Changes of structure and functional properties of rice protein in the fresh edible rice during the seed development

It has been reported that fresh edible rice has more bioactive compounds and its protein is easier to digest and has lower hypoallergenic than mature rice. In this paper, the changes in structure and functional properties of proteins at five different stages, including early milky stage(EMS), middle milky stage(MMS), late milky stage(LMS), waxy ripe stage(WS)and ripening stage(RS), during the seed development were investigated. It was found that with the seed developing, the molecular weight of fresh rice protein gradually become larger while the secondary structure changed from the highest content of disordered structure at MMS to the highest content of ordered structure at RS, which affect the surface hydrophobicity and then the functional properties of proteins, including foaming properties, emulsifying properties and oil holding capacity. Fresh rice protein at MMS has the strongest surface hydrophobicity while fresh edible rice protein at RS has the strongest oil holding capability. The results of our study can provide a theoretical basis for the application of fresh rice protein in the food industry and help to develop new fresh edible rice food.

Structure and function of the contactin-associated protein family in myelinated axons and their relationship with nerve diseases

The contactin-associated protein （Caspr） family participates in nerve excitation and conduction, and neurotransmitter release in myelinated axons. We analyzed the structures and functions of the Caspr family- CNTNAP1 （Casprl）, CNTNAP2 （Caspr2）, CNTNAP3 （Caspr3）, CNTNAP4 （Caspr4） and CNTNAP5 （Caspr5）, Casprl-5 is not only involved in the formation of myelinated axons, but also participates in maintaining the stability of adjacent connections. Casprl participates in the formation, differentiation, and proliferation of neurons and astrocytes, and in motor control and cognitive function. We also analyzed the relationship between the Caspr family and neurodegenerative diseases, multiple sclerosis, and autoimmune encephalitis. However, the effects of Caspr on disease course and prognosis remain poorly understood. The effects of Caspr on disease diagnosis and treatment need further investigation.

Inspections of Mobile Phone Microwaves Effects on Proteins Secondary Structure by Means of Fourier Transform Infrared Spectroscopy

In this study the effects of microwaves on the secondary structure of three typical proteins have been investigated. A set of samples of lysozyme, bovine serum albumin and myoglobin in D2O solutions were exposed for 8 hours to mobile phone microwaves at 900 MHz at a magnetic field intensity around 16 mA/m. The relative effects on the secondary structure of the proteins were studied by means of Fourier Transform Infrared Spectroscopy. An increase of the amide I band intensity in the secondary structure of the proteins was observed after the microwaves exposure. Furthermore, a weak shift of the amide I mode of bovine serum albumin and a heavier shift of the amide I of myoglobin occurred after the exposure. In addition, a clear increasing of the β-sheet components with respect to the α-helix content was observed in the spectra of bovine serum albumin and myoglobin after the exposure, suggesting the hypothesis of the formation of aggregates.

Elucidation of the structure, antioxidant, and interfacial properties of flaxseed proteins tailored by microwave treatment

The microwave treatment is commonly applied to flaxseed to release nutrients, inactivate enzymes, remove cyanogens,and intensify flavors. The current study aimed to explore the influences of microwave exposure on the antioxidant and interfacial properties of flaxseed protein isolates(FPI), focusing on the altering composition and molecular structure.The results showed that after microwave exposure(700 W, 1–5 min), more compact assembly of storage proteins and subsequent permeation by membrane fragments of oil bodies occurred for cold-pressing flaxseed flours. Moreover, the particle sizes of FPI was progressively reduced with the decrement ranged from 37.84 to 60.66%(P<0.05), whereas the zeta potential values initially decreased and then substantially recovered during 1–5 min of microwave exposure. The conformation unfolding, chain cross-linking, and depolymerization were sequentially induced for FPI based on the analysis of fluorescence emission spectra, secondary structure, and protein subunit profiles, thereby affecting the dispersion or aggregation properties between albumin and globulin fractions in FPI. Microwave exposure retained specific phenolic acids and superior in vitro antioxidant activities of FPI. The inferior gas–water interface absorption and the loose/porous assembly structure were observed for the foams prepared by FPI, concurrent with obviously shrinking foaming properties upon microwave exposure. Improving oil–water interface activities of FPI produced the emulsion droplets with descending sizes and dense interface coating, which were then mildly destabilized due to the lipid leakage and weakened rheological behavior with microwave exposure extended to 5 min. Our findings elucidated that microwave treatment could tailor the application functionality of protein fractions in flaxseed based on their in situ structural remodeling.

