CORD-19-Sentences  

CORD-19:bfb0852ef4dd124ba671303aee7a71a08c7c21a7 JSONTXT 8 Projects

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Id Subject Object Predicate Lexical cue
TextSentencer_T1 0-100 Sentence denotes An automated data processing and analysis pipeline for transmembrane proteins in detergent solutions
TextSentencer_T1 0-100 Sentence denotes An automated data processing and analysis pipeline for transmembrane proteins in detergent solutions
TextSentencer_T2 102-110 Sentence denotes Abstract
TextSentencer_T2 102-110 Sentence denotes Abstract
TextSentencer_T3 111-346 Sentence denotes The application of small angle X-ray scattering (SAXS) to the structural characterization of transmembrane proteins (MPs) in detergent solutions has become a routine procedure at the most synchrotron BioSAXS beamlines around the world.
TextSentencer_T3 111-346 Sentence denotes The application of small angle X-ray scattering (SAXS) to the structural characterization of transmembrane proteins (MPs) in detergent solutions has become a routine procedure at the most synchrotron BioSAXS beamlines around the world.
TextSentencer_T4 347-669 Sentence denotes SAXS provides overall parameters and low resolution shapes of solubilized MPs, but is also meaningfully employed in hybrid modeling procedures that combine scattering data with information provided by high-resolution techniques (eg. macromolecular crystallography, nuclear magnetic resonance and cryo-electron microscopy).
TextSentencer_T4 347-669 Sentence denotes SAXS provides overall parameters and low resolution shapes of solubilized MPs, but is also meaningfully employed in hybrid modeling procedures that combine scattering data with information provided by high-resolution techniques (eg. macromolecular crystallography, nuclear magnetic resonance and cryo-electron microscopy).
TextSentencer_T5 670-818 Sentence denotes Structural modeling of MPs from SAXS data is non-trivial, and the necessary computational procedures require further formalization and facilitation.
TextSentencer_T5 670-818 Sentence denotes Structural modeling of MPs from SAXS data is non-trivial, and the necessary computational procedures require further formalization and facilitation.
TextSentencer_T6 819-1104 Sentence denotes We propose an automated pipeline integrated with the laboratory-information management system ISPyB, aimed at preliminary SAXS analysis and the first-step reconstruction of MPs in detergent solutions, in order to streamline high-throughput studies, especially at synchrotron beamlines.
TextSentencer_T6 819-1104 Sentence denotes We propose an automated pipeline integrated with the laboratory-information management system ISPyB, aimed at preliminary SAXS analysis and the first-step reconstruction of MPs in detergent solutions, in order to streamline high-throughput studies, especially at synchrotron beamlines.
TextSentencer_T7 1105-1348 Sentence denotes The pipeline queries an ISPyB database for available a priori information via dedicated services, estimates model-free SAXS parameters and generates preliminary models utilizing either ab initio, high-resolution-based, or mixed/hybrid methods.
TextSentencer_T7 1105-1348 Sentence denotes The pipeline queries an ISPyB database for available a priori information via dedicated services, estimates model-free SAXS parameters and generates preliminary models utilizing either ab initio, high-resolution-based, or mixed/hybrid methods.
TextSentencer_T8 1349-1550 Sentence denotes The results of the automated analysis can be inspected online using the standard ISPyB interface and the estimated modeling parameters may be utilized for further in-depth modeling beyond the pipeline.
TextSentencer_T8 1349-1550 Sentence denotes The results of the automated analysis can be inspected online using the standard ISPyB interface and the estimated modeling parameters may be utilized for further in-depth modeling beyond the pipeline.
TextSentencer_T9 1551-1748 Sentence denotes Examples of the pipeline results for the modelling of the tetrameric alpha-helical membrane channel Aquaporin0 and mechanosensitive channel T2, solubilized by n-Dodecyl β-D-maltoside are presented.
TextSentencer_T9 1551-1748 Sentence denotes Examples of the pipeline results for the modelling of the tetrameric alpha-helical membrane channel Aquaporin0 and mechanosensitive channel T2, solubilized by n-Dodecyl β-D-maltoside are presented.
TextSentencer_T10 1749-1929 Sentence denotes We demonstrate how the increasing amount a priori information improves the model resolution and enables deeper insights into the molecular structure of protein-detergent complexes.
TextSentencer_T10 1749-1929 Sentence denotes We demonstrate how the increasing amount a priori information improves the model resolution and enables deeper insights into the molecular structure of protein-detergent complexes.
TextSentencer_T11 1930-2286 Sentence denotes Small angle X-ray scattering (SAXS) using synchrotron radiation is a powerful technique for the structural characterization of transmembrane proteins (MPs) in detergent solutions Overall structural characterization and modeling of MPs from SAXS data is non-trivial, and the necessary computational procedures require further formalization and facilitation.
TextSentencer_T11 1930-2286 Sentence denotes Small angle X-ray scattering (SAXS) using synchrotron radiation is a powerful technique for the structural characterization of transmembrane proteins (MPs) in detergent solutions Overall structural characterization and modeling of MPs from SAXS data is non-trivial, and the necessary computational procedures require further formalization and facilitation.
TextSentencer_T12 2287-2567 Sentence denotes We propose an automated pipeline integrated with the laboratory-information management system ISPyB, aimed at preliminary SAXS analysis and modelling of MPs in detergent solutions, in order to streamline high-throughput studies, especially at synchrotron beamlines. author/funder.
TextSentencer_T12 2287-2567 Sentence denotes We propose an automated pipeline integrated with the laboratory-information management system ISPyB, aimed at preliminary SAXS analysis and modelling of MPs in detergent solutions, in order to streamline high-throughput studies, especially at synchrotron beamlines. author/funder.
TextSentencer_T13 2568-2588 Sentence denotes All rights reserved.
TextSentencer_T13 2568-2588 Sentence denotes All rights reserved.
TextSentencer_T14 2589-2625 Sentence denotes No reuse allowed without permission.
TextSentencer_T14 2589-2625 Sentence denotes No reuse allowed without permission.
TextSentencer_T15 2627-2872 Sentence denotes Membrane proteins (MPs) are crucial for the normal functioning of an organism as they are involved in essential processes including signalling, nutrient and ion transport, maintaining biological membrane structure and integrity (1) (2) (3) (4) .
TextSentencer_T15 2627-2872 Sentence denotes Membrane proteins (MPs) are crucial for the normal functioning of an organism as they are involved in essential processes including signalling, nutrient and ion transport, maintaining biological membrane structure and integrity (1) (2) (3) (4) .
TextSentencer_T16 2873-2978 Sentence denotes They are encoded by about 30% of the human genome (5) and are major targets for modern therapeutic drugs.
TextSentencer_T16 2873-2978 Sentence denotes They are encoded by about 30% of the human genome (5) and are major targets for modern therapeutic drugs.
TextSentencer_T17 2979-3101 Sentence denotes This makes structural studies of MP solutions extremely important both scientifically and medically (6) (7) (8) (9) (10) .
TextSentencer_T17 2979-3101 Sentence denotes This makes structural studies of MP solutions extremely important both scientifically and medically (6) (7) (8) (9) (10) .
TextSentencer_T18 3102-3321 Sentence denotes The defining structural feature of an integral MP is the presence of a large contiguous apolar surface, facilitating the insertion of the protein into the hydrophobic lipid alkyl chain interior of a biological membrane.
TextSentencer_T18 3102-3321 Sentence denotes The defining structural feature of an integral MP is the presence of a large contiguous apolar surface, facilitating the insertion of the protein into the hydrophobic lipid alkyl chain interior of a biological membrane.
TextSentencer_T19 3322-3496 Sentence denotes In order to characterize MPs in vitro, one needs to substitute the natural phospholipid bilayer with an artificial amphiphilic environment that supports the functional state.
TextSentencer_T19 3322-3496 Sentence denotes In order to characterize MPs in vitro, one needs to substitute the natural phospholipid bilayer with an artificial amphiphilic environment that supports the functional state.
TextSentencer_T20 3497-3664 Sentence denotes At present the majority of investigators studying MPs utilize readily available and inexpensive surfactant systems or detergents (small amphiphilic molecules) (6, 8) .
