Membrane proteins are an important kind of proteins embedded in the membranes of cells and play crucial roles in living organisms, such as ion channels,transporters, receptors. Because it is difficult to determinate t...Membrane proteins are an important kind of proteins embedded in the membranes of cells and play crucial roles in living organisms, such as ion channels,transporters, receptors. Because it is difficult to determinate the membrane protein's structure by wet-lab experiments,accurate and fast amino acid sequence-based computational methods are highly desired. In this paper, we report an online prediction tool called Mem Brain, whose input is the amino acid sequence. Mem Brain consists of specialized modules for predicting transmembrane helices, residue–residue contacts and relative accessible surface area of a-helical membrane proteins. Mem Brain achieves aprediction accuracy of 97.9% of ATMH, 87.1% of AP,3.2 ± 3.0 of N-score, 3.1 ± 2.8 of C-score. Mem BrainContact obtains 62%/64.1% prediction accuracy on training and independent dataset on top L/5 contact prediction,respectively. And Mem Brain-Rasa achieves Pearson correlation coefficient of 0.733 and its mean absolute error of13.593. These prediction results provide valuable hints for revealing the structure and function of membrane proteins.Mem Brain web server is free for academic use and available at www.csbio.sjtu.edu.cn/bioinf/Mem Brain/.展开更多
Parallel DNA helices with reverse WatsonCrick pairing have been described in several papers.It has been pointed out,however,that the parallel structures may also be in equilibrium with antiparallel WatsonCrick helices...Parallel DNA helices with reverse WatsonCrick pairing have been described in several papers.It has been pointed out,however,that the parallel structures may also be in equilibrium with antiparallel WatsonCrick helices due to their closely similar properties.To avoid the problem we have prepared and characterized DNA helices which are constrained to possess parallel polarity by two dC residues,or CC+clamps,at both the ends of AT oligomer chains.The residues are hemiprotonated below neutral pH,forming two stable CC+base pairs with three hydrogen bonds at each end of the helix.The physical properties of these constructs can then be used to calibrate those of duplexes having the same sequences but lacking the terminal C residues.Though recent studies indicate that dC acid selfstructures are fourstranded with intercalated bases,gel electrophoresis indicates that these structures are not present in the molecules described here.展开更多
Aquaporin (AQP) is a water channel protein found in various subcellular membranes of both prokaryotic and eukaryotic cells. The physiological functions of AQPs have been elucidated in many organisms. However, unders...Aquaporin (AQP) is a water channel protein found in various subcellular membranes of both prokaryotic and eukaryotic cells. The physiological functions of AQPs have been elucidated in many organisms. However, understanding their biogenesis remains elusive, particularly regarding how they assemble into tetramers. Here, we investigated the amino acid residues involved in the tetramer formation of the Arabidopsis plasma membrane AQP AtPIP2;1 using extensive amino acid substitution mutagenesis. The mutant proteins V41A/ E44A, F51A/L52A, F87A/191A, F92A/193A, V95A/Y96A, and H216A/L217A, harboring alanine substitutions in the transmembrane (TM) helices of AtPIP2;1 polymerized into multiple oligomeric complexes with a vari- able number of subunits greater than four. Moreover, these mutant proteins failed to traffic to the plasma membrane, instead of accumulating in the endoplasmic reticulum (ER). Structure-based modeling revealed that these residues are largely involved in interactions between TM helices within monomers. These results suggest that inter-TM interactions occurring both within and between monomers play crucial roles in tetramer formation in the AtPIP2;1 complex. Moreover, the assembly of AtPIP2;1 tetramers is critical for their trafficking from the ER to the plasma membrane, as well as water permeability.展开更多
A novel method based on continuous wavelet transform (CWT) for predicting the number and location of helices in membrane proteins is presented. The PDB code of lyst is chosen as an example to describe the prediction o...A novel method based on continuous wavelet transform (CWT) for predicting the number and location of helices in membrane proteins is presented. The PDB code of lyst is chosen as an example to describe the prediction of transmembrane helices (HTM) by using CWT. The results indicate that CWT is a promising approach for the prediction of HTM.展开更多
