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.

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.

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 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.

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.

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.

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.

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.

Dietary bamboo leaf flavonoids improve quality and microstructure of broiler meat by changing untargeted metabolome

Background Dietary bamboo leaf flavonoids(BLFs)are rarely used in poultry production,and it is unknown whether they influence meat texture profile,perceived color,or microstructure.Results A total of 720 one-day-old Arbor Acres broilers were supplemented with a basal diet with 20 mg bacitracin/kg,50 mg BLFs/kg,or 250 mg BLFs/kg or without additions.Data showed that the dietary BLFs significantly(P<0.05)changed growth performance and the texture profile.In particular,BLFs increased birds’average daily gain and average daily feed intake,decreased the feed:gain ratio and mortality rate,improved elasticity of breast meat,enhanced the gumminess of breast and leg meat,and decreased the hardness of breast meat.Moreover,a significant(P<0.05)increase in redness(a*)and chroma(c*)of breast meat and c*and water-holding capacity of leg meat was found in BLF-supplemented broilers compared with control broilers.In addition,BLFs supplementation significantly decreased(P<0.05)theβ-sheet ratio and serum malondialdehyde and increased theβ-turn ratio of protein secondary structure,superoxide dismutase,and glutathione peroxidase of breast meat and total antioxidant capacity and catalase of serum.Based on the analysis of untargeted metabolome,BLFs treatment considerably altered 14 metabolites of the breast meat,including flavonoids,amino acids,and organic acids,as well as phenolic and aromatic compounds.Conclusions Dietary BLFs supplementation could play a beneficial role in improving meat quality and sensory color in the poultry industry by changing protein secondary structures and modulating metabolites.

Interaction between MAPKs and MKPs in hexaploid chrysanthemum illuminates functional paralogue diversification in polyploids

Mitogen-activated protein kinases(MAPKs,also known as MPKs)regulate diverse cellular and physiological functions,and dual-specificity MAPK phosphatases(MKPs)modulate MAPK signalling through MAPK dephosphorylation and inactivation.Due to lacking of overall understanding for the regulatory networks between Chrysanthemum morifolium MKPs(CmMKPs)and C.morifolium MAPKs(CmMPKs),we systematically studied the interactions between four groups of CmMPKs and eight identified CmMKPs in chrysanthemum and found that the interaction between the specific CmMKP and the specific CmMPK differed from those in other plants.Furthermore,the expression of CmMKP1 and CmMKP1-LIKE1showed opposite trends during the development of chrysanthemum flower buds under salt treatment and Alternaria alternata inoculation,but these genes could interact with the same CmMPKs,providing insight into the subfunctionalization of paralogues.Amino acid variations(M87V,T277P and V6L)in dual-specificity protein phosphatases(DsPTP1)-LIKE1/2/3 changed the interactions of these proteins with the four CmMPK groups in chrysanthemum,providing evidence for the de/neofunctionalization of paralogues in polyploids,suggesting that we can identify the key functional sites of proteins by studying polyploid paralogues.

A Novel Design Method for Protein-Like Molecules from the Perspective of Sheaf Theory

Proteins perform a variety of functions in living organisms and their functions are largely determined by their shape. In this paper, we propose a novel mathematical method for designing protein-like molecules of a given shape. In the mathematical model, molecules are represented as loops of n-simplices (2-simplices are triangles and 3-simplices are tetrahedra). We design a new molecule of a given shape by patching together a set of smaller molecules that cover the shape. The covering set of small molecules is defined using a binary relation between sets of molecules. A new molecule is then obtained as a sum of the smaller molecules, where addition of molecules is defined using transformations acting on a set of (n + 1)-dimensional cones. Due to page limitations, only the two-dimensional case (i.e., loops of triangles) is considered. No prior knowledge of Sheaf Theory, Category Theory, or Protein Science is required. The author hopes that this paper will encourage further collaboration between Mathematics and Protein Science.