TextSentencer_T20 3497-3664 Sentence denotes At present the majority of investigators studying MPs utilize readily available and inexpensive surfactant systems or detergents (small amphiphilic molecules) (6, 8) .
TextSentencer_T21 3665-3796 Sentence denotes However, a common problem observed is the destabilization of protein structure following exposure to detergent molecules (11, 12) .
TextSentencer_T21 3665-3796 Sentence denotes However, a common problem observed is the destabilization of protein structure following exposure to detergent molecules (11, 12) .
TextSentencer_T22 3797-3951 Sentence denotes Fortunately, the development of milder detergents and detergent stabilized bilayer systems (bicelles) has helped to overcome this problem (7, 8, 13, 14) .
TextSentencer_T22 3797-3951 Sentence denotes Fortunately, the development of milder detergents and detergent stabilized bilayer systems (bicelles) has helped to overcome this problem (7, 8, 13, 14) .
TextSentencer_T23 3952-4139 Sentence denotes Importantly, the solution behaviour of many commercially available detergents has been well characterised using a range of techniques, including small angle X-ray scattering (SAXS) (15) .
TextSentencer_T23 3952-4139 Sentence denotes Importantly, the solution behaviour of many commercially available detergents has been well characterised using a range of techniques, including small angle X-ray scattering (SAXS) (15) .
TextSentencer_T24 4140-4386 Sentence denotes Micellar solutions of such detergents have been shown to adopt characteristic sizes, which can be reliably separated from detergent-protein complexes of interest using chromatographic techniques, eg. high performance liquid chromatography (HPLC).
TextSentencer_T24 4140-4386 Sentence denotes Micellar solutions of such detergents have been shown to adopt characteristic sizes, which can be reliably separated from detergent-protein complexes of interest using chromatographic techniques, eg. high performance liquid chromatography (HPLC).
TextSentencer_T25 4387-4639 Sentence denotes Recently, MPs have become increasingly popular objects for small angle scattering investigations (16) (17) (18) (19) thanks to the availability of improved online size-exclusion chromatography (SEC-SAXS) set-ups at dedicated SAXS synchrotron beamlines.
TextSentencer_T25 4387-4639 Sentence denotes Recently, MPs have become increasingly popular objects for small angle scattering investigations (16) (17) (18) (19) thanks to the availability of improved online size-exclusion chromatography (SEC-SAXS) set-ups at dedicated SAXS synchrotron beamlines.
TextSentencer_T26 4640-4860 Sentence denotes Integrated HPLC facilitates simultaneous sample purification and X-ray data acquisition, separating the scattering signal from protein, detergent and protein-detergent complexes (PDCs) that appear in the elution profile.
TextSentencer_T26 4640-4860 Sentence denotes Integrated HPLC facilitates simultaneous sample purification and X-ray data acquisition, separating the scattering signal from protein, detergent and protein-detergent complexes (PDCs) that appear in the elution profile.
TextSentencer_T27 4861-5100 Sentence denotes Direct measurement of the mobile phase (ie. buffer) and elution peaks corresponding to the macromolecule(s) of interest enable a rapid and robust sample characterization following a well-defined sequence of data reduction procedures (20) .
TextSentencer_T27 4861-5100 Sentence denotes Direct measurement of the mobile phase (ie. buffer) and elution peaks corresponding to the macromolecule(s) of interest enable a rapid and robust sample characterization following a well-defined sequence of data reduction procedures (20) .
TextSentencer_T28 5101-5262 Sentence denotes These procedures are amenable to automation and can be further coupled to advanced analysis and modeling approaches for MP systems, such as those detailed below.
TextSentencer_T28 5101-5262 Sentence denotes These procedures are amenable to automation and can be further coupled to advanced analysis and modeling approaches for MP systems, such as those detailed below.
TextSentencer_T29 5263-5474 Sentence denotes Unambiguous reconstruction of protein shape from a detergent solubilised MP is hampered by the strong scattering signal of bound detergent, typically forming a corona around the lipophilic trans-membrane region.
TextSentencer_T29 5263-5474 Sentence denotes Unambiguous reconstruction of protein shape from a detergent solubilised MP is hampered by the strong scattering signal of bound detergent, typically forming a corona around the lipophilic trans-membrane region.
TextSentencer_T30 5475-5597 Sentence denotes The corona consists of hydrophobic and hydrophilic components, with significantly different scattering/electron densities.
TextSentencer_T30 5475-5597 Sentence denotes The corona consists of hydrophobic and hydrophilic components, with significantly different scattering/electron densities.
TextSentencer_T31 5598-5701 Sentence denotes Thus the results of standard SAXS modelling procedures are, in such cases, non-realistic and ambiguous.
TextSentencer_T31 5598-5701 Sentence denotes Thus the results of standard SAXS modelling procedures are, in such cases, non-realistic and ambiguous.
TextSentencer_T32 5702-5963 Sentence denotes Using complementary data from small-angle neutron scattering (SANS) including contrast matching approaches to isolate scattering from each solution component, the ambiguity of models calculated from detergent solubilised MPs can be reduced (21) (22) (23) (24) .
TextSentencer_T32 5702-5963 Sentence denotes Using complementary data from small-angle neutron scattering (SANS) including contrast matching approaches to isolate scattering from each solution component, the ambiguity of models calculated from detergent solubilised MPs can be reduced (21) (22) (23) (24) .
TextSentencer_T33 5964-6186 Sentence denotes It was recently shown that SANS data recorded at several contrast points together with an a priori estimate of detergent aggregation number, allow one to reliably reconstruct the shapes of MPs in detergent solutions (24) .
TextSentencer_T33 5964-6186 Sentence denotes It was recently shown that SANS data recorded at several contrast points together with an a priori estimate of detergent aggregation number, allow one to reliably reconstruct the shapes of MPs in detergent solutions (24) .
TextSentencer_T34 6187-6347 Sentence denotes In this publication it was suggested that a minimum of two SANS curves, collected under different contrast conditions, are required to obtain a stable solution.
TextSentencer_T34 6187-6347 Sentence denotes In this publication it was suggested that a minimum of two SANS curves, collected under different contrast conditions, are required to obtain a stable solution.
TextSentencer_T35 6348-6546 Sentence denotes This requirement is necessary to isolate the signals from the two principal contributions to the scattering intensity, from the protein itself and from the hydrophillic part of the detergent corona.
TextSentencer_T35 6348-6546 Sentence denotes This requirement is necessary to isolate the signals from the two principal contributions to the scattering intensity, from the protein itself and from the hydrophillic part of the detergent corona.
TextSentencer_T36 6547-6729 Sentence denotes For this purpose the author developed an ab initio algorithm with a four-phase bead model for a protein: (1) protein, (2) detergent heads, (3) detergent tails, and (4) solvent (24) .
TextSentencer_T36 6547-6729 Sentence denotes For this purpose the author developed an ab initio algorithm with a four-phase bead model for a protein: (1) protein, (2) detergent heads, (3) detergent tails, and (4) solvent (24) .
TextSentencer_T37 6730-6809 Sentence denotes An additional set of geometrical and symmetrical constraints was also required.
TextSentencer_T37 6730-6809 Sentence denotes An additional set of geometrical and symmetrical constraints was also required.
TextSentencer_T38 6810-7029 Sentence denotes In comparison to shape reconstruction from multi-contrast SANS data, reconstruction of MPs from a single SAXS curve is significantly more challenging as the contributions from different phases are difficult to separate.
TextSentencer_T38 6810-7029 Sentence denotes In comparison to shape reconstruction from multi-contrast SANS data, reconstruction of MPs from a single SAXS curve is significantly more challenging as the contributions from different phases are difficult to separate.
TextSentencer_T39 7030-7240 Sentence denotes Nevertheless, in view of the relative ease of access to X-ray facilities and lower sample consumption, compared to that of neutron sources, SAXS-based approaches to MP characterization are increasingly popular.
TextSentencer_T39 7030-7240 Sentence denotes Nevertheless, in view of the relative ease of access to X-ray facilities and lower sample consumption, compared to that of neutron sources, SAXS-based approaches to MP characterization are increasingly popular.
