1066 57 15279 2 48975 document 15279 Ab_initio_models.zip application/zip a0d5be4eb82e4530870e79bf4355a13f MD5 236308 2021-08-27 07:57:03 https://researchdata.bath.ac.uk/1066/1/Ab_initio_models.zip 1066 1 1 application/zip other Ab initio .pdb files constructs for polymer nanodisc samples incorporating OmpF or gramicidin. These are the final models. en public cc_by

Ab_initio_models.zip

data 15280 2 48921 document 15280 CD_spectra.zip application/zip e219b35cc0ca60c7ea9ade7c380cd974 MD5 106304 2021-08-25 16:08:13 https://researchdata.bath.ac.uk/1066/2/CD_spectra.zip 1066 2 2 application/zip other CD spectra for polymer nanodiscs incorporating OmpF protein and corresponding CD spectra comparisons from a trimer crystal structure (Protein data bank ID: 2OMF) using STRIDE. en public cc_by

CD_spectra.zip

data 15281 2 48923 document 15281 DLS_spectra.xlsx application/vnd.openxmlformats-officedocument.spreadsheetml.sheet f4b2b44497394186aaa3864bd510bb17 MD5 60910 2021-08-25 16:08:17 https://researchdata.bath.ac.uk/1066/3/DLS_spectra.xlsx 1066 3 3 application/vnd.openxmlformats-officedocument.spreadsheetml.sheet other DLS spectra for lipid-only nanodiscs, gramicidin nanodiscs and OmpF nanodiscs. en public cc_by

DLS_spectra.xlsx

data 15282 3 48976 document 15282 SANS_raw_datasets.zip application/zip 0b792e79e4813d5712d6200981210b5d MD5 9934 2021-08-27 07:57:49 https://researchdata.bath.ac.uk/1066/4/SANS_raw_datasets.zip 1066 4 4 application/zip other Raw datasets for purified OmpF-nanodiscs gramicidin and lipid-only nanodisc samples. Three different contrasts are present. en public cc_by

SANS_raw_datasets.zip

data 15283 3 48927 document 15283 SEC_chromatograms.zip application/zip 0e456a3eb21687fcdb843100c3082e4e MD5 54324 2021-08-25 16:08:23 https://researchdata.bath.ac.uk/1066/5/SEC_chromatograms.zip 1066 5 5 application/zip other Size exclusion chromatography (SEC) chromatograms for OmpF-nanodiscs and lipid-only nanodiscs detected at 254 nm. en public cc_by

SEC_chromatograms.zip

data 15284 4 48980 document 15284 README.txt text/plain 7bb8bbf53c8d91e2401b5d7feda732af MD5 2532 2021-08-27 07:59:39 https://researchdata.bath.ac.uk/1066/6/README.txt 1066 6 6 text/plain other Information on the whole dataset for this data archive request. en public cc_by

README.txt

documentation 15286 1 48941 document 15286 Doctoral_Data_Management_Plan_Kerrie_Morrison_v2.docx application/vnd.openxmlformats-officedocument.wordprocessingml.document 5f6fe0187737cff904b846e290973003 MD5 447131 2021-08-25 17:21:19 https://researchdata.bath.ac.uk/1066/8/Doctoral_Data_Management_Plan_Kerrie_Morrison_v2.docx 1066 8 8 application/vnd.openxmlformats-officedocument.wordprocessingml.document other en staffonly

Doctoral_Data_Management_Plan_Kerrie_Morrison_v2.docx

dmp 15287 1 48946 document 15287 indexcodes.txt text/plain c16b584160a4f7d6240fb9aa7662b1de MD5 641 2021-08-25 17:33:00 https://researchdata.bath.ac.uk/1066/9/indexcodes.txt 1066 9 9 text/plain other Generate index codes conversion from other to indexcodes en public

indexcodes.txt

http://eprints.org/relation/isVersionOf https://researchdata.bath.ac.uk/id/document/15284 http://eprints.org/relation/isVolatileVersionOf https://researchdata.bath.ac.uk/id/document/15284 http://eprints.org/relation/isIndexCodesVersionOf https://researchdata.bath.ac.uk/id/document/15284 15289 1 48948 document 15289 indexcodes.txt text/plain 5aeb5842d55cd306e0d6181e1ac92357 MD5 2371 2021-08-25 17:33:01 https://researchdata.bath.ac.uk/1066/11/indexcodes.txt 1066 11 11 text/plain other Generate index codes conversion from other to indexcodes en staffonly

