In this paper, a new hybrid model of amino acid substitution is developed and compared with the others in previous works. The results show that the new hybrid model can characterize the protein sequences very well by ...In this paper, a new hybrid model of amino acid substitution is developed and compared with the others in previous works. The results show that the new hybrid model can characterize the protein sequences very well by calculating Fisher weights, which can denote how much the variants contribute to the classification.展开更多
Previous molecular analyses of human astrocytomas have identified many genetic changes associated with astrocy-toma formation and progression.In an effort to identify novel gene expression changes associated with astr...Previous molecular analyses of human astrocytomas have identified many genetic changes associated with astrocy-toma formation and progression.In an effort to identify novel gene expression changes associated with astrocytomaformation,which might reveal new potential targets for glioma therapeutic drug design,we used the B8-RAS-transgenic mouse astrocytoma model.Using multiplex gene expression profiling,we found that展开更多
The realization of protein functional movement is usually accompanied by specific conformational changes,and there exist some key residues that mediate and control the functional motions of proteins in the allosteric ...The realization of protein functional movement is usually accompanied by specific conformational changes,and there exist some key residues that mediate and control the functional motions of proteins in the allosteric process.In the present work,the perturbation-response scanning method developed by our group was combined with the molecular dynamics(MD)simulation to identify the key residues controlling the functional movement of proteins.In our method,a physical quantity that is directly related to protein specific function was introduced,and then based on the MD simulation trajectories,the perturbation-response scanning method was used to identify the key residues for functional motions,in which the residues that highly correlated with the fluctuation of the function-related quantity were identified as the key residues controlling the specific functional motions of the protein.Two protein systems,i.e.,the heat shock protein 70 and glutamine binding protein,were selected as case studies to validate the effectiveness of our method.Our calculated results are in good agreement with the experimental results.The location of the key residues in the two proteins are similar,indicating the similar mechanisms behind the performance of their biological functions.展开更多
Proteins function as integral actors in essential life processes,rendering the realm of protein research a fundamental domain that possesses the potential to propel advancements in pharmaceuticals and disease investig...Proteins function as integral actors in essential life processes,rendering the realm of protein research a fundamental domain that possesses the potential to propel advancements in pharmaceuticals and disease investigation.Within the context of protein research,an imperious demand arises to uncover protein functionalities and untangle intricate mechanistic underpinnings.Due to the exorbitant costs and limited throughput inherent in experimental investigations,computational models offer a promising alternative to accelerate protein function annotation.In recent years,protein pre-training models have exhibited noteworthy advancement across multiple prediction tasks.This advancement highlights a notable prospect for effectively tackling the intricate downstream task associated with protein function prediction.In this review,we elucidate the historical evolution and research paradigms of computational methods for predicting protein function.Subsequently,we summarize the progress in protein and molecule representation as well as feature extraction techniques.Furthermore,we assess the performance of machine learning-based algorithms across various objectives in protein function prediction,thereby offering a comprehensive perspective on the progress within this field.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
OBJECTIVE:To study the functional mechanism of Pingchuanning Decoction in treatment of airway remodeling in asthmatic rats.METHODS:Eighty healthy Wistar male rats were randomized into eight groups(n=10 rats each):Norm...OBJECTIVE:To study the functional mechanism of Pingchuanning Decoction in treatment of airway remodeling in asthmatic rats.METHODS:Eighty healthy Wistar male rats were randomized into eight groups(n=10 rats each):Normal group,Asthma model group,Dexamethasone group,Guilong Kechuanning group,Xiaoqinglong Decoction group,and Pingchuanning Decoction low-,middle-,and high-dose groups.The rats of all but the Normal group were made into asthma models through intraperitoneal injection and aerosol inhalation of ovalbumin.All treatments were administered at the first stimulation of asthma onset(third week of modeling),and the