TextSentencer_T40 7241-7485 Sentence denotes A recent work on the tetrameric water-channel protein Aquaporin0 (25) showed that if an atomic structure of the protein is available, it is possible to reconstruct the entire complex by combining online SEC-SAXS with refractometry measurements.
TextSentencer_T40 7241-7485 Sentence denotes A recent work on the tetrameric water-channel protein Aquaporin0 (25) showed that if an atomic structure of the protein is available, it is possible to reconstruct the entire complex by combining online SEC-SAXS with refractometry measurements.
TextSentencer_T41 7486-7660 Sentence denotes In that case, it was essential to use the available a priori information about the PDC in order to provide sufficient restraints on the model for a meaningful reconstruction.
TextSentencer_T41 7486-7660 Sentence denotes In that case, it was essential to use the available a priori information about the PDC in order to provide sufficient restraints on the model for a meaningful reconstruction.
TextSentencer_T42 7661-7837 Sentence denotes In the present paper we further formalize this approach and develop an automatic pipeline to build models of PDC utilizing a priori information taken from a dedicated database.
TextSentencer_T42 7661-7837 Sentence denotes In the present paper we further formalize this approach and develop an automatic pipeline to build models of PDC utilizing a priori information taken from a dedicated database.
TextSentencer_T43 7838-7983 Sentence denotes Given the rapidly growing interest in the applications of SAXS to study MPs, systematic storage of the relevant information is urgently required.
TextSentencer_T43 7838-7983 Sentence denotes Given the rapidly growing interest in the applications of SAXS to study MPs, systematic storage of the relevant information is urgently required.
TextSentencer_T44 7984-8161 Sentence denotes The ISPyB information system (26) , a database dedicated to biological SAXS (BioSAXS) and crystallographic experiments on synchrotron beamlines, offers an appropriate framework.
TextSentencer_T44 7984-8161 Sentence denotes The ISPyB information system (26) , a database dedicated to biological SAXS (BioSAXS) and crystallographic experiments on synchrotron beamlines, offers an appropriate framework.
TextSentencer_T45 8162-8415 Sentence denotes ISPyB is already employed at major European synchrotrons (Petra-III, ESRF, SOLEIL, DIAMOND, MAX IV) to facilitate the data flow beginning with the sample tracking and ending with its structural characterization and visualization of the generated models.
TextSentencer_T45 8162-8415 Sentence denotes ISPyB is already employed at major European synchrotrons (Petra-III, ESRF, SOLEIL, DIAMOND, MAX IV) to facilitate the data flow beginning with the sample tracking and ending with its structural characterization and visualization of the generated models.
TextSentencer_T46 8416-8698 Sentence denotes In order to be used in this project, the ISPyB database was extended to store information on the available high-resolution structures of MPs (e.g. homologs or crystallographic models), aminoacid sequences in FASTA format and chemical formulae of the given detergent tails and heads.
TextSentencer_T46 8416-8698 Sentence denotes In order to be used in this project, the ISPyB database was extended to store information on the available high-resolution structures of MPs (e.g. homologs or crystallographic models), aminoacid sequences in FASTA format and chemical formulae of the given detergent tails and heads.
TextSentencer_T47 8699-8824 Sentence denotes The latter are used for the calculation of electron densities and approximate sizes of the detergent corona in the modelling.
TextSentencer_T47 8699-8824 Sentence denotes The latter are used for the calculation of electron densities and approximate sizes of the detergent corona in the modelling.
TextSentencer_T48 8825-9017 Sentence denotes The electron density values can also be provided directly by the user for the cases when the automatic calculations are impossible or the values are not considered to be sufficiently accurate.
TextSentencer_T48 8825-9017 Sentence denotes The electron density values can also be provided directly by the user for the cases when the automatic calculations are impossible or the values are not considered to be sufficiently accurate.
TextSentencer_T49 9018-9279 Sentence denotes Depending on the amount of a priori information, the pipeline decides whether it is possible to automatically reconstruct the model and, if so, builds it utilizing either the multiphase ab initio program MONSA (27) or the hybrid modelling program MEMPROT (28) .
TextSentencer_T49 9018-9279 Sentence denotes Depending on the amount of a priori information, the pipeline decides whether it is possible to automatically reconstruct the model and, if so, builds it utilizing either the multiphase ab initio program MONSA (27) or the hybrid modelling program MEMPROT (28) .
TextSentencer_T50 9280-9493 Sentence denotes The starting parameters for the relevant fitting procedures are evaluated based on the available data stored in ISPyB, with the hybrid approach (25) executing upon detection of a high resolution protein component.
TextSentencer_T50 9280-9493 Sentence denotes The starting parameters for the relevant fitting procedures are evaluated based on the available data stored in ISPyB, with the hybrid approach (25) executing upon detection of a high resolution protein component.
TextSentencer_T51 9494-9776 Sentence denotes In the absence of a high resolution protein structure the ab initio reconstruction is executed utilizing information about the amino-acid sequence of the MP, chemical formula of the detergent and additional data on the other solvent/solute components to assess the shape of the PDC.
TextSentencer_T51 9494-9776 Sentence denotes In the absence of a high resolution protein structure the ab initio reconstruction is executed utilizing information about the amino-acid sequence of the MP, chemical formula of the detergent and additional data on the other solvent/solute components to assess the shape of the PDC.
TextSentencer_T52 9777-10008 Sentence denotes The automated membrane protein pipeline (AMPP) described herein, is implemented at the P12 beamline of the EMBL at Petra-III storage ring (synchrotron DESY, Hamburg, Germany) as an extension of a standard SEC-SAXS pipeline SASFLOW.
TextSentencer_T52 9777-10008 Sentence denotes The automated membrane protein pipeline (AMPP) described herein, is implemented at the P12 beamline of the EMBL at Petra-III storage ring (synchrotron DESY, Hamburg, Germany) as an extension of a standard SEC-SAXS pipeline SASFLOW.
TextSentencer_T53 10009-10099 Sentence denotes It is integrated into the beamline control software BECQUEREL (29) operating the beamline.
TextSentencer_T53 10009-10099 Sentence denotes It is integrated into the beamline control software BECQUEREL (29) operating the beamline.
TextSentencer_T54 10100-10301 Sentence denotes If the MP-related fields in the ISPyB database are lacking, BECQUEREL runs a standard pipeline mode for soluble proteins, using the program DAMMIF (30) for a single-phase ab initio shape determination.
TextSentencer_T54 10100-10301 Sentence denotes If the MP-related fields in the ISPyB database are lacking, BECQUEREL runs a standard pipeline mode for soluble proteins, using the program DAMMIF (30) for a single-phase ab initio shape determination.
TextSentencer_T55 10302-10479 Sentence denotes The MPrelated extension starts by default if the connection with ISPyB is established by the control software, and the membrane-specific fields in the ISPyB database are filled.
TextSentencer_T55 10302-10479 Sentence denotes The MPrelated extension starts by default if the connection with ISPyB is established by the control software, and the membrane-specific fields in the ISPyB database are filled.
TextSentencer_T56 10480-10638 Sentence denotes The system has been optimized through extensive testing on different MPs in detergent solutions, and several examples of its applications are presented below.
TextSentencer_T56 10480-10638 Sentence denotes The system has been optimized through extensive testing on different MPs in detergent solutions, and several examples of its applications are presented below.
TextSentencer_T57 10639-10802 Sentence denotes The published SAXS data of the tetrameric α-helical membrane channel, Aquaporin0 solubilized by n-Dodecyl β-D-Maltoside (25, 28) was used for the pipeline testing.
TextSentencer_T57 10639-10802 Sentence denotes The published SAXS data of the tetrameric α-helical membrane channel, Aquaporin0 solubilized by n-Dodecyl β-D-Maltoside (25, 28) was used for the pipeline testing.
TextSentencer_T58 10803-10977 Sentence denotes This sample corresponds to a reliably reconstituted PDC with known geometrical parameters of a detergent corona providing a test case with the modeling program MEMPROT (28) .
TextSentencer_T58 10803-10977 Sentence denotes This sample corresponds to a reliably reconstituted PDC with known geometrical parameters of a detergent corona providing a test case with the modeling program MEMPROT (28) .
