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It has long been proposed that nuclear RNAs might play an important role in organizing the structure of the nucleus. Initial experiments performed more than 30 years ago found that global disruption of RNA led to visible rearrangements of nuclear organization. Yet, this idea remained controversial for many years, in large part because it was unclear what specific RNAs might be involved, and which specific nuclear structures might be dependent on RNA. Over the past few years, the contributions of RNA to organizing nuclear structures have become clearer with the discovery that many nuclear bodies are enriched for specific noncoding RNAs (ncRNAs); in specific cases, ncRNAs have been shown to be essential for establishment and maintenance of these nuclear structures. More recently, many different ncRNAs have been shown to play critical roles in initiating the three-dimensional (3D) spatial organization of DNA, RNA, and protein molecules in the nucleus. These examples, combined with global imaging and genomic experiments, have begun to paint a picture of a broader role for RNA in nuclear organization and to uncover a unifying mechanism that may explain why RNA is a uniquely suited molecule for this role. In this review, we provide an overview of the history of RNA and nuclear structure and discuss key examples of RNA-mediated bodies, the global roles of ncRNAs in shaping nuclear structure, and emerging insights into mechanisms of RNA-mediated nuclear organization.

Liquid-liquid phase separation drives the formation of biological condensates that play essential roles in transcriptional regulation and signal sensing. Computational modeling could provide high-resolution structural characterizations of these condensates and help uncover physicochemical interactions that dictate their stability. However, many protein molecules involved in phase separation often contain multiple ordered domains connected with flexible, structureless linkers. Simulating such proteins necessitates force fields with consistent accuracy for both folded and disordered proteins. We provide a critical review of existing coarse-grained force fields for disordered proteins and highlight the challenges in their application to folded proteins. After discussing existing algorithms for force field parameterization, we propose an optimization strategy that should lead to computer models with improved transferability across protein types.

Due to the enormous benefits derived from host immune response, immunotherapy has been regarded among the most effective methods for defending against cancers. Nevertheless, developing robust solutions with strong biosecurity as well as the potential to modulate immunogenicity in an effective manner, continues to be a challenge. Peptides’ structural similarities to protein molecules endow them with tremendous ability to solve such issues by either specifically inducing immune responses or enhancing therapeutic effect. Peptide-based substances have a lot of potential as immunotherapeutic agents for treating a variety of cancers. The development of cancer vaccines as well as delivery mechanisms based on peptides by imitating the biological functions of protein having extremely specialized immuno-regulatory roles has been the subject of significant research. Thus, this review gives a systemic comprehension of cancer immunotherapy, role of the immune system, and how peptides pose a huge potential in cancer immunotherapeutic. The role of peptides as vaccine antigens and adjuvants, checkpoint blockades, in targeted delivery and in combinatorial therapies has been addressed. Recent research on the same has been summarised, which demonstrates their enormous advantages, thus allowing their clinical application for cancer immunotherapy in near future.

Oral cancers are the seventh most common cancer globally. While progresses in oral cancer treatment has been made, not all patients respond to these therapies in the same way. To overcome this difficulty, numerous studies have been devoted to identifying biomarkers, which enable early identification of patients who may benefit from a particular treatment modality or at risk for poor prognosis. Biomarkers are protein molecules, gene expression, DNA variants, or metabolites that are derived from tumors, adjacent normal tissue or bodily fluids, which can be acquired prior to treatment and during follow-up, thus extending their use to the evaluation of cancer progression and prediction of treatment outcome. In this review, we employed a basic significance level (< 0.05) as the minimal requirement for candidate biomarkers. Effect sizes of the biomarkers in terms of odds ratio, hazard ratio and area under the receiver operating characteristic curves were subsequently used to evaluate the potential of their clinical use. We identified the CCND1 from the tumor, human papillomavirus, HSP70, and IL-17 from the peripheral blood, and high density of CD45RO+ tumor-infiltrating lymphocytes as the clinically relevant biomarkers for oral cancers.

Liposomes containing small amounts of porphyrin-phospholipid (PoP) have been shown to encapsulate small molecular weight cargos and then release them upon exposure to red light. A putative mechanism involves transient pore formation in the bilayer induced by PoP-mediated photo-oxidation of unsaturated lipids. However, little is known about the properties of such pores. This study assesses whether large carbohydrate and protein molecules could be released from PoP liposomes upon red light exposure. A small fluorophore with ∼0.5 kDa in molecular weight, fluorescently labeled dextrans of ∼5 and ∼500 kDa, and a ∼240 kDa fluorescent protein were passively entrapped in PoP liposomes. When exposed to 665 nm irradiation, liposomes containing PoP, but not liposomes lacking it, released all these cargos in a size-dependent manner that occurred with oxidation of unsaturated lipids included in the bilayer. Thus, this study demonstrates the feasibility of light-triggered release of large biomacromolecules from liposomes.

