KCD: A prediction web server of knowledge-based circular dichroism.

We present a web server that predicts the far-UV circular dichroism (CD) spectra of proteins by utilizing their three-dimensional (3D) structures from the Protein Data Bank (PDB). The main algorithm is based on the classical theory of optical activity together with a set of atomic complex polarizabilities, which are obtained from the analysis of a series of synchrotron radiation CD spectra and their related 3D structures from the PDB. The results of our knowledge-based CD method (KCD) are in good agreement with measured spectra that could include the effect of D-amino acids. Our method also delivers some of the most accurate predictions, in comparison with the calculated spectra from well-established models. Specifically, using a metric of closeness based on normalized absolute deviations between experimental and calculated spectra, the mean values for a series of 57 test proteins give the following figures for such models: 0.26 KCD, 0.27 PDBMD2CD, 0.30 SESCA, and 0.47 DichroCalc. From another point of view, it is worth mentioning the remarkable capabilities of the recent approaches based on artificial intelligence, which can precisely predict the native structure of proteins. The structure of proteins, however, is flexible and can be modified by a diversity of environmental factors such as interactions with other molecules, mechanical stresses, variations of temperature, pH, or ionic strength. Experimental CD spectra together with reliable predictions can be utilized to assess eventual secondary structural changes. A similar kind of evaluation can be done for the case of an incomplete protein structure that has been reconstructed by using different approaches. The KCD method can be freely accessed from: https://kcd.cinvestav.mx/.

Direct Polyphenol Attachment on the Surfaces of Magnetite Nanoparticles, Using Vitis vinifera, Vaccinium corymbosum, or Punica granatum.

This study presents an alternative approach to directly synthesizing magnetite nanoparticles (MNPs) in the presence of Vitis vinifera, Vaccinium corymbosum, and Punica granatum derived from natural sources (grapes, blueberries, and pomegranates, respectively). A modified co-precipitation method that combines phytochemical techniques was developed to produce semispherical MNPs that range in size from 7.7 to 8.8 nm and are coated with a ~1.5 nm thick layer of polyphenols. The observed structure, composition, and surface properties of the MNPs@polyphenols demonstrated the dual functionality of the phenolic groups as both reducing agents and capping molecules that are bonding with Fe ions on the surfaces of the MNPs via -OH groups. Magnetic force microscopy images revealed the uniaxial orientation of single magnetic domains (SMDs) associated with the inverse spinel structure of the magnetite (Fe3O4). The samples' inductive heating (H0 = 28.9 kA/m, f = 764 kHz), measured via the specific loss power (SLP) of the samples, yielded values of up to 187.2 W/g and showed the influence of the average particle size. A cell viability assessment was conducted via the MTT and NRu tests to estimate the metabolic and lysosomal activities of the MNPs@polyphenols in K562 (chronic myelogenous leukemia, ATCC) cells.

Processing and Physicochemical Properties of Magnetite Nanoparticles Coated with Curcuma longa L. Extract.

In this work, Curcuma longa L. extract has been used in the synthesis and direct coating of magnetite (Fe3O4) nanoparticles ~12 nm, providing a surface layer of polyphenol groups (-OH and -COOH). This contributes to the development of nanocarriers and triggers different bio-applications. Curcuma longa L. is part of the ginger family (Zingiberaceae); the extracts of this plant contain a polyphenol structure compound, and it has an affinity to be linked to Fe ions. The nanoparticles' magnetization obtained corresponded to close hysteresis loop Ms = 8.81 emu/g, coercive field Hc = 26.67 Oe, and low remanence energy as iron oxide superparamagnetic nanoparticles (SPIONs). Furthermore, the synthesized nanoparticles (G-M@T) showed tunable single magnetic domain interactions with uniaxial anisotropy as addressable cores at 90-180°. Surface analysis revealed characteristic peaks of Fe 2p, O 1s, and C 1s. From the last one, it was possible to obtain the C-O, C=O, -OH bonds, achieving an acceptable connection with the HepG2 cell line. The G-M@T nanoparticles do not induce cell toxicity in human peripheral blood mononuclear cells or HepG2 cells in vitro, but they can increase the mitochondrial and lysosomal activity in HepG2 cells, probably related to an apoptotic cell death induction or to a stress response due to the high concentration of iron within the cell.