TextSentencer_T59 10978-11094 Sentence denotes The model of the Aquaporin0-detergent complex (24, 25, 28) was used as a reference for the models generated by AMPP.
TextSentencer_T59 10978-11094 Sentence denotes The model of the Aquaporin0-detergent complex (24, 25, 28) was used as a reference for the models generated by AMPP.
TextSentencer_T60 11095-11321 Sentence denotes Additional pipeline tests were conducted using the experimental SEC-SAXS data for the mechanosensitive T2 channel solubilized n-Dodecyl β-D-Maltoside (31) downloaded from the SASBDB database (www.sasbdb.org, ID SASDCY6)) (32).
TextSentencer_T60 11095-11321 Sentence denotes Additional pipeline tests were conducted using the experimental SEC-SAXS data for the mechanosensitive T2 channel solubilized n-Dodecyl β-D-Maltoside (31) downloaded from the SASBDB database (www.sasbdb.org, ID SASDCY6)) (32).
TextSentencer_T61 11322-11455 Sentence denotes The AMPP is implemented as an extension of SASFLOW (33) , an automated data reduction and analysis pipeline currently running at P12.
TextSentencer_T61 11322-11455 Sentence denotes The AMPP is implemented as an extension of SASFLOW (33) , an automated data reduction and analysis pipeline currently running at P12.
TextSentencer_T62 11456-11594 Sentence denotes AMPP utilizes several modules and modeling programs available in the ATSAS package (34) and, in addition, calls the program MEMPROT (28) .
TextSentencer_T62 11456-11594 Sentence denotes AMPP utilizes several modules and modeling programs available in the ATSAS package (34) and, in addition, calls the program MEMPROT (28) .
TextSentencer_T63 11595-11737 Sentence denotes The primary data analysis is executed directly upon completion of a SEC-SAXS data acquisition and proceeds in the following workflow ( Figure.
TextSentencer_T63 11595-11737 Sentence denotes The primary data analysis is executed directly upon completion of a SEC-SAXS data acquisition and proceeds in the following workflow ( Figure.
TextSentencer_T64 11738-11910 Sentence denotes 1) Radial integration of 2D SAXS images by RADAVER (33) (typically 1000-3000 frames are collected for a standard SEC-SAXS run set with one second exposure per image/frame).
TextSentencer_T64 11738-11910 Sentence denotes 1) Radial integration of 2D SAXS images by RADAVER (33) (typically 1000-3000 frames are collected for a standard SEC-SAXS run set with one second exposure per image/frame).
TextSentencer_T65 11911-12099 Sentence denotes 2) Determination of the buffer and sample ranges from the elution profile using CHROMIXS (35) , an important analysis component of the pipeline specifically designed for SEC-SAXS analysis.
TextSentencer_T65 11911-12099 Sentence denotes 2) Determination of the buffer and sample ranges from the elution profile using CHROMIXS (35) , an important analysis component of the pipeline specifically designed for SEC-SAXS analysis.
TextSentencer_T66 12100-12322 Sentence denotes CHROMIXS automatically identifies both buffer and sample regions in the elution profile, and performs frame averaging and subtraction to produce the SAXS curve of the purified component for subsequent analysis (Figure 2 ).
TextSentencer_T66 12100-12322 Sentence denotes CHROMIXS automatically identifies both buffer and sample regions in the elution profile, and performs frame averaging and subtraction to produce the SAXS curve of the purified component for subsequent analysis (Figure 2 ).
TextSentencer_T67 12323-12499 Sentence denotes It is worth noting that CHROMIXS is capable of identifying multiple elution peaks, providing the users with a set of distinct SAXS curves from individual fractions, if present.
TextSentencer_T67 12323-12499 Sentence denotes It is worth noting that CHROMIXS is capable of identifying multiple elution peaks, providing the users with a set of distinct SAXS curves from individual fractions, if present.
TextSentencer_T68 12500-12819 Sentence denotes 3) Calculation of the overall parameters (radius of gyration R g , maximum size D max , excluded volume V Porod , molecular weight MW) and the generation of relevant plots (Guinier plot: ln I(s) vs s 2 ; Kratky plot: I(s)s 2 vs s; and the real-space distance distribution function: P(r) vs r) for all subtracted curves.
TextSentencer_T68 12500-12819 Sentence denotes 3) Calculation of the overall parameters (radius of gyration R g , maximum size D max , excluded volume V Porod , molecular weight MW) and the generation of relevant plots (Guinier plot: ln I(s) vs s 2 ; Kratky plot: I(s)s 2 vs s; and the real-space distance distribution function: P(r) vs r) for all subtracted curves.
TextSentencer_T69 12820-12935 Sentence denotes An example of these plots for the mechanosensitive T2 channel data is shown in the generated summary table (Figure.
TextSentencer_T69 12820-12935 Sentence denotes An example of these plots for the mechanosensitive T2 channel data is shown in the generated summary table (Figure.
TextSentencer_T70 12936-12939 Sentence denotes 3).
TextSentencer_T70 12936-12939 Sentence denotes 3).
TextSentencer_T71 12940-13107 Sentence denotes These parameters are employed for the evaluation of the search volume to conduct the ab initio reconstruction using MONSA or for the hybrid MEMPROT fitting procedures.
TextSentencer_T71 12940-13107 Sentence denotes These parameters are employed for the evaluation of the search volume to conduct the ab initio reconstruction using MONSA or for the hybrid MEMPROT fitting procedures.
TextSentencer_T72 13108-13258 Sentence denotes 4) Querying and collecting the available a priori information from the ISPyB database via dedicated Simple Object Access Protocol (SOAP) web services.
TextSentencer_T72 13108-13258 Sentence denotes 4) Querying and collecting the available a priori information from the ISPyB database via dedicated Simple Object Access Protocol (SOAP) web services.
TextSentencer_T73 13259-13366 Sentence denotes Depending on the results, one of the three modeling paths is executed for the subsequent modeling ( Figure.
TextSentencer_T73 13259-13366 Sentence denotes Depending on the results, one of the three modeling paths is executed for the subsequent modeling ( Figure.
TextSentencer_T74 13367-13370 Sentence denotes 1):
TextSentencer_T74 13367-13370 Sentence denotes 1):
TextSentencer_T75 13371-13385 Sentence denotes author/funder.
TextSentencer_T75 13371-13385 Sentence denotes author/funder.
TextSentencer_T76 13386-13406 Sentence denotes All rights reserved.
TextSentencer_T76 13386-13406 Sentence denotes All rights reserved.
TextSentencer_T77 13407-13443 Sentence denotes No reuse allowed without permission.
TextSentencer_T77 13407-13443 Sentence denotes No reuse allowed without permission.
TextSentencer_T78 13444-13582 Sentence denotes The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/714303 doi: bioRxiv preprint Figure.
TextSentencer_T78 13444-13582 Sentence denotes The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/714303 doi: bioRxiv preprint Figure.
TextSentencer_T79 13583-13585 Sentence denotes 1.
TextSentencer_T79 13583-13585 Sentence denotes 1.
TextSentencer_T80 13586-13629 Sentence denotes Workflow of the pipeline extension for MPs.
TextSentencer_T80 13586-13629 Sentence denotes Workflow of the pipeline extension for MPs.
TextSentencer_T81 13630-13792 Sentence denotes The pipeline utilizes a priori data from the ISPyB database, calculates overall SAXS parameters and decides, which software to employ for the subsequent analysis.
TextSentencer_T81 13630-13792 Sentence denotes The pipeline utilizes a priori data from the ISPyB database, calculates overall SAXS parameters and decides, which software to employ for the subsequent analysis.
TextSentencer_T82 13793-13800 Sentence denotes Figure.
TextSentencer_T82 13793-13800 Sentence denotes Figure.
TextSentencer_T83 13801-13803 Sentence denotes 2.
TextSentencer_T83 13801-13803 Sentence denotes 2.
TextSentencer_T84 13804-13945 Sentence denotes An elution profile of T2 membrane protein, built by CHROMIXS from 1600 consequent SEC-SAXS data sets (average intensity versus frame number).