The compound [Cu2(bpy)2(PDIAla)(H2O)2](ClO4)2·H2O(H2PDIAla = N,N'-(p-xylylene)dialanine,bipy = 2,2'-bipyridine) 1 has been synthesized and structurally determined by single-crystal X-ray diffraction...The compound [Cu2(bpy)2(PDIAla)(H2O)2](ClO4)2·H2O(H2PDIAla = N,N'-(p-xylylene)dialanine,bipy = 2,2'-bipyridine) 1 has been synthesized and structurally determined by single-crystal X-ray diffraction,elemental analyses and IR spectroscopy.The crystal belongs to the monoclinic system,space group P21 with a = 10.9772(6),b = 18.5464(9),c = 11.0790(6) ,β = 116.3110o,V = 2021.87(18) 3,Z = 2,Dc = 1.594 Mg/m3,Mr = 970.70,μ = 1.260 mm-1,F(000) = 996,λ(MoKα) = 0.71073 ,the final R = 0.0400 and wR = 0.1050 for all observed reflections.In the structure,the O(5)-H(52)…O(4) hydrogen bonding between aqua ligand and carbonyl oxygen of the H2PDIAla ligand along the c axis produce hydrogen-bonded helices which are assembled along the b axis through O(61)-H(61)…O(2) and N(6)-H(6N)…O(2) interactions to form 2-D layers that are further linked by π···π interactions between bpy ligands to yield a three-dimensional supramolecular network.展开更多
Estrogen mediates multiple functions in the brain through the interaction of estrogen receptor (ER)α and ERβ with a host of nuclear proteins that regulate specific gene transcription. We have identified ERAP 140, AI...Estrogen mediates multiple functions in the brain through the interaction of estrogen receptor (ER)α and ERβ with a host of nuclear proteins that regulate specific gene transcription. We have identified ERAP 140, AIB 1, Trk A, Src, pCREB and CREB as ERβ interacting proteins in the mouse brain. Earlier we showed that the interaction of ERβ with ERAP 140 decreased whereas its expression increased with aging in the brain of female mice. Here we report that the pattern of interaction and expression is different in male mice as compared to females. The interaction of ERAP 140 with ERβ decreased in adult male mouse brain as compared to young and remained almost similar in old whereas its expression was higher in adult than young and old, which were almost similar. Further in silico secondary structure analysis by self-optimized prediction method alignment (SOPMA) and PSIPRED revealed that ERβ interacting proteins were rich in alpha helices and coils. Such findings might help to design ER modulators which can regulate specific functions of estrogen in the brain during aging and degenerative diseases.展开更多
A novel 3D metal-organic framework(MOF) with remarkable thermal stability,Ni(BIC)2.2·5H2O(JUC-86)(HBIC = 1-H-benzimidazole-5-carboxylic acid and JUC = Jilin University China),has been synthesized under hydrotherm...A novel 3D metal-organic framework(MOF) with remarkable thermal stability,Ni(BIC)2.2·5H2O(JUC-86)(HBIC = 1-H-benzimidazole-5-carboxylic acid and JUC = Jilin University China),has been synthesized under hydrothermal conditions.It crystallizes in tetragonal symmetry with P43212 space group.The 3D structure consists of channels assembled from triple helices with a 4.5 × 4.52 aperture,which are formed by the parallel alignment of three infinite helical chains.The thermogravimetric analysis(TGA) and powder X-ray diffractions(PXRD) indicate JUC-86 with high thermal stability(up to 350 ℃).展开更多
Aluminum nitride(AlN)has attracted a great amount of interest due to the fact that these group III–V semiconductors present direct band gap behavior and are compatible with current micro-electro-mechanical systems.In...Aluminum nitride(AlN)has attracted a great amount of interest due to the fact that these group III–V semiconductors present direct band gap behavior and are compatible with current micro-electro-mechanical systems.In this work,three dimensional(3D)AlN architectures including tubes and helices were constructed by rolling up AlN nanomembranes grown on a silicon-on-insulator wafer via magnetron sputtering.The properties of the AlN membrane were characterized through transmission electron microscopy and X-ray diffraction.The thickness of AlN nanomembranes could be tuned via the RIE thinning method,and thus micro-tubes with different diameters were fabricated.The intrinsic strain in AlN membranes was investigated via micro-Raman spectroscopy,which agrees well with theory prediction.Whispering gallery mode was observed in AlN tubular optical microcavity in photoluminescence spectrum.A postprocess involving atomic layer deposition and R6G immersion were employed on as-fabricated AlN tubes to promote the Q-factor.The AlN tubular micro-resonators could offer a novel design route for Si-based integrated light sources.In addition,the rolled-up technology paves a new way for AlN 3D structure fabrication,which is promising for AlN application in MEMS and photonics fields.展开更多
