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Improved understanding of cellulose swelling mechanism is beneficial for increasing the hydrolysis efficiency of cellulosic substrates. Here, we report a family 5 glycoside hydrolase ArCel5 isolated from the cellulose-gelatinizing fungus Arthrobotrys sp. CX1. ArCel5 exhibited low specific hydrolysis activity and high cellulose swelling capability, which suggested that this protein might function as an accessory protein. Homology modeling glycosylation detection revealed that ArCel5 is a multi-domain protein including a family 1 carbohydrate-binding module, a glycosylation linker, and a catalytic domain. The adsorption capacity, structural changes and hydrature index of filter paper treated by different ArCel5 mutants demonstrated that CBM1 and linker played an essential role in recognizing, binding and decrystallizing cellulosic substrates, which further encouraged the synergistic action between ArCel5 and cellulases. Notably, glycosylation modification further strengthened the function of the linker region. Overall, our study provides insight into the cellulose decrystallization mechanism by a novel accessory protein ArCel5 that will benefit future applications. [ABSTRACT FROM AUTHOR]

Presents a study on the finding of abnormal protein components in a case of virus hepatitis and Laennec's cirrhosis. Importance of paper electrophoresis to the diagnosis of the disease; Role of paper electrophoresis and chemical fractionation in determining serum protein patterns; Discussion of the abnormal paper electrophoretic components.

The adsorption of a carbohydrate binding module (CBM3) from the Clostridium thermocellum scaffolding protein (CipA) to cellulose was analysed in this work. The effect of CBM-PEG on the drainability of E. globulus and P. sylvestris pulps and on the physical properties of the respective papersheets was also studied. The CBM binding to cellulose is often described as “irreversible”, but this classification does not fully characterize this interaction. Indeed, the results obtained demonstrate that, although the adsorption on cellulose is rather stable, CBM inter-fibre mobility may be observed. The results also showed that the CBM-PEG conjugate improves the drainability of E. globulus and P. sylvestris pulps without affecting the physical properties of the papersheets. [ABSTRACT FROM AUTHOR]

The article presents abstracts of medical research. They include "Dynamics of Spontaneous Apoptosis and Proliferation in Immunocompetent Organs during Perinatal Development of Rats," "A Study of Regulatory Proteins Isolated from Mammalian Liver: Identification in Tissue, Physicochemical Properties, and Biological Effects," and "Molecular-Genetic Analysis of Amphipod Populations in the Zone of Secondary Contact within 50 Years of the Volga-Don Canal Construction."

Body fluid biomarkers are very important, because they can be detected in a non-invasive or minimally invasive way. The discovery of secreted proteins in human body fluids is an essential step toward proteomic biomarker identification for human diseases. Recently, many computational methods have been proposed to predict secreted proteins and achieved some success. However, most of them are based on a manual negative dataset, which is usually biased and therefore limits the prediction performances. In this paper, we first propose a novel positive-unlabeled learning framework to predict secreted proteins in a single body fluid. The secreted protein discovery in a single body fluid is transformed into multiple binary classifications and solved via multi-task learning. Also, an effective convolutional neural network is employed to reduce the overfitting problem. After that, we then improve this framework to predict secreted proteins in multiple body fluids simultaneously. The improved framework adopts a globally shared network to further improve the prediction performances of all body fluids. The improved framework was trained and evaluated on datasets of 17 body fluids, and the average benchmarks of 17 body fluids achieved an accuracy of 89.48%, F1 score of 56.17%, and PRAUC of 58.93%. The comparative results demonstrate that the improved framework performs much better than other state-of-the-art methods in secreted protein discovery. [ABSTRACT FROM AUTHOR]

In the present paper, deep convolutional neural network (DCNN) is applied to multilocus protein subcellular localization as it is more suitable for multi-class classification. There are two main problems with this application. First, the appropriate features for correlation between multiple sites are hard to find. Second, the classifier structure is difficult to determine as it is greatly affected by the distribution of classified data. To solve these problems, a self-evoluting framework using DCNNs for multilocus protein subcellular localization is proposed. It has three characteristics that the previous algorithms do not. The first is that it combines the ant colony algorithm with the DCNN to form a self-evoluting algorithm for multilocus protein subcellular localization. The second is that it randomly groups subcellular sites using a limited random k-labelsets multi-label classification method. It also solves complex problems in a divide-and-conquer approach and proposes a flexible expansion model. The third is that it realizes the random selection feature extraction method in the positioning process and avoids the defects in individual feature extraction methods. The algorithm in the present paper is tested on the human database, and the overall correct rate is 67.17%, which is higher than that for the stacked self-encoder (SAE), support vector machine (SVM), random forest classifier (RF), or single deep convolutional neural network. Graphical abstract [ABSTRACT FROM AUTHOR]

The article discusses the molecular cue that guides the axons of neurons to their target which was developed by David Ginty and Takako Makita at the Johns Hopkins University School of Medicine in Baltimore, Maryland. It is mentioned that one model postulates that each neurons randomly connect to other neurons by using cues such as blood vessels as guides. Makita and Hopkins worked with the neurons positioned where the common carotid artery branches grow. They found out the that activity of genes from endothelin family was higher in the external carotid artery. Results showed that endothelin family of proteins acts as guides for external carotid artery.

The article discusses how Raimund Dutzler, a biochemist at the University of Zurich and his graduate student Ricarda Hilf determine the three-dimensional structures of membrane proteins. At first they could not produce enough protein to make crystals but they fused the channel protein to another protein and obtained crystals. In order to resolve the atomic structure of a protein, one needs numerous sets of extremely precise X-ray-diffraction and fortunately, the team had access to new sensitive X-ray detector called Pilatus at the Swiss Light Source. The team believes that the resulting structure is conserved among all pentameric ligand-gated ion channels and is the first piece of the puzzle.

The article focuses on the reasons why the author has spent nine years pursuing a map of the 450-protein nuclear pore complex (NPC). His fascination by how things move in and about the cell's nucleus contribute with his determination to mapping huge complexes. The author, together with his colleagues, has generated proteomics, biochemical and mass spectrometry data for all NPC proteins. Fitting each protein's volume into its hotspot gives a physical map of the pore. It is considered that this serves as a powerful approach to solve large assemblies.

