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 Tian...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.展开更多
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 p...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.展开更多
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 simultan...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展开更多
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/...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.展开更多
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...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.展开更多
This study aimed to investigate the effect of ultrasound-assisted alkaline extraction(UAE)(at 20 kHz and different powers of 0,200,300,400,500 and 600 W for 10 min)on the yield,structure and emulsifying properties of ...This study aimed to investigate the effect of ultrasound-assisted alkaline extraction(UAE)(at 20 kHz and different powers of 0,200,300,400,500 and 600 W for 10 min)on the yield,structure and emulsifying properties of chickpea protein isolate(CPI).Compared with the non-ultrasound group,ultrasound treatment at 400 W resulted in the largest increase in CPI yield,and both the particle size and turbidity decreased with increasing ultrasound power from 0 to 400 W.The scanning electron microscope results showed a uniform structural distribution of CPI.Moreover,itsα-helix content increased,β-sheet content decreased,and total sulfhydryl group content and endogenous fluorescence intensity rose,illustrating that UAE changed the secondary and tertiary structure of CPI.At 400 W,the solubility of the emulsion increased to 63.18%,and the best emulsifying properties were obtained;the emulsifying activity index(EAI)and emulsifying stability index(ESI)increased by 85.42%and 46.78%,respectively.Furthermore,the emulsion droplets formed were smaller and more uniform.In conclusion,proper UAE power conditions increased the extraction yield and protein content of CPI,and effectively improved its structure and emulsifying characteristics.展开更多
A large multi-country outbreak of Oropouche virus(OROV),a segmented negative-sense RNA virus,is emerging in Latin America.By analyzing publicly available whole-genome sequences spanning 1955 to 2024,this study reveals...A large multi-country outbreak of Oropouche virus(OROV),a segmented negative-sense RNA virus,is emerging in Latin America.By analyzing publicly available whole-genome sequences spanning 1955 to 2024,this study reveals accelerated spatiotemporal evolution of OROV,cooperatively driven by genome mutagenesis and segment reassortment.The strains responsible for the 2023-2024 outbreak are universally reassortants,but form two divergent lineages,namely the Brazil and western Amazon basin lineages.This epidemic spreading is primarily fueled by localized transmission within countries and cross-border spread.Phylogenomic analysis further suggests that the S segment of the viral genome originated in Brazil around the 1740s,underwent diversification into five distinct clusters by the 1970s,and experienced rapid proliferation during 2020-2024.In contrast,the L segment originated in Peru around the 1630s and evolved into two independent clusters by the 1850s.Divergent evolutionary pressures have driven distinct patterns of amino acid changes in viral proteins between the Brazil and the western Amazon basin lineages.These mutations are predicted to alter the protein structures and bear functional consequences for viral fitness and transmission.These findings provide critical insights into the evolutionary dynamics of OROV and underscore the necessity of genome surveillance to track the transmission pathways and spatiotemporal evolution.展开更多
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 ...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.展开更多
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 meth...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.展开更多
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 correlati...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.展开更多
Noroviruses(NoVs)are the primary cause of acute gastroenteritis worldwide.Histo-blood group antigens(HBGAs)are receptors or attachment factors that affect the prevalence and host susceptibility of NoVs.GII.6 NoV is on...Noroviruses(NoVs)are the primary cause of acute gastroenteritis worldwide.Histo-blood group antigens(HBGAs)are receptors or attachment factors that affect the prevalence and host susceptibility of NoVs.GII.6 NoV is one of the predominant genotypes in humans,which recognizes the type ABO secretor of HBGAs.However,the structural basis of GII.6 NoV's interaction with HBGAs receptors remains elusive.In this study,we investigated the binding features of the GII.6 strain to HBGAs using saliva-and glycan-ELISA assays and characterized the molecular basis of the GII.6 virus that recognizes H disaccharide.We showed that the GII.6 P domain recognized some A and O secretor's saliva samples,most B secretor's saliva samples,and H disaccharide antigen,but did not bind non-secretors’saliva.Further,we determined the crystal structures of GII.6 and its complex with H disaccharides at 1.7Å,revealing that the P domain of GII.6 shares the conventional binding interface and mode of GII HBGAs.Single residue mutations at the GII.6-H binding sites could inhibit the binding of GII.6 to HBGAs,demonstrating that the interaction residues were crucial in maintaining NoV-glycan integrity.Finally,structural and sequence analyses showed that the major residues of the GII.6-H interaction were conserved among NoVs in the GII genogroup.Taken together,our study characterized the functional and structural features of GII.6 that allow it to interact with HBGAs,and shed light on NoV evolution,epidemiology,and anti-viral drug development.展开更多