The main objective of structural biology is to model proteins and other biological macromolecules and link the structural information to function and dynamics. The biological functions of protein molecules and nucleic acids are inherently dependent on their conformational dynamics. Imaging of individual molecules and their dynamic characteristics is an ample source of knowledge that brings new insights about mechanisms of action. The atomic-resolution structural information on most of the biomolecules has been solved by biophysical techniques; either by X-ray diffraction in single crystals or by nuclear magnetic resonance (NMR) spectroscopy in solution. Cryo-electron microscopy (cryo-EM) is emerging as a new tool for analysis of a larger macromolecule that couldn’t be solved by X-ray crystallography or NMR. Now a day’s low-resolution Cryo-EM is used in combination with either X-ray crystallography or NMR. The present review intends to provide updated information on applications like X-ray crystallography, cryo-EM and NMR which can be used independently and/or together in solving structures of biological macromolecules for our full comprehension of their biological mechanisms.

Protein molecules have a unique property of transferring material or information across the impenetrable barrier of a lipid bilayer. This peculiar role of cell “gatekeepers” is especially interesting for the purposes of nanobiotechnology because membrane proteins can be successfully used for communication between two different media separated by a lipid bilayer. This review describes the structural features and properties of transmembrane proteins as the most promising components of modern biosensor devices. Another focus is the methods to produce lipid bilayers attached to a solid surface and to obtain a rigid protein “armature.” These methods make it possible to reconstruct and maintain proteins in the conformation that is functionally active toward a wide range of analytes to be determined. Being highly selective and specific in recognizing receptors or ligands, protein molecules provide an indispensable tool for biomedical analysis and molecular diagnosis.

It is important to reveal the exact cause of poor diffractivity in protein crystals in order to determine the accurate structure of protein molecules. It is shown that there is a large amount of local strain in subgrains of glucose isomerase crystals even though the overall crystal quality is rather high, as shown by clear equal-thickness fringes in X-ray topography. Thus, a large stress is exerted on the subgrains of protein crystals, which could significantly lower the resistance of the crystals to radiation damage. It is also demonstrated that this local strain can be reduced through the introduction of dislocations in the crystal. This suggests that the introduction of dislocations in protein crystals can be effective in enhancing the crystal quality of subgrains of protein crystals. By exploiting this effect, the radiation damage in subgrains could be decreased, leading to the collection of X-ray diffraction data sets with high diffractivity.

We investigate the dromion-like excitations corresponding to intramolecular chain-like proteins. In the present work, the dromion-like excitations are described by using cubic-quintic nonlinear Schrodinger equation (CQNSE) governing the dynamics of proteins and we analytically analyze the velocity (v) of dromion-like structure compared with velocity ( $$v_a$$ ) of acoustical sound waves corresponding to the longitudinal vibrations of protein molecules. Our work is motivated by the effectiveness and powerful mathematical techniques such as modified extended tanh function method and sine–cosine function method for solving CQNSE to obtain dromion-like structures.

Statistical studies of patients' sensitization to allergens make it possible to form a general picture of sensitization for the whole country, help doctors to develop competent tactics for examining patients in the regions and can be used for the development of new formulations of allergy vaccines. Objective . To study the sensitization to inhalation allergens Dermatophagoides pteronyssinus (Der. p.) and Dermatophagoides farinaе (Der. f.) in Moscow and the Moscow region in 2010–2019 and to identify the structure, features and dynamic changes in sensitization to Der. p. and Der. f. based on the analysis of the allergosensitivity profile of patients with IgE-mediated allergic diseases (IgEA). Materials and methods . Blood serum samples of Moscow and the Moscow region residents with IgEA (n = 2849) were examined by RIDA AllergyScreen method in 2010–2019. Results . According to the results of the study spanning the last ten years, about 18–21% of patients with IgEA in Moscow and the Moscow region have sensitization to Der. p. and/or Der. f. There was a statistically significant decrease in sensitization to Der. p. from 2017 to 2019. House dust mites of the type Der. f. more often cause a higher level of sensitization compared to Der. p. Discussion . The data obtained indicate the change in the sensitization of patients to Pyroglyphidae, namely Der. p. against the background of changes in the housing acarocomplex of Moscow and the Moscow region. Features of protein molecules of these species of dust mites may contribute to their varying degrees of the impact on immunological reactivity in the population studied. Conclusions . The decrease in the prevalence of Der. p. is most likely accounted for the changes in the ecosystem of homes of residents of Moscow and the Moscow region.

