Using artificially generated spectral data to improve protein secondary structure prediction from Fourier transform infrared spectra of proteins

Secondary structures of proteins have been predicted using neural networks from their Fourier transform infrared spectra. To improve the generalization ability of the neural networks, the training data set has been artificially increased by linear interpolation. The leave-one-out approach has been used to demonstrate the applicability of the method. Bayesian regularization has been used to train the neural networks and the predictions have been further improved by the maximum-likelihood estimation method. The networks have been tested and standard error of prediction (SEP) of 4.19% for alpha helix, 3.49% for beta sheet, and 3.15% for turns have been achieved. The results indicate that there is a significant decrease in the SEP for each type of structure parameter compared to previous works.     

Rapid monitoring of diabetes-induced lipid peroxidation by Fourier transform infrared spectroscopy: evidence from rat liver microsomal membranes

Increased oxidative stress is the consequence of either enhanced reactive oxygen species (ROS) production or attenuated ROS scavenging capacity, resulting in tissue damage that in most instances is assessed by the measurement of lipid peroxides. In the current study, diabetes-induced lipid peroxidation in rat liver microsomal membranes was investigated by Fourier transform infrared (FT-IR) spectroscopy at different temperatures. The olefinic (CH) band at 3012 cm-1 was used to probe diabetes-induced lipid peroxidation. The intensity and area values of this band of diabetic samples were found to be increased significantly (P<0.05) compared with nondiabetic samples. The increase in olefinic band intensity is attributed mainly to the lipid peroxidation end products. The results of the FT-IR study were found to be in agreement with biochemical studies that revealed a significant increase in malondialdehyde levels of diabetic samples compared with control samples (P<0.05) using the thiobarbituric acid test.     

Effect of progesterone on DPPC membrane: evidence for lateral phase separation and inverse action in lipid dynamics

Interactions of progesterone with zwitterionic dipalmitoyl phosphatidylcholine (DPPC) multilamellar liposomes were investigated as a function of temperature and progesterone concentration by using three non-invasive techniques namely Fourier transform infrared spectroscopy, turbidity at 440 nm, and differential scanning calorimetry. The results reveal that progesterone changes the physical properties of DPPC bilayers by decreasing the main phase-transition temperature, abolishing the pre-transition, broadening the phase-transition profile, disordering the system both in gel and liquid crystalline phase, increasing the dynamics at low concentrations whereas stabilizing the membrane at high concentrations, and inducing phase separation. Progesterone does not change the hydration of the CO groups, while it strengthens the hydrogen bonding between the PO2- groups of lipids and the water molecules around.     

Vitamin E Decreases the Order of the Phospholipid Model Membranes in the Gel Phase: An FTIR Study

The effect of -tocopherol on the frequency of the CH₂ stretching bands of infrared spectra of dipalmitoylphosphotidylcholine multibilayers has been investigated, both in H₂O and ²H₂O buffer, to determine the reason for the discrepancy in the literature between the results of different spectroscopic techniques relating to the effect of -tocopherol on membrane order in the gel phase. In contrast to previous FTIR studies, the present FTIR results indicate that T increases the frequencies of the CH₂ stretching bands in the gel phase, which implies an increase in the number of gauche conformers (increase in disordering), which is in agreement with other ESR and NMR spectroscopic studies.     

CoronaVac (Sinovac) COVID-19 vaccine-induced molecular changes in healthy human serum by infrared spectroscopy coupled with chemometrics

From the beginning of the COVID-19 coronavirus pandemic in December of 2019, the disease has infected millions of people worldwide and caused hundreds of thousands of deaths. Since then, several vaccines have been developed. One of those vaccines is inactivated CoronaVac-Sinovac COVID-19 vaccine. In this proof of concept study, we first aimed to determine CoronaVac-induced biomolecular changes in healthy human serum using infrared spectroscopy. Our second aim was to see whether the vaccinated group can be separated or not from the non-vaccinated group by applying chemometric techniques to spectral data. The results revealed that the vaccine administration induced significant changes in some functional groups belonging to lipids, proteins and nucleic acids. In addition, the non-vaccinated and vaccinated groups were successfully separated from each other by principal component analysis (PCA) and linear discriminant analysis (LDA). This proof-of-concept study will encourage future studies on CoronaVac as well as other vaccines and will lead to make a comparison between different vaccines to establish a better understanding of the vaccination outcomes on serum biomolecules.     

p38α Negatively Regulates Survival and Malignant Selection of Transformed Bronchioalveolar Stem Cells

Lung cancer is the cause of most cancer-related deaths in the Western world. Non-small cell lung cancer accounts for almost 80% of all lung cancers, and 50% of this type are adenocarcinomas. The cellular and molecular origin of this type of lung cancer remains elusive and the mechanisms are poorly known. It is known that K-Ras mutations appear in 25–30% of lung adenocarcinomas and it is the best known single mutation that can be related to lung cancers. Recently, it has been suggested that a putative population of mouse bronchioalveolar stem cells could be considered as the cell of origin of adenocarcinomas. These cells are expanded in the early stages of lung tumorigenesis. We have isolated a population of mouse bronchioalveolar stem cells and induced their transformation by oncogenic K-RasG12. Different approaches have shown that an intracellular network linking the p38α MAPK and the PI3K-Pdk1 pathways is involved in regulating the survival and malignant progression of the transformed cells. Absence of p38α catalytic activity leads to further Pdk1 activation (independent of Akt and Erk activity), enhancing the survival and proliferation of the more malignant lung cancer cells. This specifically selects high Sca-1/Sox9 cells that harbour a stronger colonizing potential, as they maintain their capacity to produce secondary tumors after serial transplantations.     

