermal–isobaric ensemble) simulations, mean-squared displacement results show that water molecules can promote the urea molecules gradually away from the lignin. Furthermore, in NVT (canonical ensemble) molecular dynamic simulations, results on diffusion constants of urea molecules in lignin–urea system show that diffusion constant of urea molecules in a urea–water–lignin system increases with an increase in the water content. Conclusions gained from two different kinds of simulation are in agreement with each other and are consistent with the experimental observations.     

A chemometric approach to the estimation of the absorption spectra of dye probe merocyanine 540 in aqueous and phospholipid environments

Merocyanine 540 (MC540) is a widely used dye probe for membranous environments. However, fundamental knowledge of the spectral features of this dye in aqueous and hydrophobic environments is still lacking. Such knowledge is important because biomembranes involve a hydrophobic environment surrounded by a hydrophilic environment. Because many investigations so far have been performed based on indistinct spectral estimations, the interpretation of the data obtained using this dye as a fluorescent transmembrane probe remains controversial. In order to determine the exact spectra in both aqueous and hydrophobic environments, we adopted principal factor analysis (PFA), a method of multivariate analysis. The PFA method can also determine the number of molecular species present in the reaction mixture, which is three in pure water and two in phospholipid suspension. Two of the species in both water and phospholipid suspension were the monomer and dimer. The third species in water was the trimer, but its amount was so small at 10 microM MC540 solution that the spectral data in water can be approximated neglecting this molecular species. The monomer spectrum changed its form markedly with a bathochromic shift when transferred from the water to phospholipid environment, whereas the dimer remained similar in its shape except for a remarkable red shift. In water, the dissociation constants, K(1) and K(2), for the assumed stacking-model reactions, M+M <--> M(2) and M+M(2) <--> M(3), were 3.1 x 10(-4) M and 5.7 x 10(-4) M, respectively. In the phospholipid environment, the dissociation constant K* for the assumed stacking-model reaction, M(*)+M(*) <--> *M(2), was 1.9x10(-5)M. The fluorescent intensities of MC540 were also measured in both water and phospholipid environments. A comparison based on the absorption and fluorescence spectra suggested that the temporal increase in the amount of the monomer on the excitable membrane contributes to the fluorescent intensity change observed in the transmembrane potential change.     

Hydrophobic and ionic effects upon the electrophoretic mobilities of the subunits of coupling factor 1 from mitochondria

A sodium dodecyl sulfate (SDS)-urea polyacrylamide gel system was used to investigate certain properties of the subunits of the beef heart mitochondrial ATPase, (native F1, nF1). By examining the affects of urea concentration and acrylamide concentration upon the electrophoretic mobilities of the polypeptides comprising the nF1 enzyme, we have obtained conditions under which all five subunits are simultaneously resolved when the discontinuous buffer system of Laemmli is used (U. K. Laemmli (1970) Nature (London) 277, 680-685). The determination of the apparent molecular weights by analysis of Ferguson plots (K. A. Ferguson (1964) Metabolism 13, 985-1002) revealed that the addition of urea to the SDS gels resulted in a decrease in the apparent molecular weight of the beta subunit. A dramatic increase in the apparent molecular weight of the delta subunit was also brought about by the presence of urea in the SDS gels. In addition, the apparent molecular weight of both the alpha and the beta subunits was dependent upon the acrylamide concentration used, indicating that these subunits contain either areas highly resistant to denaturation by the combined action of urea and SDS, or covalent modifications leading to anomalous electrophoretic mobility. The results of experiments in which urea analogs were used indicate that the interactions of urea with the beta subunit involve the formation of hydrogen bonds between urea and regions of this subunit. On the other hand, the interactions of urea with the delta subunit are primarily of a hydrophobic nature, suggesting that these interactions could involve domains of the delta subunit required for binding of the coupling factor to the mitochondrial membrane.     

Mechanism of the interactions of aliphatic alcohols with bovine serum albumin in the ternary systems—1H n.m.r. study: 1. Aqueous solutions BSA-alcohols-urea

The molecular mechanism of the interaction of aliphatic alcohols (A) with bovine serum albumin (BSA) protein was studied in aqueous solutions at increasing concentrations (0–8 m) of urea (U). ¹H n.m.r. spectra of alcohols were monitored in D₂O in the control binary systems (A—U) and (A—BSA), and in the ternary systems (A—U—BSA) at pH 7.0. Marked and selective broadening of the n.m.r. lines of alcohols in the system (A—BSA) was reduced upon addition of urea, indicating that alcohols are poorly bound by urea-denaturated BSA. The reduction in the ability to associate with BSA depends on chain position of the alcohol molecule and is much higher for α-methylenes (next to ?OH) than for other proton groups. Besides this reduction seems to be a two-step phenomenon dependent upon urea concentration. The results obtained can be explained by competition in formation by the peptide linkages of a protein of the hydrogen bonds with ?OH group of alcohols or fragments of urea molecules.     

