Bioinformatic Analysis of Structural Proteins of Paramyxovirus Tianjin Strain

The amino acid sequences of the NP, P, M, F, HN and L proteins of the paramyxovirus Tianjin strain were analyzed by using the bioinformatics methods. Phylogenetic analysis based on 6 structural proteins among the Tianjin strain and 25 paramyxoviruses showed that the Tianjin strain belonged to the genus Respirovirus, in the subfamily Paramyxovirinae, and was most closely related to Sendai virus (SeV). Phylogenetic analysis with 14 known SeVs showed that Tianjin strain represented a new evolutionary lineage. Similarities comparisons indicated that Tianjin strain P protein was poorly conserved, sharing only 78.7% - 91.9% amino acid identity with the known SeVs, while the L protein was the most conserved, having 96.0% - 98.0% amino acid identity with the known SeVs. Alignments of amino acid sequences of 6 structural proteins clearly showed that Tianjin strain possessed many unique amino acid substitutions in their protein sequences, 15 in NP, 29 in P, 6 in M, 13 in F, 18 in HN, and 29 in L. These results revealed that Tianjin strain was most likely a new genotype of SeV. The presence of unique amino acid substitutions suggests that Tianjin strain maybe has a significant difference in biological, pathological, immunological, or epidemiological characteristics from the known SeVs.

The Structural Proteins of Bdellovibrio bacteriovorus Bacteriophage MAC-1

In the present investigation the structural proteins associated with MAC-1 bacteriophage have been characterized using sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE);tandem mass spectrometry of protein bands from SDS-PAGE gel;from the open reading frames (ORFs) deduced from MAC-1 genome sequence and amino acid sequence homology searches from the Uniprot database (up000002418). Results have led to the identification of at least three structural proteins associated with MAC-1 phage genome. They are: capsid protein (~55,000-daltons);spike protein (~22,000-daltons) and a low molecular weight DNA binding protein (~4000-dal- tons). In addition, two other minor proteins were tentatively identified as replicative and scaffold proteins based on two to three unique peptides from mass spectrometry data. However, other proteins coded (ORFs) by phage genome remain to be identified.

Expression and self-assembly of HCV structural proteins into virus-like particles and their immunogenicity

Background The synthesis of virus-like particles (VLPs) provides an important tool to determine the structural requirements for viral particle assembly and virus-host interactions. Our purpose was to express simultaneously all three structural proteins of hepatitis C virus (HCV) in insect cells to investigate the proteins assembly into VLPs and the immunogenicity of these particles KH*2/5DMethods HCV gene sequences encoding the structural proteins C, E1, and E2 were amplified with PCR, and recombinant baculoviruses were constructed using recombinant DNA techniques The expression of HCV structural proteins in insect cells was analyzed by immunofluoresceoce and SDS-PAGE The interaction of expressed structural proteins was investigated by immunoprecipitation and immunoblotting The VLPs in the insect cells were visualized by electron microscopy (EM) VLPs were then purified by sucrose gradient centrifugation and used to immunize BALB/c mice Antibodies against HCV were tested for in mouse serum samples by an ELISA assay Results The recombinant baculoviruses reBV/C and reBV/E1-E2 were constructed successfully Insect cells co-infected with reBV/C and reBV/E1-E2 expressed HCV C, E1, and E2 proteins with the expected molecular weights of 20kD, 35kD, and 66kD, respectively The results of immunoprecipitation and immunoblotting assays revealed the coimmunoprecipitation of C, E1, and E2 proteins, indicating association of the three structural proteins Electron microscopy of insect cells co-infected with reBV/C and reBV/E1-E2 demonstrated spherical particles (40 to 60 nm in diameter) similar to the HCV virions from serum samples or hepatic tissue samples of HCV infected humans The VLPs were partially purified Antibodies to HCV were detectable in the serum of mice immunized with VLPs Conclusion HCV structural proteins simultaneously expressed in insect cells can interact with each other and assemble into HCV-like particles, which are shown to be immunogenic in mice

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.

Structural modeling of proteins by integrating small-angle x-ray scattering data

Elucidating the structure of large biomolecules such as multi-domain proteins or protein complexes is challenging due to their high flexibility in solution. Recently, an ＂integrative structural biology＂ approach has been proposed, which aims to determine the protein structure and characterize protein flexibility by combining complementary high- and lowresolution experimental data using computer simulations. Small-angle x-ray scattering（SAXS） is an efficient technique that can yield low-resolution structural information, including protein size and shape. Here, we review computational methods that integrate SAXS with other experimental datasets for structural modeling. Finally, we provide a case study of determination of the structure of a protein complex formed between the tandem SH3 domains in c-Cb1-associated protein and the proline-rich loop in human vinculin.