The article discusses the experimentation of the neurobiologist Guoping Feng and his colleagues concerning the causes of obsessive-compulsive disorder (OCD) through analyzing the mice which lacks one brain protein. The study has showed that the neurons of the mice have responded to glutamate which is different from the reactions of the neurons in human to dopamine or serotonin. The result of the research has illustrated significant implications for the discovery of drugs which has not focused on glutamate synapses.

The article focuses on the collaboration between scientists Antonio Iavarone and Anna Lasorella in exploring the role of a family of proteins in brain cancer. Their study has led them from gene expression to basic cell-division processes, and onto neurobiology. They discovered that a family of proteins essential to the basic processes of cell proliferation and cancer also exerts influence beyond cell division in nervous-system development.

The article focuses on the efforts of co-director Alan Aderem and his colleagues in elucidating the complex networks that regulate the body's immune system. They are using both computational and experimental approaches, with each of the techniques informing and validating the others. The team has suspected that any transcription factors in the first set of genes would turn on genes in the second set, and transcription factors in that set would turn on genes in the third, and so forth.

The article provides an overview of a study conducted by scientist Giulio Superti-Furga and his colleagues on protein complexes. The group studied yeast proteins at Cellzome, the biotechnology firm co-founded by Superti-Furga in Heidelberg, Germany. They discovered that proteins form hundreds of core complexes. They also found out that these proteins can combine with other proteins to gain additional capabilities.

Reports that Robert Sauer and his colleagues offer an insight into what molecular machines work. Focus of the researchers on enzyme called ClpX; Interests of the groups in protein degradation to be unfolded by ClpX; Interpretation of the unfolding process of protein degradation.

Porin of Haemophilus influenzae type b (341 amino acids; M(r) 37782) determines the permeability of the outer membrane to low molecular mass compounds. Purified Hib porin was subjected to chemical modification of lysine residues by succinic anhydride. Electrospray ionization mass spectrometry identified up to 12 modifications per porin molecule. Tryptic digestion of modified Hib porin followed by reverse phase chromatography and matrix assisted laser desorption ionization time-of-flight mass spectrometry mapped the succinylation sites. Most modified lysines are positioned in surface-located loops, numbers 1 and 4 to 7. Succinylated porin was reconstituted into planar lipid bilayers, and biophysical properties were analyzed and compared to Hib porin: there was an increased average single channel conductance compared to Hib porin (1.24 +/- 0.41 vs. 0.85 +/- 0.40 nanosiemens). The voltage-gating activity of succinylated porin differed considerably from that of Hib porin. The threshold voltage for gating was decreased from 75 to 40 mV. At 80 mV, steady-state conductance for succinylated porin was 50-55% of the instantaneous conductance. Hib porin at 80 mV showed a decrease to 89-91% of the instantaneous current levels. We propose that surface-located lysine residues are determinants of voltage gating for porin of Haemophilus influenzae type b. [ABSTRACT FROM AUTHOR]

To cope with environmental stresses, bacteria have developed different strategies, including the production of small heat shock proteins (sHSP). All sHSPs are described for their role as molecular chaperones. Some of them, like the Lo18 protein synthesized by Oenococcus oeni, also have the particularity of acting as a lipochaperon to maintain membrane fluidity in its optimal state following cellular stresses. Lipochaperon activity is poorly characterized and very little information is available on the domains or amino-acids key to this activity. The aim in this paper is to investigate the importance at the protein structure and function level of four highly conserved residues in sHSP exhibiting lipochaperon activity. Thus, by combining in silico, in vitro and in vivo approaches the importance of three amino-acids present in the core of the protein was shown to maintain both the structure of Lo18 and its functions. [ABSTRACT FROM AUTHOR]

Interlayer spray is proposed as a convenient ionization source for direct analysis by mass spectrometry. Two slices of non-absorbent substrate hold the liquid sample to form a sandwich structure. By applying a high voltage to the sample, spray is generated at the tip of the substrate. The sampling procedure can be operated easily in an open condition and the spray is processed in a semi-enclosed condition, which leads to a relatively stable process. An ultralow amount (<2 μL) of the liquid sample can be analyzed without dilution, which ensures that the natural concentration and properties of the target are maintained. Less influence from the substrate is achieved compared with the spray methods based on porous absorbent materials, which results in a sensitivity enhancement of large molecule samples. It is demonstrated that the interlayer spray is applicable for the analysis of various compounds, including therapeutic drugs, peptides, and proteins. Good linearity can be obtained at a concentration as low as 50 ng/mL in the quantitative analysis for imatinib. We also show the ability to identify the chemical residuals on surfaces with high sensitivity by the 'wipe-spray' method, which is useful for the fast screening of illicit substances. Interlayer spray working with mass spectrometry provides a promising method for direct analysis in an ambient environment. [Figure not available: see fulltext.] [ABSTRACT FROM AUTHOR]

Amyotrophic lateral sclerosis (ALS) is a fatal disease. As its pathological mechanisms are not well understood, there are no efficient therapeutics for it at present. While it is highly heterogenous both etiologically and clinically, it has a common salient hallmark, i.e., aberrant protein aggregation (APA). The upstream pathogenesis and the downstream effects of APA in ALS are sophisticated and the investigation of this pathology would be of consequence for understanding ALS. In this paper, the pathomechanism of APA in ALS and the candidate treatment strategies for it are discussed. [ABSTRACT FROM AUTHOR]

