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
[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
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
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
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 proper...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.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
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
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 gi...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.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 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
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 ch...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.展开更多
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...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.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
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...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.展开更多
We introduced a new method---duration Hidden Markov Model (dHMM) to predicate the secondary structure of Protein. In our study, we divide the basic second structure of protein into three parts: H (a-Helix), E (B-sheet...We introduced a new method---duration Hidden Markov Model (dHMM) to predicate the secondary structure of Protein. In our study, we divide the basic second structure of protein into three parts: H (a-Helix), E (B-sheet) and O (others, include coil and turn). HMM is a kind of probabilistic model which more thinking of the interaction between adjacent amino acids (these interaction were represented by transmit probability), and we use genetic algorithm to determine the model parameters. After improving on the model and fixed on the parameters of the model, we write a program HMMPS. Our example shows that HMM is a nice method for protein secondary structure prediction.展开更多
The algorithm based on combination learning usually is superior to a singleclassification algorithm on the task of protein secondary structure prediction. However,the assignment of the weight of the base classifier us...The algorithm based on combination learning usually is superior to a singleclassification algorithm on the task of protein secondary structure prediction. However,the assignment of the weight of the base classifier usually lacks decision-makingevidence. In this paper, we propose a protein secondary structure prediction method withdynamic self-adaptation combination strategy based on entropy, where the weights areassigned according to the entropy of posterior probabilities outputted by base classifiers.The higher entropy value means a lower weight for the base classifier. The final structureprediction is decided by the weighted combination of posterior probabilities. Extensiveexperiments on CB513 dataset demonstrates that the proposed method outperforms theexisting methods, which can effectively improve the prediction performance.展开更多
β-TCP, as one of calcium phosphates ceramics, exerts perfect biocompatibility and osteoconductivity, and is clinically used as a bone graft substitute for decades. Consequently, the effects of β-TCP ceramics on intr...β-TCP, as one of calcium phosphates ceramics, exerts perfect biocompatibility and osteoconductivity, and is clinically used as a bone graft substitute for decades. Consequently, the effects of β-TCP ceramics on intracellular Ca2+ concentration, mineralization of osteoblast and BSA protein structure were studied. Results showed that β-TCP could increase the intracelluar Ca2+ concentration and mineralization of osteoblast, indicating that β-TCP ceramics could take part in the organic metabolism and the degradation product had no detrimental effect on osteoblast in vitro. Furthermore, β-TCP ceramics could increase the content of α-helix and β-pleated sheet and change BSA into more ordering structure, those changes might be favorable for the biomineralization after β-TCP ceramics implanted.展开更多
The secondary structure of a protein is critical for establishing a link between the protein primary and tertiary structures.For this reason,it is important to design methods for accurate protein secondary structure p...The secondary structure of a protein is critical for establishing a link between the protein primary and tertiary structures.For this reason,it is important to design methods for accurate protein secondary structure prediction.Most of the existing computational techniques for protein structural and functional prediction are based onmachine learning with shallowframeworks.Different deep learning architectures have already been applied to tackle protein secondary structure prediction problem.In this study,deep learning based models,i.e.,convolutional neural network and long short-term memory for protein secondary structure prediction were proposed.The input to proposed models is amino acid sequences which were derived from CulledPDB dataset.Hyperparameter tuning with cross validation was employed to attain best parameters for the proposed models.The proposed models enables effective processing of amino acids and attain approximately 87.05%and 87.47%Q3 accuracy of protein secondary structure prediction for convolutional neural network and long short-term memory models,respectively.展开更多
A new method was described for using a recurrent neural network with bias units to predict contact maps in proteins. The main inputs to the neural network include residues pairwise, residue classification according to...A new method was described for using a recurrent neural network with bias units to predict contact maps in proteins. The main inputs to the neural network include residues pairwise, residue classification according to hydrophobicity, polar, acidic, basic and secondary structure information and residue separation between two residues. In our work, a dataset was used which was composed of 53 globulin proteins of known 3D structure. An average predictive accuracy of 0.29 was obtained. Our results demonstrate the viability of the approach for predicting contact maps.展开更多
Based on the concept of ant colony optimization and the idea of population in genetic algorithm, a novel global optimization algorithm, called the hybrid ant colony optimization (HACO), is proposed in this paper to ...Based on the concept of ant colony optimization and the idea of population in genetic algorithm, a novel global optimization algorithm, called the hybrid ant colony optimization (HACO), is proposed in this paper to tackle continuous-space optimization problems. It was compared with other well-known stochastic methods in the optimization of the benchmark functions and was also used to solve the problem of selecting appropriate dilation efficiently by optimizing the wavelet power spectrum of the hydrophobic sequence of protein, which is the key step on using continuous wavelet transform (CWT) to predict a-helices and connecting peptides.展开更多
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.
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.