Circulating extracellular vesicles (EVs)-biological nanomaterials shed from most mammalian cells-have emerged as promising biomarkers, drug delivery vesicles, and treatment modulators. While different types of vesicles are being explored for these applications, it is becoming clear that human EVs are quite heterogeneous even in homogeneous or monoclonal cell populations. Since it is the surface EV protein composition that will largely dictate their biological behavior, high-throughput single EV profiling methods are needed to better define EV subpopulations. Here, we present an antibody-based immunosequencing method that allows multiplexed measurement of protein molecules from individual nanometer-sized EVs. We use droplet microfluidics to compartmentalize and barcode individual EVs. The barcodes/antibody-DNA are then sequenced to determine protein composition. Using this highly sensitive technology, we detected specific proteins at the single EV level. We expect that this technology can be further adapted for multiplexed protein analysis of any nanoparticle.

There is substantiated the topicality of studying hygroscopic properties and porosity of glued reinforced sausage casings of intestinal raw materials. The work aim is to establish storage conditions of glued reinforced sausage casings of intestinal raw materials and their porosity determination. Studies of hygroscopic properties of glued reinforced sausage casings of intestinal raw materials have established a possibility of their long-term storage in a polymer package at a relative humidity no more 60…70 %. It has been established, that at a relative humidity more 70 %, storage is possible only in a steam-tight package. It has been noted, that a storage temperature at that must be selected in the diapason from 0 °С to 25 °С. It has been established, that the sorption isotherm for a model of a reinforcing seam material, obtained from glued intestinal casings using thermal coagulation, is lower than the one of the glued casing of intestinal raw materials relative to the axis of moisture content. The research result is explained by different porosity of samples. Differential functions of pores distribution by radiuses for studied samples have been obtained, and most probable and average radiuses for them have been calculated. The obtained distribution functions have a similar character and close maximum positions relative to the axis that the size-free pore radius is put on. They differ by lines width, testifying to the fact that samples differ by relative number of pores of different radiuses. It has been established, that most probable radiuses of pores for the studied samples differ within error, and average radiuses differ more than twice. It has been noted, that just more developed porous structure is a cause of the fact that the sorption isotherm of glued casings is higher relative to the one of a reinforcing seam material model. It has been noted, that at reinforcing protein molecules of the initial raw material change their structure because of thermal coagulation in such a way that the porous composition of the obtained raw material becomes closer to the monodispersed one

To determine experimentally how the multiple folding pathways of a protein differ, in the order in which the structural parts are assembled, has been a long-standing challenge. To resolve whether structure formation during folding can progress in multiple ways, the complex folding landscape of monellin has been characterized, structurally and temporally, using the multisite time-resolved FRET methodology. After an initial heterogeneous polypeptide chain collapse, structure formation proceeds on parallel pathways. Kinetic analysis of the population evolution data across various protein segments provides a clear structural distinction between the parallel pathways. The analysis leads to a phenomenological model that describes how and when discrete segments acquire structure independently of each other in different subensembles of protein molecules. When averaged over all molecules, structure formation is seen to progress as α-helix formation, followed by core consolidation, then β-sheet formation, and last end-to-end distance compaction. Parts of the protein that are closer in the primary sequence acquire structure before parts separated by longer sequence.

Accurate and sensitive detection of targets in practical biological matrixes such as blood, plasma, serum, or tissue fluid is a frontier issue for most biosensors since the coexistence of both potential reducing agents and protein molecules has the possibility of causing signal interference. Herein, aiming at detection in a complex environment, an advanced and robust peptide-based photocathodic biosensor, which integrated a recognition peptide with an antifouling peptide in one probe electrode, was first proposed. Selecting human chorionic gonadotropin (hCG) as a model target, the recognition peptide with the sequence PPLRINRHILTR was first anchored on the CuBi2O4/Au (CBO/Au) photocathode and then the antifouling peptide with the sequence EKEKEKEPPPPC was further anchored to generate an antifouling biointerface. The peptide-based photocathodic biosensor demonstrated excellent anti-interference to both nonspecific proteins and reducing agents because of the capability of the antifouling peptide. It also exhibited good sensitivity owing to the utilization of the recognition peptide rather than an antibody probe. This peptide-integrated method offers a new perspective for practical applications of photocathodic biosensors.

A theory was developed to explain how charge selectivity is reversed in tight junctions (TJs) between epithelial cells when the sign of the TJ fixed charge changes. An original method that allows for the ion cavity effect was used to calculate the changes in ion solvation energies that occur upon ion transfer in TJs. An equation was derived to describe the Na+ to Cl– permeability ratio of TJs as a function of the concentration and sign of TJ fixed charges and the correlation length of water. The theory agrees with published experimental data that Na+/Cl– selectivity is reversed in Madin–Darby canine kidney (MDCK) cells when claudin-15 protein molecules with a changed sign of amino acid residues are expressed in TJs.