TextSentencer_T84 13804-13945 Sentence denotes An elution profile of T2 membrane protein, built by CHROMIXS from 1600 consequent SEC-SAXS data sets (average intensity versus frame number).
TextSentencer_T85 13946-14109 Sentence denotes The frames corresponding to the buffer and sample are automatically identified (marked by red and green, respectively), averaged and subtracted one from the other.
TextSentencer_T85 13946-14109 Sentence denotes The frames corresponding to the buffer and sample are automatically identified (marked by red and green, respectively), averaged and subtracted one from the other.
TextSentencer_T86 14110-14171 Sentence denotes The resulting curve is displayed in PRIMUS interface (inset).
TextSentencer_T86 14110-14171 Sentence denotes The resulting curve is displayed in PRIMUS interface (inset).
TextSentencer_T87 14172-14381 Sentence denotes Initial estimates of the length of the detergent tail and head components are done using the Tanford formula for the detergent tail length: l c = 1.5 + 1.265n c , where n c is the total number of carbon atoms.
TextSentencer_T87 14172-14381 Sentence denotes Initial estimates of the length of the detergent tail and head components are done using the Tanford formula for the detergent tail length: l c = 1.5 + 1.265n c , where n c is the total number of carbon atoms.
TextSentencer_T88 14382-14493 Sentence denotes The starting parameters for the evaluation of the corona geometry using MEMPROT (28) are determined as follows:
TextSentencer_T88 14382-14493 Sentence denotes The starting parameters for the evaluation of the corona geometry using MEMPROT (28) are determined as follows:
TextSentencer_T89 14494-14823 Sentence denotes For a spherical (ellipticity, e = 1) detergent torus with the height (a) and cross-sectional axes (minor = b/e, major = b•e) equal to the length of a detergent tail (Tanford tail ), the geometrical parameters are set as: a = b = t = Tanford tail (28) (Figure 4) , where t is the thickness of the hydrophilic detergent head group.
TextSentencer_T89 14494-14823 Sentence denotes For a spherical (ellipticity, e = 1) detergent torus with the height (a) and cross-sectional axes (minor = b/e, major = b•e) equal to the length of a detergent tail (Tanford tail ), the geometrical parameters are set as: a = b = t = Tanford tail (28) (Figure 4) , where t is the thickness of the hydrophilic detergent head group.
TextSentencer_T90 14824-15015 Sentence denotes Although the hydrophobic tail of a detergent is typically slightly longer than its hydrophilic head, this assumption appears to be a reasonable first approximation for the further refinement.
TextSentencer_T90 14824-15015 Sentence denotes Although the hydrophobic tail of a detergent is typically slightly longer than its hydrophilic head, this assumption appears to be a reasonable first approximation for the further refinement.
TextSentencer_T91 15016-15194 Sentence denotes AMPP employs the MEMPROT minimization procedure, refining the starting parameters within a limited range, estimated empirically based on several tests conducted on different MPs.
TextSentencer_T91 15016-15194 Sentence denotes AMPP employs the MEMPROT minimization procedure, refining the starting parameters within a limited range, estimated empirically based on several tests conducted on different MPs.
TextSentencer_T92 15195-15364 Sentence denotes The a, b and t parameters are searched in the ± 1/3(Tanford tail ) range, while ellipticity and rotation parameters are kept fixed in order to speed up the computations.
TextSentencer_T92 15195-15364 Sentence denotes The a, b and t parameters are searched in the ± 1/3(Tanford tail ) range, while ellipticity and rotation parameters are kept fixed in order to speed up the computations.
TextSentencer_T93 15365-15622 Sentence denotes The hydrophobic radius of the model is taken as a + t = 2•Tanford tail , which is in a good agreement with the statistical mean value of transmembrane thickness D Transmemb ≈ 30 ±3 Å, obtained from the OPM database (36) (https://opm.phar.umich.edu/types/1).
TextSentencer_T93 15365-15622 Sentence denotes The hydrophobic radius of the model is taken as a + t = 2•Tanford tail , which is in a good agreement with the statistical mean value of transmembrane thickness D Transmemb ≈ 30 ±3 Å, obtained from the OPM database (36) (https://opm.phar.umich.edu/types/1).
TextSentencer_T94 15623-15722 Sentence denotes The maximum value of D Transmemb is checked during the modelling such that it does not exceed 45 Å.
TextSentencer_T94 15623-15722 Sentence denotes The maximum value of D Transmemb is checked during the modelling such that it does not exceed 45 Å.
TextSentencer_T95 15723-15941 Sentence denotes The electron densities can be either provided directly via the ISPyB interface or calculated from the protein primary sequence (in FASTA format) or from the chemical formula using the built-in look-up tables (37, 38) .
TextSentencer_T95 15723-15941 Sentence denotes The electron densities can be either provided directly via the ISPyB interface or calculated from the protein primary sequence (in FASTA format) or from the chemical formula using the built-in look-up tables (37, 38) .
TextSentencer_T96 15942-16079 Sentence denotes Knowledge of the detergent chemical formula is mandatory as it provides additional information to constrain the geometry of the MP model.
TextSentencer_T96 15942-16079 Sentence denotes Knowledge of the detergent chemical formula is mandatory as it provides additional information to constrain the geometry of the MP model.
TextSentencer_T97 16080-16344 Sentence denotes When the high resolution models are not available, ab initio low resolution bead modeling is performed by MONSA (27), allowing for three phases with distinct contrasts corresponding to the protein (phase 1), detergent tails (phase 2) and detergent heads (phase 3).
TextSentencer_T97 16080-16344 Sentence denotes When the high resolution models are not available, ab initio low resolution bead modeling is performed by MONSA (27), allowing for three phases with distinct contrasts corresponding to the protein (phase 1), detergent tails (phase 2) and detergent heads (phase 3).
TextSentencer_T98 16345-16568 Sentence denotes For each phase the contrast is calculated and the search space confined to a cylinder and two coaxial spherical hemi-tori ( Figure 5A ), thus avoiding contacts between the hydrophobic regions and solvent in the final model.
TextSentencer_T98 16345-16568 Sentence denotes For each phase the contrast is calculated and the search space confined to a cylinder and two coaxial spherical hemi-tori ( Figure 5A ), thus avoiding contacts between the hydrophobic regions and solvent in the final model.
TextSentencer_T99 16569-16750 Sentence denotes A spherical region is fixed for the protein phase in the vicinity of the origin of coordinates, while the rest of the cylindrical region is free to become either protein or solvent.
TextSentencer_T99 16569-16750 Sentence denotes A spherical region is fixed for the protein phase in the vicinity of the origin of coordinates, while the rest of the cylindrical region is free to become either protein or solvent.
TextSentencer_T100 16751-16897 Sentence denotes Penalties for the model discontinuity and looseness are applied during the simulated annealing procedure as described in the original paper (27) .
TextSentencer_T100 16751-16897 Sentence denotes Penalties for the model discontinuity and looseness are applied during the simulated annealing procedure as described in the original paper (27) .
TextSentencer_T101 16898-17073 Sentence denotes Three additional boundary regions between the phases ( Figure 5A ) have a thickness of a few Angstrom allowing MONSA to select the optimum phase assignment during the fitting.
TextSentencer_T101 16898-17073 Sentence denotes Three additional boundary regions between the phases ( Figure 5A ) have a thickness of a few Angstrom allowing MONSA to select the optimum phase assignment during the fitting.
TextSentencer_T102 17074-17192 Sentence denotes The boundary beads (eg. between phases 1 and 2) are allowed to be assigned to either phase 1 or phase 2 ( Figure 5A ).
TextSentencer_T102 17074-17192 Sentence denotes The boundary beads (eg. between phases 1 and 2) are allowed to be assigned to either phase 1 or phase 2 ( Figure 5A ).
TextSentencer_T103 17193-17419 Sentence denotes The model is sought within a spherical search volume of diameter d = D max , where the protein can be surrounded by twostacked tori (detergent tails and heads) with the lengths evaluated from the Tanford formula ( Figure 5B ).
TextSentencer_T103 17193-17419 Sentence denotes The model is sought within a spherical search volume of diameter d = D max , where the protein can be surrounded by twostacked tori (detergent tails and heads) with the lengths evaluated from the Tanford formula ( Figure 5B ).