indexcodes.txt

http://eprints.org/relation/isVersionOf https://researchdata.bath.ac.uk/id/document/15286 http://eprints.org/relation/isVolatileVersionOf https://researchdata.bath.ac.uk/id/document/15286 http://eprints.org/relation/isIndexCodesVersionOf https://researchdata.bath.ac.uk/id/document/15286 15290 2 48977 document 15290 SANS_edits_for_ab_initio_modelling.zip application/zip 0bdbe5662c657f73d90e78ddcc32d649 MD5 4167 2021-08-27 07:58:08 https://researchdata.bath.ac.uk/1066/12/SANS_edits_for_ab_initio_modelling.zip 1066 12 12 application/zip other SANS data files editied for ab initio modelling. en public cc_by

SANS_edits_for_ab_initio_modelling.zip

data archive 9042 disk0/00/00/10/66 2021-12-21 14:37:54 2024-07-22 10:40:50 2021-12-21 14:37:54 data_collection show Morrison Kerrie K.A.Morrison@bath.ac.uk 0000-0001-7130-1183 University of Bath TRUE Whitley Paul P.R.Whitley@bath.ac.uk 0000-0001-9796-8488 University of Bath FALSE Price Gareth G.J.Price@bath.ac.uk 0000-0003-4983-5722 University of Bath FALSE Edler Karen K.Edler@bath.ac.uk 0000-0001-5822-0127 University of Bath FALSE DataCollector Doutch James james.doutch@stfc.ac.uk 0000-0003-0747-8368 ISIS Neutron and Muon Source BY0080 BY0130 dept_chem dept_bio SANS, CD, DLS, SMA, SMALP, Ab initio modelling Details of the data and labelling is available in the README.txt file. The purpose behind this dataset is to investigate the use of form-factor based SANS fitting methods and compare them to dummy-models generated using the ab initio modelling tools. The paper focusses on two different membrane proteins, outer membrane protein F (OmpF) and gramicidin incorporated into polymer nanodiscs with styene maleic acid (SMA). These constructs were compared to other techniques (DLS and CD) to discuss the differences that arise from investigating these complex systems using various methods. These were also compared to known crystal structures. This dataset holds the raw data files for the paper titled: "Ab initio reconstruction of small angle scattering data for membrane proteins in copolymer nanodiscs". Techniques include; size exclusion chromatography (SEC) for purification prior to other techniques; circular dichroism (CD); dynamic light scattering (DLS); small angle neutron scattering (SANS) and ab initio modelling constructs. 2021-12-16 University of Bath public RightsHolder University of Bath Science and Technology Facilities Council https://doi.org/10.13039/501100000271 SA-54 ISIS Studentship Agreement Engineering and Physical Sciences Research Council https://doi.org/10.13039/501100000266 EP/L016354/1 EPSRC Centre for Doctoral Training in Sustainable Chemical Technologies cent_sus_tech Samples were generated as described in "Ab initio reconstruction of small angle scattering data for membrane proteins in copolymer nanodiscs". In summary; Gramicidin sample preparation: A stock of 20 mM DMPC with 320 µM gramicidin liposomes were prepared and solubilised using SMA. Final concentrations were 10 mM DMPC, 160 µM gramicidin and 2.5 % (w/v) SMA. OmpF enrichment: Endogenous OmpF enrichment was adapted from previous literature (Efremov and Sazanov, 2012). E.coli cells are homogenised and broken, and membranes are harvested. Membranes were incubated with 1% (w/v) Triton X-100 for 15 minutes before ultracentrifugation. The resulting pellet was resuspended and incubated with 2% (w/v) Triton X-100 for 10 minutes before ultracentrifugation. The resulting pellet was solubilised with 2.5 % (w/v) SMA for 1 hour prior to ultracentrifugation, and the supernatant containing soluble OmpF-nanodiscs was collected. Excess polymer and aggregates were removed by size exclusion chromatography (SEC). Purified samples underwent lipid-exchange and buffer exchange for SANS and CD experimentation. Lipid exchange: To obtain lipid contrasts for SANS datasets, samples underwent lipid-exchange with deuterated-DMPC (d-DMPC) nanodiscs (10 mM d-DMPC