Protein-Protein Interaction (PPI) is a network of protein interconnections which regulates most of the biological methods. A sound state of biota largely depends on synchronized interactions between protein molecules, and any aberrant interactions between protein molecules may lead to complications, including cervical leukemia, tuberculosis, and other neural disorders. In PPI investigation, a plethora of computational methods have been developed over the years to analyze and predict PPI conclusively; however, a majority of these techniques proved to be strenuous and expensive. Therefore, the need for faster, accurate, and critical analysis of PPI warrants the adoption of Machine Learning (ML) methods such as Support Vector Machine (SVM), Artificial Neural Network (ANN), and Random Forest Model (RFM). These classifiers are useful in PPI unfolding in terms of amino acid sequence data. The SVM classifier, in particular, is serviceable in solving a majority of complex classification problems producing robust results in a reasonable time frame. This publication summarizes some state-of-art SVM based PPI investigations and challenges incurred in the application of the SVM method.

Residual dipolar couplings (RDCs) are commonly used in NMR for protein structure and dynamics studies, but it is challenging to generate five independent RDC data sets (required for simultaneous structure and dynamics determination) for most protein molecules in the magnetic field. In this work, a reporter protein with a lanthanide tag is introduced to create five independent alignments. This reporter protein is then attached to target proteins where five independent sets of RDCs are also obtained for the target proteins. The fitting of RDCs provides important information about the structure and dynamics of the target proteins. The method is simple and effective and, in principle, can be used to generate complete sets of RDCs for different protein molecules.

To help investigate the relationship between inflammatory and other symptoms of coronavirus and the protein-protein interactions (PPI) that occur between viral proteins and protein molecules of the host cell, I propose that the electrostatic discharge (ESD) exists including corona discharge to lead to ozone gas. I cite evidence in support of this hypothesis. I hope that the proposed will inspire new studies in finding effective treatments and vaccines for individuals with coronavirus disease in 2019. I suggest possible future studies that may lend more credibility to the proposed.

Pore-forming proteins/toxins (PFPs/PFTs) are the distinct class of membrane-damaging proteins. They act by forming oligomeric pores in the plasma membranes. PFTs and PFPs from diverse organisms share a common mechanism of action, in which the designated pore-forming motifs of the membrane-bound protein molecules insert into the membrane lipid bilayer to create the water-filled pores. One common characteristic of these pore-forming motifs is that they are amphipathic in nature. In general, the hydrophobic sidechains of the pore-forming motifs face toward the hydrophobic core of the membranes, while the hydrophilic residues create the lining of the water-filled pore lumen. Interestingly, pore-forming motifs of the distinct subclass of PFPs/PFTs share very little sequence similarity with each other. Therefore, the common guiding principle that governs the sequence-to-structure paradigm in the mechanism of action of these PFPs/PFTs still remains an enigma. In this article, we discuss this notion using the examples of diverse groups of membrane-damaging PFPs/PFTs.

The article describes the current practice of the relationship between clinicians and laboratory doctors.The dependence in the formation of the list and content of laboratory services on the tasks put forward by the clinician is traced. These may be tests based solely on extractable markers, tests may include extract components, it is possible that in the future the tests will be epitope.The process of protein resorption into the internal environment of a macroorganism is described. The extremely important role of the microbiome of the mucous membranes and the skin in the translational destruction of protein structures is emphasized. The determining factor is that the path of penetration, bypassing the habitat of the microbiome, does not exist. The emphasis is placed on the fact that an allergological reaction is possible only in the case where protein destruction does not lead to complete degradation to amino acids, preserved protein structures, penetrating into the internal environment, are perceived by the immune system as an antigen (allergen) with the subsequent launch of a cascade of humoral and cellular reactions. This suggests that the basis of the pathogenesis of an allergic disease is the insufficiency of protein destruction factors, which are involved both from the macroorganism and from the microbiome.Normalization of the functioning of these factors should lead to the recovery of the allergic patient. ASIT should be considered as a palliative. The main and only resorption mechanism is passive diffusion. The determining role of the degree of dissociation of electrolyte solutions created by protein molecules is estimated. The microbiome is presented as an additional organ, chimeric for a macroorganism, whose role is to form barrier, protective functions, preventing the penetration of antigenic structures into the internal environment. It is concluded that the main task of the allergist doctor at the stage of diagnosis should be the desire to identify sensitization to protein homologs that make up one group. This approach makes it possible to assess the spread of sensitizationamong proteins of homologs of various nature of origin, thereby assessing the most widespread pathological process in a particular patient. Laboratory tests for the production of Simesta take into account the ideas presented, for this reason they are arranged in a system with a thought-out sequence of use, depending on the clinical manifestations and the results of the previous study. In the line of proposals there are tests of the original layout, not offered by other manufacturers. These are linear blots collected exclusively on a group basis, namely the Profilins Polcalcins blot, the PR-10, nsLTP blot, the Storageproteins blot, the Serum albumins, Lipocalins blot, the Tropomyosins blot. The test application algorithm is divided into three levels, flexibly using with reference to a specific clinical situation, the clinician’s doctor has the opportunity to obtain the most possible information at the lowest possible cost. Assessing the prospects for the development of allergology, an assumption is made about the development with subsequent implementation of epitope tests into practice, the results of the study on which will make it possible using mathematical tools to model the structure of the protein structure that has penetrated the internal environment. This will determine the missing factors of the destruction of the allergen in a particular patient, which will lead to pathogenetic treatment.