The bcl-2 protein plays an essential role in preventing cell death. Its activity is regulated through association with bcl-2 homologous and nonhomologous proteins and also by serine phosphorylation. We now report that bcl-2 can be proteolytically cleaved towards its N-terminus by a cysteine proteinase present in RL-7 lymphoma cell lysates, yielding a major product of apparent MW 20 kDa, different from the products of bcl-2 cleavage by HIV protease. Moreover, bcl-2 proteins mutated for Asp residues at positions 31 and 34 were efficiently cleaved by RL-7 cell lysates, indicating that this proteolytic activity is distinct from the caspase-3 that cleaves bcl-2 at Asp 34. This bcl-2 cleaving activity is inhibited by E-64 and is therefore distinct from the proteinases of the ICE/Ced-3 family (caspases), whereas reciprocally, ICE (caspase-1) is unable to cleave bcl-2. It is optimally active at pH 5, a feature distinguishing it from calpain, another non-ICE cysteine proteinase which has been associated with apoptosis. This novel bcl-2 cleaving protease, although constitutively present in RL-7 cells and resting peripheral blood lymphocytes (PBL) was upregulated following induction of apoptosis in RL-7 cells or mitogen activation in PBL. The N-terminus of bcl-2 which contains the BH4 domain that binds the kinase Raf-1 and the phosphatase calcineurin is essential for anti-apoptotic activity. Its cleavage might provide a novel post-translational mechanism for regulating bcl-2 function and could amplify ongoing programmed cell death. [ABSTRACT FROM AUTHOR]

Rice (Oryza sativa L.) cultivation under non-flooded conditions using polyethylene film as ground mulching materials, namely plastic film-mulching cultivation system (PFMCS), is an alternative to the conventional rice cultivation system in regions where rainfall and fresh water resources are limited. Two-year field trials (1998–1999) were performed in this study to investigate the growth-stage-dependent changes in activities of antioxidative enzymes and lipid peroxidation in leaves of rice subjected to mulching with plastic film or kraft paper and zero mulching under non-flooded conditions compared with continuously flooded treatment. Significantly higher activities of peroxidase (POD), catalase (CAT), ascorbate peroxidase (APX) but lower concentration of malondialdehyde (MDA) were observed in mulching treatments than in zero mulching treatment at all growth stages in the drier growing season (1999). The concentration of MDA was significantly higher especially at late growth stages in zero mulching treatment than in the other treatments. In contrast, essentially no significant difference existed in the activities of the major antioxidant enzymes (except POD) or in the concentration of MDA between any two treatments in the wetter growing season (1998). This change tendency of antioxidant enzyme activity and MDA level over two contrasting growing seasons was in line with both soil and leaf moisture status, and rice yields of different treatments. These results strongly suggest that plastic film-mulching treatment or paper mulching treatment significantly alleviated oxidative damages induced by water-deficit stress in rice. The efficacy of ground-mulching-induced enhancement of antioxidative defense to drought stress is discussed with respect to water deficit status in both soils and rice plants. [ABSTRACT FROM AUTHOR]

Over the last few years, an increasing number of protein mis-localization events have been reported under various conditions. It is important to understand these events and their relationship with complex disorders. Although many efforts had been made in establishing models with statistical or machine learning algorithms, a comprehensive database resource is still missing. Since the records of experimental-validated protein mis-localization events spread across many literatures, a collection of all these reports in a unique website is demanded. In this paper, we created the dbMisLoc database by manually curating conditional protein mis-localization events from various literatures. The dbMisLoc database records the protein localizations, mis-localizations, conditions for mis-localization, and the original reports. The dbMisLoc database allows the users to intuitively view, search, visualize and download protein mis-localization records. The dbMisLoc database integrates a BLAST search engine, which can search mis-localized proteins that are similar to user queries. The dbMisLoc database can be accessed directly through (https://dbml.pufengdu.org). The source code of dbMisLoc database is available from the GitHub repository (https://github.com/quinlanW/dbMisLoc) for free. Users can host their own mirrors of dbMisLoc database on their own servers. [ABSTRACT FROM AUTHOR]

Rhodopsins are light-sensitive proteins which universally exist in prokaryotes and eukaryotes. Type I rhodopsins exist in microbes and are known as microbial rhodopsins, which include various kinds such as bacteriorhodopsins (BR), halorhodopsins (HR), and sensory rhodopsins (SR). Type II rhodopsins, which belong to G-protein-coupled receptors (GPCR), exist in animals, and are collectively known as animal rhodopsins. Type III rhodopsins, also known as heliorhodopsins discovered by Alina Pushkarev in 2018, are distributed globally and exist in eukaryotes, prokaryotes, and even some viruses. Since type III rhodopsin is distinct in its protein sequence when compared to type I and II rhodopsins, it is not considered in this research. Past research has shown that there exists a clear evolution relationship between different kinds of microbial rhodopsins. However, the evolutionary relationship between microbial and animal rhodopsins hasn't been verified yet due to the huge difference between their sequences. Thus, this paper aims to explore the evolution process within microbial rhodopsins as well as the evolutionary relationship between microbial and animal rhodopsins, utilizing phylogenetic trees and transmembrane domain analysis. Results show that HR and SR both evolved from BR. Additionally, by comparing the phylogenetic tree of BR with phylogenetic tree of microbial 16S rRNA, it is discovered that evolution of microbial rhodopsins is significantly different from their host microbes. [ABSTRACT FROM AUTHOR]

Objective: This paper was aimed at unveiling the effect of low-molecular-weight heparin calcium (LMWH) combined with magnesium sulfate and labetalol on coagulation, vascular endothelial function, and pregnancy outcome in early-onset severe preeclampsia (EOSP). Methods: Pregnant women with EOSP were divided into the control group and the study group, each with 62 cases. Patients in the control group were treated with labetalol and magnesium sulfate, and those in the study group were treated with LMWH in combination with the control grou Blood pressure (systolic blood pressure [SBP] and diastolic blood pressure [DBP]), 24-h urine protein, coagulation indices [D-dimer (D-D), plasma fibrinogen (Fg), prothrombin time (PT), activated partial thromboplastin time (APTT), and prothrombin time (TT)], endothelial function [endothelin (ET-1) and nitric oxide (NO)], oxidative stress indices [oxidized low-density lipoproteins (ox-LDL), lipid peroxidation (LPO), superoxide dismutase (SOD), and malondialdehyde (MDA)], pregnancy outcome, and adverse effects occurred in the two groups were compared. Results: After treatment, lower SBP, DBP, and 24-h urine protein levels; lower Fg and D-D levels; higher PT, APPT, and TT levels; higher NO levels; lower ET-1 levels; lower ox-LDL, MDA, and LPO levels; higher SOD levels; and lower incidence of adverse pregnancy and adverse reactions were noted in the study group in contrast to the control group. Conclusion: EOSP patients given with LMWH combined with magnesium sulfate and labetalol can effectively reduce the patient's blood pressure and urinary protein level; improve coagulation function, oxidative stress, and vascular endothelial function indices; reduce the adverse pregnancy outcomes; and improve the safety of treatment. [ABSTRACT FROM AUTHOR]