TextSentencer_T104 17420-17464 Sentence denotes The transmembrane diameter is calculated as:
TextSentencer_T104 17420-17464 Sentence denotes The transmembrane diameter is calculated as:
TextSentencer_T105 17465-17642 Sentence denotes where Length (head) is considered to be the same as the Tanford (tail) , given that for the most common detergent molecules it is typically smaller or equal to that of the tail.
TextSentencer_T105 17465-17642 Sentence denotes where Length (head) is considered to be the same as the Tanford (tail) , given that for the most common detergent molecules it is typically smaller or equal to that of the tail.
TextSentencer_T106 17643-17670 Sentence denotes The expected author/funder.
TextSentencer_T106 17643-17670 Sentence denotes The expected author/funder.
TextSentencer_T107 17671-17691 Sentence denotes All rights reserved.
TextSentencer_T107 17671-17691 Sentence denotes All rights reserved.
TextSentencer_T108 17692-17728 Sentence denotes No reuse allowed without permission.
TextSentencer_T108 17692-17728 Sentence denotes No reuse allowed without permission.
TextSentencer_T109 17729-18037 Sentence denotes The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/714303 doi: bioRxiv preprint values for toroidal volumes and R g values of detergent phases are calculated on the fly from geometrical considerations (39) and serve as additional constrains while modelling.
TextSentencer_T109 17729-18037 Sentence denotes The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/714303 doi: bioRxiv preprint values for toroidal volumes and R g values of detergent phases are calculated on the fly from geometrical considerations (39) and serve as additional constrains while modelling.
TextSentencer_T110 18038-18164 Sentence denotes The total computed volume and R g of the particle is then compared to the experimental V Porod and R g , obtained from step 2.
TextSentencer_T110 18038-18164 Sentence denotes The total computed volume and R g of the particle is then compared to the experimental V Porod and R g , obtained from step 2.
TextSentencer_T111 18165-18311 Sentence denotes If available, information from complementary methods (e.g. phase volumes or phase R g ) can be used to improve the reliability of the final model.
TextSentencer_T111 18165-18311 Sentence denotes If available, information from complementary methods (e.g. phase volumes or phase R g ) can be used to improve the reliability of the final model.
TextSentencer_T112 18312-18583 Sentence denotes Using a spherical 40 beads-per-diameter MONSA grid, together with the above mentioned geometrical restrictions, reliable low resolution models were obtained in a reasonable processing time about 10-15 minutes on a desktop PC (Intel Xeon CPU 3.7 GHz 8 Cores, 12.5 GB RAM).
TextSentencer_T112 18312-18583 Sentence denotes Using a spherical 40 beads-per-diameter MONSA grid, together with the above mentioned geometrical restrictions, reliable low resolution models were obtained in a reasonable processing time about 10-15 minutes on a desktop PC (Intel Xeon CPU 3.7 GHz 8 Cores, 12.5 GB RAM).
TextSentencer_T113 18584-18699 Sentence denotes This algorithm is generally applicable to the reconstruction of both transmembrane and membraneassociated proteins.
TextSentencer_T113 18584-18699 Sentence denotes This algorithm is generally applicable to the reconstruction of both transmembrane and membraneassociated proteins.
TextSentencer_T114 18700-18920 Sentence denotes In the case of membrane-associated proteins one can simply shift the fixed "protein" phase to the edge/surface of the detergent disc and extend the protein/solvent phase cylinder outside the entire detergent disc region.
TextSentencer_T114 18700-18920 Sentence denotes In the case of membrane-associated proteins one can simply shift the fixed "protein" phase to the edge/surface of the detergent disc and extend the protein/solvent phase cylinder outside the entire detergent disc region.
TextSentencer_T115 18922-18982 Sentence denotes In this case neither MONSA nor MEMPROT modeling is employed.
TextSentencer_T115 18922-18982 Sentence denotes In this case neither MONSA nor MEMPROT modeling is employed.
TextSentencer_T116 18983-19132 Sentence denotes The pipeline works in the standard SEC-SAXS mode and the low-resolution model is built by DAMMIF (the phase choice only between the PDC and solvent).
TextSentencer_T116 18983-19132 Sentence denotes The pipeline works in the standard SEC-SAXS mode and the low-resolution model is built by DAMMIF (the phase choice only between the PDC and solvent).
TextSentencer_T117 19133-19401 Sentence denotes The pipeline reconstructs low-resolution models from the low-s region (typically s max < 1.0 nm -1 ) of the experimental SAXS data ab initio, minimizing the contribution from the inhomogeneous internal structrure and describing only the overall particle author/funder.
TextSentencer_T117 19133-19401 Sentence denotes The pipeline reconstructs low-resolution models from the low-s region (typically s max < 1.0 nm -1 ) of the experimental SAXS data ab initio, minimizing the contribution from the inhomogeneous internal structrure and describing only the overall particle author/funder.
TextSentencer_T118 19402-19422 Sentence denotes All rights reserved.
TextSentencer_T118 19402-19422 Sentence denotes All rights reserved.
TextSentencer_T119 19423-19459 Sentence denotes No reuse allowed without permission.
TextSentencer_T119 19423-19459 Sentence denotes No reuse allowed without permission.
TextSentencer_T120 19460-19597 Sentence denotes The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/714303 doi: bioRxiv preprint shape.
TextSentencer_T120 19460-19597 Sentence denotes The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/714303 doi: bioRxiv preprint shape.
TextSentencer_T121 19598-19735 Sentence denotes The value of s max for the initial reconstruction is automatically estimated from the first local minimum of the experimental SAXS curve.
TextSentencer_T121 19598-19735 Sentence denotes The value of s max for the initial reconstruction is automatically estimated from the first local minimum of the experimental SAXS curve.
TextSentencer_T122 19736-19933 Sentence denotes MP model have been computed, the pipeline builds a file in the xml format with the final summary table, gathering together all the results in a compact and human/machine-readable form (Figure 3 ).
TextSentencer_T122 19736-19933 Sentence denotes MP model have been computed, the pipeline builds a file in the xml format with the final summary table, gathering together all the results in a compact and human/machine-readable form (Figure 3 ).
TextSentencer_T123 19934-20110 Sentence denotes Upon completion the pipeline compresses the calculated 1D SEC-SAXS profiles into a single HDF5 file and reports them back together with the final model into the ISPyB database.
TextSentencer_T123 19934-20110 Sentence denotes Upon completion the pipeline compresses the calculated 1D SEC-SAXS profiles into a single HDF5 file and reports them back together with the final model into the ISPyB database.
TextSentencer_T124 20111-20303 Sentence denotes The data from the buffer and sample regions, subtracted curves and overall SAXS parameters for each detected peak in the elution profile are displayed in a convenient tabular form (Figure 3 ).
TextSentencer_T124 20111-20303 Sentence denotes The data from the buffer and sample regions, subtracted curves and overall SAXS parameters for each detected peak in the elution profile are displayed in a convenient tabular form (Figure 3 ).
TextSentencer_T125 20304-20482 Sentence denotes It is worth noting that the summary table generated is applicable to all SEC-SAXS runs conducted at the P12 beamline and is not restricted to the measurement and analysis of MPs.
TextSentencer_T125 20304-20482 Sentence denotes It is worth noting that the summary table generated is applicable to all SEC-SAXS runs conducted at the P12 beamline and is not restricted to the measurement and analysis of MPs.
TextSentencer_T126 20483-20683 Sentence denotes For example, it is often the case that the sample exists in solution as a mixture of different states (eg. multiple oligomeric states of a protein or complex), which are separated chromatographically.
TextSentencer_T126 20483-20683 Sentence denotes For example, it is often the case that the sample exists in solution as a mixture of different states (eg. multiple oligomeric states of a protein or complex), which are separated chromatographically.
TextSentencer_T127 20684-20795 Sentence denotes In this case, AMPP will determine the shapes of individual components in the mixture using the modeling path 3.
TextSentencer_T127 20684-20795 Sentence denotes In this case, AMPP will determine the shapes of individual components in the mixture using the modeling path 3.
TextSentencer_T128 20796-20843 Sentence denotes The pipeline is therefore generally applicable.