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.

Microwave based reversible unfolding and refolding of alcohol oxidase protein probed by fluorescence and circular dichroism spectroscopy

The reversible effect of microwave mediated denaturation of protein at low exposure time of 10 s has been demonstrated for the first time. The effect of microwave (2.45 GHz and 900 W) was confirmed in a homo-octameric alcohol oxidase in aqueous solution of pH 7.5. The unfolding events did not transverse through any intermediate states and no subunits of the protein were detached during the process. The refolding of the protein achieved at 4℃ for 24 h had regenerated the native enzyme. This reversible refolding approach excludes any chemical reagent and therefore established as simple technique for protein unfolding-folding studies.

QAUST:Protein Function Prediction Using Structure Similarity,Protein Interaction,and Functional Motifs

The number of available protein sequences in public databases is increasing exponentially.However,a sig-nificant percentage of these sequences lack functional annotation,which is essential for the understanding of how bio-logical systems operate.Here,we propose a novel method,Quantitative Annotation of Unknown STructure(QAUST),to infer protein functions,specifically Gene Ontology(GO)terms and Enzyme Commission(EC)numbers.QAUST uses three sources of information:structure information encoded by global and local structure similarity search,biological network information inferred by protein–protein interaction data,and sequence information extracted from functionally discriminative sequence motifs.These three pieces of information are combined by consensus averaging to make the final prediction.Our approach has been tested on 500 protein targets from the Critical Assessment of Functional Annotation(CAFA)benchmark set.The results show that our method provides accurate functional annotation and outperforms other prediction methods based on sequence similarity search or threading.We further demonstrate that a previously unknown function of human tripartite motif-containing 22(TRIM22)protein predicted by QAUST can be experimentally validated.

A versatile building block:the structures and functions of negative-sense single-stranded RNA virus nucleocapsid proteins

Nucleocapsid protein(NPs)of negative-sense single-stranded RNA(-ssRNA)viruses function in different stages of viral replication,transcription,and maturation.Structural investigations show that-ssRNA viruses that encode NPs preliminarily serve as structural building blocks that encapsidate and protect the viral genomic RNA and mediate the interaction between genomic RNA and RNA-dependent RNA polymerase.However,recent structural results have revealed other bio-logical functions of-ssRNA viruses that extend our understanding of the versatile roles of virally encoded NPs.

Comparative Analysis of Different Evaluation Functions for Protein Structure Prediction Under the HP Model

The HP model for protein structure prediction abstracts the fact that hydrophobicity is a dominant force in the protein folding process. This challenging combinatorial optimization problem has been widely addressed through metaheuristics. The evaluation function is a key component for the success of metaheuristics; the poor discrimination of the conventional evaluation function of the HP model has motivated the proposal of alternative formulations for this component. This comparative analysis inquires into the effectiveness of seven different evaluation functions for the HP model. The degree of discrimination provided by each of the studied functions, their capability to preserve a rank ordering among potential solutions which is consistent with the original objective of the HP model, as well as their effect on the performance of local search methods are analyzed. The obtained results indicate that studying alternative evaluation schemes for the HP model represents a highly valuable direction which merits more attention.

Changes in structure and functional properties of whey proteins induced by high hydrostatic pressure:A review

High hydrostatic pressure(HHP)is an alternative technology to heat processing for food product modifications.It does not cause environmental pollution and eliminates the use of chemical additives in food products.This review covers the research conducted to understand the effect of HHP on structure and functional properties of whey proteins.In this paper,the mechanism underlying pressure-induced changes inβ-lactoglobulin andα-lactabumin is also discussed and how they related to functional properties such as hydrophobicity,foam stability,and flavor-binding capacity.