Antimicrobial peptides (AMPs) are small sized protein molecules which play a crucial role in host inborn immune framework. AMPs with their specific properties are often considered as a barrier against various harmful foreign particles including bacteria, yeast, fungi and virus. These peptides from different sources exhibit diverse functions and structural features. It exploits the unique property of membrane interaction to destroy target organisms and even cellular components are targeted. However, to combat the emerging resistance towards antibiotics, the use of AMPs as natural drugs has gained importance. Efficiency of these peptides can be enhanced by modification in different aspects through in silico approach. In this article we focus on the areas on antimicrobial peptides like source, properties, classification, mechanism of action, resistance and strategies for its applications.

The performance of a sub-100-nm gate-length p-channel TFET-based biosensor (pTFET-BS) covering a wide range of protein-molecules is presented, and for the first time the optimized length-range of t...

Purification and collection of industrial products from oil-water mixtures are commonly implemented processes. However, the efficiencies of such processes can be severely influenced by the presence of emulsifiers that induce the formation of small oil droplets dispersed in the mixtures. Understanding of this emulsifying effect and its counteractions which occur at the oil/water interface is therefore necessary for the improvement of designs of these processes. In this paper, we investigated the interfacial mechanisms of protein-induced emulsification and the opposing surfactant-induced demulsification related to corn oil refinement. At corn oil/water interfaces, the pH-dependent emulsifying function of zein protein, which is the major storage protein of corn, was elucidated by the surface/interface-sensitive sum frequency generation (SFG) vibrational spectroscopy technique. The effective stabilization of corn oil droplets by zein protein was illustrated and correlated to its ordered amide I group at the oil/water interface. Substantial decrease of this ordering with the addition of three industrial surfactants to corn oil-zein solution mixtures was also observed using SFG, which explains the surfactant-induced destabilization and coalescence of small oil droplets. Surfactant-protein interaction was then demonstrated to be the driving force for the disordering of interfacial proteins, either by disrupting protein layers or partially excluding protein molecules from the interface. The ordered zein proteins at the interface were therefore revealed to be the critical factor for the formation of corn oil-water emulsion.

In this work, we present graph-convolutional neural networks for the prediction of binding constants of protein-ligand complexes. We derived the model using multi task learning, where the target variables are the dissociation constant (Kd), inhibition constant (Ki), and half maximal inhibitory concentration (IC50). Being rigorously trained on the PDBbind dataset, the model achieves the Pearson correlation coefficient of 0.87 and the RMSE value of 1.05 in pK units, outperforming recently developed 3D convolutional neural network model Kdeep. ©

Proteins are essential nutrients for humans, but why is there a small amount of proteins excreted through urine? Although healthy people have low levels of protein in the urine, they are rich in variety. The proteins in them may be unnecessary wastes of the body or may even have a toxic effect on the body and must be excreted. Compared with small-molecule metabolites, proteins have a complex structure and various functions. Even a small change at the molecular level will affect their subsequent biological functions. A comprehensive comparison of the molecular level modifications of plasma and urine proteome, the difference may provide clues to the presence of protein in the urine. In this study, a total of 9 healthy people’s urine and 9 healthy people’s plasma samples were collected. The samples were analyzed by high-resolution tandem mass spectrometry and unlabeled quantitative proteomics techniques, and the non-limiting modification identification algorithm was used to to compare molecular modifications between two types of samples as a whole. The results showed that the amount of cysteine (Cys) modification to dehydroalanine (Dha) in the urine proteome was higher than that in plasma. The molecular modification [Cys→Dha] destroys the disulfide bond of the original protein, thereby affecting or even changing the structure and biological function of the protein. Therefore, this study revealed the differences in the overall proteome modification of plasma and urine and pointed out that the structure of protein may be irreversibly changed due to the difference in modification of protein molecules, which in turn caused proteins which lost their functions and even toxic proteins from the blood to be excreted into the urine.

