The discovery of intrinsically disordered proteins （IDP） （i.e., biologically active proteins that do not possess stable secondary and/or tertiary structures） came as an unexpected surprise, as the existence of suc...The discovery of intrinsically disordered proteins （IDP） （i.e., biologically active proteins that do not possess stable secondary and/or tertiary structures） came as an unexpected surprise, as the existence of such proteins is in contradiction to the traditional ＂sequence →structure →function＂ paradigm. Accurate prediction of a protein＇s predisposition to be intrinsically disordered is a necessary prerequisite for the further understanding of principles and mechanisms of protein folding and function, and is a key for the elaboration of a new structural and functional hierarchy of proteins. Therefore, prediction of IDPs has attracted the attention of many researchers, and a number of prediction tools have been developed. Predictions of disorder, in turn, are playing major roles in directing laboratory experiments that are leading to the discovery of ever more disordered proteins, and thereby leading to a positive feedback loop in the investigation of these proteins. In this review of algorithms for intrinsic disorder prediction, the basic concepts of various prediction methods for IDPs are summarized, the strengths and shortcomings of many of the methods are analyzed, and the difficulties and directions of future development of IDP prediction techniques are discussed.展开更多
A symptom of chilling injury is development of water deficit in shoots, resulting from an imbalance of water transport and transpiration. In this work, two rice varieties （Oryza sativa L. var. Wasetoitsu and Somewake...A symptom of chilling injury is development of water deficit in shoots, resulting from an imbalance of water transport and transpiration. In this work, two rice varieties （Oryza sativa L. var. Wasetoitsu and Somewake） seedlings were chilled at 7 ℃, followed by recovery at 28 ℃. Based on the growth phenotype and electrolyte leakage tests, Somewake was shown to be a chilling-tolerant variety, and Wasetoitsu a chilling-sensitive one. The chilling stress reduced markedly the relative water content （RWC） of leaves, accumulative transpiration and osmotic root hydraulic conductivity （Lp） in both varieties. But when retumed to 28 ℃, the water relation balance of Somewake recovered better. The mRNA expression profile of all the 11 plasma membrane intrinsic proteins （PIPs）, a subgroup of aquaporins, was subsequently determined by real-time reverse transcription （RT）-PCR with TaqMan-minor grove binder （MGB） probes derived from rice var. Nipponbare during chilling treatment and recovery. Most of the PIP genes was down-regulated at the low temperature, and recovered at the warm temperature. The relative expression of some PIPs in both Somewake and Wasetoitsu decreased in parallel during the chilling. However during the recovery, the relative expression of OsPIP1;1, OsPIP2;1, OsPIP2;7 in shoots and OsPIP1：1, OsPIP2：1 in roots were significantly higher in Somewake than Wasetoitsu. This supports the role of PIPs in re-establishing water balance after chilling conditions. We discuss the diversified roles played by members of the aquaporin PIP subfamily in plant chilling tolerance depending on aquaporin isoforms, plant tissue and the stage of chilling duration.展开更多
The prediction of intrinsically disordered proteins is a hot research area in bio-information.Due to the high cost of experimental methods to evaluate disordered regions of protein sequences,it is becoming increasingl...The prediction of intrinsically disordered proteins is a hot research area in bio-information.Due to the high cost of experimental methods to evaluate disordered regions of protein sequences,it is becoming increasingly important to predict those regions through computational methods.In this paper,we developed a novel scheme by employing sequence complexity to calculate six features for each residue of a protein sequence,which includes the Shannon entropy,the topological entropy,the sample entropy and three amino acid preferences including Remark 465,Deleage/Roux,and Bfactor(2STD).Particularly,we introduced the sample entropy for calculating time series complexity by mapping the amino acid sequence to a time series of 0-9.To