Temperature and urea induced denaturation of the TRP‐cage mini protein TC5b: A simulation study consistent with experimental observations

The effects of temperature and urea denaturation (6M urea) on the dominant structures of the 20‐residue Trp‐cage mini‐protein TC5b are investigated by molecular dynamics simulations of the protein at different temperatures in aqueous and in 6M urea solution using explicit solvent degrees of freedom and the GROMOS force‐field parameter set 45A3. In aqueous solution at 278 K, TC5b is stable throughout the 20 ns of MD simulation and the trajectory structures largely agree with the NMR‐NOE atom–atom distance data available. Raising the temperature to 360 K and to 400 K, the protein denatures within 22 ns and 3 ns, showing that the denaturation temperature is well below 360 K using the GROMOS force field. This is 40–90 K lower than the denaturation temperatures observed in simulations using other much used protein force fields. As the experimental denaturation temperature is about 315 K, the GROMOS force field appears not to overstabilize TC5b, as other force fields and the use of continuum solvation models seem to do. This feature may directly stem from the GROMOS force‐field parameter calibration protocol, which primarily involves reproduction of condensed phase thermodynamic quantities such as energies, densities, and solvation free energies of small compounds representative for protein fragments. By adding 6M urea to the solution, the onset of denaturation is observed in the simulation, but is too slow to observe a particular side‐chain side‐chain contact (Trp6‐Ile4) that was experimentally observed to be characteristic for the denatured state. Interestingly, using temperature denaturation, the process is accelerated and the experimental data are reproduced.     

Electronic spectrum,optical activity,and structure of the acridine orange complex with poly-α,L-glutamic acid

The electronic absorption and circular dichroism spectra of the complex formed by acridine orange with poly-α,L -glutamic acid in the α-helix conformation have been measured in aqueous solution over a range of glutamate residue-to-dye ratios. Three Cotton effects (circular dichroism bands) associated with the long wavelength absorption band of acridine orange at 4950 A. are induced by complex formation between the dye and the polypeptide, and further circular dichroism bands are observed in the ultraviolet region associated with the 2700 A., but not with the 2950 A. absorption band of the dye. The induced optical activity is found to be relatively insensitive to the glutamate residue-to-dye ratio and to be more dependent upon the ionic strength of the solution. By Measuring the circular dichroism spectrum of the complex in aqueous solution under streaming conditions with the light propagated along the direction of flow the observed circular dichroism bands are assigned to electronic transitions polarized parallel or perpendicular to the axis of the polypeptide α-helix. From the spectroscopic data it is inferred that the dye aggregate in the L -PGA–AO complex has the form of a left-handed superhelix bound to the core of the right-handed α-helix of poly-α,L -glutamic acid. It is shown that the longer and the shorter of the in-plane axes of the dye molecule are probably orientated respectively at a small angle, and radially, with respect to the axis of the α-helix in the complex.     

Maturation of somatic embryos in conifers: Morphogenesis,physiology, biochemistry,and molecular biology

Summary In the past 15 years tremendons progress has been made towards the development of systems for the induction and development of somatic embryos of coniferous species. Since the first report in 1985, several species have been induced to produce somatic embryos. This has been rendered possible by the development of rational media and improvement of culture conditions, which have resulted in increased embryo quality and higher conversion frequency. Understanding the physiological and biochemical events occurring during in vivo embryogenesis has been fundamental in the design of new protocols for improving the somatic embryogenic process. Specifically, the inclusions of abscisic acid (ABA) and osmotic agents, such as polyethylene glycol (PEG), have been shown to be necessary for the functional development of somatic embryos. In the past few years, physiological and biochemical investigations have been useful in increasing our knowledge on the mode of action of ABA and PEG during embryo development. In comparison with the flowering plants, our understanding on the molecular mechanisms regulating the embryogenic process in coniferous species is still very limited. The application of new molecular techniques is therefore fundamental towards this end. The emphasis of this review is on recent information dealing with the maturation of conifer somatic embryos.