An amendment to this paper has been published and can be accessed via a link at the top of the paper. [ABSTRACT FROM AUTHOR]

Proteomics is a field dedicated to the analysis of proteins in cells, tissues, and organisms, aiming to gain insights into their structures, functions, and interactions. A crucial aspect within proteomics is protein family prediction, which involves identifying evolutionary relationships between proteins by examining similarities in their sequences or structures. This approach holds great potential for applications such as drug discovery and functional annotation of genomes. However, current methods for protein family prediction have certain limitations, including limited accuracy, high false positive rates, and challenges in handling large datasets. Some methods also rely on homologous sequences or protein structures, which introduce biases and restrict their applicability to specific protein families or structures. To overcome these limitations, researchers have turned to machine learning (ML) approaches that can identify connections between protein features and simplify complex high-dimensional datasets. This paper presents a comprehensive survey of articles that employ various ML techniques for predicting protein families. The primary objective is to explore and improve ML techniques specifically for protein family prediction, thus advancing future research in the field. Through qualitative and quantitative analyses of ML techniques, it is evident that multiple methods utilizing a range of classifiers have been applied for protein family prediction. However, there has been limited focus on developing novel classifiers for protein family classification, highlighting the urgent need for improved approaches in this area. By addressing these challenges, this research aims to enhance the accuracy and effectiveness of protein family prediction, ultimately facilitating advancements in proteomics and its diverse applications. [ABSTRACT FROM AUTHOR]

Orange carotenoid protein (OCP) is a photoactive carotenoprotein involved in photoprotection of cyanobacteria, which uses a keto-catorenoid as a chromophore. When it absorbs blue-green light, it converts from an inactive OCPO orange form to an activated OCPR red form, the latter being able to bind the light-harvesting complexes facilitating thermal dissipation of the excess of absorbed light energy. Several research groups have focused their attention on the photoactivation mechanism, characterized by several steps, involving both carotenoid photophysics and protein conformational changes. Among the used techniques, time-resolved IR spectroscopy have the advantage of providing simultaneously information on both the chromophore and the protein, giving thereby the possibility to explore links between carotenoid dynamics and protein dynamics, leading to a better understanding of the mechanism. However, an appropriate interpretation of data requires previous assignment of marker IR bands, for both the carotenoid and the protein. To date, some assignments have concerned specific α-helices of the OCP backbone, but no specific marker band for the carotenoid was identified on solid ground. This paper provides evidence for the assignment of putative marker bands for three carotenoids bound in three different OCPs: 3′-hydroxyechineone (3′-hECN), echinenone (ECN), canthaxanthin (CAN). Light-induced FTIR difference spectra were recorded in H2O and D2O and compared with spectra of isolated carotenoids. The use of DFT calculations allowed to propose a description for the vibrations responsible of several IR bands. Interestingly, most bands are located at the same wavenumber for the three kinds of OCPs suggesting that the conformation of the three carotenoids is the same in the red and in the orange form. These results are discussed in the framework of recent time-resolved IR studies on OCP. [ABSTRACT FROM AUTHOR]

The protein contents of hydrolyzed sludge supernatant are commonly determined with the Kjeldahl method, but this method suffers from complicated operations, long process times, and large quantities of chemicals consumed. In this paper, the Lowry, bicinchoninic acid (BCA), and Bradford methods were used to test the precision and spiked recovery of proteins from sludge supernatants hydrolyzed by alkaline-thermal hydrolysis (ATH), enzymatic hydrolysis (EH), and ultrasound-assisted enzymatic hydrolysis (UEH), and the results were compared with those obtained with the Kjeldahl method. For all the hydrolytic processes, the sludge protein values determined with the three tested methods were within 0.05 of each other, which met the experimental requirement for accuracy. Both the Lowry and BCA methods had recovery rates of 95–105%, while the Bradford method showed large deviations and was not highly reliable. The three protein determination methods showed significant differences with the Kjeldahl method (P<0.05). However, the relative deviation between the Kjeldahl and BCA methods was the smallest (3–5%), followed by those between the Kjeldahl and the Lowry (11–21%) and Bradford methods (21–90%), and the causes of the deviations were analyzed based on the protein hydrolysate components and the mechanisms for the different detection methods. On the basis of these results, the BCA method was chosen as the most appropriate quantification method for use with sludge protein extraction, and it was used to analyze the protein contents extracted from residual sludge samples obtained from two sewage treatment plants. The reliability of the method was verified, and this lays a foundation for the extraction and reclamation of sludge proteins. [ABSTRACT FROM AUTHOR]

