Computational and bioinformatics tools for understanding disease mechanisms

Computational methods have significantly transformed biomedical research,offering a comprehensive exploration of disease mechanisms and molecular protein functions.This article reviews a spectrum of computational tools and network analysis databases that play a crucial role in identifying potential interactions and signaling networks contributing to the onset of disease states.The utilization of protein/gene interaction and genetic variation databases,coupled with pathway analysis can facilitate the identification of potential drug targets.By bridging the gap between molecular-level information and disease understanding,this review contributes insights into the impactful utilization of computational methods,paving the way for targeted interventions and therapeutic advancements in biomedical research.

Effect of a Post-Anthesis Foliar Application of Nitrogen on Grain Protein and Milling and Baking Quality of Spring Wheat

Hard red spring wheat in North America must be high in protein in order to avoid costly discounts when marketed. Many newer cultivars have higher yield potential but produce relatively lower grain protein levels. A post-anthesis foliar application of urea-ammonium nitrate mixed with equal part water at 33 kg·ha-1 nitrogen (N) can increase grain protein levels by up to one percent. This increase can be profitable when market premiums/discounts for protein are moderate to high. Nitrogen applied post-anthesis consistently increased grain protein content more than the application of the same rate of N to the soil prior to planting. Milling and baking analysis reveals augmenting the protein in this way does not diminish its functionality.

A Simulated Annealing Algorithm for Training Empirical Potential Functions of Protein Folding

In this paper are reported the local minimum problem by means of current greedy algorithm for training the empirical potential function of protein folding on 8623 non-native structures of 31 globular proteins and a solution of the problem based upon the simulated annealing algorithm. This simulated annealing algorithm is indispensable for developing and testing highly refined empirical potential functions.

The biological function of type I receptors of bone morphogenetic protein in bone

Bone morphogenetic proteins （BMPs） have multiple roles in skeletal development, homeostasis and regeneration. BMPs signal via type I and type II serine/threonine kinase receptors （BMPRI and BMPRII）. In recent decades, genetic studies in humans and mice have demonstrated that perturbations in BMP signaling via BMPRI resulted in various diseases in bone, cartilage, and muscles. In this review, we focus on all three types of BMPRI, which consist of activin-like kinase 2 （ALK2, also called type IA activin receptor）, activin- llke kinase 3 （ALK3, also called BMPRIA）, and activin-like kinase 6 （ALK6, also called BMPRIB）. The research areas covered include the current progress regarding the roles of these receptors during myogenesis, chondrogenesis, and osteogenesis. Understanding the physiological and pathological functions of these receptors at the cellular and molecular levels will advance drug development and tissue regeneration for treating musculoskeletal diseases and bone defects in the future.

Chaos game representation of functional protein sequences,and simulation and multifractal analysis of induced measures

Investigating the biological function of proteins is a key aspect of protein studies. Bioinformatic methods become important for studying the biological function of proteins. In this paper, we first give the chaos game representation （CGR） of randomly-linked functional protein sequences, then propose the use of the recurrent iterated function systems （RIFS） in fractal theory to simulate the measure based on their chaos game representations. This method helps to extract some features of functional protein sequences, and furthermore the biological functions of these proteins. Then multifractal analysis of the measures based on the CGRs of randomly-linked functional protein sequences are performed. We find that the CGRs have clear fractal patterns. The numerical results show that the RIFS can simulate the measure based on the CGR very well. The relative standard error and the estimated probability matrix in the RIFS do not depend on the order to link the functional protein sequences. The estimated probability matrices in the RIFS with different biological functions are evidently different. Hence the estimated probability matrices in the RIFS can be used to characterise the difference among linked functional protein sequences with different biological functions. From the values of the Dq curves, one sees that these functional protein sequences are not completely random. The Dq of all linked functional proteins studied are multifractal-like and sufficiently smooth for the Cq （analogous to specific heat） curves to be meaningful. Furthermore, the Dq curves of the measure μ based on their CCRs for different orders to link the functional protein sequences are almost identical if q 〉 0. Finally, the Ca curves of all linked functional proteins resemble a classical phase transition at a critical point.