How the “Folding Funnel” Depends on Size and Structure of Proteins?A View from the Scoring Function Perspective

It has been well accepted that the folding energy landscape may resemble a funnel according to the theory of protein folding. This theory of ＂folding funnel＂ has been extensively studied and thought to play an important role in guiding the sampling process of the protein folding and refinement in protein structure prediction. Here, we have investigated the relationship between the ＂funnel likeness＂ of protein folding and the size/structure of the proteins based on a set of non-homologous proteins we have recently evaluated using a statistical mechanicsbased scoring function ITScorePro. It was found that larger proteins that consist of more helix/sheet structures tend to have a higher score-Root Mean Square Deviation（RMSD） correlation（or a more funnel like energy landscape）.Another measurement in protein folding, Z-score, has also shown some correlation with the size of the proteins.As expected, proteins with a better ＂olding funnel likeness＂（or score-RMSD correlation） tend to have a betterpredicted conformation with a lower RMSD from their native structures. These findings can be extremely valuable for the development and improvement of sampling and scoring algorithms for protein structure prediction.

Solution structure and function of proteins relevant to pre-mRNA splicing

Pre-mRNA splicing is a dynamic process. It is catalyzed by the spliceosome which is a large machine formed by an ordered interactions of several small nuclear ribonucleoproteins, U1,

Effects of fabrication of conjugates between different polyphenols and bovine bone proteins on their structural and functional properties

Covalent complexes of bovine bone proteins(BBP)with four polyphenols(chlorogenic acid(CA),quercetin(Q),rutin(R),epigallocatechin gallate(EGCG))with were prepared to increase the high-value utilization degree of bovine bone.The differences in coupling effect and structural and functional properties between the conjugates were also investigated.The results showed that EGCG-BBP had the highest polyphenolic equivalent at 88.05 mg/g protein and the lowest sulfhydryl group content.EGCG-BBP also had the best covalent effect.The SDS-PAGE and fluorescence spectra results revealed that the molecular weight of the conjugates increased significantly as different polyphenols conjugated with the aromatic amino acids in BBP,resulting in significant changes in the structure of EGCG-BBP.Fourier Transform infrared spectroscopy(FTIR)analysis demonstrated that the amide I band of conjugates was slightly shifted,indicating that the polyphenols were covalently bonded with BBP.Based on the results of this study and well-established mechanisms,it could be speculated that the best covalent effect of EGCG may be not only due to the eight phenolic hydroxyl groups but also to its two benzene rings,which are greatly increased in its reaction site.In terms of functional characteristics,EGCG-BBP had the highest 1-diphenyl-2-picryl-hydrazyl radical(DPPH·)scavenging capacity,while Q-BBP had the best solubility.Thus,this study provides a theoretical basis for different polyphenols’structural and functional effects on covalently modified proteins.

Changes in physicochemical characteristics of wheat flour and quality of fresh wet noodles induced by microwave treatment

Fresh wet noodles(FWN) are popular staple foods due to its unique chewy texture and favorable taste. However,the development of FWN is limited by its short shelf life and high browning rate. It has been found that the quantity of original microorganisms in wheat flour produced by traditional method is relatively high, which is detrimental to the processing quality and storage stability of FWN. Consequently, it becomes imperative to decrease microorganisms in wheat flour. Microwave treatment has been regarded as a promising method in the food industry due to its potential in inhibiting microbial growth and inactivating enzymes without causing adverse effect on the food quality. This study aims to investigate the effects of microwave treatment of wheat kernels under different powers(1, 2, 3, 4, 5 kW) on the physicochemical properties of wheat flour and the quality of FWN. The results revealed that microwave treatment had a significant effect on microbial inhibition and enzyme inactivation, wherein the total plate count(TPC) and yeast and mold counts(YMC) decreased by 0.87 lg(CFU/g) and 1.13 lg(CFU/g) respectively, and PPO activity decreased from 11.40 U to 6.31 U. The dough quality properties, such as stability, extensibility, and starch viscosity, improved significantly under different microwave conditions. Confocal laser scanning microscopy(CLSM) images indicated that starch and proteins aggregated gradually in treated flour, altering rheological properties of dough. From the results of scanning electron microscopy(SEM), microwave treatment led to the appearance of disrupted structure in the gluten proteins, but the secondary structure of proteins altered slightly. Rheological properties of dough confirmed that the microwave treatment greatly affected processing characteristics of wheat flour products, with significant advantageous consequences on product quality, especially for textural properties of FWN. Furthermore, FWN darkening could be inhibited noticeably after microwave treatment, thereby prolonging its shelf life. Therefore, microwave treatment could thus be an effective, practical technology to produce low-bacterial flour and thereby enhance its product quality.