rats were killed after stimulating asthma attacks for 4 weeks.The general conditions of rats and pathomorphological changes of the lung tissues were observed.The expression of nerve growth factor(NGF) of the lung tissues was measured with immunohistochemical methods,and the content of Clara cell secretory protein(CCSP) mRNA was determined with RT-PCR.RESULTS:Compared with the Normal group,the contents of NGF and CCSP mRNA in the lung tissues of the Model group were significantly changed(P<0.01).Compared with the Model group,the indices of Pingchuanning Decoction and other treatment groups were improved to some extent(P<0.05 or P<0.01).CONCLUSIONS:Pathological changes of airway inflammation and remodeling were present in these rat asthma models.Pingchuanning Decoction had an intervention effect on these experimental models.Its functional mechanism may be related to multiple factors,including alleviation of airway inflammation,relief of bronchial smooth muscle spasm,and inhibition of airway remodeling.展开更多
The number of available protein sequences in public databases is increasing exponentially.However,a sig-nificant percentage of these sequences lack functional annotation,which is essential for the understanding of how...The number of available protein sequences in public databases is increasing exponentially.However,a sig-nificant percentage of these sequences lack functional annotation,which is essential for the understanding of how bio-logical systems operate.Here,we propose a novel method,Quantitative Annotation of Unknown STructure(QAUST),to infer protein functions,specifically Gene Ontology(GO)terms and Enzyme Commission(EC)numbers.QAUST uses three sources of information:structure information encoded by global and local structure similarity search,biological network information inferred by protein–protein interaction data,and sequence information extracted from functionally discriminative sequence motifs.These three pieces of information are combined by consensus averaging to make the final prediction.Our approach has been tested on 500 protein targets from the Critical Assessment of Functional Annotation(CAFA)benchmark set.The results show that our method provides accurate functional annotation and outperforms other prediction methods based on sequence similarity search or threading.We further demonstrate that a previously unknown function of human tripartite motif-containing 22(TRIM22)protein predicted by QAUST can be experimentally validated.展开更多
Predicting protein functions is an important issue in the post-genomic era. This paper studies several network-based kernels including local linear embedding （LLE） kernel method, diffusion kernel and laplacian kerne...Predicting protein functions is an important issue in the post-genomic era. This paper studies several network-based kernels including local linear embedding （LLE） kernel method, diffusion kernel and laplacian kernel to uncover the relationship between proteins functions and protein-protein interactions （PPI）. The author first construct kernels based on PPI networks, then apply support vector machine （SVM） techniques to classify proteins into different functional groups. The 5-fold cross validation is then applied to the selected 359 GO terms to compare the performance of different kernels and guilt-by-association methods including neighbor counting methods and Chi-square methods. Finally, the authors conduct predictions of functions of some unknown genes and verify the preciseness of our prediction in part by the information of other data source.展开更多
Many eukaryotic genes are members of multi-gene families due to gene duplications, which generate new copies that allow functional divergence. However, the relationship between
Investigating the biological function of proteins is a key aspect of protein studies. Bioinformatic methods become important for studying the biological function of proteins. In this paper, we first give the chaos gam...Investigating the biological function of proteins is a key aspect of protein studies. Bioinformatic methods become important for studying the biological function of proteins. In this paper, we first give the chaos game representation （CGR） of randomly-linked functional protein sequences, then propose the use of the recurrent iterated function systems （RIFS） in fractal theory to simulate the measure based on their chaos game representations. This method helps to extract some features of functional protein sequences, and furthermore the biological functions of these proteins. Then multifractal analysis of the measures based on the CGRs of randomly-linked functional protein sequences are performed. We find that the CGRs have clear fractal patterns. The numerical results show that the RIFS can simulate the measure based on the CGR very well. The relative standard error and the estimated probability matrix in the RIFS do not depend on the order to link the functional protein sequences. The estimated probability matrices in the RIFS with different biological functions are evidently different. Hence the estimated probability matrices in the RIFS can be used to characterise the difference among linked functional protein sequences with different biological functions. From the values of the Dq curves, one sees that these functional protein sequences are not completely random. The Dq of all linked functional proteins studied are multifractal-like and sufficiently smooth for the Cq （analogous to specific heat） curves to be meaningful. Furthermore, the Dq curves of the measure μ based on their CCRs for different orders to link the functional protein sequences are almost identical if q 〉 0. Finally, the Ca curves of all linked functional proteins resemble a classical phase transition at a critical point.展开更多
