CORD-19-Sentences  

CORD-19:d819ba39c114acf69059a2d37f21246f30edaf56 JSONTXT 8 Projects

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Id Subject Object Predicate Lexical cue
TextSentencer_T1 0-40 Sentence denotes SUPPLEMENTARY INFORMATION TO MANUSCRIPT:
TextSentencer_T1 0-40 Sentence denotes SUPPLEMENTARY INFORMATION TO MANUSCRIPT:
TextSentencer_T2 41-149 Sentence denotes The Disulfide Bonds in Glycoprotein E2 of Hepatitis C Virus Reveal the Tertiary Organization of the Molecule
TextSentencer_T2 41-149 Sentence denotes The Disulfide Bonds in Glycoprotein E2 of Hepatitis C Virus Reveal the Tertiary Organization of the Molecule
TextSentencer_T3 151-159 Sentence denotes Abstract
TextSentencer_T3 151-159 Sentence denotes Abstract
TextSentencer_T4 162-508 Sentence denotes the divalent metal ions used for induction with the histidine tag used for purification of the secreted protein, we replaced the region including the V5 epitope and the 6-Histidine tag by a segment coding for a specific proteolytic cleavage site, followed by a tandem strep-tag (IBA, www.iba-go.com) with a linker region (GlyGlySer) 4 in between.
TextSentencer_T4 162-508 Sentence denotes the divalent metal ions used for induction with the histidine tag used for purification of the secreted protein, we replaced the region including the V5 epitope and the 6-Histidine tag by a segment coding for a specific proteolytic cleavage site, followed by a tandem strep-tag (IBA, www.iba-go.com) with a linker region (GlyGlySer) 4 in between.
TextSentencer_T5 509-613 Sentence denotes The proteolytic cleavage site was added to allow the specific removal of the tag for structural studies.
TextSentencer_T5 509-613 Sentence denotes The proteolytic cleavage site was added to allow the specific removal of the tag for structural studies.
TextSentencer_T6 614-844 Sentence denotes We avoided the use of cysteine proteases (like Prescission, TEV or 3C proteases) which, although are very specific, require a reducing agent for activity, which could also reduce some of the exposed disulfides of the glycoprotein.
TextSentencer_T6 614-844 Sentence denotes We avoided the use of cysteine proteases (like Prescission, TEV or 3C proteases) which, although are very specific, require a reducing agent for activity, which could also reduce some of the exposed disulfides of the glycoprotein.
TextSentencer_T7 845-1103 Sentence denotes We instead engineered an enterokinase (EK) cleavage site, which is a serine-protease relatively specific for the sequence (Asp) 4 Lys↓X, cleaving at the site indicated by the arrow with a cleavage efficiency between 60 and 80 % (X being any amino acid) [4] .
TextSentencer_T7 845-1103 Sentence denotes We instead engineered an enterokinase (EK) cleavage site, which is a serine-protease relatively specific for the sequence (Asp) 4 Lys↓X, cleaving at the site indicated by the arrow with a cleavage efficiency between 60 and 80 % (X being any amino acid) [4] .
TextSentencer_T8 1104-1238 Sentence denotes This resulted in the following amino acid sequence downstream of the ApaI and BstBI sites ...DDDDKAGWSHPQFEKGGGSGGGSGGGSWSHPQFEK-COOH.
TextSentencer_T8 1104-1238 Sentence denotes This resulted in the following amino acid sequence downstream of the ApaI and BstBI sites ...DDDDKAGWSHPQFEKGGGSGGGSGGGSWSHPQFEK-COOH.
TextSentencer_T9 1239-1542 Sentence denotes All synthetic HCV glycoprotein genes were purchased from GeneCust (Dudelange, Luxemburg) and amplified by PCR using strain specific 5'-oligonucleotides containing Bgl II, which allows insertion immediately downstream of the BiP secretion signal, and strain specific 3'-oligonucleotides containing Apa I.