Quantitative determination of tear proteins is critical to our understanding of those ocular diseases with tear protein changes, but remains technically complex due to the small sample volumes available from patients. The aim of this study was to efficiently quantify the tear proteins by SDS-PAGE with an internal standard protein in small tear volumes. Schirmer test paper and capillary tubes were used to collect tear samples. Soybean trypsin inhibitor (SBTI) was used as an external standard or an internal standard to analyze tear samples in 15% SDS-PAGE gel. The total tear protein and its major components were quantified by band densitometry. Total tear protein concentrations were also measured by Bradford assay. Using this internal standard method, we compared differences between tear samples collected by the Schirmer test paper and capillary tube, and then examined the differences detected between tear samples obtained from young and elderly people. Using SBTI as an internal standard in SDS-PAGE, the total tear protein concentrations were determined to be 12.03 ± 0.45 mg/ml, showing no difference from the result determined by the Bradford assay ( P > 0.05). The quantities of the eight major tear protein bands were 2.26 ± 0.07(18.8%), 0.10 ± 0.01(0.8%), 0.63 ± 0.13(5.3%), 0.52 ± 0.07(4.3%), 1.14 ± 0.18(9.5%), 1.33 ± 0.21(11.1%), 2.76 ± 0.16(23.0%), and 2.95 ± 0.13 mg/ml (24.5%), similar to the result obtained by using SBTI as an external standard ( P > 0.05). Comparing the methods of collection, we identified that the Schirmer test paper sampling induced increased concentrations of band 2 (mainly HSA) in tears, and decreased five other major tear protein bands. Comparing total protein concentrations among different age groups, we noted a higher total protein concentration in young people ( P < 0.05). This high protein level was contributed equally by all major tear protein components. Using SBTI as an internal standard, we can simultaneously quantify total tear protein and the major tear protein components by SDS-PAGE densitometry using small volume tears. This method appears promising for use as a diagnostic tool for identifying the occurrence of ocular diseases with tear protein changes. [ABSTRACT FROM AUTHOR]

Hypomagnetic conditions (HMCs) will be an integral part of the complex of factors affecting astronauts in long-term interplanetary missions outside Earth's magnetic field. The adaptation of the human body under these conditions will affect the regulatory processes in various physiological systems, the molecular pathways of which, with the participation of proteins, have not yet been studied. In order to fill this gap, dry blood spots collected on a special paper from healthy volunteers were studied by proteomic methods in two sessions of a model experiment: with HMCs and in a placebo session. The experiment was carried out by the method of double-blind control, with the participation of the same volunteers in both sessions. 1219 different proteins were semiquantitatively determined in the samples. In the HMC series, changes relative to individual values before the experiment series were detected in three proteins: tropomyosin alpha-3 chain (TPM3), abhydrolase domain-containing protein 14B (ABHD14B), and acetylcholinesterase-associated protein (CUTA). However, comparison of the data obtained in the placebo session smoothed out the effect of HMCs on changes in the above proteins. The results may mean either the absence of HMC influence with a short exposure and the absence of a cumulative effect, or they are unreliable due to the insufficient number of subjects in the sample. [ABSTRACT FROM AUTHOR]

One of the most popular measures in the analysis of protein sequence evolution is the ratio of nonsynonymous distance (dN) to synonymous distance (dS). Under the assumption that synonymous substitutions in the coding region are selectively neutral, the dN/dS ratio can be used to statistically detect the adaptive evolution (or purifying selection) if dN/dS > 1 (or dN/dS < 1) significantly. However, due to strong structural constraints and/or variable functional constraints imposed on amino acid sites, most encoding genes in most species have demonstrated dN/dS < 1. Consequently, the statistical power for testing dN/dS = 1 may be insufficient to distinguish between different selection modes. In this paper, we propose a more powerful test, called dN/dS-H, in which a new parameter H, a relative measure of rate variation among sites, was introduced. Given the condition of strong purifying selections at some sites, the dN/dS-H model predicts dN/dS = 1-H for neutral evolution, dN/dS < 1-H for nearly neutral selection, and dN/dS > 1-H for adaptive evolution. The potential of this new method for resolving the neutral-adaptive debates is illustrated by the protein sequence evolution in vertebrates, Drosophila and yeasts, as well as somatic cancer evolution (specialized as the CN/CS-H test). [ABSTRACT FROM AUTHOR]

Three-dimensional protein structure prediction is one of the major challenges in bioinformatics. According to recent research findings, real-valued distance prediction plays a vital role in determining the unique three-dimensional protein structure. This paper proposes a novel methodology involving a deep residual dense network (DRDN) for predicting protein real-valued distance. The features extracted from the given query protein sequence and its corresponding homologous sequences are used for training the model. Multi-aligned homologous sequences for each query protein sequence are retrieved from five different databases using DeepMSA, HHblits, and HITS_PR_HHblits methods. The proposed method yielded outcomes of 3.89, 0.23, 0.45, and 0.63, respectively, corresponding to the evaluation metrics such as Absolute Error, Relative Error, High-accuracy Pairwise Distance Test (PDA), and Pairwise Distance Test (PDT). Further, the contact map is computed based on CASP criteria by converting the predicted real-valued distance, and it is evaluated using the precision metric. It is observed that precision of long-range top L/5 contact prediction on the CASP13 dataset by the proposed method, RaptorX, Zhang, trRosetta, JinboXu & JinLu, and Deepdist are 0.834, 0.657, 0.70, 0.785, 0.786, and 0.812, respectively. Also, Top-L/5 contact prediction on the CASP14 dataset evaluated using average precision resulted in 0.847, 0.707, 0.752, 0.783, 0.792, 0.817, and 0.825 respectively, corresponding to the proposed method, Zhang, RaptorX, trRosetta, Deepdist, JinboXu & JinLu, and Alphafold2. [ABSTRACT FROM AUTHOR]

Recent data suggest that the majority of proteins bind specific metabolites and that such interactions are relevant to metabolic and gene regulation. However, there are no methods to systematically identify functional allosteric protein-metabolite interactions. Here we present an experimental and computational approach for using dynamic metabolite data to discover allosteric regulation that is relevant in vivo. By switching the culture conditions of Escherichia coli every 30 s between medium containing either pyruvate or 13C-labeled fructose or glucose, we measured the reversal of flux through glycolysis pathways and observed rapid changes in metabolite concentration. We fit these data to a kinetic model of glycolysis and systematically tested the consequences of 126 putative allosteric interactions on metabolite dynamics. We identified allosteric interactions that govern the reversible switch between gluconeogenesis and glycolysis, including one by which pyruvate activates fructose-1,6-bisphosphatase. Thus, from large sets of putative allosteric interactions, our approach can identify the most likely ones and provide hypotheses about their function. [ABSTRACT FROM AUTHOR]