with 1.5 % (w/v) SMA). Samples were then purified using SEC to remove excess polymer, followed by concentration using centrifugal filters. Circular Dichroism: Circular dichroism (CD) spectra were measured between 260 – 185 nm at 20°C using a 1.00 mm quartz cuvette using a Chirascan CD spectrometer (Applied Photophysics, UK) with the protein sample at 0.2 mg/mL for CD analysis. DMPC-only nanodiscs were used as a control. To remove any ‘background’ interference from the CD spectrum, the signal from the DMPC-only nanodisc sample was subtracted from that from the OmpF samples. The data was analysed using Dichroweb to determine the nature of the protein structure within the nanodiscs. SANS: Measurements were made on the SANS2d instrument at ISIS Neutron and Muon source (Harwell, UK) using 1mm thick quartz Hellma cells and placed in a temperature-controlled sample holding rack at 25C. Three contrasts were used for gramicidin; d-DMPC with hydrogenated-PBS (h-PBS), d-DMPC with 32% deuterated-PBS (d-PBS) and hydrogenated-DMPC with d-PBS; OmpF contrasts were partially deuterated bacterial lipids (d-bact) with h-PBS, d-bact with 32% d-PBS and d-bact with d-PBS. Dynamic light scattering: All DLS measurements were performed using a Malvern Panalytical Zetasizer Nano ZS. Size distribution was measured and is shown on a log scale, plotted using Igor Pro 6 (Wavemetrics) software. CD: Background was subtracted from CD data using lipid-only nanodiscs to remove any polymer inference. The data were analysed using Dichroweb and compared using predicted CD spectra for OmpF crystal structure (PDB ID: 2OMF), determined by PDBMD2CD. SANS: Data were corrected, solvent subtracted and reduced to 1-D curves using Mantid software. Gramicidin nanodisc SANS data ab initio modelling: To create an overall shape of the gramicidin nanodisc, DAMMIF was used before further refinement using; DAMSEL, DAMSUP, DAMAVER, DAMFILT, and DAMSTART. Lastly, the models were passed through DAMMIN, to compare against the original data file. OmpF nanodisc SANS data ab initio modelling: A multi-phase construct was generated using MONSA for the OmpF-nanodiscs. Further refinement was conducted for each phase separately using; DAMSEL, DAMSUP, DAMAVER, DAMSTART and DAMFILT. The two refines phases were then superimposed using SUPCOMB to correct their orientation to one another. CD: CD spectra obtained by a Chirascan CD spectrometer (Applied Photophysics, UK). Data was analysed using DICROWEB web interface and compared to predicted CD spectra from crystal structures (PDB ID: 2OMF) using PDBMD2CD web interface. Data was visualised using Igor Pro 6 (Wavemetrics) software. DLS: DLS measurements were performed using a Malvern Panalytical Zetasizer Nano ZS and visualised using Igor Pro 6 (Wavemetrics) software. SANS: SANS data obtained by SANS2d instrument at ISIS Neutron and Muon source (Harwell, UK) and reduced to 1-D curves using Mantid software. Resulting datasets can be visualised using Igor Pro 6 (Wavemetrics) and fitted using cylindrical nanodisc models (part of the SANS analysis software developed at NIST, modified to incorporate the water content in the shell). Ab initio model constructs: Initial models are generated using Data analysis software (ATSAS). For gramicidin nanodiscs, DAMMIF, DAMSEL, DAMSUP, DAMAVER, DAMFILT, DAMSTART and DAMMIN, were used to refine and generate the final model construct against the original data file. These create a .pdb file which can be visualised using Visual Molecular Dynamics (VMD) software. For OmpF nanodiscs, MONSA, DAMSEL, DAMSUP, DAMAVER, DAMSTART, DAMFILT and SUPCOMB were used to refine, generate the final model construct against the original data file and to correct the multiple phase orientations to one another. These create a .pdb file which can be visualised using Visual Molecular Dynamics (VMD) software. en 1 10.15125/BATH-01066 https://doi.org/10.1016/j.bbadva.2021.100033 pub open