our knowledge,the sample entropy has not been previously used for predicting IDPs and hence is being used for the first time in our study.In addition,the scheme used a properly sized sliding window in every protein sequence which greatly improved the prediction performance.Finally,we used seven machine learning algorithms and tested with 10-fold cross-validation to get the results on the dataset R80 collected by Yang et al.and of the dataset DIS1556 from the Database of Protein Disorder(DisProt)(https://www.disprot.org)containing experimentally determined intrinsically disordered proteins(IDPs).The results showed that k-Nearest Neighbor was more appropriate and an overall prediction accuracy of 92%.Furthermore,our method just used six features and hence required lower computational complexity.展开更多
Accurately,reliably and rapidly identifying intrinsically disordered(IDPs)proteins is essential as they often play important roles in various human diseases;moreover,they are related to numerous important biological a...Accurately,reliably and rapidly identifying intrinsically disordered(IDPs)proteins is essential as they often play important roles in various human diseases;moreover,they are related to numerous important biological activities.However,current computational methods have yet to develop a network that is sufficiently deep tomake predictions about IDPs and demonstrate an improvement in performance.During this study,we constructed a deep neural network that consisted of five identical variant models,ResNet18,combined with an MLP network,for classification.Resnet18 was applied for the first time as a deep model for predicting IDPs,which allowed the extraction of information fromIDP residues in greater detail and depth,and this information was then passed through the MLP network for the final identification process.Two well-known datasets,MXD494 and R80,were used as the blind independent datasets to compare their performance with that of our method.The simulation results showed that Matthew’s correlation coefficient obtained using our deep network model was 0.517 on the blind R80 dataset and 0.450 on the MXD494 dataset;thus,our method outperformed existing methods.展开更多
Nodulin 26-like intrinsic proteins(NIPs) are a family of channel-forming transmembrane proteins that function in the transport of water and other small molecules.Some NIPs can mediate silicon transport across plasma m...Nodulin 26-like intrinsic proteins(NIPs) are a family of channel-forming transmembrane proteins that function in the transport of water and other small molecules.Some NIPs can mediate silicon transport across plasma membranes and lead to silicon accumulation in plants,which is beneficial for the growth and development of plants.Cucumber is one of the most widely consumed vegetables;however,the functions of NIPs in this crop are still largely unknown.Here,we report the functional characteristics of Cs NIP2;2.It was found that Cs NIP2;2 is a tandem repeat of Cs NIP2;1,which had been demonstrated to be a silicon influx transporter gene.Cs NIP2;2 has a selectivity filter composed of cysteine,serine,glycine and arginine(CSGR),which is different from all previously characterized silicon influx transporters in higher plants at the second helix position.Xenopus laevis oocytes injected with Cs NIP2;2 c RNA demonstrated a higher uptake of silicon than the control,and the uptake remained unchanged under low temperature.Cs NIP2;2 was found to be expressed in the root,stem,lamina and petiole,and exogenous silicon treatment decreased its expression in the stem but not in other tissues.Transient expression of Cs NIP2;2-e GFP fusion sequence in onion epidermal cells showed that Cs NIP2;2 was localized to the cell nucleus,plasma membrane and an unknown structure inside the cell.The results suggest that Cs NIP2;2 is a silicon influx transporter in cucumber,and its subcellular localization and the selectivity filter are different from those of the previously characterized silicon influx transporters in other plants.These findings may be helpful for understanding the functions of NIPs in cucumber plants.展开更多