A method for constructing protein semantic networks using MEDLINE abstracts is proposed. The publications retrieved by the context search for protein names (relevant) and the related publications were used. The proposed method is based on estimation of semantic connectivity between proteins. The connectivity score was calculated as a function of the number of relevant or related papers found for a pair of proteins. This score was used to construct a semantic network for 150 human proteins belonging to five different metabolic pathways. Analysis of the network demonstrated that the proteins involved in associated molecular processes formed the subgraphs with a high edge density. [ABSTRACT FROM AUTHOR]

An amendment to this paper has been published and can be accessed via a link at the top of the paper. [ABSTRACT FROM AUTHOR]

The original publication of this paper contains a mistake. [ABSTRACT FROM AUTHOR]

This paper describes the start of the Biophysical Chemistry group of prof. Herman J.C. Berendsen (1934-2019) in Groningen, The Netherlands in the years from 1964 to 1974. [ABSTRACT FROM AUTHOR]

In this paper we give the overview of our latest results on the complexation between polyelectrolytes and oppositely charged low-molar mass species, proteins, homopolymers and block copolymers. First, we review the results on the study of the interaction of polythiophene-based polycations with phosphonium and ammonium pendants and their complexation with negatively charged multivalent species followed by fluorescence quenching. We proved that multivalent solutes bind to polyelectrolyte stronger than to previously studied polythiophene, thus, allowing for their application as luminescence sensors. Secondly, we investigated the co-assembly of polyanion with double hydrophilic block copolymer composed of polycationic block and neutral hydrophilic block and followed the complex formation by quenching of fluorescence of the indicator attached to the end of polyanion chain. We discovered that the formed interpolyelectrolyte (IPEC) core of core/shell micelles remains dynamical even after equilibrium was reached thus making such systems suitable materials for targeted delivery of multivalent species. In addition, the formation of micelles with fluid cores was observed as a result of self-assembly of di- and triblock polyelectrolytes containing a hydrophobic block with low glass transition temperature and a positively charged block. We proved their ability to encapsulate and release hydrophobic species from the soft core upon dilution. Moreover, we confirmed their ability to complex with multivalent negatively charged species. The morphology of the formed complex strongly depends on ionic strength: the aggregates formed by micelles bonded at the periphery disrupt with increasing salt concentration and a part of multivalent ions releases into solution. Finally, the multilayered nanoparticles with both soft hydrophobic and IPEC layers were designed by co-assembly between core/shell micelles with a soft core and a positively charged shell, and block polyelectrolyte composed of polyanion and neutral hydrophilic blocks. We showed that the morphology of the particles and the charge of IPEC layer of such multicompartment nanostructures can be controlled by the ratio of oppositely charged monomeric units. [ABSTRACT FROM AUTHOR]

Toxoplasma gondii is a pathogenic protozoan parasite belonging to the apicomplexan phylum that infects the nucleated cells of warm-blooded hosts leading to an infectious disease known as toxoplasmosis. Apicomplexan parasites such as T. gondii can display different mechanisms to control or manipulate host cells signaling at different levels altering the host subcellular genome and proteome. Indeed, Toxoplasma is able to modulate host cell responses (especially immune responses) during infection to its advantage through both structural and functional changes in the proteome of different infected cells. Consequently, parasites can transform the invaded cells into a suitable environment for its own replication and the induction of infection. Proteomics as an applicable tool can identify such critical proteins involved in pathogen (Toxoplasma)-host cell interactions and consequently clarify the cellular mechanisms that facilitate the entry of pathogens into host cells, and their replication and transmission, as well as the central mechanisms of host defense against pathogens. Accordingly, the current paper reviews several proteins (identified using proteomic approaches) differentially expressed in the proteome of Toxoplasma-infected host cells (macrophages and human foreskin fibroblasts) and tissues (brain and liver) and highlights their plausible functions in the cellular biology of the infected cells. The identification of such modulated proteins and their related cell impact (cell responses/signaling) can provide further information regarding parasite pathogenesis and biology that might lead to a better understanding of therapeutic strategies and novel drug targets. [ABSTRACT FROM AUTHOR]

Monocrotophos (MCP) is a broad spectrum organophosphorus insecticide, which is widely used as foliar spray to the different important crops. MCP may reach the soil and the aquatic environment directly or indirectly during and after the application, which leads to the different environmental issues. MCP is found to be associated with neurotoxicity and its toxic effects have been monitored during different stages of neuronal development. Identification of gene expression in MCP-induced neurotoxicity during neuronal developmental stage is a major area of genomic research interest. In accordance with this identification, screening of potential neuroprotective, natural resources are also required as a preventive aspects by targeting the impaired genes. In this current course of work, microarray experiment has been used to identify genes that were expressed in monocrotophos (MCP)-induced mesenchymal stem cells (MSC) and also the neuroprotectant activity of RV on MCP-exposed MSCs. Microarray experiment data have been deposited in NCBI's Gene Expression Omnibus database and are accessible through GEO Series accession number GSE121261. In this paper, we have discussed two important genes NIPBL (nipped-B-like protein) and POU4F1 (POU domain, class 4, transcription factor 1). These genes were found to be significantly expressed in MCP-exposed MSC and show minimum expression in presence of RV. Homology modelling and docking study was done to identify the interaction and binding affinity of resveratrol and its derivatives with NIPBL and POU4F1 protein. Docking analysis shows that RV and its derivatives have strong interaction with NIPBL and POU4F1 protein hence proves the significance of resveratrol as potential neuroprotectant. This paper highlights the hazardous impact of MCP on neuronal development disorders and repairing potentiality of RV and its derivatives on altered genes involved in neuronal diseases. [ABSTRACT FROM AUTHOR]

In this paper the answer to O. B. Ptitsyn's question "What is the role of conserved non-functional residues in apomyoglobin" is presented, which is based on the research results of three laboratories. The role of conserved non-functional apomyoglobin residues in formation of native topology in the molten globule state of this protein is revealed. This fact allows suggesting that the conserved non-functional residues in this protein are indispensable for fixation and maintaining main elements of the correct topology of its secondary structure in the intermediate state. The correct topology is a native element in the intermediate state of the protein. [ABSTRACT FROM AUTHOR]