In this paper are reported the local minimum problem by means of current greedy algorithm for training the empirical potential function of protein folding on 8623 non-native structures of 31 globular proteins and a so...In this paper are reported the local minimum problem by means of current greedy algorithm for training the empirical potential function of protein folding on 8623 non-native structures of 31 globular proteins and a solution of the problem based upon the simulated annealing algorithm. This simulated annealing algorithm is indispensable for developing and testing highly refined empirical potential functions.展开更多
The paper summarizes and discusses the recent advances of proteins as functional interlayers in organic field-effect transistors（OFETs）.Specific focus is given on the proteins integrated into the device structure,ei...The paper summarizes and discusses the recent advances of proteins as functional interlayers in organic field-effect transistors（OFETs）.Specific focus is given on the proteins integrated into the device structure,either to act as dielectric materials or to perform as the functional interlayer between the dielectric and the organic semiconductor（OSC）.The main emphasis is give to the location and the specific effect of protein layers in the structure of OFETs.Besides,the possibility of amyloid serving as useful building blocks for OFET is discussed.展开更多
The skeleton is a dynamic organ that is constantly remodeled. Proteins secreted from bone cells, namely osteoblasts, osteocytes,and osteoclasts exert regulation on osteoblastogenesis, osteclastogenesis, and angiogenes...The skeleton is a dynamic organ that is constantly remodeled. Proteins secreted from bone cells, namely osteoblasts, osteocytes,and osteoclasts exert regulation on osteoblastogenesis, osteclastogenesis, and angiogenesis in a paracrine manner. Osteoblasts secrete a range of different molecules including RANKL/OPG, M-CSF, SEMA3A, WNT5A, and WNT16 that regulate osteoclastogenesis. Osteoblasts also produce VEGFA that stimulates osteoblastogenesis and angiogenesis. Osteocytes produce sclerostin（SOST） that inhibits osteoblast differentiation and promotes osteoclast differentiation. Osteoclasts secrete factors including BMP6, CTHRC1, EFNB2, S1P, WNT10B, SEMA4D, and CT-1 that act on osteoblasts and osteocytes, and thereby influencea A osteogenesis. Osteoclast precursors produce the angiogenic factor PDGF-BB to promote the formation of Type H vessels, which then stimulate osteoblastogenesis. Besides, the evidences over the past decades show that at least three hormones or ＂osteokines＂from bone cells have endocrine functions. FGF23 is produced by osteoblasts and osteocytes and can regulate phosphate metabolism. Osteocalcin（OCN） secreted by osteoblasts regulates systemic glucose and energy metabolism, reproduction, and cognition. Lipocalin-2（LCN2） is secreted by osteoblasts and can influence energy metabolism by suppressing appetite in the brain.We review the recent progresses in the paracrine and endocrine functions of the secretory proteins of osteoblasts, osteocytes, and osteoclasts, revealing connections of the skeleton with other tissues and providing added insights into the pathogenesis of degenerative diseases affecting multiple organs and the drug discovery process.展开更多
To simplify the assessment method of soy protein isolate （SPI） functionalities, the viscosity and functionalities of commercial SPI products were studied. Viscosity value （y） increases With increasing concentrati...To simplify the assessment method of soy protein isolate （SPI） functionalities, the viscosity and functionalities of commercial SPI products were studied. Viscosity value （y） increases With increasing concentration （x） and exhibits a highly significant correlation with the exponential equation y = a. ebx. The b values of products are gradually enhanced from dispersion, emulsion and injected to gel type. Products with low b values （〈0.2）, and high dispersivity were dispersion-type. Products having high b values （〉0.4） and gel springiness were gel-type. The other products with centered b value （0.2-0.4）, high solubility and emulsifying capacity were emulsion-type.展开更多