Purpose:To analyze the change of water-soluble-protein(WSP),urea-soluble-protein(USP)and membrane intrinsic protein(MIP)in human senile catarct.Methods:The water-soluble-fractions(WSF)were prepared basically according...Purpose:To analyze the change of water-soluble-protein(WSP),urea-soluble-protein(USP)and membrane intrinsic protein(MIP)in human senile catarct.Methods:The water-soluble-fractions(WSF)were prepared basically according to the method of Kibbelear,et al.But in this study,5mmol/LB-mercaptoethanol was added to the buffer solution.The urea-soluble-fractions(USF)were pre-pared basically according to the method of Kibbelear,et al.Lens fiber cell mem-branes were purified basically according to the method of Russell,et al.SDS-PAGE were performed according to the procedure of Laemmili,et al.using re-solving gel13%and3%stacking gel.Results:The WSPwas fractionated intoHM^+α^-,β1-3^-andγ-crystallin compo-nents.In nuclear cataractous lenses HM^+α^-and B-crystallin increase,while r-crystallin decrease.The USP from clear lenses contains mainlyαβchains of22KD,whereas in cataractous lenses,especially in nuclear cataractous lenses,the relative amount of the 28-and23KDpolypeptide(the components of β-crys-tallin)increased markedly.Lens fiber cell MIP,clear lens and cataract lens con-tained the main polypeptide of 27KD(MIP)and23KD(MP23).Conclusion:The water-insolube protein,whether in quantity or in quality,plays an important role in cataract formation.Eye Science 1995,11:124-127.展开更多
●AIM:To identify disease-causative mutations in families with congenital cataract.●METHODS:Two Chinese families with autosomaldominant congenital cataract(ADCC)were recruited and underwent comprehensive eye examinat...●AIM:To identify disease-causative mutations in families with congenital cataract.●METHODS:Two Chinese families with autosomaldominant congenital cataract(ADCC)were recruited and underwent comprehensive eye examinations.Gene panel next-generation sequencing of common pathogenic genes of congenital cataract was performed in the proband of each family.Sanger sequencing was used to valid the candidate gene mutations and sequence the other family members for co-segregation analysis.The effect of sequence changes on protein structure and function was predicted through bioinformatics analysis.Major intrinsic protein(MIP)-wildtype and MIP-G29R plasmids were constructed and microinjected into zebrafish single-cell stage embryos.Zebrafish embryonic lens phenotypes were screened using confocal microscopy.●RESULTS:A novel heterozygous mutation(c.85G>A;p.G29R)in the MIP gene was identified in the proband of one family.A known heterozygous mutation(c.97C>T;p.R33C;rs864309693)in MIP was found in the proband of another family.In-silico prediction indicated that the novel mutation might affect the MIP protein function.Zebrafish embryonic lens was uniformly transparent in both wild-type PCS2+MIP and mutant PCS2+MIP.●CONCLUSION:Two missense mutations in the MIP gene in Chinese cataract families are identified,and one of which is novel.These findings expand the genetic spectrum of MIP mutations associated with cataracts.The functional studies suggest that the novel MIP mutation might not be a gain-of-function but a loss-of-function mutation.展开更多
文摘The discovery of intrinsically disordered proteins （IDP） （i.e., biologically active proteins that do not possess stable secondary and/or tertiary structures） came as an unexpected surprise, as the existence of such proteins is in contradiction to the traditional ＂sequence →structure →function＂ paradigm. Accurate prediction of a protein＇s predisposition to be intrinsically disordered is a necessary prerequisite for the further understanding of principles and mechanisms of protein folding and function, and is a key for the elaboration of a new structural and functional hierarchy of proteins. Therefore, prediction of IDPs has attracted the attention of many researchers, and a number of prediction tools have been developed. Predictions of disorder, in turn, are playing major roles in directing laboratory experiments that are leading to the discovery of ever more disordered proteins, and thereby leading to a positive feedback loop in the investigation of these proteins. In this review of algorithms for intrinsic disorder prediction, the basic concepts of various prediction methods for IDPs are summarized, the strengths and shortcomings of many of the methods are analyzed, and the difficulties and directions of future development of IDP prediction techniques are discussed.