Izumiya and Takeuchi (2003) obtained some characterizations for Ruled surfaces. Turgut and Haclsalihoglu (1998) defined timelike Ruled surfaces and obtained some characterizations in timelike Ruled surfaces. Choi ...Izumiya and Takeuchi (2003) obtained some characterizations for Ruled surfaces. Turgut and Haclsalihoglu (1998) defined timelike Ruled surfaces and obtained some characterizations in timelike Ruled surfaces. Choi (1995) and Jung and Pak (1996) studied Ruled surfaces. This study uses the method in (lzumiya and Takeuchi, 2003) to investigate cylindrical helices and Bertrand curves as curves on timelike Ruled surfaces in Minkowski 3-space R1^3. We have studied singularities of the rectifying developable (surface) of a timelike curve. We observed that the rectifying developable along a timelike curve a is non-singular if and only if a is a cylindrical helice. In this case the rectifying developable is a cylindrical surface.展开更多
基金supported by the National Natural Science Foundation of China(Nos.61671288,91530321,61603161)Science and Technology Commission of Shanghai Municipality(Nos.16JC1404300,17JC1403500,16ZR1448700)
文摘Membrane proteins are an important kind of proteins embedded in the membranes of cells and play crucial roles in living organisms, such as ion channels,transporters, receptors. Because it is difficult to determinate the membrane protein's structure by wet-lab experiments,accurate and fast amino acid sequence-based computational methods are highly desired. In this paper, we report an online prediction tool called Mem Brain, whose input is the amino acid sequence. Mem Brain consists of specialized modules for predicting transmembrane helices, residue–residue contacts and relative accessible surface area of a-helical membrane proteins. Mem Brain achieves aprediction accuracy of 97.9% of ATMH, 87.1% of AP,3.2 ± 3.0 of N-score, 3.1 ± 2.8 of C-score. Mem BrainContact obtains 62%/64.1% prediction accuracy on training and independent dataset on top L/5 contact prediction,respectively. And Mem Brain-Rasa achieves Pearson correlation coefficient of 0.733 and its mean absolute error of13.593. These prediction results provide valuable hints for revealing the structure and function of membrane proteins.Mem Brain web server is free for academic use and available at www.csbio.sjtu.edu.cn/bioinf/Mem Brain/.
文摘Parallel DNA helices with reverse WatsonCrick pairing have been described in several papers.It has been pointed out,however,that the parallel structures may also be in equilibrium with antiparallel WatsonCrick helices due to their closely similar properties.To avoid the problem we have prepared and characterized DNA helices which are constrained to possess parallel polarity by two dC residues,or CC+clamps,at both the ends of AT oligomer chains.The residues are hemiprotonated below neutral pH,forming two stable CC+base pairs with three hydrogen bonds at each end of the helix.The physical properties of these constructs can then be used to calibrate those of duplexes having the same sequences but lacking the terminal C residues.Though recent studies indicate that dC acid selfstructures are fourstranded with intercalated bases,gel electrophoresis indicates that these structures are not present in the molecules described here.
文摘Aquaporin (AQP) is a water channel protein found in various subcellular membranes of both prokaryotic and eukaryotic cells. The physiological functions of AQPs have been elucidated in many organisms. However, understanding their biogenesis remains elusive, particularly regarding how they assemble into tetramers. Here, we investigated the amino acid residues involved in the tetramer formation of the Arabidopsis plasma membrane AQP AtPIP2;1 using extensive amino acid substitution mutagenesis. The mutant proteins V41A/ E44A, F51A/L52A, F87A/191A, F92A/193A, V95A/Y96A, and H216A/L217A, harboring alanine substitutions in the transmembrane (TM) helices of AtPIP2;1 polymerized into multiple oligomeric complexes with a vari- able number of subunits greater than four. Moreover, these mutant proteins failed to traffic to the plasma membrane, instead of accumulating in the endoplasmic reticulum (ER). Structure-based modeling revealed that these residues are largely involved in interactions between TM helices within monomers. These results suggest that inter-TM interactions occurring both within and between monomers play crucial roles in tetramer formation in the AtPIP2;1 complex. Moreover, the assembly of AtPIP2;1 tetramers is critical for their trafficking from the ER to the plasma membrane, as well as water permeability.
文摘A novel method based on continuous wavelet transform (CWT) for predicting the number and location of helices in membrane proteins is presented. The PDB code of lyst is chosen as an example to describe the prediction of transmembrane helices (HTM) by using CWT. The results indicate that CWT is a promising approach for the prediction of HTM.
