Vlad Tudor Popa

Mechanism of Protein Supercharging by Sulfolane and m-Nitrobenzyl Alcohol: Molecular Dynamics Simulations of the Electrospray Process

Electrospray ionization (ESI) allows the production of intact gas-phase ions from proteins in solution. Nondenaturing solvent conditions usually culminate in low ESI charge states. However, many mass spectrometric applications benefit from protein ions that are more highly charged. One way to boost protein charge is the addition of supercharging agents (SCAs) such as sulfolane or m-nitrobenzyl alcohol (m-NBA) to the aqueous solution. The supercharging mechanism remains controversial. We use molecular dynamics (MD) simulations to examine how SCAs affect the behavior of ESI nanodroplets. Simulations were conducted on myoglobin in water, water/sulfolane, and water/m-NBA. Na(+) ions served as surrogate charge carriers instead of H(+). We focus on conditions where the protein initially adopts its native conformation. MD-generated charge states show remarkable agreement with experimental data. Droplet shrinkage is accompanied by Na(+) ejection, consistent with the ion evaporation model (IEM). The droplets segregate into an outer SCA shell and an aqueous core. This core harbors protein and Na(+). Unfavorable SCA solvation restricts Na(+) access to the droplet surface, thereby impeding IEM ejection. Rapid water loss causes SCA enrichment, ultimately forcing all remaining Na(+) to bind the protein. IEM ejection is no longer feasible after this point, such that the protein becomes supercharged by Na(+) trapping. SCA-free droplets produce lower charge states because the aqueous environment ensures a higher IEM efficiency. For all scenarios examined here, proteins are released via solvent evaporation to dryness, as envisioned by the charged residue model. Our data provide the first atomistic view of the supercharging mechanism.

FTIR, XRD, and DSC analysis of the rosemary extract effect on polyethylene structure and biodegradability

Differential scanning calorimetry (DSC) technique enabled the study of the effect of the rosemary (Rosmarinus officinalis) extract on polyethylene foils structure and biodegradability. The polyethylene used for food packaging contains synthetic antioxidants which are often able to migrate and to contaminate the food. Natural extracts with antioxidant properties may be an interesting alternative for the polyethylene fabrication. The influence of the rosemary present in different concentrations in non-irradiated and irradiated polyethylene samples was studied. The biodegradability studies were carried out by incubating the modified polyethylene with the yeast Candida lipolytica. The changes of physical properties and morphological aspects before and after fungal attack were studied by Fourier Transform Infrared Spectroscopy, X-ray diffraction, and DSC. With some exceptions due to the nonuniform character of the investigated samples, the melting peak temperature and crystallization degree were found to decrease with increasing of rosemary content and irradiation. Synergic effects of rosemary and irradiation on the film biodegradability were directly confirmed by optical microscopy.

Analysis of bimodal thermally-induced denaturation of type I collagen extracted from calfskin

The most widely occurring collagen in the extracellular matrix of the mammalian tissues – type I collagen has attracted huge interest from both theoretical and practical points of view. The results presented herein are mainly confined to a study of the thermal stability of type I collagen (CI) extracted from calfskin in acidic solutions (10−2 M HCl). A two-step process associated with the heat-induced denaturation of CI was revealed by using ultra sensitive differential scanning calorimetry. The minor endothermic transition (peak temperatures of about 30.5–30.8 °C) has been assigned to the defibrillation of small supramolecular CI assemblies (occurring in solution) while the major endothermic transition (about 34.8–35.0 °C) has been ascribed to denaturation of CI, consisting of a complete unfolding of the native triple-helical conformation of the collagen molecule. The calorimetric data were supported by information obtained from capillary viscometry performed on the same solutions. The native state of CI (molecular integrity and triple-helical conformation) for all the systems studied in this paper was confirmed by transmission electron microscopy, ultraviolet circular dichroism and capillary viscometry. At the same time, based on the sodium dodecyl sulphate-polyacrylamide gel electrophoresis and an appropriate image processing of the corresponding electropherogram, a certain degree of intramolecular crosslinking of CI was detected, mainly between α1 and α2 chains of the collagen triple-helix. Such a feature seems to be caused by both the nature of the extraction procedure and the storage conditions.

Thermoanalytical study of some salts of3d metals withd-tartaric acid

The processes of dehydration and decomposition of the Mn(II), Fe(II), Co(II), Ni(II), Cu(II) and Zn(II) salts ofd-tartaric acid were studied by using TG, DTG and DTA methods in air or in argon, and also IR-spectroscopy.The equations of thermal decomposition were established. For the dehydration processes, the kinetic parametersn, E andInA were determined.

MicroDSC study of Staphylococcus epidermidis growth

BackgroundA microcalorimetric study was carried out using a Staphylococcus epidermidis population to determine the reproducibility of bacterial growth and the variability of the results within certain experimental parameters (temperature, bacterial concentration, sample thermal history). Reproducibility tests were performed as series of experiments within the same conditions using either freshly prepared populations or samples kept in cold storage. In both cases, the samples were obtained by serial dilution from a concentrated TSB bacterial inoculum incubated overnight.ResultsThe results show that experiments are fairly reproducible and that specimens can be preserved at low temperatures (1 - 2°C) at least 4 days. The thermal signal variations at different temperatures and initial bacterial concentrations obey a set of rules that we identified.ConclusionOur study adds to the accumulating data and confirms available results of isothermal microcalorimetry applications in microbiology and can be used to standardize this method for either research or clinical setting.