TextSentencer_T128 20796-20843 Sentence denotes The pipeline is therefore generally applicable.
TextSentencer_T129 20844-20923 Sentence denotes The results generated can be inspected online using the ISPyB web-server (26) .
TextSentencer_T129 20844-20923 Sentence denotes The results generated can be inspected online using the ISPyB web-server (26) .
TextSentencer_T130 20924-21148 Sentence denotes The ISPyB database and web services were extended to accommodate the information on chemical formulae and electron densities of detergents, as well as FASTA amino acid sequences and electron densities of the MPs and buffers.
TextSentencer_T130 20924-21148 Sentence denotes The ISPyB database and web services were extended to accommodate the information on chemical formulae and electron densities of detergents, as well as FASTA amino acid sequences and electron densities of the MPs and buffers.
TextSentencer_T131 21149-21312 Sentence denotes The SEC-SAXS elution profile and the final model can be visualized in the existing ISPyB GUI, as the pipeline output files are compatible with the required format.
TextSentencer_T131 21149-21312 Sentence denotes The SEC-SAXS elution profile and the final model can be visualized in the existing ISPyB GUI, as the pipeline output files are compatible with the required format.
TextSentencer_T132 21313-21483 Sentence denotes To test the modelling components of the AMPP, we performed an automatic structural characterization of a tetrameric α-helical membrane channel Aquaporin0 in DDM solution.
TextSentencer_T132 21313-21483 Sentence denotes To test the modelling components of the AMPP, we performed an automatic structural characterization of a tetrameric α-helical membrane channel Aquaporin0 in DDM solution.
TextSentencer_T133 21484-21726 Sentence denotes The AMPP was utilized in all three pipeline regimes: i) with the high resolution model available ii) with detergent composition and the protein primary structure (FASTA sequence) known iii) plain ab initio modelling (no a priori information).
TextSentencer_T133 21484-21726 Sentence denotes The AMPP was utilized in all three pipeline regimes: i) with the high resolution model available ii) with detergent composition and the protein primary structure (FASTA sequence) known iii) plain ab initio modelling (no a priori information).
TextSentencer_T134 21727-21904 Sentence denotes The models generated from these three modelling trajectories are displayed in Figure 6 (as the protein was known to be tetrameric, P4 symmetry was utilized in MONSA and DAMMIF).
TextSentencer_T134 21727-21904 Sentence denotes The models generated from these three modelling trajectories are displayed in Figure 6 (as the protein was known to be tetrameric, P4 symmetry was utilized in MONSA and DAMMIF).
TextSentencer_T135 21905-21912 Sentence denotes Figure.
TextSentencer_T135 21905-21912 Sentence denotes Figure.
TextSentencer_T136 21913-21915 Sentence denotes 6.
TextSentencer_T136 21913-21915 Sentence denotes 6.
TextSentencer_T137 21916-22307 Sentence denotes Examples of automatically reconstructed Aquaporin0 PDC models by the AMPP pipeline utilizing MEMPROT (hybrid modeling with known protein model (PDB:2B6P) and unknown detergent belt) (A), MONSA (multi-phase ab initio, the model was built from precalculated searching volume; fourfold symmetry around z-axis is imposed) (B) and DAMMIF(C) (single phase ab initio also with P4 symmetry applied).
TextSentencer_T137 21916-22307 Sentence denotes Examples of automatically reconstructed Aquaporin0 PDC models by the AMPP pipeline utilizing MEMPROT (hybrid modeling with known protein model (PDB:2B6P) and unknown detergent belt) (A), MONSA (multi-phase ab initio, the model was built from precalculated searching volume; fourfold symmetry around z-axis is imposed) (B) and DAMMIF(C) (single phase ab initio also with P4 symmetry applied).
TextSentencer_T138 22308-22601 Sentence denotes The first row shows the side view cross-section of the PDC components that is represented with a section inside the detergent corona; protein beads are green for ab initio models and colored according to atom type for the hybrid model, detergent tails and heads are blue and red, respectively.
TextSentencer_T138 22308-22601 Sentence denotes The first row shows the side view cross-section of the PDC components that is represented with a section inside the detergent corona; protein beads are green for ab initio models and colored according to atom type for the hybrid model, detergent tails and heads are blue and red, respectively.
TextSentencer_T139 22602-22678 Sentence denotes The second and third rows represent the top and the side view of the models.
TextSentencer_T139 22602-22678 Sentence denotes The second and third rows represent the top and the side view of the models.
TextSentencer_T140 22679-22825 Sentence denotes Expectedly, the automatically generated Aquaporin0 models display more adequate structural details with increasing amount of a priori information.
TextSentencer_T140 22679-22825 Sentence denotes Expectedly, the automatically generated Aquaporin0 models display more adequate structural details with increasing amount of a priori information.
TextSentencer_T141 22826-22987 Sentence denotes The single phase based model generated ab initio by DAMMIF (Fig. 6C) provides only the overall shape roughly approximating that of the protein-detergent complex.
TextSentencer_T141 22826-22987 Sentence denotes The single phase based model generated ab initio by DAMMIF (Fig. 6C) provides only the overall shape roughly approximating that of the protein-detergent complex.
TextSentencer_T142 22988-23120 Sentence denotes This reflects the limitation of the ab initio shape determination procedure, which must assume constant density inside the particle.
TextSentencer_T142 22988-23120 Sentence denotes This reflects the limitation of the ab initio shape determination procedure, which must assume constant density inside the particle.
TextSentencer_T143 23121-23350 Sentence denotes The more information-rich multi-phase MONSA and MEMPROT models (Fig. 6B, A) display a good level of similarity, with the hybrid model generated using the latter program being more detailed and arguably having a higher resolution.
TextSentencer_T143 23121-23350 Sentence denotes The more information-rich multi-phase MONSA and MEMPROT models (Fig. 6B, A) display a good level of similarity, with the hybrid model generated using the latter program being more detailed and arguably having a higher resolution.
TextSentencer_T144 23351-23599 Sentence denotes For the multi-phase MONSA modeling path the starting cylindrical search volume used for protein-solvent phases was considerably larger than the final model and contains a spherical core with the fixed protein phase (green area shown in Figure 5B ).
TextSentencer_T144 23351-23599 Sentence denotes For the multi-phase MONSA modeling path the starting cylindrical search volume used for protein-solvent phases was considerably larger than the final model and contains a spherical core with the fixed protein phase (green area shown in Figure 5B ).
TextSentencer_T145 23600-23858 Sentence denotes However, after the minimization procedure the volume occupied by the protein phase becomes only slightly larger than the central fixed spherical volume, and the MONSA models do display protrusions resembling the four α-helical "legs" expected for Aquaporin0.
TextSentencer_T145 23600-23858 Sentence denotes However, after the minimization procedure the volume occupied by the protein phase becomes only slightly larger than the central fixed spherical volume, and the MONSA models do display protrusions resembling the four α-helical "legs" expected for Aquaporin0.
TextSentencer_T146 23859-23999 Sentence denotes These models are similar to those generated using the hybrid modeling path with MEMPROT, where the protein structure is assumed to be known.
TextSentencer_T146 23859-23999 Sentence denotes These models are similar to those generated using the hybrid modeling path with MEMPROT, where the protein structure is assumed to be known.
TextSentencer_T147 24000-24217 Sentence denotes The automatically generated models using the three modeling paths of the pipeline provide good fits to the experimental data at low angles, thus the overall particle shapes coincide and are well described by the data.
TextSentencer_T147 24000-24217 Sentence denotes The automatically generated models using the three modeling paths of the pipeline provide good fits to the experimental data at low angles, thus the overall particle shapes coincide and are well described by the data.
TextSentencer_T148 24218-24435 Sentence denotes The deviations observed at higher resolution ( Figure 7) reflect contributions from the detergents including the complex contrast situation, which is not accurately captured by the simplified modeling procedures used.
TextSentencer_T148 24218-24435 Sentence denotes The deviations observed at higher resolution ( Figure 7) reflect contributions from the detergents including the complex contrast situation, which is not accurately captured by the simplified modeling procedures used.