基金supported by the National Natural Science Foundation of China (20571035)the Ministry of Education,Singapore through NUS (FRC Grant No. R143-000-371-112)
文摘The compound [Cu2(bpy)2(PDIAla)(H2O)2](ClO4)2·H2O(H2PDIAla = N,N'-(p-xylylene)dialanine,bipy = 2,2'-bipyridine) 1 has been synthesized and structurally determined by single-crystal X-ray diffraction,elemental analyses and IR spectroscopy.The crystal belongs to the monoclinic system,space group P21 with a = 10.9772(6),b = 18.5464(9),c = 11.0790(6) ,β = 116.3110o,V = 2021.87(18) 3,Z = 2,Dc = 1.594 Mg/m3,Mr = 970.70,μ = 1.260 mm-1,F(000) = 996,λ(MoKα) = 0.71073 ,the final R = 0.0400 and wR = 0.1050 for all observed reflections.In the structure,the O(5)-H(52)…O(4) hydrogen bonding between aqua ligand and carbonyl oxygen of the H2PDIAla ligand along the c axis produce hydrogen-bonded helices which are assembled along the b axis through O(61)-H(61)…O(2) and N(6)-H(6N)…O(2) interactions to form 2-D layers that are further linked by π···π interactions between bpy ligands to yield a three-dimensional supramolecular network.
文摘Estrogen mediates multiple functions in the brain through the interaction of estrogen receptor (ER)α and ERβ with a host of nuclear proteins that regulate specific gene transcription. We have identified ERAP 140, AIB 1, Trk A, Src, pCREB and CREB as ERβ interacting proteins in the mouse brain. Earlier we showed that the interaction of ERβ with ERAP 140 decreased whereas its expression increased with aging in the brain of female mice. Here we report that the pattern of interaction and expression is different in male mice as compared to females. The interaction of ERAP 140 with ERβ decreased in adult male mouse brain as compared to young and remained almost similar in old whereas its expression was higher in adult than young and old, which were almost similar. Further in silico secondary structure analysis by self-optimized prediction method alignment (SOPMA) and PSIPRED revealed that ERβ interacting proteins were rich in alpha helices and coils. Such findings might help to design ER modulators which can regulate specific functions of estrogen in the brain during aging and degenerative diseases.
基金supported by the National Basic Research Program of china (2011CB808703)the National Natural Science Foundation of China (91022030)+1 种基金"111" project(B07016)Jilin Young Scientist Foundation (20090131)
文摘A novel 3D metal-organic framework(MOF) with remarkable thermal stability,Ni(BIC)2.2·5H2O(JUC-86)(HBIC = 1-H-benzimidazole-5-carboxylic acid and JUC = Jilin University China),has been synthesized under hydrothermal conditions.It crystallizes in tetragonal symmetry with P43212 space group.The 3D structure consists of channels assembled from triple helices with a 4.5 × 4.52 aperture,which are formed by the parallel alignment of three infinite helical chains.The thermogravimetric analysis(TGA) and powder X-ray diffractions(PXRD) indicate JUC-86 with high thermal stability(up to 350 ℃).
基金the National Natural Science Foundation of China(Nos.61905270,51961145108)Natural Science Foundation of Shanghai(19ZR1467100)+1 种基金Science and Technology Commission of Shanghai Municipality(17JC1401700)the Program of Shanghai Academic Research Leader(19XD1400600).
文摘Aluminum nitride(AlN)has attracted a great amount of interest due to the fact that these group III–V semiconductors present direct band gap behavior and are compatible with current micro-electro-mechanical systems.In this work,three dimensional(3D)AlN architectures including tubes and helices were constructed by rolling up AlN nanomembranes grown on a silicon-on-insulator wafer via magnetron sputtering.The properties of the AlN membrane were characterized through transmission electron microscopy and X-ray diffraction.The thickness of AlN nanomembranes could be tuned via the RIE thinning method,and thus micro-tubes with different diameters were fabricated.The intrinsic strain in AlN membranes was investigated via micro-Raman spectroscopy,which agrees well with theory prediction.Whispering gallery mode was observed in AlN tubular optical microcavity in photoluminescence spectrum.A postprocess involving atomic layer deposition and R6G immersion were employed on as-fabricated AlN tubes to promote the Q-factor.The AlN tubular micro-resonators could offer a novel design route for Si-based integrated light sources.In addition,the rolled-up technology paves a new way for AlN 3D structure fabrication,which is promising for AlN application in MEMS and photonics fields.
文摘Izumiya and Takeuchi (2003) obtained some characterizations for Ruled surfaces. Turgut and Haclsalihoglu (1998) defined timelike Ruled surfaces and obtained some characterizations in timelike Ruled surfaces. Choi (1995) and Jung and Pak (1996) studied Ruled surfaces. This study uses the method in (lzumiya and Takeuchi, 2003) to investigate cylindrical helices and Bertrand curves as curves on timelike Ruled surfaces in Minkowski 3-space R1^3. We have studied singularities of the rectifying developable (surface) of a timelike curve. We observed that the rectifying developable along a timelike curve a is non-singular if and only if a is a cylindrical helice. In this case the rectifying developable is a cylindrical surface.