Banana bunchy top virus(BBTV)poses a serious danger to banana crops worldwide.BBTV-encoded protein B4 is a determinant of pathogenicity.However,the relevant molecular mechanisms underlying its effects remain unknown.I...Banana bunchy top virus(BBTV)poses a serious danger to banana crops worldwide.BBTV-encoded protein B4 is a determinant of pathogenicity.However,the relevant molecular mechanisms underlying its effects remain unknown.In this study,we found that a functional peptide could be liberated from protein B4,likely via proteolytic processing.Site-directed mutagenesis indicated that the functional processing of protein B4 is required for its pathogenic effects,including dwarfism and sterility,in plants.The released protein fragment targets host proteins,such as the large subunit of RuBisCO(RbcL)and elongation factor 2(EF2),involved in protein synthesis.Therefore,the peptide released from B4(also a precursor)may act as a non-canonical modifier to influence host-pathogen interactions involving BBTV and plants.展开更多
Considering huge number of insect species in the world,studies of heat shock proteins on insects are still very limited.Special focus of＂Insect heat shock proteins and their underlying functions＂provides a comprehen...Considering huge number of insect species in the world,studies of heat shock proteins on insects are still very limited.Special focus of＂Insect heat shock proteins and their underlying functions＂provides a comprehensive knowledge for the given topics,which focuses on the heat shock proteins from four insect species：i）Five heat shock proteins（HSPs）from Cotesia chilonis were identified,and their expressional patterns under different temperatures were examined.展开更多
Compound probiotics were used to ferment compound wheat embryo Chinesemedicine(CWECM)at 37°C for a given period,and the fermentation end pointwas determined based on pHvalue.The full spectrumof the proteinswithin...Compound probiotics were used to ferment compound wheat embryo Chinesemedicine(CWECM)at 37°C for a given period,and the fermentation end pointwas determined based on pHvalue.The full spectrumof the proteinswithin the fermentation supernatant was determined by ion mass spectrometry,and then the fermentation was analyzed by proteomics.The difference of functional protein ofCWECMwas analyzed before and after fermentation.Additionally,the changes in flavor of peptides were examined.Our results indicated that when the fermentationwas performed for 96 h,the pH value became stable over time,which it shifted froman initial 3.98±0.04 to a stable 2.78±0.04.Proteomicbased analysis of the fermentation supernatant indicated that the fermentation of the probiotics increased.The amount of functional proteome and protein within the supernatant increased from 60 proteomes and 136 proteins before fermentation to 70 proteomes and 149 proteins post fermentation.These proteins were primarily members of the Ubiquitin and Histone families.These families contain more specific peptides after fermentation,and the coverage was reduced.Analysis of the unique P0C512 protein after fermentation indicated that this protein is an unstable,3Deffect columnar protein.We also found that probiotic fermentation can reduce the proportion of bitter peptideswithin fermentation broth from 47.49%to 36.98%,and the proportion of sweet peptides increased after fermentation from 35.29%to 51.01%.Based on testing,we concluded that fermentation of CWECM by compound probiotics can reduce the pH of the CWECM solution,increase the number of functional proteomes and proteins,improve the taste of CWECM solutions,and improve the therapeutic efficacy of CWECM.展开更多
Background: High protein (HP) diets are increasingly being recommended as one of the management strategies for weight control in overweight and obese individuals. The health benefits of high protein diets are well-est...Background: High protein (HP) diets are increasingly being recommended as one of the management strategies for weight control in overweight and obese individuals. The health benefits of high protein diets are well-established, but the mechanisms of action on body systems responsible for the changes in body weight and glycaemic control are not well-clear. Objective: The present study aimed to examine the effect of HP diets on the kidney functions of diabetic obese albino rats. Material and Methods: Eighty male adult male albino rats were used in this study. The animals were divided into eight equal groups (10 rats for each). Type 2 DM and obesity were induced. At the end of the 12 weeks, samples were collected for biochemical analysis. Results: The high protein diet led to significant decrease in BW, FI, BG, TC, LDL, TG, Lactate dehydrogenase, albumin, urine pH and urine citrate;while serum insulin, HDL, urea, creatinine, total protein, urine volume and urinary excretion of Ca were significantly higher in high protein diet groups. Conclusion: A high protein intake in diabetic obese albino rats for 12 weeks led to changes in the serum and urine levels of markers of renal function which indicated abnormalities in the functions of the kidney.展开更多
基金supported by the National Natural Science Foundation of China(No 29877016).