Characterization of physicochemical and immunogenic properties of allergenic proteins altered by food processing:a review

Food allergens are mainly naturally-occurring proteins with immunoglobulin E(IgE)-binding epitopes.Understanding the structural and immunogenic characteristics of allergenic proteins is essential in assessing whether and how food processing techniques reduce allergenicity.We here discuss the impacts of food processing technologies on the modification of physicochemical,structural,and immunogenic properties of allergenic proteins.Detection techniques for characterizing changes in these properties of food allergens are summarized.Food processing helps to reduce allergenicity by aggregating or denaturing proteins,which masks,modifies,or destroys antigenic epitopes,whereas,it cannot eliminate allergenicity completely,and sometimes even improves allergenicity by exposing new epitopes.Moreover,most food processing techniques have been tested on purified food allergens rather than food products due to potential interference of other food components.We provide guidance for further development of processing operations that can decrease the allergenicity of allergenic food proteins without negatively impacting the nutritional profile.

Advances of Studies on the Viral Proteins of PRRSV

Porcine reproductive and respiratory syndrome( PRRS) is one of viral diseases with severe reproductive obstacle of pregnant sows and respiratory tract symptoms and higher mortality of piglets as characteristics,which is caused by porcine reproductive and respiratory syndrome virus( PRRSV). PRRS has brought great threats to swine industry in the world. The advances of studies on the viral proteins of PRRSV were reviewed from the genome,non-structural proteins and structural proteins of PRRSV.

Quantum Chemical Studies on Proteins in the Reaction Center of Rhodobacter sphaeroides

The electronic structure of protein chains L and M in photosynthetic reaction center (PRC) of Rhodobacter sphaeroides (Van Niel) Imhoff, Truper et Pfennig) was studied by using the Overlapping Dimer Approximation method and the Extended Negative Factor Counter method at ab initio level. The result indicated that: (1) Amino acid residues, the molecular orbitals of which composed the main components of frontier orbitals of protein chain L (M), are located at the random coil areas of chain L (alpha helix areas of chain M). Since the random coil is flexible and more easy to change its conformation in the electron transfer process and to reduce the energy of the system, and the structure of the alpha helix is reletively stable, this difference might be one of the causes for the electron transfer in photosynthetic reaction center (PRC) only takes place along the L branch. (2) The His residues which axially coordinated to the 'special pair' P and accessory chlorophyll molecules (ABChls) are essentially important for the E-LUMO levels of P and ABChl. But, the corresponding molecular orbitals of these His residues do not appear in the composition of frontier orbitals of protein chains. It means that the interaction between pigment molecules and protein chains do not influence the contribution to the frontier orbitals of protein chains explicitly, but influences the corresponding E-LUMO levels significantly.

Proteins:From sequence to structure

Protein sequences as special heterogeneous sequences are rare in the amino acid sequence space. The specific sequen- tial order of amino acids of a protein is essential to its 3D structure. On the whole, the correlation between sequence and structure of a protein is not so strong. How well would a protein sequence contain its structural information？ How does a sequence determine its native structure？ Keeping the globular proteins in mind, we discuss several problems from sequence to structure.

Discrete Exterior Calculus of Proteins and Their Cohomology

This paper proposes a novel application of cohomology to protein structure analysis. Since proteins interact each other by forming transient protein complexes, their shape (e.g., shape complementarity) plays an important role in their functions. In our mathematical toy models, proteins are represented as a loop of triangles (2D model) or tetrahedra (3D model), where their interactions are defined as fusion of loops. The purpose of this paper is to describe the conditions for loop fusion using the language of cohomology. In particular, this paper uses cohomology to describe the conditions for “allosteric regulation”, which has been attracted attention in safer drug discovery. I hope that this paper will provide a new perspective on the mechanism of allosteric regulation. Advantages of the model include its topological nature. That is, we can deform the shape of loops by deforming the shape of triangles (or tetrahedra) as long as their folded structures are preserved. Another advantage is the simplicity of the “allosteric regulation” mechanism of the model. Furthermore, the effect of the “post-translational modification” can be understood as a resolution of singularities of a flow of triangles (or tetrahedra). No prior knowledge of either protein science, exterior calculus, or cohomology theory is required. The author hopes that this paper will facilitate the interaction between mathematics and protein science.

Prokaryotic Expression and Immunogenicity of Dominant Epitope Region of Goose Parvovirus Structural Protein VP3

[Objective] The paper was to develop a subunit vaccine candidate for prevention and control of goose parvovirus infection. [Method]Based on the prokaryotic expression system, the antigenic epitopes and locations of the structural protein VP3 were predicted by software analysis,and the region displaying a large portion of antigenic epitopes was amplified by PCR. The target VP3 DNA fragment was inserted into pET-30 a-VP3 vector, was transformed into Escherichia coli BL21 competent cells for protein expression and animal test. The SPF chickens were immunized with the recombinant protein and the antisera were collected for neutralization test by using a goose embryo fibroblast. [Result] The recombinant plasmid was constructed, and the target region of VP3 protein was expressed efficiently in a soluble form. The neutralizing titers of antisera could reach up to-2.608. [Conclusion] The target region displaying a large portion of antigenic epitopes of the structural protein VP3 could be expressed efficiently in soluble form, and the expressed protein could induce neutralizing antibodies in SFP chicken.