Local thermodynamic consistency for integral equations describing single-component fluids.

A new closure approximation is presented here, and it is based on two thermodynamic relations, namely, a particular case of a local expression together with a global thermodynamic condition. The results obtained from this local approximation are compared with thermodynamic and structural properties determined by using well-established closure approximations as well as numerical simulations for different kinds of interaction potentials. In terms of numerical simulations, the new closure delivers results similar to and sometimes better than the well-known closure relations that are specialized in certain types of interactions.

Knowledge-Based Atomic Polarizabilities Used to Model Circular Dichroism Spectra of Proteins.

We present a model of circular dichroism for proteins, which is mainly based on both the classical theory of optical activity and a series of effective atomic polarizabilities. Such polarizabilities are extracted from the analysis of a set of synchrotron radiation circular dichroism spectra and their corresponding three-dimensional structures from the Protein Data Bank. Each modeled spectrum is obtained from the protein atomic coordinates and the identification of its secondary structure elements. The resulting spectra are in good agreement with additional experimental data and also with the predictions of some other models. Among them, only our approach is able to describe the effect of d-amino acids. Moreover, our model is also utilized to evaluate protein reconstructions as well as structural changes.

Secondary structure specified polarizabilities of residues for an evaluation of circular dichroism spectra of proteins.

We present a model of circular dichroism for proteins that is based on the classical electromagnetic theory for optical activity. The two additional constituents of the model are as follows: an appropriate characterization of the secondary structure of the protein residues and the assignment of an effective polarizability to each type of classified residue. The set of effective polarizabilities is obtained by means of a Monte Carlo statistical method, which is used to analyze a series of synchrotron radiation circular dichroism spectra together with their corresponding crystallographic structures. As a result, the predicted spectra from our model are in good accord with experimental data, as well as with the results of some other theoretical approaches.

Brownian-particle motion used to characterize mechanical properties of lipid vesicles.

We present a method that takes advantage of the Brownian motion of a colloidal particle to experimentally determine the area stretch modulus of giant liposomes in solution, in regard to the continuum mechanics theory of elasticity. The characteristic parameters of the corresponding model are measured by using the three-dimensional version of digital video microscopy. Such an approach makes use of the diffraction pattern generated by fluorescent spheres found below the focal plane of the microscope objective, allowing the spatial location of the sphere and, thus, the reconstruction of its trajectory. When this particle probe is localized in the neighborhood of a bilayer membrane, its motion causes an elastic distortion of the membrane that is quantifiable. More importantly, such deformation is related to the mentioned modulus, whose measured values are consistent with experimental data obtained through well-known techniques.

A molecular dynamics study proposing the existence of statistical structural heterogeneity due to chain orientation in the POPC-cholesterol bilayer.

We performed molecular dynamics simulations of a lipid bilayer consisting of POPC and cholesterol at temperatures from 283 to 308K and cholesterol concentrations from 0 to 50% mol/mol. The purpose of this study was to look for the existence of structural differences in the region delimited by these parameters and, in particular, in a region where coexistence of liquid disordered and liquid ordered phases has been proposed. Our interest in this range of concentration and temperature responds to the fact that polyene ionophore activity varies considerably along it. Two force fields, CHARMM36 and Slipids, were compared in order to determine the most suitable. Both force fields predict non-monotonic behaviors consistent with the existence of phase transitions. We found the presence of lateral structural heterogeneity, statistical in nature, in some of the bilayers occurring in this range of temperatures and sterol concentrations. This heterogeneity was produced by correlated ordering of the POPC tails and not due to cholesterol enrichment, and lasts for tens of nanoseconds. We relate these observations to the action of polyenes in these membranes.

One-bead coarse-grained model for RNA dynamics.

We present a revised version of a coarse-grained model for RNA dynamics. In such approach, the description of nucleotides is reduced to single points that interact between them through a series of effective pair potentials that were obtained from an improved analysis of RNA structures from the Protein Data Bank. These interaction potentials are the main constituents of a Brownian dynamics simulation algorithm that allows to perform a variety of tasks by taking advantage of the reduced number of variables. Such tasks include the prediction of the three-dimensional configuration of a series of test molecules. Moreover, the model permits the inclusion of effective magnesium ions and the ends of the RNA chains can be pulled with an external force to study the process of unfolding. In spite of the simplicity of the model, we obtain a good agreement with the experimental results.