The effects of flock size and human presence on vigilance and feeding behavior in the Eurasian Coot (<Emphasis Type="Italic">Fulica atra</Emphasis> L.) during breeding season

Group size influences individual vigilance in different bird species. Most studies have shown that animals spend more time for feeding and less time on vigilance when in groups. Apart from group size, additional factors, such as group density, age, sex, and season, are considered to influence vigilance behaviors. The aim of the present study was to investigate the effects of flock size and human presence on vigilance and feeding in the Eurasian Coot (Fulica atra) during the breeding season. This work was performed in Yorukkirka Lake (Eskisehir, Turkey) from March to August 2005. No correlation was found between flock size and vigilance rates during either human absence or presence. On the other hand, when comparing behavioral differences between human presence and absence, humans appeared to have an important negative effect on vigilance rates, vigilance duration, and feeding behavior, regardless of flock size.     

Early alterations in myocardia and vessels of the diabetic rat heart: an FTIR microspectroscopic study

Diabetes mellitus is associated with a high incidence and poor prognosis of cardiovascular disease. The aim of the present study was to examine the effect of relatively short-term (5 weeks) Type I diabetes on the left ventricle, the right ventricle and the vessel (vein) on the left ventricle of the myocardium at molecular level by FTIR (Fourier-transform infrared) microspectroscopy. The rats were categorized into two groups: control group (for the left ventricle myocardium, n=8; for the right ventricle myocardium, n=9; for the vein, n=9) and streptozotocin-induced diabetic group (for the left ventricle myocardium, n=7; for the right ventricle myocardium, n=9; for the vein, n=8). Two adjacent cross-sections of 9 microm thickness were taken from the ventricles of the hearts in two groups of rats by using a cryotome. The first sections were used for FTIR microspectroscopy measurements. The second serial sections were stained by haematoxylin/eosin for comparative purposes. Diabetes caused an increase in the content of lipids, an alteration in protein profile with a decrease in alpha-helix and an increase in beta-sheet structure as well as an increase in glycogen and glycolipid contents in both ventricles and the vein. Additionally, the collagen content was found to be increased in the vein of the diabetic group. The present study demonstrated that diabetes-induced alterations in the rat heart can be detected by correlating the IR spectral changes with biochemical profiles in detail. The present study for the first time demonstrated the diabetes-induced alterations at molecular level in both ventricle myocardia and the veins in relatively short-term diabetes.     

IR and turbidity studies of vitamin E-cholesterol-phospholipid membrane interactions

Binary and tertiary mixture of -tocophenol, cholesterol and dimyristoylphosphatidylcholine in the form of multilamellar liposomes were investigated by Fourier Transform Infrared and visible spectroscopy. Results of the FTIR and turbidity experiments indicate that T decreases or diminishes the effect of cholesterol on the frequency and the bandwidth of the C-H stretching, CH₂ scissoring and C=O stretching bands in FTIR spectra and the turbidity measurements (recorded as absorbance values at 440 nm) in phospholipid model membranes.     

Fourier transform infrared spectroscopy suggests unfolding of loop structures precedes complete unfolding of pig citrate synthase

Pig citrate synthase (PCS) can be used as a model enzyme to gain some insight into the structural basis of protein thermostability. The thermal unfolding characteristics of the specific secondary structure elements within PCS were monitored in detail by following changes in its amide I band components. The result of our study indicates that PCS undergoes irreversible thermal denaturation. Detailed analysis reveals that the different secondary structures display a multistep transition with a major and a minor transition at different temperatures and a very small initial transition at the same temperature (30 degrees C). A plot of temperature-induced changes in (1)H-(2)H exchange, the decrease in the absorbance of the alpha-helical structures, and the increase in the absorbance of aggregated structures all have in common a multistep transition, the minor one centered at 45 degrees C and the major one around 59 degrees C. In contrast, a band that is tentatively assigned to loop structures displays these same minor and major transitions but at lower temperatures (39 and 52 degrees C, respectively). The transition, which occurs at 39-45 degrees C, is not associated with the appearance of aggregated structures. This transition may reflect a change in the tertiary structure of the protein. However, the final transition, which occurs at a higher temperature (52-59 degrees C), reflects unfolding and aggregation of the polypeptide chains. The Fourier transform infrared (FTIR) analysis suggests that PCS has a thermolabile region that unfolds first, some 7 degrees C below the main unfolding of the protein. We propose that this reflects the unfolding of the highly flexible loop segments, which in turn triggers the unfolding of the predominantly helical core structure of PCS.