The Influence of Newcastle Disease Virus Major Proteins on Virulence

The Newcastle disease virus(NDV)negative-strand RNA genome contains six genes.These genes encode nucleoprotein(NP),phosphoprotein(P),matrix protein(M),fusion protein(F),hemagglutinin-neuraminidase(HN),and RNA-dependent RNA polymerase(L)proteins.The six proteins affect the virulence of NDV in different ways,but available information on the six proteins is disparate and scattered across many databases and sources.A comprehensive overview of the proteins determining NDV virulence is lacking.This review summarizes the virulence of NDV as a complex trait determined by these six different proteins.

Physical and chemical changes of rapeseed meal proteins during toasting and their effects on in vitro digestibility

Background： Toasting during the production of rapeseed meal（RSM） decreases ileal crude protein（CP） and amino acid（AA） digestibility. The mechanisms that determine the decrease in digestibility have not been fully elucidated. A high protein quality, low-denatured, RSM was produced and toasted up to 120 min, with samples taken every 20 min. The aim of this study was to characterize secondary structure and chemical changes of proteins and glucosinolates occurring during toasting of RSM and the effects on its in vitro CP digestibility.Results： The decrease in protein solubility and the increase of intermolecular β-sheets with increasing toasting time were indications of protein aggregation. The contents of NDF and ADIN increased with increasing toasting time.Contents of arginine, lysine and O-methylisourea reactive lysine（OMIU-RL） linearly decreased with increasing toasting time, with a larger decrease of OMIU-RL than lysine. First-order reactions calculated from the measured parameters show that glucosinolates were degraded faster than lysine, OMIU-RL and arginine and that physical changes to proteins seem to occur before chemical changes during toasting. Despite the drastic physical and chemical changes noticed on the proteins, the coefficient of in vitro CP digestibility ranged from 0.776 to 0.750 and there were no effects on the extent of protein hydrolysis after 120 min. In contrast, the rate of protein hydrolysis linearly decreased with increasing toasting time, which was largely correlated to the decrease in protein solubility, lysine and OMIU-RL observed. Rate of protein hydrolysis was more than 2-fold higher for the untoasted RSM compared to the 120 min toasted material.Conclusions： Increasing the toasting time for the production of RSM causes physical and chemical changes to the proteins that decrease the rate of protein hydrolysis. The observed decrease in the rate of protein hydrolysis could impact protein digestion and utilization.

Half a century after their discovery:Structural insights into exonuclease and annealase proteins catalyzing recombineering

Recombineering is an essential tool for molecular biologists,allowing for the facile and efficient manipulation of bacterial genomes directly in cells without the need for costly and laborious in vitro manipulations involving restriction enzymes.The main workhorses behind recombineering are bacteriophage proteins that promote the single-strand annealing(SSA)homologous recombination pathway to repair double-stranded DNA breaks.While there have been several reviews examining recombineering methods and applications,comparatively few have focused on the mechanisms of the proteins that are the key players in the SSA pathway:a 5′→3′exonuclease and a single-strand annealing protein(SSAP or“annealase”).This review dives into the structures and functions of the two SSA recombination systems that were the first to be developed for recombineering in E.coli:the RecET system from E.coli Rac prophage and the𝜆Red system from bacteriophageλ.By comparing the structures of the RecT and Red𝛽annealases,and the RecE and𝜆Exo exonucleases,we provide new insights into how the structures of these proteins dictate their function.Examining the sequence conservation of the𝜆λExo and RecE exonucleases gives more profound insights into their critical functional features.Ultimately,as recombineering accelerates and evolves in the laboratory,a better understanding of the mechanisms of the proteins behind this powerful technique will drive the development of improved and expanded capabilities in the future.

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.

Plant Anthocyanin Synthesis and Gene Regulation

This paper aims to explain the biochemistry of anthocyanin synthesis based on an overview of plant anthocyanin synthesis genes and environmental factors in the regulation of anthocyanin metabolism. The results show that： ① The metabolism of anthocyanins in plants is affected by the temperature, light, ultraviolet, fertilization status, hormone levels and other factors, which affect the military anthocyanin biosynthetic genes, and then induce or inhibit the synthesis of anthocyanins. ② In the regulation of genes, some of the structural genes of anthocyanin synthesis showed promoting effect, while others showed inhibitory effect. At different environ- mental conditions, the regulation of gene activation and inhibition of the amount of different regulatory genes that anthocyanin accumulation is different, and cause different colors of plant-organs production. ③ In different environmental factors or hor-mones induced to produce the same or different regulation of gene expression changes in regulatory genes, resulting in several different anthocyanins or anthocyanin ratio changes, so that the color of plant organs in different colors.