Based on the concept of the pseudo amino acid composition （PseAAC）, protein structural classes are predicted by using an approach of increment of diversity combined with support vector machine （ID-SVM）, in which t...Based on the concept of the pseudo amino acid composition （PseAAC）, protein structural classes are predicted by using an approach of increment of diversity combined with support vector machine （ID-SVM）, in which the dipeptide amino acid composition of proteins is used as the source of diversity. Jackknife test shows that total prediction accuracy is 96.6% and higher than that given by other approaches. Besides, the specificity （Sp） and the Matthew＇s correlation coefficient （MCC） are also calculated for each protein structural class, the Sp is more than 88%, the MCC is higher than 92%, and the higher MCC and Sp imply that it is credible to use ID-SVM model predicting protein structural class. The results indicate that： 1 the choice of the source of diversity is reasonable, 2 the predictive performance of IDSVM is excellent, and3 the amino acid sequences of proteins contain information of protein structural classes.展开更多
Dear Editor,Enterovirus 71(EV71)is the main pathogen of hand,foot,and mouth disease(HFMD),which is a serious public health threat,especially in the Asia-Pacific region(Wu et al.,2013).Due to the lack of effective anti...Dear Editor,Enterovirus 71(EV71)is the main pathogen of hand,foot,and mouth disease(HFMD),which is a serious public health threat,especially in the Asia-Pacific region(Wu et al.,2013).Due to the lack of effective antivirals for treatment,supportive therapy remains to be the primary measure for severe infections of EV71.EV71 belongs to the genus Enterovirus in the family of Picornavirridae.EV71 encodes a polyprotein that is proteolytically cleaved into four structural proteins and seven nonstructural proteins,i.e.,VP1 to VP4,2A to 2C,and 3A to 3D.Moreover,an alternative encoding strategy of harboring a novel open reading frame encoding a short peptide has been recently reported in gut epithelial cells infected with some enteroviruses(Lulla et al.,2019).Structural proteins play a key role in the packaging and maturation of virus particles,while non-structural proteins are mainly involved in the replication process of virus.Among them,the 3D polymerase(3Dpol)protein functions as an RNA-dependent RNA polymerase(RdRP)that is essential for viral RNA synthesis(Wu et al.,2010).展开更多
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 ...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.展开更多
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,
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 import...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.展开更多
[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 th...[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.展开更多
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-dependen...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.展开更多
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 ful...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.展开更多
With the broad spread of the chikungunya virus(CHIkV),there is an increasing demand for more effective and broadly protective vaccines.Here,we designed CHIkV mRNA vaccines containing full-length structural proteins or...With the broad spread of the chikungunya virus(CHIkV),there is an increasing demand for more effective and broadly protective vaccines.Here,we designed CHIkV mRNA vaccines containing full-length structural proteins or part of structural proteins(envelope proteins)based on conserved sequences from 769 viral strains encompassing four lineages.The vaccine induced strong cellular and humoral immune responses in BALB/c mice and provided robust protection.Immunization of BALB/c mice with either of the two vaccines induced high levels of neutralizing antibodies against pseudoviruses from four distinct lineages,highlighting their potential for broad cross-lineage protective efficacy.Immunoglobulin repertoire analysis revealed two important BCR V-J gene combinations,IgHV1-4-lgHJ3 and IgHV1-4-lgHJ2,and lineage-specific immunity analysis revealed significant upregulation of TCRs containing V19 and V20.BCR and TCR immunodiversity may be a potential reason for the broad-spectrum protection against CHIkV afforded by the vaccine.In A129 mice,it elicited lower levels of neutralizing antibodies but prevented mouse mortality and cleared chronic infection.In the rhesus macaque model,both vaccines elicited a certain level of humoral and cellular immune responses and protected the rhesus macaques from the CHikV challenge.In conclusion,the results from both mouse and rhesus macaque models indicate that the vaccine could be a candidate for clinical useagainst CHIKV.展开更多
基金National natural science foundation of China (30471530)
文摘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.
文摘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.
基金ThisstudywassupportedbyagrantfromtheYunnanCommissionofScienceandTechnology,China (No 2 0 0 2C0 0 74M)
文摘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
基金Supported by the Ministry of Education,Science and Technological Development of the Republic of Serbia,No.451-03-9/2021-14/200019.
文摘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.
基金Project supported by the National Key Basic Research Program of China(Grant Nos.2013CB910203 and 2011CB911104)the National Natural Science Foundation of China(Grant No.31270760)+1 种基金the Strategic Priority Research Program of the Chinese Academy of Sciences(Grant No.XDB08030102)the Specialized Research Fund for the Doctoral Program of Higher Education of China(Grant No.20113402120013)
文摘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.