文摘In this paper, a new hybrid model of amino acid substitution is developed and compared with the others in previous works. The results show that the new hybrid model can characterize the protein sequences very well by calculating Fisher weights, which can denote how much the variants contribute to the classification.
文摘Previous molecular analyses of human astrocytomas have identified many genetic changes associated with astrocy-toma formation and progression.In an effort to identify novel gene expression changes associated with astrocytomaformation,which might reveal new potential targets for glioma therapeutic drug design,we used the B8-RAS-transgenic mouse astrocytoma model.Using multiplex gene expression profiling,we found that
文摘The realization of protein functional movement is usually accompanied by specific conformational changes,and there exist some key residues that mediate and control the functional motions of proteins in the allosteric process.In the present work,the perturbation-response scanning method developed by our group was combined with the molecular dynamics(MD)simulation to identify the key residues controlling the functional movement of proteins.In our method,a physical quantity that is directly related to protein specific function was introduced,and then based on the MD simulation trajectories,the perturbation-response scanning method was used to identify the key residues for functional motions,in which the residues that highly correlated with the fluctuation of the function-related quantity were identified as the key residues controlling the specific functional motions of the protein.Two protein systems,i.e.,the heat shock protein 70 and glutamine binding protein,were selected as case studies to validate the effectiveness of our method.Our calculated results are in good agreement with the experimental results.The location of the key residues in the two proteins are similar,indicating the similar mechanisms behind the performance of their biological functions.
基金supported in part by the National Natural Science Foundation of China(22033001)the National Key R&D Program of China(2022YFA1303700)the Chinese Academy of Medical Sciences(2021-I2M-5-014).
文摘Proteins function as integral actors in essential life processes,rendering the realm of protein research a fundamental domain that possesses the potential to propel advancements in pharmaceuticals and disease investigation.Within the context of protein research,an imperious demand arises to uncover protein functionalities and untangle intricate mechanistic underpinnings.Due to the exorbitant costs and limited throughput inherent in experimental investigations,computational models offer a promising alternative to accelerate protein function annotation.In recent years,protein pre-training models have exhibited noteworthy advancement across multiple prediction tasks.This advancement highlights a notable prospect for effectively tackling the intricate downstream task associated with protein function prediction.In this review,we elucidate the historical evolution and research paradigms of computational methods for predicting protein function.Subsequently,we summarize the progress in protein and molecule representation as well as feature extraction techniques.Furthermore,we assess the performance of machine learning-based algorithms across various objectives in protein function prediction,thereby offering a comprehensive perspective on the progress within this field.
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Supported by the National Natural Science Fund(No. 81173187)the Natural Science Fund of Anhui Province (No.11040606M217)
文摘OBJECTIVE:To study the functional mechanism of Pingchuanning Decoction in treatment of airway remodeling in asthmatic rats.METHODS:Eighty healthy Wistar male rats were randomized into eight groups(n=10 rats each):Normal group,Asthma model group,Dexamethasone group,Guilong Kechuanning group,Xiaoqinglong Decoction group,and Pingchuanning Decoction low-,middle-,and high-dose groups.The rats of all but the Normal group were made into asthma models through intraperitoneal injection and aerosol inhalation of ovalbumin.All treatments were administered at the first stimulation of asthma onset(third week of modeling),and the rats were killed after stimulating asthma attacks for 4 weeks.The general conditions of rats and pathomorphological changes of the lung tissues were observed.The expression of nerve growth factor(NGF) of the lung tissues was measured with immunohistochemical methods,and the content of Clara cell secretory protein(CCSP) mRNA was determined with RT-PCR.RESULTS:Compared with the Normal group,the contents of NGF and CCSP mRNA in the lung tissues of the Model group were significantly changed(P<0.01).Compared with the Model group,the indices of Pingchuanning Decoction and other treatment groups were improved to some extent(P<0.05 or P<0.01).CONCLUSIONS:Pathological changes of airway inflammation and remodeling were present in these rat asthma models.Pingchuanning Decoction had an intervention effect on these experimental models.Its functional mechanism may be related to multiple factors,including alleviation of airway inflammation,relief of bronchial smooth muscle spasm,and inhibition of airway remodeling.