文摘A symptom of chilling injury is development of water deficit in shoots, resulting from an imbalance of water transport and transpiration. In this work, two rice varieties （Oryza sativa L. var. Wasetoitsu and Somewake） seedlings were chilled at 7 ℃, followed by recovery at 28 ℃. Based on the growth phenotype and electrolyte leakage tests, Somewake was shown to be a chilling-tolerant variety, and Wasetoitsu a chilling-sensitive one. The chilling stress reduced markedly the relative water content （RWC） of leaves, accumulative transpiration and osmotic root hydraulic conductivity （Lp） in both varieties. But when retumed to 28 ℃, the water relation balance of Somewake recovered better. The mRNA expression profile of all the 11 plasma membrane intrinsic proteins （PIPs）, a subgroup of aquaporins, was subsequently determined by real-time reverse transcription （RT）-PCR with TaqMan-minor grove binder （MGB） probes derived from rice var. Nipponbare during chilling treatment and recovery. Most of the PIP genes was down-regulated at the low temperature, and recovered at the warm temperature. The relative expression of some PIPs in both Somewake and Wasetoitsu decreased in parallel during the chilling. However during the recovery, the relative expression of OsPIP1;1, OsPIP2;1, OsPIP2;7 in shoots and OsPIP1：1, OsPIP2：1 in roots were significantly higher in Somewake than Wasetoitsu. This supports the role of PIPs in re-establishing water balance after chilling conditions. We discuss the diversified roles played by members of the aquaporin PIP subfamily in plant chilling tolerance depending on aquaporin isoforms, plant tissue and the stage of chilling duration.
文摘The prediction of intrinsically disordered proteins is a hot research area in bio-information.Due to the high cost of experimental methods to evaluate disordered regions of protein sequences,it is becoming increasingly important to predict those regions through computational methods.In this paper,we developed a novel scheme by employing sequence complexity to calculate six features for each residue of a protein sequence,which includes the Shannon entropy,the topological entropy,the sample entropy and three amino acid preferences including Remark 465,Deleage/Roux,and Bfactor(2STD).Particularly,we introduced the sample entropy for calculating time series complexity by mapping the amino acid sequence to a time series of 0-9.To our knowledge,the sample entropy has not been previously used for predicting IDPs and hence is being used for the first time in our study.In addition,the scheme used a properly sized sliding window in every protein sequence which greatly improved the prediction performance.Finally,we used seven machine learning algorithms and tested with 10-fold cross-validation to get the results on the dataset R80 collected by Yang et al.and of the dataset DIS1556 from the Database of Protein Disorder(DisProt)(https://www.disprot.org)containing experimentally determined intrinsically disordered proteins(IDPs).The results showed that k-Nearest Neighbor was more appropriate and an overall prediction accuracy of 92%.Furthermore,our method just used six features and hence required lower computational complexity.
文摘Accurately,reliably and rapidly identifying intrinsically disordered(IDPs)proteins is essential as they often play important roles in various human diseases;moreover,they are related to numerous important biological activities.However,current computational methods have yet to develop a network that is sufficiently deep tomake predictions about IDPs and demonstrate an improvement in performance.During this study,we constructed a deep neural network that consisted of five identical variant models,ResNet18,combined with an MLP network,for classification.Resnet18 was applied for the first time as a deep model for predicting IDPs,which allowed the extraction of information fromIDP residues in greater detail and depth,and this information was then passed through the MLP network for the final identification process.Two well-known datasets,MXD494 and R80,were used as the blind independent datasets to compare their performance with that of our method.The simulation results showed that Matthew’s correlation coefficient obtained using our deep network model was 0.517 on the blind R80 dataset and 0.450 on the MXD494 dataset;thus,our method outperformed existing methods.