文摘This study aimed to investigate the effect of ultrasound-assisted alkaline extraction(UAE)(at 20 kHz and different powers of 0,200,300,400,500 and 600 W for 10 min)on the yield,structure and emulsifying properties of chickpea protein isolate(CPI).Compared with the non-ultrasound group,ultrasound treatment at 400 W resulted in the largest increase in CPI yield,and both the particle size and turbidity decreased with increasing ultrasound power from 0 to 400 W.The scanning electron microscope results showed a uniform structural distribution of CPI.Moreover,itsα-helix content increased,β-sheet content decreased,and total sulfhydryl group content and endogenous fluorescence intensity rose,illustrating that UAE changed the secondary and tertiary structure of CPI.At 400 W,the solubility of the emulsion increased to 63.18%,and the best emulsifying properties were obtained;the emulsifying activity index(EAI)and emulsifying stability index(ESI)increased by 85.42%and 46.78%,respectively.Furthermore,the emulsion droplets formed were smaller and more uniform.In conclusion,proper UAE power conditions increased the extraction yield and protein content of CPI,and effectively improved its structure and emulsifying characteristics.
基金supported by the National Natural Science Foundation of China,32270161,82302506.Research Grant of Jiangsu Commission of Health,ZD2021036The Starting Grant for Talents of Xuzhou Medical University,D2021007,D2021008,D2024017The Natural Science Foundation of the Jiangsu Higher Education Institutions of China(23KJD310005,23KJB310028,24KJD310005).
文摘A large multi-country outbreak of Oropouche virus(OROV),a segmented negative-sense RNA virus,is emerging in Latin America.By analyzing publicly available whole-genome sequences spanning 1955 to 2024,this study reveals accelerated spatiotemporal evolution of OROV,cooperatively driven by genome mutagenesis and segment reassortment.The strains responsible for the 2023-2024 outbreak are universally reassortants,but form two divergent lineages,namely the Brazil and western Amazon basin lineages.This epidemic spreading is primarily fueled by localized transmission within countries and cross-border spread.Phylogenomic analysis further suggests that the S segment of the viral genome originated in Brazil around the 1740s,underwent diversification into five distinct clusters by the 1970s,and experienced rapid proliferation during 2020-2024.In contrast,the L segment originated in Peru around the 1630s and evolved into two independent clusters by the 1850s.Divergent evolutionary pressures have driven distinct patterns of amino acid changes in viral proteins between the Brazil and the western Amazon basin lineages.These mutations are predicted to alter the protein structures and bear functional consequences for viral fitness and transmission.These findings provide critical insights into the evolutionary dynamics of OROV and underscore the necessity of genome surveillance to track the transmission pathways and spatiotemporal evolution.
基金Supported by Program of National Natural Science Foundation of China(No.31272564)The Joint Fund of NSFC-Guangdong(U0931003)+1 种基金Special Program of Modern Agricultural Industry Technology System(CARS-36)Hainan Program of Scientific Operating Expenses(Qiong Cai Yu[2013]131)
文摘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.
文摘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.
基金supported by the National Natural Science Foundation of China (Grant Nos. 11175224 and 11121403)
文摘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.
基金supported by grants from the National Natural Science Foundation of China(no.32100111,21934005)Guangdong Basic and Applied Basic Reuter Foundation(no.2019A1515110220)+1 种基金China Postdoctoral Science Foundation(no.2020M682900)Shenzhen High-level Hospital Construction Fund.
文摘Noroviruses(NoVs)are the primary cause of acute gastroenteritis worldwide.Histo-blood group antigens(HBGAs)are receptors or attachment factors that affect the prevalence and host susceptibility of NoVs.GII.6 NoV is one of the predominant genotypes in humans,which recognizes the type ABO secretor of HBGAs.However,the structural basis of GII.6 NoV's interaction with HBGAs receptors remains elusive.In this study,we investigated the binding features of the GII.6 strain to HBGAs using saliva-and glycan-ELISA assays and characterized the molecular basis of the GII.6 virus that recognizes H disaccharide.We showed that the GII.6 P domain recognized some A and O secretor's saliva samples,most B secretor's saliva samples,and H disaccharide antigen,but did not bind non-secretors’saliva.Further,we determined the crystal structures of GII.6 and its complex with H disaccharides at 1.7Å,revealing that the P domain of GII.6 shares the conventional binding interface and mode of GII HBGAs.Single residue mutations at the GII.6-H binding sites could inhibit the binding of GII.6 to HBGAs,demonstrating that the interaction residues were crucial in maintaining NoV-glycan integrity.Finally,structural and sequence analyses showed that the major residues of the GII.6-H interaction were conserved among NoVs in the GII genogroup.Taken together,our study characterized the functional and structural features of GII.6 that allow it to interact with HBGAs,and shed light on NoV evolution,epidemiology,and anti-viral drug development.