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the financial support from the Postdoctoral Research Project of Heilongjiang Provincial Department of Human Resources and Social Security (LBH-Q21156)Heilongjiang BaYi Agricultural University Support Program for San Zong San Heng (ZDZX202104)+3 种基金Science Foundation Project of Heilongjiang Province (QC2015028)National Natural Science Foundation of China (32072258)Major Science and technology Program of Heilongjiang (2019ZX08B02,2020ZX08B02)Central financial support for the development of local colleges and universities,Graduate research and innovation project of Harbin University of Commerce (YJSCX2020636HSD)。
文摘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.
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.
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.
文摘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.
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 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financially supported by Beijing Municipal Commission of Education Co-Constructed Programand Chinese Universities Scientific Fund(2009-4-25)
文摘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.
基金supported by the start-up grant from“Top 100 Talents Program”of Sun Yat-sen University to JRY(50000-31131114)General Program of National Natural Science Foundation of China to JRY(31671320)
文摘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.
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.
文摘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.
基金Supported by the National Natural Science Foundation of China(30170214)
文摘We introduced a new method---duration Hidden Markov Model (dHMM) to predicate the secondary structure of Protein. In our study, we divide the basic second structure of protein into three parts: H (a-Helix), E (B-sheet) and O (others, include coil and turn). HMM is a kind of probabilistic model which more thinking of the interaction between adjacent amino acids (these interaction were represented by transmit probability), and we use genetic algorithm to determine the model parameters. After improving on the model and fixed on the parameters of the model, we write a program HMMPS. Our example shows that HMM is a nice method for protein secondary structure prediction.
文摘The algorithm based on combination learning usually is superior to a singleclassification algorithm on the task of protein secondary structure prediction. However,the assignment of the weight of the base classifier usually lacks decision-makingevidence. In this paper, we propose a protein secondary structure prediction method withdynamic self-adaptation combination strategy based on entropy, where the weights areassigned according to the entropy of posterior probabilities outputted by base classifiers.The higher entropy value means a lower weight for the base classifier. The final structureprediction is decided by the weighted combination of posterior probabilities. Extensiveexperiments on CB513 dataset demonstrates that the proposed method outperforms theexisting methods, which can effectively improve the prediction performance.
基金Funded by the Research Fund of Key Laboratory for Advanced Technology in Environmental Protection of Jiangsu Province (AE201037)the Foundation for Talent Recruitment of Yancheng Institute of Technology (XKR2011007)"973" Chinese National Key Fundamental Research and Development Program (No.G1999064701)
文摘β-TCP, as one of calcium phosphates ceramics, exerts perfect biocompatibility and osteoconductivity, and is clinically used as a bone graft substitute for decades. Consequently, the effects of β-TCP ceramics on intracellular Ca2+ concentration, mineralization of osteoblast and BSA protein structure were studied. Results showed that β-TCP could increase the intracelluar Ca2+ concentration and mineralization of osteoblast, indicating that β-TCP ceramics could take part in the organic metabolism and the degradation product had no detrimental effect on osteoblast in vitro. Furthermore, β-TCP ceramics could increase the content of α-helix and β-pleated sheet and change BSA into more ordering structure, those changes might be favorable for the biomineralization after β-TCP ceramics implanted.
文摘The secondary structure of a protein is critical for establishing a link between the protein primary and tertiary structures.For this reason,it is important to design methods for accurate protein secondary structure prediction.Most of the existing computational techniques for protein structural and functional prediction are based onmachine learning with shallowframeworks.Different deep learning architectures have already been applied to tackle protein secondary structure prediction problem.In this study,deep learning based models,i.e.,convolutional neural network and long short-term memory for protein secondary structure prediction were proposed.The input to proposed models is amino acid sequences which were derived from CulledPDB dataset.Hyperparameter tuning with cross validation was employed to attain best parameters for the proposed models.The proposed models enables effective processing of amino acids and attain approximately 87.05%and 87.47%Q3 accuracy of protein secondary structure prediction for convolutional neural network and long short-term memory models,respectively.
文摘A new method was described for using a recurrent neural network with bias units to predict contact maps in proteins. The main inputs to the neural network include residues pairwise, residue classification according to hydrophobicity, polar, acidic, basic and secondary structure information and residue separation between two residues. In our work, a dataset was used which was composed of 53 globulin proteins of known 3D structure. An average predictive accuracy of 0.29 was obtained. Our results demonstrate the viability of the approach for predicting contact maps.
基金the National Natural Science Foundation of China(No.20475068) the Guangdong Provincial Natural Science Foundation(No.031577).
文摘Based on the concept of ant colony optimization and the idea of population in genetic algorithm, a novel global optimization algorithm, called the hybrid ant colony optimization (HACO), is proposed in this paper to tackle continuous-space optimization problems. It was compared with other well-known stochastic methods in the optimization of the benchmark functions and was also used to solve the problem of selecting appropriate dilation efficiently by optimizing the wavelet power spectrum of the hydrophobic sequence of protein, which is the key step on using continuous wavelet transform (CWT) to predict a-helices and connecting peptides.