基金supported by the King Abdullah University of Science and Technology(KAUST)Office of Sponsored Research(OSR)(Grant Nos.URF/1/1976-04,URF/1/1976-06)。
文摘The number of available protein sequences in public databases is increasing exponentially.However,a sig-nificant percentage of these sequences lack functional annotation,which is essential for the understanding of how bio-logical systems operate.Here,we propose a novel method,Quantitative Annotation of Unknown STructure(QAUST),to infer protein functions,specifically Gene Ontology(GO)terms and Enzyme Commission(EC)numbers.QAUST uses three sources of information:structure information encoded by global and local structure similarity search,biological network information inferred by protein–protein interaction data,and sequence information extracted from functionally discriminative sequence motifs.These three pieces of information are combined by consensus averaging to make the final prediction.Our approach has been tested on 500 protein targets from the Critical Assessment of Functional Annotation(CAFA)benchmark set.The results show that our method provides accurate functional annotation and outperforms other prediction methods based on sequence similarity search or threading.We further demonstrate that a previously unknown function of human tripartite motif-containing 22(TRIM22)protein predicted by QAUST can be experimentally validated.
基金This research is supported in part by HKRGC Grant 7017/07P, HKU CRCG Grants, HKU strategic theme grant on computational sciences, HKU Hung Hing Ying Physical Science Research Grant, National Natural Science Foundation of China Grant No. 10971075 and Guangdong Provincial Natural Science Grant No. 9151063101000021. The preliminary version of this paper has been presented in the OSB2009 conference and published in the corresponding conference proceedings[25]. The authors would like to thank the anonymous referees for their helpful comments and suggestions.
文摘Predicting protein functions is an important issue in the post-genomic era. This paper studies several network-based kernels including local linear embedding （LLE） kernel method, diffusion kernel and laplacian kernel to uncover the relationship between proteins functions and protein-protein interactions （PPI）. The author first construct kernels based on PPI networks, then apply support vector machine （SVM） techniques to classify proteins into different functional groups. The 5-fold cross validation is then applied to the selected 359 GO terms to compare the performance of different kernels and guilt-by-association methods including neighbor counting methods and Chi-square methods. Finally, the authors conduct predictions of functions of some unknown genes and verify the preciseness of our prediction in part by the information of other data source.
文摘Many eukaryotic genes are members of multi-gene families due to gene duplications, which generate new copies that allow functional divergence. However, the relationship between
基金Project partially supported by the National Natural Science Foundation of China (Grant No.30570426)the Chinese Program for New Century Excellent Talents in University (Grant No.NCET-08-06867)+1 种基金Fok Ying Tung Education Foundation (Grant No.101004)Australian Research Council (Grant No.DP0559807)
文摘Investigating the biological function of proteins is a key aspect of protein studies. Bioinformatic methods become important for studying the biological function of proteins. In this paper, we first give the chaos game representation （CGR） of randomly-linked functional protein sequences, then propose the use of the recurrent iterated function systems （RIFS） in fractal theory to simulate the measure based on their chaos game representations. This method helps to extract some features of functional protein sequences, and furthermore the biological functions of these proteins. Then multifractal analysis of the measures based on the CGRs of randomly-linked functional protein sequences are performed. We find that the CGRs have clear fractal patterns. The numerical results show that the RIFS can simulate the measure based on the CGR very well. The relative standard error and the estimated probability matrix in the RIFS do not depend on the order to link the functional protein sequences. The estimated probability matrices in the RIFS with different biological functions are evidently different. Hence the estimated probability matrices in the RIFS can be used to characterise the difference among linked functional protein sequences with different biological functions. From the values of the Dq curves, one sees that these functional protein sequences are not completely random. The Dq of all linked functional proteins studied are multifractal-like and sufficiently smooth for the Cq （analogous to specific heat） curves to be meaningful. Furthermore, the Dq curves of the measure μ based on their CCRs for different orders to link the functional protein sequences are almost identical if q 〉 0. Finally, the Ca curves of all linked functional proteins resemble a classical phase transition at a critical point.