基金Supported by the National Natural Science Foundation of China (30660044)
文摘Based on the concept of the pseudo amino acid composition （PseAAC）, protein structural classes are predicted by using an approach of increment of diversity combined with support vector machine （ID-SVM）, in which the dipeptide amino acid composition of proteins is used as the source of diversity. Jackknife test shows that total prediction accuracy is 96.6% and higher than that given by other approaches. Besides, the specificity （Sp） and the Matthew＇s correlation coefficient （MCC） are also calculated for each protein structural class, the Sp is more than 88%, the MCC is higher than 92%, and the higher MCC and Sp imply that it is credible to use ID-SVM model predicting protein structural class. The results indicate that： 1 the choice of the source of diversity is reasonable, 2 the predictive performance of IDSVM is excellent, and3 the amino acid sequences of proteins contain information of protein structural classes.
基金supported by Hubei Provincial Natural Science Foundation of China(2025AFB822)National Key Research and Development Program of China(No.2022YFD1800100)National Natural Science Foundation of China(32100110).
文摘Dear Editor,Enterovirus 71(EV71)is the main pathogen of hand,foot,and mouth disease(HFMD),which is a serious public health threat,especially in the Asia-Pacific region(Wu et al.,2013).Due to the lack of effective antivirals for treatment,supportive therapy remains to be the primary measure for severe infections of EV71.EV71 belongs to the genus Enterovirus in the family of Picornavirridae.EV71 encodes a polyprotein that is proteolytically cleaved into four structural proteins and seven nonstructural proteins,i.e.,VP1 to VP4,2A to 2C,and 3A to 3D.Moreover,an alternative encoding strategy of harboring a novel open reading frame encoding a short peptide has been recently reported in gut epithelial cells infected with some enteroviruses(Lulla et al.,2019).Structural proteins play a key role in the packaging and maturation of virus particles,while non-structural proteins are mainly involved in the replication process of virus.Among them,the 3D polymerase(3Dpol)protein functions as an RNA-dependent RNA polymerase(RdRP)that is essential for viral RNA synthesis(Wu et al.,2010).
基金supported by the National Natural Science Foundation of China (32102605)the Agricultural Science and Technology Innovation Program under Grant (CAAS-ASTIP-2020IAR)the Earmarked Fund for CARS (CARS-44)。
文摘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.
文摘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,
文摘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.
基金Supported by Youth Fund Project of Natural Science Foundation of Shandong Province(ZR2014CQ009)Science and Technology Development Program of Binzhou City(2013GG0304)
文摘[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.
文摘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.
基金the financial support from the Wageningen UR“IPOP Customized Nutrition”programme financed by Wageningen UR,the Dutch Ministry of Economic Affairs,WIAS,Agrifirm Innovation Center,ORFFA Additives BV,Ajinomoto Eurolysine s.a.s and Stichting VICTAM BV.SSV acknowledgesthe support from the Universidad de Costa Rica
文摘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.
基金supported by the CAMS Innovation Fund for Medical Sciences(2022-I2M-CoV19-002,2021-12M-1-038,2023-12M-2-001)Key project of basic research in Yunnan Province(202401As070049)Major project of basic research in Yunnan Province(202401BC070008)。
文摘With the broad spread of the chikungunya virus(CHIkV),there is an increasing demand for more effective and broadly protective vaccines.Here,we designed CHIkV mRNA vaccines containing full-length structural proteins or part of structural proteins(envelope proteins)based on conserved sequences from 769 viral strains encompassing four lineages.The vaccine induced strong cellular and humoral immune responses in BALB/c mice and provided robust protection.Immunization of BALB/c mice with either of the two vaccines induced high levels of neutralizing antibodies against pseudoviruses from four distinct lineages,highlighting their potential for broad cross-lineage protective efficacy.Immunoglobulin repertoire analysis revealed two important BCR V-J gene combinations,IgHV1-4-lgHJ3 and IgHV1-4-lgHJ2,and lineage-specific immunity analysis revealed significant upregulation of TCRs containing V19 and V20.BCR and TCR immunodiversity may be a potential reason for the broad-spectrum protection against CHIkV afforded by the vaccine.In A129 mice,it elicited lower levels of neutralizing antibodies but prevented mouse mortality and cleared chronic infection.In the rhesus macaque model,both vaccines elicited a certain level of humoral and cellular immune responses and protected the rhesus macaques from the CHikV challenge.In conclusion,the results from both mouse and rhesus macaque models indicate that the vaccine could be a candidate for clinical useagainst CHIKV.