TextSentencer_T149 24436-24645 Sentence denotes This intentional simplification was justified for the sake of speed, such that preliminary models are generated that describe the gross structure of PDCs and do not attempt to describe internal inhomogeneties.
TextSentencer_T149 24436-24645 Sentence denotes This intentional simplification was justified for the sake of speed, such that preliminary models are generated that describe the gross structure of PDCs and do not attempt to describe internal inhomogeneties.
TextSentencer_T150 24646-24812 Sentence denotes One of the simplifications we implemented for the MEMPROT modeling was to assume a horizontal detergent torus with a circular geometry, and a fixed ellipticity e = 1.
TextSentencer_T150 24646-24812 Sentence denotes One of the simplifications we implemented for the MEMPROT modeling was to assume a horizontal detergent torus with a circular geometry, and a fixed ellipticity e = 1.
TextSentencer_T151 24813-25219 Sentence denotes It should be stressed, that further model refinement is recommended in order to obtain more accurate and detailed models, using initial parameters suggested by the pipeline, and as necessary additional penalties as required (such as increased penalty for looseness and/or discontinuity, a higher number of experimental points and dummy beads in the MONSA grid, free ellipticity parameter for MEMPROT, etc).
TextSentencer_T151 24813-25219 Sentence denotes It should be stressed, that further model refinement is recommended in order to obtain more accurate and detailed models, using initial parameters suggested by the pipeline, and as necessary additional penalties as required (such as increased penalty for looseness and/or discontinuity, a higher number of experimental points and dummy beads in the MONSA grid, free ellipticity parameter for MEMPROT, etc).
TextSentencer_T152 25220-25350 Sentence denotes Similar results were obtained from the mechanosensitive channel T2 experimental data obtained at the P12 beamline (Figures 7b-8 ).
TextSentencer_T152 25220-25350 Sentence denotes Similar results were obtained from the mechanosensitive channel T2 experimental data obtained at the P12 beamline (Figures 7b-8 ).
TextSentencer_T153 25351-25542 Sentence denotes There is a high degree of similarity between the three types of models generated, and interestingly, MONSA does reconstruct models with a void in the protein phase (green beads in Figure 8 ).
TextSentencer_T153 25351-25542 Sentence denotes There is a high degree of similarity between the three types of models generated, and interestingly, MONSA does reconstruct models with a void in the protein phase (green beads in Figure 8 ).
TextSentencer_T154 25543-25659 Sentence denotes This void is maintained also when an increased penalty for the bead discontinuity during minimization is introduced.
TextSentencer_T154 25543-25659 Sentence denotes This void is maintained also when an increased penalty for the bead discontinuity during minimization is introduced.
TextSentencer_T155 25660-25776 Sentence denotes Upon inspection, the high resolution model of a homologous structure, the MscS ion channel of T. tengcongensis (PDB:
TextSentencer_T155 25660-25776 Sentence denotes Upon inspection, the high resolution model of a homologous structure, the MscS ion channel of T. tengcongensis (PDB:
TextSentencer_T156 25777-25849 Sentence denotes 3T9N) also displays a void in the extracellular domain of the structure.
TextSentencer_T156 25777-25849 Sentence denotes 3T9N) also displays a void in the extracellular domain of the structure.
TextSentencer_T157 25850-25977 Sentence denotes Thus the multiphase ab initio reconstruction reliably generates features consistent with those expected for the T2 ion channel.
TextSentencer_T157 25850-25977 Sentence denotes Thus the multiphase ab initio reconstruction reliably generates features consistent with those expected for the T2 ion channel.
TextSentencer_T158 25978-25985 Sentence denotes Figure.
TextSentencer_T158 25978-25985 Sentence denotes Figure.
TextSentencer_T159 25986-25988 Sentence denotes 8.
TextSentencer_T159 25986-25988 Sentence denotes 8.
TextSentencer_T160 25989-26083 Sentence denotes Automatically reconstructed T2 models by the AMPP pipeline utilizing MEMPROT (hybrid modeling:
TextSentencer_T160 25989-26083 Sentence denotes Automatically reconstructed T2 models by the AMPP pipeline utilizing MEMPROT (hybrid modeling:
TextSentencer_T161 26084-26246 Sentence denotes 3T9N pdb model with found shape of detergent corona) (A), MONSA (multi-phase ab initio with P7 symmetry) (B) and DAMMIF (single phase ab initio, P7 symmetry) (C).
TextSentencer_T161 26084-26246 Sentence denotes 3T9N pdb model with found shape of detergent corona) (A), MONSA (multi-phase ab initio with P7 symmetry) (B) and DAMMIF (single phase ab initio, P7 symmetry) (C).
TextSentencer_T162 26247-26540 Sentence denotes The first row shows the side view cross-section of the PDC components that is represented with a section inside the detergent corona; protein beads are green for ab initio models and colored according to atom type for the hybrid model, detergent tails and heads are blue and red, respectively.
TextSentencer_T162 26247-26540 Sentence denotes The first row shows the side view cross-section of the PDC components that is represented with a section inside the detergent corona; protein beads are green for ab initio models and colored according to atom type for the hybrid model, detergent tails and heads are blue and red, respectively.
TextSentencer_T163 26541-26617 Sentence denotes The second and third rows represent the top and the side view of the models.
TextSentencer_T163 26541-26617 Sentence denotes The second and third rows represent the top and the side view of the models.
TextSentencer_T164 26618-26724 Sentence denotes The reconstructed MONSA model of the T2 channel protein fit the data reasonably well up to s = 0.25 Å -1 .
TextSentencer_T164 26618-26724 Sentence denotes The reconstructed MONSA model of the T2 channel protein fit the data reasonably well up to s = 0.25 Å -1 .
TextSentencer_T165 26725-26859 Sentence denotes The on-the-fly generated MEMPROT model fits only up to s = 0.09 Å -1 , which corresponds to the real-space resolution D = 2π/s ~ 60 Å.
TextSentencer_T165 26725-26859 Sentence denotes The on-the-fly generated MEMPROT model fits only up to s = 0.09 Å -1 , which corresponds to the real-space resolution D = 2π/s ~ 60 Å.
TextSentencer_T166 26860-27014 Sentence denotes It is also worth noting that atomistic models are often incomplete, missing eg. density for flexible loops which could not be resolved at high resolution.
TextSentencer_T166 26860-27014 Sentence denotes It is also worth noting that atomistic models are often incomplete, missing eg. density for flexible loops which could not be resolved at high resolution.
TextSentencer_T167 27015-27176 Sentence denotes In general, to reliably reconstruct a PDC it is recommended to utilize both methods (full ab initio with MONSA, and hybrid with MEMPROT) and compare the results.
TextSentencer_T167 27015-27176 Sentence denotes In general, to reliably reconstruct a PDC it is recommended to utilize both methods (full ab initio with MONSA, and hybrid with MEMPROT) and compare the results.
TextSentencer_T168 27177-27290 Sentence denotes Thus, the ab initio modelling is an important component of the automated MP modelling procedure implemented here.
TextSentencer_T168 27177-27290 Sentence denotes Thus, the ab initio modelling is an important component of the automated MP modelling procedure implemented here.
TextSentencer_T169 27291-27474 Sentence denotes In summary, an automated SAXS-based data analysis pipeline modified for multi-contrast systems has been developed and implemented at the P12 beamline of the EMBL (Petra-III, Hamburg).
TextSentencer_T169 27291-27474 Sentence denotes In summary, an automated SAXS-based data analysis pipeline modified for multi-contrast systems has been developed and implemented at the P12 beamline of the EMBL (Petra-III, Hamburg).
TextSentencer_T170 27475-27620 Sentence denotes The pipeline facilitates the determination of the overall parameters and automated construction of low-resolution structures of solubilized PDCs.
TextSentencer_T170 27475-27620 Sentence denotes The pipeline facilitates the determination of the overall parameters and automated construction of low-resolution structures of solubilized PDCs.
TextSentencer_T171 27621-27747 Sentence denotes Given that the interpretation of the SAXS data from membrane proteins is by far non-trivial task, these results and models are
TextSentencer_T171 27621-27747 Sentence denotes Given that the interpretation of the SAXS data from membrane proteins is by far non-trivial task, these results and models are