Structural changes of proteins in liver cirrhosis and consequential changes in their function

The liver is the site of synthesis of the majority of circulating proteins.Besides initial polypeptide synthesis,sophisticated machinery is involved in the further processing of proteins by removing parts of them and/or adding functional groups and small molecules tailoring the final molecule to suit its physiological purpose.Posttranslational modifications(PTMs)design a network of molecules with the common protein ancestor but with slightly or considerably varying activity/localization/purpose.PTMs can change under pathological conditions,giving rise to aberrant or overmodified proteins.Undesired changes in the structure of proteins most often accompany undesired changes in their function,such as reduced activity or the appearance of new effects.Proper protein processing is essential for the reactions in living beings and crucial for the overall quality control.Modifications that occur on proteins synthesized in the liver whose PTMs are cirrhosis-related are oxidation,nitration,glycosylation,acetylation,and ubiquitination.Some of them predominantly affect proteins that remain in liver cells,whereas others predominantly occur on proteins that leave the liver or originate from other tissues and perform their function in the circulation.Altered PTMs of certain proteins are potential candidates as biomarkers of liver-related diseases,including cirrhosis.This review will focus on PTMs on proteins whose structural changes in cirrhosis exert or are suspected to exert the most serious functional consequences.

The43,000Growth - associated Protein Functions as a Negative Growth Regulator in Glioma.

Previous molecular analyses of human astrocytomas have identified many genetic changes associated with astrocy-toma formation and progression.In an effort to identify novel gene expression changes associated with astrocytomaformation,which might reveal new potential targets for glioma therapeutic drug design,we used the B8-RAS-transgenic mouse astrocytoma model.Using multiplex gene expression profiling,we found that

Identification of key residues in protein functional movements by using molecular dynamics simulations combined with a perturbation-response scanning method

The realization of protein functional movement is usually accompanied by specific conformational changes,and there exist some key residues that mediate and control the functional motions of proteins in the allosteric process.In the present work,the perturbation-response scanning method developed by our group was combined with the molecular dynamics(MD)simulation to identify the key residues controlling the functional movement of proteins.In our method,a physical quantity that is directly related to protein specific function was introduced,and then based on the MD simulation trajectories,the perturbation-response scanning method was used to identify the key residues for functional motions,in which the residues that highly correlated with the fluctuation of the function-related quantity were identified as the key residues controlling the specific functional motions of the protein.Two protein systems,i.e.,the heat shock protein 70 and glutamine binding protein,were selected as case studies to validate the effectiveness of our method.Our calculated results are in good agreement with the experimental results.The location of the key residues in the two proteins are similar,indicating the similar mechanisms behind the performance of their biological functions.

Insect heat shock proteins and their underlying functions

Considering huge number of insect species in the world,studies of heat shock proteins on insects are still very limited.Special focus of＂Insect heat shock proteins and their underlying functions＂provides a comprehensive knowledge for the given topics,which focuses on the heat shock proteins from four insect species：i）Five heat shock proteins（HSPs）from Cotesia chilonis were identified,and their expressional patterns under different temperatures were examined.

Identification of Three Interactions to Determine the Conformation Change and to Maintain the Function of Kir2.1 Channel Protein

We find that a conserved mutation residue Glu to residue Asp （E303D）, which both have the same polar and charged properties, makes Kit2.1 protein lose its function. To understand the mechanism, we identify three interactions which control the conformation change and maintain the function of the Kit2.1 protein by combining homology modeling and molecular dynamics with targeted molecular dynamics. We find that the E303D mutation weakens these interactions and results in the loss of the related function. Our data indicate that not only the amino residues but also the interactions determine the function of proteins.

Overview on pulse proteins for future foods:ingredient development and novel applications

We are facing the challenge of climate change and food insecurity for a growing population.The current mode of animal protein production via animal agriculture is resource-intensive and unsustainable.Therefore,there is a need to find alternative sources of food protein that are environmentally sustainable.Plant-based proteins,specifically pulse-based proteins,provide a promising solution to the problem.This review aims to provide an overview and perspective on extraction,functionality,digestibility,sensory,and new food applications of pulse proteins.Two main methods,namely wet fractionation and dry fractionation are used to extract pulse-based proteins.As compared to dry fractionation,wet fractionation yields high purity protein,but the process alters the structure and function of the proteins.Various biochemical and physical techniques can be used to assist wet extraction process to increase protein yield and/or reduce extraction time.The main techno-functional properties of plant-based proteins determining their practical applicability are solubility,water/oil holding capacity(WHC/OHC),gelation,emulsification,foaming,and rheological properties.Nutritionally,pulse proteins are deficient in one or more essential amino acids.Strategies to overcome the deficiency are discussed.Volatile and non-volatile compounds inherent to pulses or developed during processing are mostly responsible for the off flavors in the extracted protein.Approaches to improve the pulse protein flavor and remove or modify off-flavors are discussed.Pulse-based protein ingredients have applications in bakery products,pasta,meat analogues,dairy alternatives,and beverages.Beyond these applications,there is a need to explore novel applications of pulse proteins in infant and children’s formula,beverages,breakfast cereals,flavor development,and extruded snack products,develop new applications such as personalized and precision nutrition and bioactive peptides,and employ innovative technologies such as 3D printing,extrusion,and artificial intelligence for pulse protein research.This review presents the current status,limitations,and future perspectives for developing pulse protein ingredients as future foods.This review aims to foster thinking and generate novel ideas for future research.