Experimental Determination of High-Order Bending Elastic Constants of Lipid Bilayers.

We present a method to describe the formation of small lipid vesicles in terms of three bending elastic constants that can be experimentally measured. Our method combines a general expression of the elastic free energy of the bilayer and the thermodynamic description of molecular aggregation. The resulting model requires the size distribution of liposomes, which is determined from the X-ray scattered intensity spectra of vesicular dispersions. By using two different preparation methods, we studied a series of vesicular solutions made of distinct lipids and we obtained their corresponding bending elastic constants that are consistent with known bending rigidities.

RNA pseudo-knots simulated with a one-bead coarse-grained model.

We present a revised version of a Monte Carlo simulation model for RNA molecules that was introduced in a previous communication [O. Taxilaga-Zetina, P. Pliego-Pastrana, and M. D. Carbajal-Tinoco, Phys. Rev. E 81, 041914 (2010)]. The basic model consists of a series of knowledge-based pair potentials that were obtained from the statistical analysis of large RNAs belonging to the Protein Data Bank. These effective interactions are then used to dress a polymeric chain that reproduces relatively simple secondary structures (e.g., small hairpins). In order to describe more complicated three-dimensional structures such as pseudo-knots, here we include orientational information for the interaction between nucleotides forming hydrogen bonds, as in the case of the Watson-Crick base pairs. As a result, the simulated molecules obtained through the modified model are now consistent with their corresponding experimental configurations.

Thermodynamically consistent closure approximation for hard spheres systems.

We present a new closure relation that is an extension of the Percus-Yevick approximation. In the proposed closure, we introduce an additional term and a mixing coefficient that can be determined by imposing a condition of thermodynamic self-consistency. Moreover, the mixing coefficient is calculated analytically within a linear approximation. In the case of a monodisperse system of hard spheres, we compare the results of our model to well-established thermodynamic expressions and also to the structural properties of fairly known closure approximations. In the second case, and using an equivalent scheme, the new closure relation is extended to the depletion potential between two large hard spheres immersed in a liquid of small hard spheres. In both cases, the results of our model are in good agreement with numerical simulations performed at intermediate concentrations.

Three-dimensional structures of RNA obtained by means of knowledge-based interaction potentials.

We derive a set of effective potentials describing the interaction between pairs of nucleotides that belong to an RNA molecule. Such interaction potentials are then used as the main constituents of a simplified simulation model, which is tested in the description of small secondary structure motifs. Our simulated RNA hairpins are consistent with the experimental structures obtained by NMR.

Thermodynamically consistent integral equation for soft repulsive spheres.

We present a new closure relation that is an extension of the thermodynamically consistent approximation of Rogers and Young [Phys. Rev. A 30, 999 (1984)]. In the proposed closure, we introduce a nonlinear term along with an additional thermodynamic consistency equation. We compare some thermodynamic and structural properties obtained within our scheme with the corresponding results emerging from other approaches that include numerical simulations and other closure approximations. For the systems considered here, the results derived from our scheme are in better agreement with the reference values of the simulations.

Asymmetry in colloidal diffusion near a rigid wall.

The three-dimensional motion of single colloidal particles close to a plane wall is measured by optical microscopy. In accordance with classical theoretical predictions, we find an asymmetric motion of the particles in the directions parallel and perpendicular to the wall. We also find that, close to the wall, the distribution functions of perpendicular steps are asymmetric, being shorter toward the wall and longer away from it.

Micelles and reverse micelles in the nickel bis(2-ethylhexyl) sulfosuccinate/water/isooctane microemulsion.

The ternary system Ni(2+)(AOT)(2) (nickel 2-bis[2-ethylhexyl] sulfosuccinate)/water/isooctane presents w/o and o/w microemulsions with a Winsor progression (2Phi-3Phi-2Phi), without the addition of salt; the "fish diagram" was obtained for alpha=0.5 and gamma=0.02-0.22. Using static and dynamic light scattering the micellar size, the ratio of water to surfactant, and the density of micelles for this system were estimated. In addition, the mean interfacial curvature as a function of temperature was obtained.