TextSentencer_T9 1239-1542 Sentence denotes All synthetic HCV glycoprotein genes were purchased from GeneCust (Dudelange, Luxemburg) and amplified by PCR using strain specific 5'-oligonucleotides containing Bgl II, which allows insertion immediately downstream of the BiP secretion signal, and strain specific 3'-oligonucleotides containing Apa I.
TextSentencer_T10 1543-1619 Sentence denotes A full list of oligonucleotides used in this study is available upon request
TextSentencer_T10 1543-1619 Sentence denotes A full list of oligonucleotides used in this study is available upon request
TextSentencer_T11 1620-1632 Sentence denotes Transfection
TextSentencer_T11 1620-1632 Sentence denotes Transfection
TextSentencer_T12 1634-1847 Sentence denotes For large scale production of E2e the cells were cultured in spinner flasks or in Wave Bioreactors (2/10, Wave Biotech, Somerset, USA) and induced with 4µM CdCl 2 at a density of approximately 7x10 6 cells per ml.
TextSentencer_T12 1634-1847 Sentence denotes For large scale production of E2e the cells were cultured in spinner flasks or in Wave Bioreactors (2/10, Wave Biotech, Somerset, USA) and induced with 4µM CdCl 2 at a density of approximately 7x10 6 cells per ml.
TextSentencer_T13 1848-2124 Sentence denotes After 8 days at 28°C cells were pelleted and E2e was purified by affinity chromatography from the supernatant using a StrepTactin Superflow column (IBA, Goettingen, Germany) followed by gel filtration chromatography using a Superdex200 column (GE Healthcare, Uppsala, Sweden).
TextSentencer_T13 1848-2124 Sentence denotes After 8 days at 28°C cells were pelleted and E2e was purified by affinity chromatography from the supernatant using a StrepTactin Superflow column (IBA, Goettingen, Germany) followed by gel filtration chromatography using a Superdex200 column (GE Healthcare, Uppsala, Sweden).
TextSentencer_T14 2125-2224 Sentence denotes Pure protein was quantified using adsorption at UV 280nm and concentrated to approximately 1 mg/ml.
TextSentencer_T14 2125-2224 Sentence denotes Pure protein was quantified using adsorption at UV 280nm and concentrated to approximately 1 mg/ml.
TextSentencer_T15 2225-2447 Sentence denotes 25µg of H77 E2e and 70µg of either mAb H53 or CBH-4D, respectively, were incubated as isolated proteins as well as in complex for 1h at 10°C followed by analysis on a Superdex200 Mini column (column volume 3 ml, Amersham).
TextSentencer_T15 2225-2447 Sentence denotes 25µg of H77 E2e and 70µg of either mAb H53 or CBH-4D, respectively, were incubated as isolated proteins as well as in complex for 1h at 10°C followed by analysis on a Superdex200 Mini column (column volume 3 ml, Amersham).
TextSentencer_T16 2448-2583 Sentence denotes 25µg of E2e was bound to a StrepTactin Superflow mini column (column volume 0.2ml) and washed with 10 column volumes of washing buffer.
TextSentencer_T16 2448-2583 Sentence denotes 25µg of E2e was bound to a StrepTactin Superflow mini column (column volume 0.2ml) and washed with 10 column volumes of washing buffer.
TextSentencer_T17 2584-2602 Sentence denotes Subsequently, 10µg
TextSentencer_T17 2584-2602 Sentence denotes Subsequently, 10µg
TextSentencer_T18 2603-2769 Sentence denotes of CD81 large extracellular loop (produced as described before [5] ) or 50µg of conformation dependent antibodies CBH-4B, CBH-4D against HCV E2 (kindly provided by S.
TextSentencer_T18 2603-2769 Sentence denotes of CD81 large extracellular loop (produced as described before [5] ) or 50µg of conformation dependent antibodies CBH-4B, CBH-4D against HCV E2 (kindly provided by S.
TextSentencer_T19 2770-2869 Sentence denotes Foung, Stanford, USA) or a control antibody were added, followed by washing with 10 column volumes.
