Calculation of the proton chemical shifts as a tool to explain the peculiarities of 1H NMR spectra of protein in a compact denatured state

Using the protein crystal structure the chemical shift dispersions of binase α-CH protons were calculated for protein in native state and in a compact denatured one. The same models of internal fields with different adjusting parameters were used to describe data for protons disposed in regions of both regular and irregular secondary structures. It was shown that peculiarities of 1H NMR spectra, observed for compact denatured proteins, could be explained through fluctuations of hydrogen bonds network in conserved secondary structures

Investigation of compact denatured state of protein by molecular dynamics simulation

The native state can be considered as a unique conformation of the protein molecule with the lowest free energy of residue contacts. In this case, all other conformations correspond to the denatured state. The degree of their compactness varies significantly. Under folding conditions, the compact denatured state rather than the random coil is in equilibrium with native protein. The balance between the main forces of protein folding, the solvophobic interactions and conformational entropy, suggests that some properties of the compact denatured state are close to those of native protein, whereas other properties are close to those of the random coil. To investigate the molecular structure of the compact denatured state, the method of molecular dynamics simulation seems to be very useful

Study of the compact denatured state of a protein by molecular dynamics simulation | Issledovanie kompaktnogo denaturirovannogo sostoianiia belka metodom imitatsii molekuliarnoi dinamiki.

The native state can be considered as a unique conformation of the protein molecule with the lowest free energy of residue contacts. In this case, all other conformations correspond to the denatured state. The degree of their compactness varies significantly. Under folding conditions, the compact denatured state rather than the random coil is in equilibrium with native protein. The balance between the main forces of protein folding, the solvophobic interactions and conformational entropy, suggests that some properties of the compact denatured state are close to those of native protein, whereas other properties are close to those of the random coil. To investigate the molecular structure of the compact denatured state, the method of molecular dynamics simulation seems to be very useful

Calculation of chemical shift dispersion for α-CH protons in binase

Crystallographic data on binase (109 aa) were used to calculate the chemical shift dispersion (CSD) for 99 α-CH protons, taking into account the effects of internal electric and magnetic fields of C=O, C-N, O-H, and aromatic rings of Phe, Tyr, and Trp. Most of the small CSDs (up to ±0.6 ppm) could be described by close sets of fitting parameters reflecting the proton microenvironment. The larger CSDs observed for α-CH protons of residues involved in secondary structure could be explained assuming that the characteristics of peptide groups (orientation of the magnetic anisotropy tensor, dipole moments) change markedly upon hydrogen bonding, and depend on the orientation and lifespan of H-bonds

Analyzing and Mapping Sweat Metabolomics by High-Resolution NMR Spectroscopy

The content of human sweat is studied by high-resolution NMR, and the majority of organic components most often found in sweat of conditionally healthy people are identified. Original and simple tools are designed for sweat sampling from different areas of human body. The minimal surface area needed for sampling is in the range of 50–100 cm2. On all the surface parts of the human body examined in this work, the main constituents forming a sweat metabolic profile are lactate, glycerol, pyruvate, and serine. The only exception is the sole of the foot (planta pedis), where trace amounts of glycerol are found. An attempt is made to explain the presence of specified metabolites and their possible origin