High density lipoprotein and cardiovascular diseases

Several epidemiological studies have clearly shown that low plasma levels of high density lipoprotein cholesterol (HDL-C) represent a cardiovascular disease (CVD) risk factor. However, it is unclear if there is a causal association between HDL-C concentration and CVD. A recent study published in the Lancet, which performed two Mendelian randomization analyses, showed that increased HDL-C levels were not associated with a decreased risk of myocardial infarction. These findings, together with the termination of the niacin-based AIM-HIGH trial and the discontinuation of cholesteryl ester transfer protein inhibitor dalcetrapib, challenge the concept that raising of plasma HDL-C will uniformly translate into reductions in CVD risk. HDL particles exhibit several anti-atherosclerotic properties, such as anti-inflammatory and anti-oxidative activities and cellular cholesterol efflux activity. Furthermore, HDL particles are very heterogeneous in terms of size, structure, composition and metabolism. HDL functionality may be associated more strongly with CVD risk than the traditional HDL-C levels. More research is needed to assess the association of the structure of HDL particle with its functionality and metabolism.

Bioinformatic Analysis of Non-VP1 Capsid Protein of Coxsackievirus A6

This study bioinformatically analyzed the non-VP1 capsid proteins（VP2-VP4） of Coxasckievirus A6（CVA6）, with an attempt to predict their basic physicochemical properties, structural/functional features and linear B cell eiptopes. The online tools Sub Loc, Target P and the others from Ex PASy Bioinformatics Resource Portal, and SWISS-MODEL（an online protein structure modeling server）, were utilized to analyze the amino acid（AA） sequences of VP2-VP4 proteins of CVA6. Our results showed that the VP proteins of CVA6 were all of hydrophilic nature, contained phosphorylation and glycosylation sites and harbored no signal peptide sequences and acetylation sites. Except VP3, the other proteins did not have transmembrane helix structure and nuclear localization signal sequences. Random coils were the major conformation of the secondary structure of the capsid proteins. Analysis of the linear B cell epitopes by employing Bepipred showed that the average antigenic indices（AI） of individual VP proteins were all greater than 0 and the average AI of VP4 was substantially higher than that of VP2 and VP3. The VP proteins all contained a number of potential B cell epitopes and some eiptopes were located at the internal side of the viral capsid or were buried. We successfully predicted the fundamental physicochemical properties, structural/functional features and the linear B cell eiptopes and found that different VP proteins share some common features and each has its unique attributes. These findings will help us understand the pathogenicity of CVA6 and develop related vaccines and immunodiagnostic reagents.

iORbase:A database for the prediction of the structures andfunctions of insect olfactory receptors

Insect olfactory receptors(iORs)with atypical 7-transmembrane domains,unlike Chordata olfactory receptors,are not in the GPCR protein family.iORs selectively bind to volatile ligands in the environment and affect essential insect behaviors.In this study,we constructed a new platform(iORbase,https://www.iorbase.com)for the structural and functional analysis of iORs based on a combined algorithm for gene annotation and protein structure prediction.Moreover,it provides the option to calculate the binding affinities and binding residues between iORs and pheromone molecules by virtual screening of docking.Furthermore,iORbase supports the automatic structural and functional prediction of user-submitted iORs or pheromones.iORbase contains the well-analyzed results of approximately 6000 iORs and their 3D protein structures identified from 59 insect species and 2077 insect pheromones from the literature,as well as approximately 12 million pairs of simulated interactions between functional iORs and pheromones.We also built 4 online modules,iORPDB,iInteraction,iModelTM,and iOdorTool to easily retrieve and visualize the 3D structures and interactions.iORbase can help greatly improve the experimental efficiency and success rate,identify new insecticide targets,or develop electronic nose technology.This study will shed light on the olfactory recognition mechanism and evolutionary characteristics from the perspectives of omics and macroevolution.