TextSentencer_T19 2770-2869 Sentence denotes Foung, Stanford, USA) or a control antibody were added, followed by washing with 10 column volumes.
TextSentencer_T20 2870-2973 Sentence denotes Complexes were eluted in 4.5 column volumes elution buffer and concentrated 20-fold by ultrafiltration.
TextSentencer_T20 2870-2973 Sentence denotes Complexes were eluted in 4.5 column volumes elution buffer and concentrated 20-fold by ultrafiltration.
TextSentencer_T21 2974-3044 Sentence denotes This concentrate was analysed by SDS-PAGE and Coomassie Blue staining.
TextSentencer_T21 2974-3044 Sentence denotes This concentrate was analysed by SDS-PAGE and Coomassie Blue staining.
TextSentencer_T22 3045-3106 Sentence denotes Huh7.5 cells plated on glass coverslips in 24-well plates (4.
TextSentencer_T22 3045-3106 Sentence denotes Huh7.5 cells plated on glass coverslips in 24-well plates (4.
TextSentencer_T23 3107-3353 Sentence denotes Secondary structure contents were estimated from the far-UV CD spectra using the CDSSTR routine [6] of the DICHROWEB server [7, 8] run on the SP175 reference dataset [9] , containing 72 proteins representing a large panel of secondary structures.
TextSentencer_T23 3107-3353 Sentence denotes Secondary structure contents were estimated from the far-UV CD spectra using the CDSSTR routine [6] of the DICHROWEB server [7, 8] run on the SP175 reference dataset [9] , containing 72 proteins representing a large panel of secondary structures.
TextSentencer_T24 3354-3451 Sentence denotes Similar results were obtained on different datasets [10] or by using the CONTIN/LL routine [11] .
TextSentencer_T24 3354-3451 Sentence denotes Similar results were obtained on different datasets [10] or by using the CONTIN/LL routine [11] .
TextSentencer_T25 3452-3618 Sentence denotes Soluble HCV E2 and Dengue virus 3 E protein in a concentration of 5-10mg/ml in After 8h, 0.25µg of trypsin were added and the digestion was continued for another 16h.
TextSentencer_T25 3452-3618 Sentence denotes Soluble HCV E2 and Dengue virus 3 E protein in a concentration of 5-10mg/ml in After 8h, 0.25µg of trypsin were added and the digestion was continued for another 16h.
TextSentencer_T26 3619-3711 Sentence denotes The peptides were eluted from the gel using 200µl water and two times 100µl 60% Acetonitril.
TextSentencer_T26 3619-3711 Sentence denotes The peptides were eluted from the gel using 200µl water and two times 100µl 60% Acetonitril.
TextSentencer_T27 3712-3853 Sentence denotes As a control, the trypsin digestion experiment was carried out as described above, but in the presence of 5% DMSO, acting as oxidizing agent.
TextSentencer_T27 3712-3853 Sentence denotes As a control, the trypsin digestion experiment was carried out as described above, but in the presence of 5% DMSO, acting as oxidizing agent.
TextSentencer_T28 3854-3991 Sentence denotes The deglycosylated 8 protein was analysed by SDS-PAGE followed by transfer onto a Nitrocellulose membrane and staining with Poinceau-Red.
TextSentencer_T28 3854-3991 Sentence denotes The deglycosylated 8 protein was analysed by SDS-PAGE followed by transfer onto a Nitrocellulose membrane and staining with Poinceau-Red.
TextSentencer_T29 3992-4027 Sentence denotes Bands containing approximately 15µg
TextSentencer_T29 3992-4027 Sentence denotes Bands containing approximately 15µg
TextSentencer_T30 4028-4188 Sentence denotes E2e were cut out of the membrane and saturated with 1ml of 0.2% PVP K30 for 15 minutes followed by six washes, four with water and two with 50mM TrisHCl pH 7.6.