Ginkgolide B promotes the proliferation and differentiation of neural stem cells following cerebral ischemia/reperfusion injury,both in vivo and in vitro

Neural stem cells have great potential for the development of novel therapies for nervous system diseases.However,the proliferation of endogenous neural stem cells following brain ischemia is insufficient for central nervous system self-repair.Ginkgolide B has a robust neuroprotective effect.In this study,we investigated the cell and molecular mechanisms underlying the neuroprotective effect of ginkgolide B on focal cerebral ischemia/reperfusion injury in vitro and in vivo.Neural stem cells were treated with 20,40 and 60 mg/L ginkgolide B in vitro.Immunofluorescence staining was used to assess cellular expression of neuron-specific enolase,glial fibrillary acid protein and suppressor of cytokine signaling 2.After treatment with 40 and 60 mg/L ginkgolide B,cells were large,with long processes.Moreover,the proportions of neuron-specific enolase-,glial fibrillary acid protein-and suppressor of cytokine signaling 2-positive cells increased.A rat model of cerebral ischemia/reperfusion injury was established by middle cerebral artery occlusion.Six hours after ischemia,ginkgolide B（20 mg/kg） was intraperitoneally injected,once a day.Zea Longa＇s method was used to assess neurological function.Immunohistochemistry was performed to evaluate the proportion of nestin-,neuron-specific enolase-and glial fibrillary acid protein-positive cells.Real-time quantitative polymerase chain reaction was used to measure m RNA expression of brain-derived neurotrophic factor and epidermal growth factor.Western blot assay was used to analyze the expression levels of brain-derived neurotrophic factor and suppressor of cytokine signaling 2.Ginkgolide B decreased the neurological deficit score,increased the proportion of nestin-,neuron-specific enolase-and glial fibrillary acid protein-positive cells,increased the m RNA expression of brain-derived neurotrophic factor and epidermal growth factor,and increased the expression levels of brain-derived neurotrophic factor and suppressor of cytokine signaling 2 in the ischemic penumbra.Together,the in vivo and in vitro findings suggest that ginkgolide B improves neurological function by promoting the proliferation and differentiation of neural stem cells in rats with cerebral ischemia/reperfusion injury.

Physiological Processes Contributing to the Difference in Grain Amino Acid Content Between Two Hybrid Rice(Oryza sativa L.)Cultivars

Improving grain amino acid content of rice(Oryza sativa L.)is essential for the health of consumers.This study was conducted to identify the physiological processes that contribute to the higher grain amino acid content in hybrid rice cultivar Lingliangyou 268 compared to Luliangyou 996.The results showed that total amino acid content in grains was 9%higher in Lingliangyou 268 than in Luliangyou 996.There was no significant difference in grain nitrogen(N)content between Lingliangyou 268 and Luliangyou 996,while ratio of amino acid to N was 6%higher in Lingliangyou 268 compared to Luliangyou 996.A total of 16 differentially expressed proteins related to amino acid metabolism(e.g.,erythronate-4-phosphate dehydrogenase domain containing protein)were identified in grains between Lingliangyou 268 and Luliangyou 996.The identified proteins were involved in 10 molecular functions.Six of the 10 defined functions were related to binding(heterocyclic compound binding,nucleoside phosphate binding,nucleotide binding,organic cyclic compound binding,protein binding,and small molecule binding)and the other 4 defined functions were catalytic activity,enzyme regulator activity,hydrolase activity,and transferase activity.These results indicate that the higher grain amino acid content in Lingliangyou 268 compared to Luliangyou 996 is attributed to increased efficiency of converting N to amino acid that results from altered expression of proteins related to amino acid metabolism.

Fine motor skill training enhances functional plasticity of the corticospinal tract after spinal cord injury

Following central nervous system injury, axonal sprouts form distal to the injury site and extend into the denervated area, reconstructing neural circuits through neural plasticity. How to facilitate this plasticity has become the key to the success of central nervous system repair. It remains controversial whether fine motor skill training contributes to the recovery of neurological function after spinal cord injury. Therefore, we established a rat model of unilateral corticospinal tract injury using a pyramidal tract cutting method. Horizontal ladder crawling and food ball grasping training procedures were conducted 2 weeks before injury and 3 days after injury. The neurological function of rat forelimbs was assessed at 1, 2, 3, 4, and 6 weeks after injury. Axon growth was observed with biotinylated dextran amine anterograde tracing in the healthy corticospinal tract of the denervated area at different time periods. Our results demonstrate that compared with untrained rats, functional recovery was better in the forelimbs and forepaws of trained rats. The number of axons and the expression of growth associated protein 43 were increased at the injury site 3 weeks after corticospinal tract injury. These findings confirm that fine motor skill training promotes central nervous system plasticity in spinal cord injury rats.