The water-soluble Moringa oleifera lectin (WSMoL) exhibits larvicidal, ovicidal, and oviposition-stimulant effects on Aedes aegypti. Here, we evaluated the influence of gamma irradiation on the activity of WSMoL against A. aegypti. Irradiation with 10 mGy and 10 Gy did not result in the loss of protein molecules; however, irradiated samples presented a distinct profile on gel filtration chromatography. Bis-ANS probe fluorescence was similar when incubated with non-irradiated and 10 mGy-irradiated samples, but less intense fluorescence was observed when incubated with 10 Gy-irradiated WSMoL, indicating the exposure of lectin hydrophobic pockets to water. Irradiation of WSMoL with 10 mGy potentiated its larvicidal and ovicidal activities, while irradiated WSMoL with 10 Gy did not affect the survival of larvae and eggs. The stimulation of oviposition by WSMoL was not observed with irradiated samples. Nevertheless, the hatching rate of eggs laid on vessels containing 10 mGy-irradiated lectin (37%) was lower than that in vessels containing non-irradiated WSMoL (59%). In conclusion, a low dose of gamma irradiation (10 mGy) can be used to improve the deleterious effects of WSMoL on A. aegypti larvae and eggs, while a higher dose (10 Gy) was found to impair the insecticidal effects on this mosquito. These changes are probably linked to conformational changes in the structure of WSMoL.

Obesity is characterized by a certain pathological imbalance in the mechanisms of proteolysis, which results in an increase in the number of degraded protein molecules, their fragments and the peptide pool in the tissues. Despite a significant number of literature on the biochemistry of obesity, the issue of the participation of proteolytic processes in the pathogenesis of obesity, their features and potential effects on metabolism is not well understood. At the same time, the appearance in the bloodstream of atypical protein molecules can be an important component of this pathology. Studying the processes of formation of these molecules can be very useful in planning strategies for correcting the development of this pathological condition, and the molecules described can be used as marker molecules for the development of obesity. The results of this work are the identification of changes in the quantitative and qualitative composition of the peptide component of the fraction of medium-weight molecules in rat tissues under experimental obesity. Chromatography, which separates by size, shows changes in the number of peaks and molecular weight of the peptide molecules in homogenates of obese rat tissue. The results indicate a certain imbalance in the proteolysis system with the development of obesity caused by the consumption of high-calorie diets, which in turn can be a potential cause of the appearance of certain non-physiological mechanisms in the functioning of metabolism in this pathology. This, in turn, can be triggers for the development of concomitant pathology and complicate the correction of the metabolic profile in the development of obesity. Further studies of the characteristics of changes in the peptide pool in rat tissues can contribute to a better understanding of biochemical processes in the context of this pathology, which is important for the development of approaches for the diagnosis and treatment of obesity. The study of potential mechanisms for the development of a dysfunction of the proteolysis system and methods for its correction can be successfully applied when working out strategies for treating various pathological conditions of the body, where a certain imbalance in the functioning of this system occurs.