TextSentencer_T30 4028-4188 Sentence denotes E2e were cut out of the membrane and saturated with 1ml of 0.2% PVP K30 for 15 minutes followed by six washes, four with water and two with 50mM TrisHCl pH 7.6.
TextSentencer_T31 4189-4297 Sentence denotes Subsequently the protein was digested with 1µg Trypsin for 3h at 37°C in the absence or presence of 5mM NEM.
TextSentencer_T31 4189-4297 Sentence denotes Subsequently the protein was digested with 1µg Trypsin for 3h at 37°C in the absence or presence of 5mM NEM.
TextSentencer_T32 4298-4362 Sentence denotes The peptides were eluted from the membrane using 200µl of water.
TextSentencer_T32 4298-4362 Sentence denotes The peptides were eluted from the membrane using 200µl of water.
TextSentencer_T33 4363-4416 Sentence denotes The tryptic digest was divided in two half fractions.
TextSentencer_T33 4363-4416 Sentence denotes The tryptic digest was divided in two half fractions.
TextSentencer_T34 4417-4523 Sentence denotes One half was submitted directly to reverse-phase HPLC using DEAE-C18 columns (1mm diameter) and a gradient
TextSentencer_T34 4417-4523 Sentence denotes One half was submitted directly to reverse-phase HPLC using DEAE-C18 columns (1mm diameter) and a gradient
TextSentencer_T35 4525-4603 Sentence denotes N-terminal sequencing was performed using a ABI 494 Protein Sequencer (Applied
TextSentencer_T35 4525-4603 Sentence denotes N-terminal sequencing was performed using a ABI 494 Protein Sequencer (Applied
TextSentencer_T36 4604-4785 Sentence denotes ChipReader System 4000 using a H4 (reversed phase, Ciphergen Biosystems, Fremont, CA, USA) surface and a SPA matrix, which was prepared according to the manufacturer's instructions.
TextSentencer_T36 4604-4785 Sentence denotes ChipReader System 4000 using a H4 (reversed phase, Ciphergen Biosystems, Fremont, CA, USA) surface and a SPA matrix, which was prepared according to the manufacturer's instructions.
TextSentencer_T37 4786-4865 Sentence denotes Peak identification was carried out using ProteinChip Software 3.1 (Ciphergen).
TextSentencer_T37 4786-4865 Sentence denotes Peak identification was carried out using ProteinChip Software 3.1 (Ciphergen).
TextSentencer_T38 4866-5044 Sentence denotes Molecular weight prediction of disulfide-connected peptides was performed using MS-BRIDGE [12] , while molecular weight of reduced peptides was predicted using PeptideMass [13] .
TextSentencer_T38 4866-5044 Sentence denotes Molecular weight prediction of disulfide-connected peptides was performed using MS-BRIDGE [12] , while molecular weight of reduced peptides was predicted using PeptideMass [13] .
TextSentencer_T39 5045-5166 Sentence denotes In order to identify the disulfide bridges of HCV E2e we first performed a tryptic digestion of E2e of the JFH-1 isolate.
TextSentencer_T39 5045-5166 Sentence denotes In order to identify the disulfide bridges of HCV E2e we first performed a tryptic digestion of E2e of the JFH-1 isolate.
TextSentencer_T40 5167-5297 Sentence denotes The HPLC chromatogram of the resulting digest revealed peaks 6-3, 12-3 and 16-3 to be TCEP sensitive and disappear upon reduction.
TextSentencer_T40 5167-5297 Sentence denotes The HPLC chromatogram of the resulting digest revealed peaks 6-3, 12-3 and 16-3 to be TCEP sensitive and disappear upon reduction.
TextSentencer_T41 5298-5492 Sentence denotes Peak 6-3 revealed a mixture of peptides, the N-terminal sequencing of which showed that only J1 and J2 (Table S1 and Fig. S3A ) contained a cysteine residue (position 452 and 459, respectively).