Expression,Purification and Activity Detection of VP1 of A-type FMDV

[Objective] The research aimed to induce the expression of FMDV structural protein VP1 in E.coli and purify the protein,then detect the activity.[Method] The fragment coding VP1 was amplified by PCR and doubly digested with BamH Ⅰ and XhoⅠ,then cloned into expression vector pGEX-4T-1 and pPROExHTb respectively to get recombinant plasmid pGEX-4T-1-VP1 and pPROExHTb-VP1.The recombinant plasmid pGEX-4T-1-VP1 and pPROExHTb-VP1 was transformed into E.coli BL21(DE3)and induced by IPTG,fusion protein was identifie...

The structural and accessory proteins M,ORF 4a,ORF 4b,and ORF 5 of Middle East respiratory syndrome coronavirus(MERS-CoV)are potent interferon antagonists

The newly emerged Middle East respiratory syndrome coronavirus(MERS-CoV)is a highly pathogenic respira-tory virus with pathogenic mechanisms that may be driven by innate immune pathways.The goal of this study is to characterize the expression of the structural(S,E,M,N)and accessory(ORF 3,ORF 4a,ORF 4b,ORF 5)proteins of MERS-CoV and to determine whether any of these pro-teins acts as an interferon antagonist.Individual structural and accessory protein-coding plasmids with an N-terminal HA tag were constructed and transiently transfected into cells,and their native expression and subcellular localiza-tion were assessed using Wes tern blotting and indirect immunofl uorescence.While ORF 4b demonstrated majorly nuclear localization,all of the other proteins demonstrated cytoplasmic localization.In addition,for the fi rst time,our experiments revealed that the M,ORF 4a,ORF 4b,and ORF 5 proteins are potent interferon antagonists.Further exami-nation revealed that the ORF 4a protein of MERS-CoV has the most potential to counteract the antiviral effects of IFN via the inhibition of both the interferon production(IFN-βpromoter activity,IRF-3/7 and NF-κB activation)and ISRE promoter element signaling pathways.Together,our re-sults provide new insights into the function and pathogenic role of the structural and accessory proteins of MERS-CoV.

Proteomic Analyses of the Shrimp White Spot Syndrome Virus

White spot syndrome virus (WSSV), a unique member within the virus family Nimaviridae, is the most notorious aquatic virus infecting shrimp and other crustaceans and has caused enormous economic losses in the shrimp farming industry worldwide. Therefore, a comprehensive understanding of WSSV morphogenesis, structural proteins, and replication is essential for developing prevention measures of this serious parasite. The viral genome is approximately 300kb and contains more than 180 open reading frames (ORF). However, most of proteins encoded by these ORF have not been characterized. Due to the importance of WSSV structural proteins in the composition of the virion structure, infection process and interaction with host cells, knowledge of structural proteins is essential to understanding WSSV entry and infection as well as for exploring effective prevention measures. This review article summarizes mainly current investigations on WSSV structural proteins including the relative quantities, localization, function and protein-protein interactions. Traditional proteomic studies of 1D or 2D gel electrophoresis separations and mass spectrometry (MS) followed by database searches have identified a total of 39 structural proteins. Shotgun proteomics and iTRAQ were initiated to identify more structural proteins. To date, it is estimated that WSSV is assembled by at least 59 structural proteins, among them 35 are defined as the envelope fraction (including tegument proteins) and 9 as nucleocapsid proteins. Furthermore, the interaction within several major structural proteins has also been investigated. This identitification and characterization of WSSV protein components should help in the understanding of the viral assembly process and elucidate the roles of several major structural proteins.

Prediction of Protein OmpH in Structure of C47-8 Pasteurella multocida

[Objective] This study aimed to predict the structure of protein OmpH from Pasteurella multocida C47-8 （PmC47-8） strain of yak. [Method] Online BLAST, signal peptide prediction, secondary structure prediction and protein characteristics of sequencing result of gene OmpH from PmC47-8 strain were analyzed. [Result] The similarities of gene OmpH from PmC47-8 with the published 81 OmpH genes were between 84% and 99%; a signal peptide was found with the cleavage sites between 20 and 21 in the polypeptide; secondary structure prediction showed that folding structure accounted for 49.8% and loop structure for 50.2%; it predicted that there were 7 O-glycosylation sites in OmpH protein with the amino acid residual sites of 2, 45, 48, 330, 716, 721, 723, respectively, and 2 N-glycosylation sites with the amino acid residual sites of 15 and 35. [Conclusion] This study lays the foundation for the study on the immunity of OmpH gene from yak.