Human saliva is rich in proteins of variable functions (e.g., enzymes, immunoglobulins, cytokines) and origin (blood plasma, salivary glands, or oral microflora). Circadian dynamics, volume and composition (electrolytes, pH, protein, etc.) of secreted saliva vary with local and systemic physiological and pathophysiological conditions. Therefore, the composition of saliva, protein in particular, has been intensively investigated to identify the potential markers and/or mechanisms of systemic and local diseases. Proteomic techniques used for the analysis of biological fluids have enabled great advances in salivary protein stabilization (as the main precondition for their analysis) and detection of those found in saliva in very low concentrations, including small proteins and peptides. This review brings the main characteristics of current proteomic techniques such as liquid chromatography-mass spectrometry, two-dimensional electrophoresis-mass spectrometry, and surfaceenhanced laser desorption ionization/time of flight/mass spectrometry. These techniques enable simultaneous identification of hundreds and thousands of protein molecules, as well as identifying those of a potential biological value in particular states. This literature review is focused on the state-of-the-art and possibilities offered by proteomic techniques in analyzing the effects of orthodontic appliances on salivary protein composition and searching for potential markers of therapeutic success/failure or for the molecules by which therapeutic effects are achieved., Ljudska slina obiluje proteinima raznolikih funkcija (enzimi, imunoglobulini, citokini) i podrijetla (krvna plazma, žlijezde slinovnice, mikroflora usne šupljine). Dinamika i volumen izlučene sline kao i njezin sastav (elektroliti, pH, proteini) promjenjivi su tijekom dana, u različitim fiziološkim i patofiziološkim stanjima, lokalnim ali i sustavnim. Stoga se sastav sline, osobito proteinski, intenzivno istražuje u smislu identifikacije potencijalnih biljega i/ili mehanizama sustavnih i lokalnih bolesti. Nove tehnike analize proteina (tzv. proteomske tehnike) u biološkim tekućinama omogućile su velik napredak u stabilizaciji proteina sline (temeljni uvjet za njihovu analizu) te otkrivanje i onih koji se u slini nalaze u vrlo malim koncentracijama, uključujući i male proteine i peptide. U ovom članku prikazana su temeljna svojstva suvremenih proteomskih tehnika poput tekućinske kromatografije povezane s masenom spektrometrijom (LC-MS), dvodimenzionalne elektroforezemasene spektrometrije (2-DE-MS) ili surface-enhaced laser desorption/ionization/time of flight/mass spectrometry (SELDITOF- MS). One omogućuju simultano traženje/identifikaciju stotina i tisuća proteinskih molekula i pružaju mogućnost identifikacije onih od potencijalne biološke važnosti u pojedinim stanjima. Ovaj pregled literature usredotočen je na dosadašnje znanje i mogućnosti koje proteomske tehnike pružaju u analizi učinaka ortodontskih aparata na proteinski sastav sline i potragu za potencijalnim biljezima (ne)uspješnosti liječenja ili izvršnim molekulama putem kojih ovaj terapijski postupak ostvaruje učinke.

The degree of oxidation of graphene oxide (GO) has been shown to be important for its toxicity and drug-loading efficiency. However, the effect of its variations on GO-protein interaction remains unclear. Here, we evaluate the effect of the different oxidation degrees of GO on its interaction with human ubiquitin (8.6 kDa) using solution state nuclear magnetic resonance (NMR) spectroscopy in combination with other biophysical techniques. Our findings show that the interaction between the protein and the different GO samples is weak and electrostatic in nature. It involves fast dynamic exchange of the protein molecules from the surface of the GO. As the oxidation degree of the GO increases, the extent of the interaction with the protein changes. The interaction of the protein with GO can thus be modulated by tuning the degree of oxidation. This study opens up new avenues to design appropriate graphenic materials for use in various biomedical fields such as drug delivery, biomedical devices and imaging.

A shift in the fluorescence emission maxima with gradual increase in excitation wavelength is termed as red edge excitation shift (REES). Tryptophan residues are widely utilized as intrinsic fluorescence probe to investigate the protein structures. Wavelength selective tryptophan fluorescence can explore the dynamics of surrounded water molecules, the ubiquitous biological solvent. Thus REES experiment of various protein conformational states can provide significant input to the study of protein folding pathway and it can also be useful to study interaction of proteins with others. In this review article, we shall focus on red edge effect of various multi-tryptophan proteins in their respective native, intermediate and denatured state.

Efforts to sequence single protein molecules in nanopores1-5 have been hampered by the lack of techniques with sufficient sensitivity to discern the subtle molecular differences among all twenty amino acids. Here we report ionic current detection of all twenty proteinogenic amino acids in an aerolysin nanopore with the help of a short polycationic carrier. Application of molecular dynamics simulations revealed that the aerolysin nanopore has a built-in single-molecule trap that fully confines a polycationic carrier-bound amino acid inside the sensing region of the aerolysin. This structural feature means that each amino acid spends sufficient time in the pore for sensitive measurement of the excluded volume of the amino acid. We show that distinct current blockades in wild-type aerolysin can be used to identify 13 of the 20 natural amino acids. Furthermore, we show that chemical modifications, instrumentation advances and nanopore engineering offer a route toward identification of the remaining seven amino acids. These findings may pave the way to nanopore protein sequencing.

A cell contains numerous protein molecules. One of the fundamental goals in molecular cell biology is to determine their subcellular locations since this information is extremely important to both basic research and drug development. In this paper, we report a novel and very powerful predictor called "pLoc_bal-mHum" for predicting the subcellular localization of human proteins based on their sequence information alone. Cross-validation tests on exactly the same experiment-confirmed dataset have indicated that the new predictor is remarkably superior to the existing state-of-the-art predictor in identifying the subcellular localization of human proteins. To maximize the convenience for the majority of experimental scientists, a user-friendly web-server for the new predictor has been established at http://www.jci-bioinfo.cn/pLoc_bal-mHum/, by which users can easily get their desired results without the need to go through the detailed mathematics.