TextSentencer_T41 5298-5492 Sentence denotes Peak 6-3 revealed a mixture of peptides, the N-terminal sequencing of which showed that only J1 and J2 (Table S1 and Fig. S3A ) contained a cysteine residue (position 452 and 459, respectively).
TextSentencer_T42 5493-5716 Sentence denotes In the respective mass spectrum a peak corresponding to the disulfide linked dipeptide could be identified (1471.71 Da), which disappeared upon reduction (Fig. S3A) , indicating a disulfide bridge between Cys452 and Cys459.
TextSentencer_T42 5493-5716 Sentence denotes In the respective mass spectrum a peak corresponding to the disulfide linked dipeptide could be identified (1471.71 Da), which disappeared upon reduction (Fig. S3A) , indicating a disulfide bridge between Cys452 and Cys459.
TextSentencer_T43 5717-5825 Sentence denotes Peak 12-3 contained peptides J6 and J7, each of them with one cysteine (position 607 and 644, respectively).
TextSentencer_T43 5717-5825 Sentence denotes Peak 12-3 contained peptides J6 and J7, each of them with one cysteine (position 607 and 644, respectively).
TextSentencer_T44 5826-6064 Sentence denotes While peptides J6 and J7 were found as single peptides in the mass spectrum, indicating partial reduction, we also observed a peak at the predicted molecular weight of the two peptides linked by a disulfide bond (Fig. S3A, 2045 .37 Da).
TextSentencer_T44 5826-6064 Sentence denotes While peptides J6 and J7 were found as single peptides in the mass spectrum, indicating partial reduction, we also observed a peak at the predicted molecular weight of the two peptides linked by a disulfide bond (Fig. S3A, 2045 .37 Da).
TextSentencer_T45 6065-6116 Sentence denotes This peak disappeared, as expected, upon reduction.
TextSentencer_T45 6065-6116 Sentence denotes This peak disappeared, as expected, upon reduction.
TextSentencer_T46 6117-6185 Sentence denotes This clearly suggested a disulfide bridge between Cys607 and Cys644.
TextSentencer_T46 6117-6185 Sentence denotes This clearly suggested a disulfide bridge between Cys607 and Cys644.
TextSentencer_T47 6186-6379 Sentence denotes Peak 16-3 contained a mixture of peptides with one dominant sequence corresponding to peptide J4, containing two cysteines (position 503 and 508, respectively) and a proline residue in between.
TextSentencer_T47 6186-6379 Sentence denotes Peak 16-3 contained a mixture of peptides with one dominant sequence corresponding to peptide J4, containing two cysteines (position 503 and 508, respectively) and a proline residue in between.
TextSentencer_T48 6380-6502 Sentence denotes This peptide was unambiguously identified in the mass spectrum of peak 16-3 (Fig. 5B, Fig. S3B and Table S1 , 2341.37 Da).
TextSentencer_T48 6380-6502 Sentence denotes This peptide was unambiguously identified in the mass spectrum of peak 16-3 (Fig. 5B, Fig. S3B and Table S1 , 2341.37 Da).
TextSentencer_T49 6503-6726 Sentence denotes Reduction with TCEP resulted in a molecular weight shift by 2 Da, which was interpreted as two hydrogen atoms added upon reduction of the cysteines, demonstrating an intrapeptidic disulfide bridge between Cys503 and Cys508.
TextSentencer_T49 6503-6726 Sentence denotes Reduction with TCEP resulted in a molecular weight shift by 2 Da, which was interpreted as two hydrogen atoms added upon reduction of the cysteines, demonstrating an intrapeptidic disulfide bridge between Cys503 and Cys508.
TextSentencer_T50 6727-6950 Sentence denotes Two more peptides, which could not be observed by mass spectrometry, were identified by N-terminal sequencing in peak 16-3: peptide J3 and peptide J5, containing Cys486 and Cys494 as well as Cys581 and Cys585, respectively.
TextSentencer_T50 6727-6950 Sentence denotes Two more peptides, which could not be observed by mass spectrometry, were identified by N-terminal sequencing in peak 16-3: peptide J3 and peptide J5, containing Cys486 and Cys494 as well as Cys581 and Cys585, respectively.