Corporate business management in banks in the conditions of digitalization

Метою статті є аналіз сучасного стану банківського обслуговування корпоративного бізнесу та формування пропозицій щодо його подальшого розвитку в умовах цифровізації. Дослідження проведено з використанням порівняльного аналізу цифрових банківських послуг для корпоративного бізнесу. У статті наведено визначення цифровізації банків. Викормлено еволюцію промислових революцій, яку є рушійною силою цифровізації банківського бізнесу. . Надано перелік обов’язкових та додаткових інструментів оцінки операційного ризику. Викормлено ТОП-10 найбільших банків щодо залучення коштів та кредитування корпоративного бізнесу в Україні у 2021 р. Проведено факторний аналіз, за яким визначено влив чинників на капітал для покриття операційного ризику. Проаналізовано банки України щодо повноти їх політики з управління операційним ризиком та визначено особливості застосування банками інструментарію оцінки операційного ризику. Практична значимість даної роботи полягає у встановленому взаємозв’язку між розвитком цифрових технологій та збільшенням фактів реалізації операційного ризику. Також банкам рекомендовано вести власну базу даних подій операційного ризику і створити спеціальний структурний підрозділ з управління операційним ризиком.The purpose of this article is the analyze of the methodological tools for assessing the operational risk of the bank in a digital economy. The methods used to conduct the research are a comparative analysis of operational risk assessment tools, factor analysis of factors that affect the capital to cover operational risk. Results of the article. The article lists the main digital technologies that affect the economy and banking, and, accordingly, are the causes of operational risk. The connection between the growing necessity for the use of digital technologies and the increase in the number of facts of occurrence of operational risk is established. The need for operational risk assessment and management has been proven. A list of required and additional operational risk assessment tools is provided. A factor analysis was performed, according to which the influence of factors on capital to cover operational risk was determined on the example of one bank. Banks of Ukraine are analyzed for the completeness of their operational risk management policy and the features of banks' using of operational risk assessment tools are identified. Systemically important banks have been identified in which there is no specially authorized unit for operational risk management and which do not accumulate information on operational risk events. The scientific novelty of the article is to prove the relationship between the widespread of digital technologies in the banking sector and the increase in the implementation of operational risk. We also propose to use factor analysis as a tool for assessing operational risk, as well as to create databases in which to record cases of operational risk. The practical importance of this work lies in the established relationship between the development of digital technologies and increasing the facts of operational risk. Banks are also recommended to maintain their own database of operational risk events and to create a special structural unit for operational risk management

Disorder Predictors Also Predict Backbone Dynamics for a Family of Disordered Proteins

Several algorithms have been developed that use amino acid sequences to predict whether or not a protein or a region of a protein is disordered. These algorithms make accurate predictions for disordered regions that are 30 amino acids or longer, but it is unclear whether the predictions can be directly related to the backbone dynamics of individual amino acid residues. The nuclear Overhauser effect between the amide nitrogen and hydrogen (NHNOE) provides an unambiguous measure of backbone dynamics at single residue resolution and is an excellent tool for characterizing the dynamic behavior of disordered proteins. In this report, we show that the NHNOE values for several members of a family of disordered proteins are highly correlated with the output from three popular algorithms used to predict disordered regions from amino acid sequence. This is the first test between an experimental measure of residue specific backbone dynamics and disorder predictions. The results suggest that some disorder predictors can accurately estimate the backbone dynamics of individual amino acids in a long disordered region

Study of the compact denatured state of a protein by molecular dynamics simulation | Issledovanie kompaktnogo denaturirovannogo sostoianiia belka metodom imitatsii molekuliarnoi dinamiki.

The native state can be considered as a unique conformation of the protein molecule with the lowest free energy of residue contacts. In this case, all other conformations correspond to the denatured state. The degree of their compactness varies significantly. Under folding conditions, the compact denatured state rather than the random coil is in equilibrium with native protein. The balance between the main forces of protein folding, the solvophobic interactions and conformational entropy, suggests that some properties of the compact denatured state are close to those of native protein, whereas other properties are close to those of the random coil. To investigate the molecular structure of the compact denatured state, the method of molecular dynamics simulation seems to be very useful

Differences in the processes of beta-lactoglobulin cold and heat denaturations.

The changes in beta-lactoglobulin upon cold and heat denaturation were studied by scanning calorimetry, CD, and NMR spectroscopy. It is shown that, in the presence of urea, these processes of beta-lactoglobulin denaturation below and above 308 K are accompanied by different structural and thermodynamic changes. Analysis of the NOE spectra of beta-lactoglobulin shows that changes in the spin diffusion of beta-lactoglobulin after disruption of the unique tertiary structure upon cold denaturation are much more substantial than those upon heat denaturation. In cold denatured beta-lactoglobulin, the network of residual interactions in hydrophobic and hydrophilic regions of the molecules is more extensive than after heat denaturation. This suggests that upon cold- and heat-induced unfolding, the molecule undergoes different structural rearrangements, passing through different denaturation intermediates. From this point of view, cold denaturation can be considered to be a two stage process with a stable intermediate. A similar equilibrium intermediate can be obtained at 35 degrees C in 6.0 M urea solution, where the molecule has no tertiary structure. Cooling or heating of the solution from this temperature leads to unfolding of the intermediate. However, these processes differ in cooperativity, showing noncommensurate sigmoidal-like changes in efficiency of spin diffusion, ellipticity at 222 nm, and partial heat capacity. The disruption with cooling is accompanied by cooperative changes in heat capacity, whereas with heating the heat capacity changes only gradually. Considering the sigmoidal shape of the heat capacity change an extended heat absorption peak, we propose that the intermediate state is stabilized by enthalpic interactions