Proteins physiologically exist as "proteoforms" that arise from one gene and acquire additional function by post-translational modifications (PTM). When multiple PTMs coexist on single protein molecules, top-down proteomics becomes the only feasible method of characterization; however, most top-down methods have limited quantitative capacity and insufficient throughput to truly address proteoform biology. Here we demonstrate that top-down proteomics can be quantitative, reproducible, sensitive, and high throughput. The proteoforms of histone H4 are well studied both as a challenging proteoform identification problem and due to their essential role in the regulation of all eukaryotic DNA-templated processes. Much of histone H4's function is obfuscated from prevailing methods due to combinatorial mechanisms. Starting from cells or tissues, after an optimized protein purification process, the H4 proteoforms are physically separated by on-line C3 chromatography, narrowly isolated in MS1 and sequenced with ETD fragmentation. We achieve more than 30 replicates from a single 35-mm tissue culture dish by loading 55 ng of H4 on column. Parallelization and automation yield a sustained throughput of 12 replicates per day. We achieve reproducible quantitation (average biological Pearson correlations of 0.89) of hundreds of proteoforms (about 200-300) over almost six orders of magnitude and an estimated LLoQ of 0.001% abundance. We demonstrate the capacity of the method to precisely measure well-established changes with sodium butyrate treatment of SUM159 cells. We show that the data produced by a quantitative top-down method can be amenable to parametric statistical comparisons and is capable of delineating relevant biological changes at the full proteoform level.

This investigation examines the validity of employing single-solute theory to interpret SAXS measurements on buffered protein solutions—the current practice despite the necessity to regard the buffer components as additional non-scattering solutes rather than as part of the solvent. The present study of bovine serum albumin in phosphate-buffered saline supplemented with 20–100 g/L sucrose as small cosolute has certainly verified the prediction that the experimentally obtained second virial coefficient should contain protein–cosolute contributions. Nevertheless, the second virial coefficient determined for protein solutions supplemented with high cosolute concentrations on the basis of single-solute theory remains a valid means for identifying conditions conducive to protein crystallization, because the return of a slightly negative second virial coefficient based on single-solute theory $$A_{2}^{\text{app}}$$ still establishes the existence of slightly associative interactions between protein molecules, irrespective of the molecular source–protein self-interactions and/or protein–cosolute contributions.

Flexibility had been determined to be an important indicator governing the surface properties of proteins and it was identified using the protease digestion method. In this study, the Maillard reaction between glucose and soy protein isolate was reacted under wet reaction conditions to obtain different flexible protein molecules. The effects of different reaction times (0, 2, 3, 4, 5, 6 h) on the flexibility, emulsifying and foaming properties of conjugates compared with soy protein isolate were studied and the correlation between them was analyzed by SPSS 20 Statistical Software. At the same time, the other structural indexes were also measured. These indexes changes responsible for the variation of flexibility were given detailed analysis. The results showed that emulsifying activity and emulsion stability were positively correlated with flexibility, the correlation coefficients were 0.976 (P

The molecular motors are protein molecules which can be teamed up to form the active mobile nanomachine with special functions. As a new type of therapeutic target different from normal enzymes or receptors, molecular motor plays a unique role in the transportation of intracellular substances, mitosis, and the construction of cytoskeleton. It has also been reported that molecular motors were capable of regulate the tumor cells' proliferation, related to the occurrence of neurodegenerative diseases, and can be used as a nano carrier to deliver drugs. Molecular motors could be divided into linear and rotary molecular motors according to their different forms of motion. The former includes dynein, kinesin, and myosin, and the latter includes ATP synthase and flagellar motors. In addition, there are also some chemically or biologically modified molecular motors to expand or enhance their therapeutic applications. In this review, after the introduction of the classification, structures, main functions and motion mechanism of molecular motors in detail, the application progress of molecular motors in recent years is summarized. Finally, the current problems and future prospect are also discussed in this paper.

We present a detailed heuristic method to quantify the degree of local energetic frustration manifested by protein molecules. Current applications are realized in computational experiments where a protein structure is visualized highlighting the energetic conflicts or the concordance of the local interactions in that structure. Minimally frustrated linkages highlight the stable folding core of the molecule. Sites of high local frustration, in contrast, often indicate functionally relevant regions such as binding, active, or allosteric sites.

Digital proximity ligation assay (PLA) detects single protein molecules with a pair of oligonucleotide-conjugated antibodies and digital PCR (dPCR) readout, which allows absolute quantitation of proteins in single cells with high sensitivity. The pipeline also allows simultaneous measurement of protein and mRNA from the same single cell. The sensitivity of the assay has been further improved with implementation of the assay on a microfluidic system, which enables quantitation of rare protein species, with expression level as low as ~3000 protein molecules per cell.