TextSentencer_T51 6951-7029 Sentence denotes Subsequently we subjected the E2e from isolate UKN2b_2.8 to trypsin digestion.
TextSentencer_T51 6951-7029 Sentence denotes Subsequently we subjected the E2e from isolate UKN2b_2.8 to trypsin digestion.
TextSentencer_T52 7030-7264 Sentence denotes HPLC separation of the resulting peptides revealed that peaks 13-1, 20-1, 29-3, 42-observed by N-terminal sequencing in all three control experiments (data not shown), strongly suggesting that it is also present in the native protein.
TextSentencer_T52 7030-7264 Sentence denotes HPLC separation of the resulting peptides revealed that peaks 13-1, 20-1, 29-3, 42-observed by N-terminal sequencing in all three control experiments (data not shown), strongly suggesting that it is also present in the native protein.
TextSentencer_T53 7265-7423 Sentence denotes Peak 20-1 contained exclusively peptide U3, which corresponds to peptide J4 in JFH-1 E2e, thereby confirming the presence of a disulfide bridge between Cys503
TextSentencer_T53 7265-7423 Sentence denotes Peak 20-1 contained exclusively peptide U3, which corresponds to peptide J4 in JFH-1 E2e, thereby confirming the presence of a disulfide bridge between Cys503
TextSentencer_T54 7424-7472 Sentence denotes and Cys508 (Table S1 and Fig. S3C, 2194 .94 Da).
TextSentencer_T54 7424-7472 Sentence denotes and Cys508 (Table S1 and Fig. S3C, 2194 .94 Da).
TextSentencer_T55 7473-7543 Sentence denotes Analysis of peak 29-3 revealed two TCEP sensitive peptides, U2 and U3.
TextSentencer_T55 7473-7543 Sentence denotes Analysis of peak 29-3 revealed two TCEP sensitive peptides, U2 and U3.
TextSentencer_T56 7544-7709 Sentence denotes We had identified U3 previously to carry an internal disulfide bridge, thus suggesting an additional internal disulfide bond between Cys486 and Cys494 in peptide U2.
TextSentencer_T56 7544-7709 Sentence denotes We had identified U3 previously to carry an internal disulfide bridge, thus suggesting an additional internal disulfide bond between Cys486 and Cys494 in peptide U2.
TextSentencer_T57 7710-7717 Sentence denotes Cys552.
TextSentencer_T57 7710-7717 Sentence denotes Cys552.
TextSentencer_T58 7718-7899 Sentence denotes Although the disulfide linked peptides could not be identified by mass spectrometry, upon reduction a peak corresponding to the reduced peptide U1 was observed (Fig. S3D , 2308 Da).
TextSentencer_T58 7718-7899 Sentence denotes Although the disulfide linked peptides could not be identified by mass spectrometry, upon reduction a peak corresponding to the reduced peptide U1 was observed (Fig. S3D , 2308 Da).
TextSentencer_T59 7900-8030 Sentence denotes Likely the high molecular weight of the disulfide linked dipeptide (U1 + U4 -6890.68 Da) prevented its appearance in the spectrum.
TextSentencer_T59 7900-8030 Sentence denotes Likely the high molecular weight of the disulfide linked dipeptide (U1 + U4 -6890.68 Da) prevented its appearance in the spectrum.
TextSentencer_T60 8031-8206 Sentence denotes One peak (19-1) was found to contain a mixture of sequences, with one dominant sequence corresponding to peptide U5, in which two cysteines (position 581 and 585) are present.
TextSentencer_T60 8031-8206 Sentence denotes One peak (19-1) was found to contain a mixture of sequences, with one dominant sequence corresponding to peptide U5, in which two cysteines (position 581 and 585) are present.
TextSentencer_T61 8207-8356 Sentence denotes We observed a peak corresponding to the peptide harboring an intrapeptidic disulfide bridge in the mass spectrum (Table S1 and Fig. S3D, 1849.64 Da).