弹状病毒基质蛋白(Matrix protein)的研究进展

弹状病毒的基因组由1段线性单股不分节的负链RNA组成,主要编码5个结构蛋白,分别为核蛋白(Nucleoprotein,N)、磷蛋白(Phosphoprotein,P)、基质蛋白(Matrix protein,M)、糖蛋白(Glycoprotein,G)和RNA聚合酶(RNA polymerase,L)。其中,基质蛋白(M)是一种多功能性蛋白,在病毒的侵染过程中参与病毒粒子的出芽、装配,抑制核质运输,调控宿主的基因转录,诱导细胞凋亡等。本文综述M蛋白的研究进展。

Oligomerization of drug transporters:Forms,functions,and mechanisms

Drug transporters are essential players in the transmembrane transport of a wide variety of clinical drugs.The broad substrate spectra and versatile distribution pattern of these membrane proteins infer their pharmacological and clinical significance.With our accumulating knowledge on the three-dimensional structure of drug transporters,their oligomerization status has become a topic of intense study due to the possible functional roles carried out by such kind of post-translational modification(PTM).In-depth studies of oligomeric complexes formed among drug transporters as well as their interactions with other regulatory proteins can help us better understand the regulatory mechanisms of these membrane proteins,provide clues for the development of novel drugs,and improve the therapeutic efficacy.In this review,we describe different oligomerization forms as well as their structural basis of major drug transporters in the ATP-binding cassette and solute carrier superfamilies,summarize our current knowledge on the influence of oligomerization for protein expression level and transport function of these membrane proteins,and discuss the regulatory mechanisms of oligomerization.Finally,we highlight the challenges associated with the current oligomerization studies and propose some thoughts on the pharmaceutical application of this important drug transporter PTM.

Algorithmic challenges in structure-based drug design and NMR structural biology

The three-dimensional structure of a biomolecule rather than its one-dimensionM sequence determines its biological function. At present, the most accurate structures are derived from experimental data measured mainly by two techniques： X-ray crystallog- raphy and nuclear magnetic resonance （NMR） spec- troscopy. Because neither X-ray crystallography nor NMR spectroscopy could directly measure the positions of atoms in a biomolecule, algorithms must be designed to compute atom coordinates from the data. One salient feature of most NMR structure computation algorithms is their reliance on stochastic search to find the lowest energy conformations that satisfy the experimentally- derived geometric restraints. However, neither the cor- rectness of the stochastic search has been established nor the errors in the output structures could be quantified. Though there exist exact algorithms to compute struc- tures from angular restraints, similar algorithms that use distance restraints remain to be developed. An important application of structures is rational drug design where protein-ligand docking plays a crit- ical role. In fact, various docking programs that place a compound into the binding site of a target protein have been used routinely by medicinal chemists for both lead identification and optimization. Unfortunately, de- spite ongoing methodological advances and some success stories, the performance of current docking algorithms is still data-dependent. These algorithms formulate the docking problem as a match of two sets of feature points. Both the selection of feature points and the search for the best poses with the minimum scores are accomplished through some stochastic search methods. Both the un- certainty in the scoring function and the limited sam- pling space attained by the stochastic search contribute to their failures. Recently, we have developed two novel docking algorithms： a data-driven docking algorithm and a general docking algorithm that does not rely on experimental data. Our algorithms search the pose space exhaustively with the pose space itself being limited to a set of hierarchical manifolds that represent, respectively, surfaces, curves and points with unique geometric and energetic properties. These algorithms promise to be es- pecially valuable for the docking of fragments and small compounds as well as for virtual screening.