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.

Application value of biofluid-based biomarkers for the diagnosis and treatment of spinal cord injury

Recent studies in patients with spinal cord injuries(SCIs)have confirmed the diagnostic potential of biofluid-based biomarkers,as a topic of increasing interest in relation to SCI diagnosis and treatment.This paper reviews the research progress and application prospects of recently identified SCI-related biomarkers.Many structural proteins,such as glial fibrillary acidic protein,S100-β,ubiquitin carboxy-terminal hydrolase-L1,neurofilament light,and tau protein were correlated with the diagnosis,American Spinal Injury Association Impairment Scale,and prognosis of SCI to different degrees.Inflammatory factors,including interleukin-6,interleukin-8,and tumor necrosis factorα,are also good biomarkers for the diagnosis of acute and chronic SCI,while non-coding RNAs(micro RNAs and long non-coding RNAs)also show diagnostic potential for SCI.Trace elements(Mg,Se,Cu,Zn)have been shown to be related to motor recovery and can predict motor function after SCI,while humoral markers can reflect the pathophysiological changes after SCI.These factors have the advantages of low cost,convenient sampling,and ease of dynamic tracking,but are also associated with disadvantages,including diverse influencing factors and complex level changes.Although various proteins have been verified as potential biomarkers for SCI,more convincing evidence from large clinical and prospective studies is thus required to identify the most valuable diagnostic and prognostic biomarkers for SCI.

FTIR Analysis of Protein Secondary Structure in Cheddar Cheese during Ripening

Proteolysis is one of the most important biochemical reactions during cheese ripening.Studies on the secondary structure of proteins during ripening would be helpful for characterizing protein changes for assessing cheese quality.Fourier transform infrared spectroscopy(FTIR),with self-deconvolution,second derivative analysis and band curve-fitting,was used to characterize the secondary structure of proteins in Cheddar cheese during ripening.The spectra of the amide I region showed great similarity,while the relative contents of the secondary structures underwent a series of changes.As ripening progressed,the α-helix content decreased and the β-sheet content increased.This structural shift was attributed to the strengthening of hydrogen bonds that resulted from hydrolysis of caseins.In summary,FTIR could provide the basis for rapid characterization of cheese that is undergoing ripening.

Does mRNA structure contain genetic information for regulating co-translational protein folding？

Currently many facets of genetic information are illdefined. In particular, how protein folding is genetically regulated has been a long-standing issue for genetics and protein biology. And a generic mechanistic model with supports of genomic data is still lacking. Recent technological advances have enabled much needed genome-wide experiments. While putting the effect of codon optimality on debate, these studies have supplied mounting evidence suggesting a role of m RNA structure in the regulation of protein folding by modulating translational elongation rate. In conjunctions with previous theories, this mechanistic model of protein folding guided by m RNA structure shall expand our understandings of genetic information and offer new insights into various biomedical puzzles.

Characterization of Protein in Old Myocardial Infarction by FTIR Micro-spectroscopy

The aim of the present study was to assess whether Fourier transform infrared spectrometry (FTIR) micro-spectroscopy could produce distinct spectral information on protein of old myocardial infarction (OMI) and to set them as molecular markers to diagnose atypical OMI. Paraffin-embedded heart samples were derived from victims dying of OMI. In combination with histological stain, FTIR and infrared micro-spectroscopy, the characteristics of OMI were analyzed morphologically and molecularly. The most relevant bands identified were the amide A, B, Ⅰ and Ⅱ, showing crucial spectral differences between apparent normal region and OMI region, including the peak position blue shift and the increased intensity of OMI, moreover relative increase in α-helix and decrease in β-sheet of protein secondary structures in OMI. Comparing to single spectral band, the I1650/I1550 ratio was increased and rationally used as a molecular marker for diagnosing OMI. These novel preliminary findings supported further exploration of FTIR molecular profiling in clinical or forensic study, and were in accordance with histopathology.