In this paper, we demonstrate the coupling of synchrotron small angle X-ray scattering (SAXS) to asymmetrical flow-field flow fractionation (AF4) for protein characterization. To the best of our knowledge, this is the first time AF4 is successfully coupled to a synchrotron for on-line measurements on proteins. This coupling has potentially high impact, as it opens the possibility to characterize individual constituents of sensitive and/or complex samples, not suited for separation using other techniques, and for low electron density samples where high X-ray flux is required, e.g., biomolecules and biologics. AF4 fractionates complex samples in native or close to native environment, with low shear forces and system surface area. Many orders of magnitude in size can be fractionated in one measurement, without having to reconfigure the experimental setup. We report AF4 fractionations with correlated UV and statistically adequate SAXS data of bovine serum albumin and a monoclonal antibody and evaluate SAXS data recorded for the two protein systems. [ABSTRACT FROM AUTHOR]

The paper reports on the absorption dynamics of chlorophyll a in a symmetric tetrameric complex of the water-soluble chlorophyll-binding protein BoWSCP. It was measured by a broadband femtosecond laser pump-probe spectroscopy within the range from 400 to 750 nm and with a time resolution of 20 fs-200 ps. When BoWSCP was excited in the region of the Soret band at a wavelength of 430 nm, nonradiative intramolecular conversion S3→S1 was observed with a characteristic time of 83 ± 9 fs. When the complex was excited in the region of the Qy band at 670 nm, relaxation transition between two excitonic states of the chlorophyll dimer was observed in the range of 105 ± 10 fs. Absorption spectra of the excited singlet states S1 and S3 of chlorophyll a were obtained. The delocalization of the excited state between exciton-coupled Chl molecules in BoWSCP tetramer changed in time and depended on the excitation energy. When BoWSCP is excited in the Soret band region, an ultrafast photochemical reaction is observed. This could result from the reduction of tryptophan in the vicinity of chlorophyll. [ABSTRACT FROM AUTHOR]

As an important research field in bioinformatics, protein subcellular location prediction is critical to reveal the protein functions and provide insightful information for disease diagnosis and drug development. Predicting protein subcellular locations remains a challenging task due to the difficulty of finding representative features and robust classifiers. Many feature fusion methods have been widely applied to tackle the above issues. However, they still suffer from accuracy loss due to feature redundancy. Furthermore, multiple protein subcellular locations prediction is more complicated since it is fundamentally a multi-label classification problem. The traditional binary classifiers or even multi-class classifiers cannot achieve satisfactory results. This paper proposes a novel method for protein subcellular location prediction with both single and multiple sites based on deep convolutional neural networks. Specifically, we first obtain the integrated features by simultaneously considering the pseudo amino acid, amino acid index distribution, and physicochemical property. We then adopt deep convolutional neural networks to extract high-dimensional features from the fused feature, removing the redundant preliminary features and gaining better representations of the raw sequences. Moreover, we use the self-attention mechanism and a customized loss function to ensure that the model is more inclined to positive data. In addition, we use random k-label sets to reduce the number of prediction labels. Meanwhile, we employ a hybrid strategy of over-sampling and under-sampling to tackle the data imbalance problem. We compare our model with three representative classification alternatives. The experiment results show that our model achieves the best performance in terms of accuracy, demonstrating the efficacy of the proposed model. [ABSTRACT FROM AUTHOR]

Melibiose-derived AGE (MAGE) is an advanced glycation end-product formed in vitro in anhydrous conditions on proteins and protein-free amino acids during glycation with melibiose. Our previous studies revealed the presence of MAGE antigen in the human body and tissues of several other species, including muscles, fat, extracellular matrix, and blood. MAGE is also antigenic and induces generation of anti-MAGE antibody. The aim of this paper was to identify the proteins modified by MAGE present in human body fluids, such as serum, plasma, and peritoneal fluids. The protein-bound MAGE formed in vivo has been isolated from human blood using affinity chromatography on the resin with an immobilized anti-MAGE monoclonal antibody. Using mass spectrometry and immunochemistry it has been established that MAGE epitope is present on several human blood proteins including serum albumin, IgG, and IgA. In serum of diabetic patients, mainly the albumin and IgG were modified by MAGE, while in healthy subjects IgG and IgA carried this modification, suggesting the novel AGE can impact protein structure, contribute to auto-immunogenicity, and affect function of immunoglobulins. Some proteins in peritoneal fluid from cancer patients modified with MAGE were also observed and it indicates a potential role of MAGE in cancer. [ABSTRACT FROM AUTHOR]

Rapid, non-destructive, and high-throughput analytical methods for samples with complex matrices play an important role in food analysis. Two-dimensional liquid chromatography (2D-LC) is a suitable technique for the efficient separation and sensitive detection of non-volatile organic compounds. It has the characteristics of fast response, high sensitivity, and simple operation. This paper briefly introduces the working principle of 2D-LC, and the research and application in different food analysis by 2D-LC in recent years were reviewed. Against this background, the following conclusions are summarized: 2D-LC can be a powerful tool for the analysis of various food components. Its combination with mass spectrum (MS) contributes to establishing a relatively complete database to achieve the rapid, sensitive, and automatic characterization, which would be the future trend for food analysis. [ABSTRACT FROM AUTHOR]

Protein hot spot residues are functional sites in protein–protein interactions. Biological experimental methods are traditionally used to identify hot spot residues, which is laborious and time-consuming. Thus a variety of computational methods were widely used in recent years. Despite the success of computational methods in hot spot identification, most of them are impractical in reality because they can recognize hot spot residues only from known protein–protein interface residues. Therefore, identifying hot spots from whole protein sequence is a meaningful and interesting issue. However, it will bring extreme imbalance between positive and negative samples. Hot spot residues only account for about 1–2% of whole protein sequences. To address the issue, this paper proposes a two-step ensemble model for identifying hot spot residues from extremely unbalanced data set. The model is composed of 134 classifiers constructed by base KNN and SVM. Compared to the previous methods, our model yields good performance with an F1 score of 0.593 on the BID test set. Furthermore, to validate the robustness of our model, it was tested on other three independent test sets and also achieved good predictions. More importantly, the performance of our model tested on unbalanced data set is comparable with other methods tested on balanced hot spot data set. [ABSTRACT FROM AUTHOR]