TextSentencer_T61 8207-8356 Sentence denotes We observed a peak corresponding to the peptide harboring an intrapeptidic disulfide bridge in the mass spectrum (Table S1 and Fig. S3D, 1849.64 Da).
TextSentencer_T62 8357-8435 Sentence denotes Reduction resulted as expected in an increase of the molecular weight by 2 Da.
TextSentencer_T62 8357-8435 Sentence denotes Reduction resulted as expected in an increase of the molecular weight by 2 Da.
TextSentencer_T63 8436-8561 Sentence denotes In addition, peptide U2 was found in the same peak, which has previously been shown to carry an intrapeptidic disulfide bond.
TextSentencer_T63 8436-8561 Sentence denotes In addition, peptide U2 was found in the same peak, which has previously been shown to carry an intrapeptidic disulfide bond.
TextSentencer_T64 8562-8759 Sentence denotes Finally, we performed a tryptic digestion of the of E2e of H77 followed by HPLC of the resulting peptides, which revealed that peaks 15-2, 6-2, 26-2, 32-2, 43-2 and 33-2 disappeared upon reduction.
TextSentencer_T64 8562-8759 Sentence denotes Finally, we performed a tryptic digestion of the of E2e of H77 followed by HPLC of the resulting peptides, which revealed that peaks 15-2, 6-2, 26-2, 32-2, 43-2 and 33-2 disappeared upon reduction.
TextSentencer_T65 8760-8847 Sentence denotes Peptides H5 and H6, which correspond to J6/ J7 and U6/ U7 were identified in peak 15-2.
TextSentencer_T65 8760-8847 Sentence denotes Peptides H5 and H6, which correspond to J6/ J7 and U6/ U7 were identified in peak 15-2.
TextSentencer_T66 8848-8982 Sentence denotes For both E2 of JFH-1 and UKN2b_2.8 a disulfide bridge between the respective cysteines (position 607 and 644) was shown in this study.
TextSentencer_T66 8848-8982 Sentence denotes For both E2 of JFH-1 and UKN2b_2.8 a disulfide bridge between the respective cysteines (position 607 and 644) was shown in this study.
TextSentencer_T67 8983-9143 Sentence denotes Mass spectrometry clearly demonstrated the presence of a disulfide bridge between Cys607 and Cys644 in the ectodomain of H77 E2 as well (Table S1 and Fig. S3E ,
TextSentencer_T67 8983-9143 Sentence denotes Mass spectrometry clearly demonstrated the presence of a disulfide bridge between Cys607 and Cys644 in the ectodomain of H77 E2 as well (Table S1 and Fig. S3E ,
TextSentencer_T68 9144-9188 Sentence denotes Peptide H1 was found in two different peaks.
TextSentencer_T68 9144-9188 Sentence denotes Peptide H1 was found in two different peaks.
TextSentencer_T69 9189-9409 Sentence denotes Together with peptide H2, which corresponds to peptide J2, it was observed in peak 6-2, suggesting the presence of a disulfide bridge between Cys452 and Cys459, which has already been identified in E2e from strain JFH-1.
TextSentencer_T69 9189-9409 Sentence denotes Together with peptide H2, which corresponds to peptide J2, it was observed in peak 6-2, suggesting the presence of a disulfide bridge between Cys452 and Cys459, which has already been identified in E2e from strain JFH-1.
TextSentencer_T70 9410-9538 Sentence denotes A peak in the mass spectrum corresponding to this peptide confirmed the presence of this disulfide bond (Fig. S3E, 1544 .29 Da).
TextSentencer_T70 9410-9538 Sentence denotes A peak in the mass spectrum corresponding to this peptide confirmed the presence of this disulfide bond (Fig. S3E, 1544 .29 Da).