Application of Thermal Analysis to the Study of Some Waste Agricultural Products for the Preparation of Active Carbons

TG, DTG and DTA methods were used for the investigation of some waste agricultural products, such as grape seeds, walnut shells, plum and peach stones, which can serve as raw materials for the production of active carbons. It was demonstrated that thermo analytical methods are appropriate to study the thermal characteristics of the above wastes and the data obtained can be applied to the technological processes of active carbon preparation.

Functional, fractal nonlinear response with application to rate processes with memory, allometry, and population genetics

We give a functional generalization of fractal scaling laws applied to response problems as well as to probability distributions. We consider excitations and responses, which are functions of a given state vector. Based on scaling arguments, we derive a general nonlinear response functional scaling law, which expresses the logarithm of a response at a given state as a superposition of the values of the logarithms of the excitations at different states. Such a functional response law may result from the balance of different growth processes, characterized by variable growth rates, and it is the first order approximation of a perturbation expansion similar to the phase expansion. Our response law is a generalization of the static fractal scaling law and can be applied to the study of various problems from physics, chemistry, and biology. We consider some applications to heterogeneous and disordered kinetics, organ growth (allometry), and population genetics. Kinetics on inhomogeneous reconstructing surfaces leads to rate equations described by our nonlinear scaling law. For systems with dynamic disorder with random energy barriers, the probability density functional of the rate coefficient is also given by our scaling law. The relative growth rates of different biological organs (allometry) can be described by a similar approach. Our scaling law also emerges by studying the variation of macroscopic phenotypic variables in terms of genotypic growth rates. We study the implications of the causality principle for our theory and derive a set of generalized Kramers–Kronig relationships for the fractal scaling exponents.

Quercetin Influence on Thermal Denaturation of Bovine Serum Albumin

The effect of quercetin (QUER) binding on bovine serum albumin (BSA) thermal denaturation was systematically investigated by means of differential scanning calorimetry (DSC). Additional information concerning thermodynamic and structural binding parameters was provided by isothermal titration calorimetry (ITC) and molecular docking. The most relevant effect of QUER is manifested in the modification of the two-step thermal fingerprint of protein denaturation. Higher QUER concentrations result in a single-step denaturation thermogram, ascribed to the interplay between specific and nonspecific binding and enhancement of the solvent unfolding action. Analysis of ITC data indicate sequential binding of two molecules of QUER occurring spontaneously at different binding sites of BSA involving hydrophobic, electrostatic and hydrogen binding forces. Identification of QUER binding sites was possible through corroboration of DSC runs in the presence of site markers and molecular docking. Modeling of ligand-protein interaction confirmed the experimental data. On one hand, a neutral form of QUER binds in a nonplanar conformation to Sudlows site I, a large hydrophobic cavity of subdomain IIA of BSA and decreases its thermal stability. On the other hand, a second molecule of QUER, the anionic form, is bound in planar conformation to Sudlows site II, situated in the subdomain IIIA of the folded protein, and increases the thermal stability of the corresponding structural domain of the protein.

Complex interaction of caffeic acid with bovine serum albumin: calorimetric, spectroscopic and molecular docking evidence

Herein, the interaction between caffeic acid (CA), a hydroxycinnamic acid with favorable health impacts through the prevention of degenerative pathologies, and bovine serum albumin (BSA) was investigated. The effect of CA on the conformation and thermal stability of BSA was studied using isothermal titration calorimetry (ITC), differential scanning calorimetry (DSC), circular dichroism (CD) spectroscopy, and molecular docking. Thermodynamic parameters (ΔH, ΔS, and ΔG), number of site types (N), and binding constant (K) were determined by ITC. Competitive binding of ITC with warfarin (WAR) and Ibuprofen (IBP) suggested that one of the BSA binding sites for CA was missed in the fluorescence measurements. Molecular docking studies indicate that CA binds to BSA at two sites located in the IIIA and IIA subdomains of the protein native structure. This confirmed the ITC results of competitive binding. Comprehensive DSC and CD experiments revealed a protein stability enhancement in the presence of CA. At higher concentrations, CA induces a slight decrease in the α-helix content of BSA, as observed in the far-UV CD spectra, whereby a partial unfolding of the protein occurs, as proven via both the DSC and CD experiments. This extensive study provides substantial data regarding the ligand binding effect on the protein structure that is significant for understanding the biological activity of BSA in vivo.

On anti-portfolio effects in science and technology with application to reaction kinetics, chemical synthesis, and molecular biology

The portfolio effect is the increase of the stability of a system to random fluctuations with the increase of the number of random state variables due to spreading the risk among these variables; many examples exist in various areas of science and technology. We report the existence of an opposite effect, the decrease of stability to random fluctuations due to an increase of the number of random state variables. For successive industrial or biochemical processes of independent, random efficiencies, the stability of the total efficiency decreases with the increase of the number of processes. Depending on the variables considered, the same process may display both a portfolio as well as an anti-portfolio behavior. In disordered kinetics, the activation energy of a reaction or transport process is the result of a sum of random components. Although the total activation energy displays a portfolio effect, the rate coefficient displays an anti-portfolio effect. For random-channel kinetics, the stability of the total rate coefficient increases with the average number of reaction pathways, whereas the stability of the survival function has an opposite behavior: it decreases exponentially with the increase of the average number of reaction pathways (anti-portfolio effect). In molecular biology, the total rate of a nucleotide substitution displays a portfolio effect, whereas the probability that no substitutions occur displays an anti-portfolio effect, resulting in faster evolutionary processes due to fluctuations. The anti-portfolio effect emerges for products of random variables or equations involving multiplicative convolution products.