Protein oxidation is a topic of indisputable scientific interest given the impact of oxidized proteins on food quality and safety. Carbonylation is regarded as one of the most notable post-translational modifications in proteins and yet, this reaction and its consequences are poorly understood. From a mechanistic perspective, primary protein carbonyls (i.e. α-aminoadipic and γ-glutamic semialdehydes) have been linked to radical-mediated oxidative stress, but recent studies emphasize the role alternative carbonylation pathways linked to the Maillard reaction. Secondary protein carbonyls are introduced in proteins via covalent linkage of lipid carbonyls (i.e. protein-bound malondialdehyde). The high reactivity of protein carbonyls in foods and other biological systems indicates the intricate chemistry of these species and urges further research to provide insight into these molecular mechanisms and pathways. In particular, protein carbonyls are involved in the formation of aberrant and dysfunctional protein aggregates, undergo further oxidation to yield carboxylic acids of biological relevance and establish interactions with other biomolecules such as oxidizing lipids and phytochemicals. From a methodological perspective, the routine dinitrophenylhydrazine (DNPH) method is criticized not only for the lack of accuracy and consistency but also authors typically perform a poor interpretation of DNPH results, which leads to misleading conclusions. From a practical perspective, the biological relevance of protein carbonyls in the field of food science and nutrition is still a topic of debate. Though the implication of carbonylation on impaired protein functionality and poor protein digestibility is generally recognized, the underlying mechanism of such connections requires further clarification. From a medical perspective, protein carbonyls are highlighted as markers of protein oxidation, oxidative stress and disease. Yet, the specific role of specific protein carbonyls in the onset of particular biological impairments needs further investigations. Recent studies indicates that regardless of the origin (in vivo or dietary) protein carbonyls may act as signalling molecules which activate not only the endogenous antioxidant defences but also implicate the immune system. The present paper concisely reviews the most recent advances in this topic to identify, when applicable, potential fields of interest for future studies. [ABSTRACT FROM AUTHOR]

The combination of dried blood spots (DBS) and bottom-up LC-MS-based protein analysis was investigated in the present paper using six model proteins (1 mg/mL of each protein) with different physicochemical properties. Two different materials for DBS were examined: a water-soluble DBS material (carboxymethyl cellulose, (CMC)) and a commercially available (non-soluble) material (DMPK-C). The sample preparation was optimised regarding the water-soluble material and achieving acceptable repeatability of the signal was emphasised. Five microlitres of whole blood were deposited and dried on either CMC or DMPK-C. The samples were dissolved (CMC) or extracted (DMPK-C) prior to tryptic digest and matrix precipitation. The optimization of the sample preparation showed that an increased buffer concentration (100 mM ammonium bicarbonate) for dissolving the DBS samples gave better repeatability combined with a decrease in analyte signal. CMC seemed to add extra variability (RSD 8-60%) into the analysis compared to sample prepared without CMC (RSD 6-36%), although equal performance compared to DMPK-C material (RSD 13-60%) was demonstrated. The stability of the analytes was examined for different storage periods (1 and 4 weeks) and different storage temperatures (−25, 25, and 40 °C). The stability on both CMC (> 70% compared to reference) and DMPK-C (> 50% compared to reference) was acceptable for most of the peptides. This paper shows that both DBS materials can be used in targeted LC-MS-based protein analysis of proteins with different physicochemical properties. [ABSTRACT FROM AUTHOR]

The acute toxicity of polychlorinated dibenzo- p-dioxins/dibenzofurans (PCDD/Fs) was investigated in the earthworm Eisenia andrei using filter paper toxicity test. Protein content, catalase (CAT) activity, and histology of intestinal wall (chloragogen cells and intestinal epithelium) were investigated in earthworms exposed for 48 h to 0 (control), 0.5, 1.0, and 1.5 ng/cm PCDD/Fs. The results showed an increase in the total protein content 1.56- ( p = 0.104), 1.66- ( p = 0.042), and 2.26-fold ( p < 0.001), respectively, compared to control. The average ± standard deviation of tissular CAT activity showed no significant differences; it was 36.01 ± 7.65, 36.17 ± 9.45, 36.08 ± 9.80, and 40.01 ± 6.98 U/g tissue, respectively. However, the average specific activity of CAT ± standard deviation was significantly decreased ( p < 0.001) at all doses compared to control; it was 2.93 ± 0.42, 1.93 ± 0.53, 1.80 ± 0.38, and 1.53 ± 0.44 U/mg protein, respectively. There was a progressive damage in both of the intestinal villi and the chloragogenous tissue associated with the incrementing doses. Since the toxic mixture altered the investigated biomarkers of E. andrei within 48 h, the cellular and molecular alterations resulted from the filter paper contact test could be utilized as a rapid toxicity assessment tool of environmental contamination with dioxins/furans and to assess consequent potential adverse effects on soil biota and other organisms in the ecosystem. [ABSTRACT FROM AUTHOR]

During neurosurgery the freshly secreted extracellular fluid (ECF) from the choroid plexus was sampled with small pieces of application paper in three patients with intractable epilepsy. The samples were analyzed for free amino acids and for soluble proteins. The results were compared with corresponding data on extracellular fluid from the brain surface obtained with dialysis-perfusion as well as with the cerebrospinal fluid (CSF) acquired by lumbar punction. The dialysis data were calibrated against the paper results. The choroid plexus secretion had a high concentration of transthyretin as well as of an unidentified protein with an isoelectric point of 7.4. The cortical ECF exhibited high concentrations of tau-globulin and gamma-trace protein. Among the amino acids, glutamine had lower concentration in the choroid plexus secretion and higher concentrations in the ECF of the brain compared to the CSF. The amino acid derivative ethanolamine exhibited a similar pattern. This was interpreted to demonstrate that these compounds enter the CSF from the brain tissue. In contrast, alanine, serine, and taurine had a lower concentration in the CSF than in the plexus secretion which suggests that they are removed from the CSF by brain tissue. [ABSTRACT FROM AUTHOR]