TextSentencer_T71 9539-9815 Sentence denotes However, peptide H1 was also found together with peptide H6 in peak 26-2, which clearly suggested a disulfide rearrangement for these cysteines (Fig. S3F) Peak 43-2 consisted of the peptides H7 and H8, each containing one cysteine residue (position 652 and 677, respectively).
TextSentencer_T71 9539-9815 Sentence denotes However, peptide H1 was also found together with peptide H6 in peak 26-2, which clearly suggested a disulfide rearrangement for these cysteines (Fig. S3F) Peak 43-2 consisted of the peptides H7 and H8, each containing one cysteine residue (position 652 and 677, respectively).
TextSentencer_T72 9816-10041 Sentence denotes In the mass spectrum we observed a peak corresponding to the disulfide linked dipeptide (Fig. S3G and Table S1 , 6849.91 Da), unambiguously identifying a disulfide bridge between Cys652 and Cys677 in the ectodomain of H77 E2.
TextSentencer_T72 9816-10041 Sentence denotes In the mass spectrum we observed a peak corresponding to the disulfide linked dipeptide (Fig. S3G and Table S1 , 6849.91 Da), unambiguously identifying a disulfide bridge between Cys652 and Cys677 in the ectodomain of H77 E2.
TextSentencer_T73 10042-10259 Sentence denotes Comparing the sequence alignment of E2 in the region between Cys569 and Cys581 we noticed that while UKN2b_2.8 and JFH-1 E2 contain three trypsin cleavage sites, H77 E2 has no cleavage sites in this region (Fig. S2 ).
TextSentencer_T73 10042-10259 Sentence denotes Comparing the sequence alignment of E2 in the region between Cys569 and Cys581 we noticed that while UKN2b_2.8 and JFH-1 E2 contain three trypsin cleavage sites, H77 E2 has no cleavage sites in this region (Fig. S2 ).
TextSentencer_T74 10260-10471 Sentence denotes Thus trypsin cleavage prediction in this region resulted in one peptide containing 4 cysteines, aligned sequentially in a way that the first two cysteines and the last two each have a proline residue in between.
TextSentencer_T74 10260-10471 Sentence denotes Thus trypsin cleavage prediction in this region resulted in one peptide containing 4 cysteines, aligned sequentially in a way that the first two cysteines and the last two each have a proline residue in between.
TextSentencer_T75 10472-10634 Sentence denotes Analysis of peak 33-2 revealed only peptide H4, which corresponds to the predicted peptide containing 4 cysteines (positions 564, 569, 581 and 585, respectively).
TextSentencer_T75 10472-10634 Sentence denotes Analysis of peak 33-2 revealed only peptide H4, which corresponds to the predicted peptide containing 4 cysteines (positions 564, 569, 581 and 585, respectively).
TextSentencer_T76 10635-10786 Sentence denotes Mass spectrometry revealed a peak matching the predicted mass of this peptide containing two intrapeptidic disulfide bridges (Fig. S3G , 2504.50 Da).
TextSentencer_T76 10635-10786 Sentence denotes Mass spectrometry revealed a peak matching the predicted mass of this peptide containing two intrapeptidic disulfide bridges (Fig. S3G , 2504.50 Da).
TextSentencer_T77 10787-10969 Sentence denotes Under non-reducing conditions two minor peaks could be observed, which are shifted by exactly 2 Da and thus likely correspond to partially reduced peptides in the original HPLC peak.
TextSentencer_T77 10787-10969 Sentence denotes Under non-reducing conditions two minor peaks could be observed, which are shifted by exactly 2 Da and thus likely correspond to partially reduced peptides in the original HPLC peak.
TextSentencer_T78 10970-11156 Sentence denotes Since we had already identified the disulfide bond between Cys581 and Cys585 in UKN2b_2.8 E2, this result strongly indicates the presence of a disulfide bridge between Cys564 and Cys569.
TextSentencer_T78 10970-11156 Sentence denotes Since we had already identified the disulfide bond between Cys581 and Cys585 in UKN2b_2.8 E2, this result strongly indicates the presence of a disulfide bridge between Cys564 and Cys569.