基金supported by the National Key Research and Development Program of China (2018YFD1000800)the National Natural Science Foundation of China (32072561 and 31772290)。
文摘Nodulin 26-like intrinsic proteins(NIPs) are a family of channel-forming transmembrane proteins that function in the transport of water and other small molecules.Some NIPs can mediate silicon transport across plasma membranes and lead to silicon accumulation in plants,which is beneficial for the growth and development of plants.Cucumber is one of the most widely consumed vegetables;however,the functions of NIPs in this crop are still largely unknown.Here,we report the functional characteristics of Cs NIP2;2.It was found that Cs NIP2;2 is a tandem repeat of Cs NIP2;1,which had been demonstrated to be a silicon influx transporter gene.Cs NIP2;2 has a selectivity filter composed of cysteine,serine,glycine and arginine(CSGR),which is different from all previously characterized silicon influx transporters in higher plants at the second helix position.Xenopus laevis oocytes injected with Cs NIP2;2 c RNA demonstrated a higher uptake of silicon than the control,and the uptake remained unchanged under low temperature.Cs NIP2;2 was found to be expressed in the root,stem,lamina and petiole,and exogenous silicon treatment decreased its expression in the stem but not in other tissues.Transient expression of Cs NIP2;2-e GFP fusion sequence in onion epidermal cells showed that Cs NIP2;2 was localized to the cell nucleus,plasma membrane and an unknown structure inside the cell.The results suggest that Cs NIP2;2 is a silicon influx transporter in cucumber,and its subcellular localization and the selectivity filter are different from those of the previously characterized silicon influx transporters in other plants.These findings may be helpful for understanding the functions of NIPs in cucumber plants.
文摘Purpose:To analyze the change of water-soluble-protein(WSP),urea-soluble-protein(USP)and membrane intrinsic protein(MIP)in human senile catarct.Methods:The water-soluble-fractions(WSF)were prepared basically according to the method of Kibbelear,et al.But in this study,5mmol/LB-mercaptoethanol was added to the buffer solution.The urea-soluble-fractions(USF)were pre-pared basically according to the method of Kibbelear,et al.Lens fiber cell mem-branes were purified basically according to the method of Russell,et al.SDS-PAGE were performed according to the procedure of Laemmili,et al.using re-solving gel13%and3%stacking gel.Results:The WSPwas fractionated intoHM^+α^-,β1-3^-andγ-crystallin compo-nents.In nuclear cataractous lenses HM^+α^-and B-crystallin increase,while r-crystallin decrease.The USP from clear lenses contains mainlyαβchains of22KD,whereas in cataractous lenses,especially in nuclear cataractous lenses,the relative amount of the 28-and23KDpolypeptide(the components of β-crys-tallin)increased markedly.Lens fiber cell MIP,clear lens and cataract lens con-tained the main polypeptide of 27KD(MIP)and23KD(MP23).Conclusion:The water-insolube protein,whether in quantity or in quality,plays an important role in cataract formation.Eye Science 1995,11:124-127.
基金Supported by the Science,Technology and Innovation Commission of Shenzhen Municipality(No.GJHZ20220913142618036,No.JCYJ20210324113610029).
文摘●AIM:To identify disease-causative mutations in families with congenital cataract.●METHODS:Two Chinese families with autosomaldominant congenital cataract(ADCC)were recruited and underwent comprehensive eye examinations.Gene panel next-generation sequencing of common pathogenic genes of congenital cataract was performed in the proband of each family.Sanger sequencing was used to valid the candidate gene mutations and sequence the other family members for co-segregation analysis.The effect of sequence changes on protein structure and function was predicted through bioinformatics analysis.Major intrinsic protein(MIP)-wildtype and MIP-G29R plasmids were constructed and microinjected into zebrafish single-cell stage embryos.Zebrafish embryonic lens phenotypes were screened using confocal microscopy.●RESULTS:A novel heterozygous mutation(c.85G>A;p.G29R)in the MIP gene was identified in the proband of one family.A known heterozygous mutation(c.97C>T;p.R33C;rs864309693)in MIP was found in the proband of another family.In-silico prediction indicated that the novel mutation might affect the MIP protein function.Zebrafish embryonic lens was uniformly transparent in both wild-type PCS2+MIP and mutant PCS2+MIP.●CONCLUSION:Two missense mutations in the MIP gene in Chinese cataract families are identified,and one of which is novel.These findings expand the genetic spectrum of MIP mutations associated with cataracts.The functional studies suggest that the novel MIP mutation might not be a gain-of-function but a loss-of-function mutation.