基金Supported by the National Nataral Science Foundation of China(No.39980 0 0 5 )
文摘In this paper are reported the local minimum problem by means of current greedy algorithm for training the empirical potential function of protein folding on 8623 non-native structures of 31 globular proteins and a solution of the problem based upon the simulated annealing algorithm. This simulated annealing algorithm is indispensable for developing and testing highly refined empirical potential functions.
基金funding from the National Natural Science Foundation of China(NSFC,Nos.21374057,51303100)the Fundamental Research Funds for the Central Universities(No.GK201502001,GK201301006)+6 种基金the 111 Project(No.B14041)Program for Changjiang Scholars and Innovative Research Team in University(No.IRT_14R33)Natural Science Basic Research Plan in Shaanxi Province of China(No.2015JM2048)Open Project of State Key Laboratory of Supramolecular Structure and Materials(No.sklssm201626)the support of the Project funded by China Postdoctoral Science Foundation(No.2014M560747)Natural Science Basic Research Plan in Shaanxi Province of China(No.2016JM5024)the Scientific Research Program funded by Shaanxi Provincial Education Department(No.14JK1801)
文摘The paper summarizes and discusses the recent advances of proteins as functional interlayers in organic field-effect transistors（OFETs）.Specific focus is given on the proteins integrated into the device structure,either to act as dielectric materials or to perform as the functional interlayer between the dielectric and the organic semiconductor（OSC）.The main emphasis is give to the location and the specific effect of protein layers in the structure of OFETs.Besides,the possibility of amyloid serving as useful building blocks for OFET is discussed.
基金supported in part by grants from 973 Program from the Chinese Ministry of Science and Technology (MOST) (2014CB964704 and 2015CB964503)the Strategic Priority Research Program of the Chinese Academy of Sciences (Grant No. XDB19000000)the National Natural Science Foundation of China (NSFC) (31371463, 81672119, and 81725010)
文摘The skeleton is a dynamic organ that is constantly remodeled. Proteins secreted from bone cells, namely osteoblasts, osteocytes,and osteoclasts exert regulation on osteoblastogenesis, osteclastogenesis, and angiogenesis in a paracrine manner. Osteoblasts secrete a range of different molecules including RANKL/OPG, M-CSF, SEMA3A, WNT5A, and WNT16 that regulate osteoclastogenesis. Osteoblasts also produce VEGFA that stimulates osteoblastogenesis and angiogenesis. Osteocytes produce sclerostin（SOST） that inhibits osteoblast differentiation and promotes osteoclast differentiation. Osteoclasts secrete factors including BMP6, CTHRC1, EFNB2, S1P, WNT10B, SEMA4D, and CT-1 that act on osteoblasts and osteocytes, and thereby influencea A osteogenesis. Osteoclast precursors produce the angiogenic factor PDGF-BB to promote the formation of Type H vessels, which then stimulate osteoblastogenesis. Besides, the evidences over the past decades show that at least three hormones or ＂osteokines＂from bone cells have endocrine functions. FGF23 is produced by osteoblasts and osteocytes and can regulate phosphate metabolism. Osteocalcin（OCN） secreted by osteoblasts regulates systemic glucose and energy metabolism, reproduction, and cognition. Lipocalin-2（LCN2） is secreted by osteoblasts and can influence energy metabolism by suppressing appetite in the brain.We review the recent progresses in the paracrine and endocrine functions of the secretory proteins of osteoblasts, osteocytes, and osteoclasts, revealing connections of the skeleton with other tissues and providing added insights into the pathogenesis of degenerative diseases affecting multiple organs and the drug discovery process.
基金supported by the National Key Technologies Research and Development Program(No. 2012BAD34B04)Ministry of Science and Technology of the People's Republic of China
文摘To simplify the assessment method of soy protein isolate （SPI） functionalities, the viscosity and functionalities of commercial SPI products were studied. Viscosity value （y） increases With increasing concentration （x） and exhibits a highly significant correlation with the exponential equation y = a. ebx. The b values of products are gradually enhanced from dispersion, emulsion and injected to gel type. Products with low b values （〈0.2）, and high dispersivity were dispersion-type. Products having high b values （〉0.4） and gel springiness were gel-type. The other products with centered b value （0.2-0.4）, high solubility and emulsifying capacity were emulsion-type.