In silico protein function prediction:the rise of machine learning-based approaches

Proteins function as integral actors in essential life processes,rendering the realm of protein research a fundamental domain that possesses the potential to propel advancements in pharmaceuticals and disease investigation.Within the context of protein research,an imperious demand arises to uncover protein functionalities and untangle intricate mechanistic underpinnings.Due to the exorbitant costs and limited throughput inherent in experimental investigations,computational models offer a promising alternative to accelerate protein function annotation.In recent years,protein pre-training models have exhibited noteworthy advancement across multiple prediction tasks.This advancement highlights a notable prospect for effectively tackling the intricate downstream task associated with protein function prediction.In this review,we elucidate the historical evolution and research paradigms of computational methods for predicting protein function.Subsequently,we summarize the progress in protein and molecule representation as well as feature extraction techniques.Furthermore,we assess the performance of machine learning-based algorithms across various objectives in protein function prediction,thereby offering a comprehensive perspective on the progress within this field.

NetGO 3.0:Protein Language Model Improves Large-scale Functional Annotations

As one of the state-of-the-art automated function prediction(AFP)methods,NetGO 2.0 integrates multi-source information to improve the performance.However,it mainly utilizes the proteins with experimentally supported functional annotations without leveraging valuable information from a vast number of unannotated proteins.Recently,protein language models have been proposed to learn informative representations[e.g.,Evolutionary Scale Modeling(ESM)-1b embedding] from protein sequences based on self-supervision.Here,we represented each protein by ESM-1b and used logistic regression(LR)to train a new model,LR-ESM,for AFP.The experimental results showed that LR-ESM achieved comparable performance with the best-performing component of NetGO 2.0.Therefore,by incorporating LR-ESM into NetGO 2.0,we developed NetGO 3.0 to improve the performance of AFP extensively.

Characterization of goat whey proteins and their bioactivity and toxicity assay

Goat whey is an industry-discarded dairy by-product that has interesting nutritional value and a nutrient composition with important functional potential,where proteins have a high biological value and play an important role in the organism’s physiology.Therefore,the aim of this study was to identify,quantify,concentrate and investigate the capacity of goat whey proteins to perform different biological activities and to evaluate their acute toxicity.Concentrated proteins were quantified and identified by Bradford,Kjehdal and SDS-PAGE methods.Antibacterial activity was performed against Listeria monocytogenes,Salmonella spp.,Staphylococcus aureus,Pseudomonas aeruginosa and Escherichia coli microorganisms and showed MIC ranging from 15 to 120μg mL-1,with the highest inhibition for L.monocytogenes growth.Antiproliferative activity was performed against human malignant melanoma cells and their proliferation inhibition was up to 66.8%within 72 h of exposure.The highest antioxidant capacity was obtained at concentration 2 mg that showed 29.69%of inhibition of DPPH radical oxidation.The acute toxicity test was performed using Artemia franciscana larvae in which whey proteins were able to preserve larval survival throughout exposure.Thus,we can conclude that goat’s whey has proteins that can play a positive effect on health,with antimicrobial activity and without toxicity.The present study highlights the great potential of goat’s whey to be developed as a safe biopreservative or as a functional ingredient in the food industry.

Molecular evolutionary analysis of gene families encoding DNA recombination and repair proteins and histone demethylases,and their functional implications

Many eukaryotic genes are members of multi-gene families due to gene duplications, which generate new copies that allow functional divergence. However, the relationship between

Prolonging the plasma circulation of proteins by nano- encapsulation with phosphorylcholine-based polymer

Short in vivo circulation is a major hindrance to the widespread adoption of protein therapeutics. Protein nanocapsules generated by encapsulating proteins with a thin layer of phosphorylcholine-based polymer via a two-step encapsulation process exhibited significantly prolonged plasma half-life. Furthermore, by constructing nanocapsules with similar sizes but different surface charges and chemistry, we demonstrated a generic strategy for prolonging the plasma half-life of therapeutic proteins. In an in vitro experiment, four types of bovine serum albumin （BSA） nanocapsules were incubated with fetal bovine serum （FBS） in phosphate buffer saline （PBS）; the cell uptake by HeLa cells was monitored to systematically evaluate the characteristics of the surface chemistry during drculation. Single positron emission tomography-computed tomography （SPECT） was employed to allow real-time observation of the BSA nanoparticle distribution in vivo, as well as quantification of the plasma concentration after intravenous administration. This study offers a practical method for translating a broad range of proteins for clinical use.