基金supported by grants from the Natural Science Foundation of China (No. 31301641 to J.Z.)the Program for Qualified Personnel of Taiwan Strait West Coast (No. K8812007 to L.H.X.)
文摘Banana bunchy top virus(BBTV)poses a serious danger to banana crops worldwide.BBTV-encoded protein B4 is a determinant of pathogenicity.However,the relevant molecular mechanisms underlying its effects remain unknown.In this study,we found that a functional peptide could be liberated from protein B4,likely via proteolytic processing.Site-directed mutagenesis indicated that the functional processing of protein B4 is required for its pathogenic effects,including dwarfism and sterility,in plants.The released protein fragment targets host proteins,such as the large subunit of RuBisCO(RbcL)and elongation factor 2(EF2),involved in protein synthesis.Therefore,the peptide released from B4(also a precursor)may act as a non-canonical modifier to influence host-pathogen interactions involving BBTV and plants.
文摘Considering huge number of insect species in the world,studies of heat shock proteins on insects are still very limited.Special focus of＂Insect heat shock proteins and their underlying functions＂provides a comprehensive knowledge for the given topics,which focuses on the heat shock proteins from four insect species：i）Five heat shock proteins（HSPs）from Cotesia chilonis were identified,and their expressional patterns under different temperatures were examined.
基金supported by Centaline Thousand Talents Program Centaline Scholars Funding Program (No. 192101510004)the Natural Science Foundation of Henan Province (No. 182300410056)Green Manufacturing 2025 (Ministry of Industry and Information Technology [2018] No. 272-3)
文摘Compound probiotics were used to ferment compound wheat embryo Chinesemedicine(CWECM)at 37°C for a given period,and the fermentation end pointwas determined based on pHvalue.The full spectrumof the proteinswithin the fermentation supernatant was determined by ion mass spectrometry,and then the fermentation was analyzed by proteomics.The difference of functional protein ofCWECMwas analyzed before and after fermentation.Additionally,the changes in flavor of peptides were examined.Our results indicated that when the fermentationwas performed for 96 h,the pH value became stable over time,which it shifted froman initial 3.98±0.04 to a stable 2.78±0.04.Proteomicbased analysis of the fermentation supernatant indicated that the fermentation of the probiotics increased.The amount of functional proteome and protein within the supernatant increased from 60 proteomes and 136 proteins before fermentation to 70 proteomes and 149 proteins post fermentation.These proteins were primarily members of the Ubiquitin and Histone families.These families contain more specific peptides after fermentation,and the coverage was reduced.Analysis of the unique P0C512 protein after fermentation indicated that this protein is an unstable,3Deffect columnar protein.We also found that probiotic fermentation can reduce the proportion of bitter peptideswithin fermentation broth from 47.49%to 36.98%,and the proportion of sweet peptides increased after fermentation from 35.29%to 51.01%.Based on testing,we concluded that fermentation of CWECM by compound probiotics can reduce the pH of the CWECM solution,increase the number of functional proteomes and proteins,improve the taste of CWECM solutions,and improve the therapeutic efficacy of CWECM.
文摘Background: High protein (HP) diets are increasingly being recommended as one of the management strategies for weight control in overweight and obese individuals. The health benefits of high protein diets are well-established, but the mechanisms of action on body systems responsible for the changes in body weight and glycaemic control are not well-clear. Objective: The present study aimed to examine the effect of HP diets on the kidney functions of diabetic obese albino rats. Material and Methods: Eighty male adult male albino rats were used in this study. The animals were divided into eight equal groups (10 rats for each). Type 2 DM and obesity were induced. At the end of the 12 weeks, samples were collected for biochemical analysis. Results: The high protein diet led to significant decrease in BW, FI, BG, TC, LDL, TG, Lactate dehydrogenase, albumin, urine pH and urine citrate;while serum insulin, HDL, urea, creatinine, total protein, urine volume and urinary excretion of Ca were significantly higher in high protein diet groups. Conclusion: A high protein intake in diabetic obese albino rats for 12 weeks led to changes in the serum and urine levels of markers of renal function which indicated abnormalities in the functions of the kidney.
