http://www.sarajweaver.com/platformpaper daily 0.75 2019-04-12 https://images.squarespace-cdn.com/content/v1/567a0c9bd8af105908588eb8/1554950920186-HDYNO79Q19UQX6PIYAW5/FoilHole_4903258_Data_4904250_4904251_20180905_1034-4971_lpf5+copy.png Visualizing small proteins by single particle cryoEM https://images.squarespace-cdn.com/content/v1/567a0c9bd8af105908588eb8/1554920810802-IS7D63BNM40MZ3HB1XW1/Screen+Shot+2019-04-10+at+11.26.36+AM.png Visualizing small proteins by single particle cryoEM - bioRxiv preprint https://static1.squarespace.com/static/567a0c9bd8af105908588eb8/5cae29190d92977242834fe1/5cae29aaee6eb079bcf5d914/1554917802085/ Visualizing small proteins by single particle cryoEM https://images.squarespace-cdn.com/content/v1/567a0c9bd8af105908588eb8/1554920663579-1LLARI1A48ROE66ATEDJ/image-asset.jpeg Visualizing small proteins by single particle cryoEM - Video S1: movie of GFP:DARPin-aldolase model Available space to bind a target is indicated in the second half of the video using spheres of 60 Å radius. https://images.squarespace-cdn.com/content/v1/567a0c9bd8af105908588eb8/1554920650268-C6D38OU09M6GS5X7NGGJ/image-asset.jpeg Visualizing small proteins by single particle cryoEM - Video S2: model fit into cryoEM density and local resolution https://images.squarespace-cdn.com/content/v1/567a0c9bd8af105908588eb8/1554920630668-32YF4X3E7RWMJ34OM3BC/image-asset.jpeg Visualizing small proteins by single particle cryoEM - cryoEM Density of sharpened GFP:DARPin-aldolase complex Sharpened cryoEM density (right, clipped, blue mesh, PyMOL level 5, carved to 50 Å of atoms) of the best GFP:DARPin-aldolase subunit in the C1 reconstruction. https://images.squarespace-cdn.com/content/v1/567a0c9bd8af105908588eb8/1554950831387-9D58SCRYXPW5GVCLJBP2/FoilHole_4903258_Data_4904250_4904251_20180905_1034-4971_lpf5+copy.png Visualizing small proteins by single particle cryoEM - 5 Å low pass filtered cryoEM micrograph of the GFP:DARPin-aldolase complex https://images.squarespace-cdn.com/content/v1/567a0c9bd8af105908588eb8/1555005383103-S1JB0LAAL5O9BTI5ESXS/image-asset.jpeg Visualizing small proteins by single particle cryoEM - cryoEM density of DARPin-aldolase linker helix Sharpened cryoEM density of the DARPin-aldolase platform in complex with GFP. The linker helix region is visualized in PyMOL and carved to within 10 Å of the selected atoms. DARPin residues are orange while aldolase residues are yellow. https://images.squarespace-cdn.com/content/v1/567a0c9bd8af105908588eb8/1555005695078-4OE51AKSRWID172V4K8I/image-asset.jpeg Visualizing small proteins by single particle cryoEM - Video S3: 3D focused classification of GFP:DARPin-aldolase monomer https://images.squarespace-cdn.com/content/v1/567a0c9bd8af105908588eb8/1555005742381-E3T5Q0XT86HVVMH2IH42/image-asset.jpeg Visualizing small proteins by single particle cryoEM - DARPin-aldolase monomer simulation 50 ns simulation of a DARPin-aldolase monomer. All atom molecular dynamics simulations All software was run through using SBGrid unless otherwise stated(Morin et al., 2013). The PDB model 6MWQ was used for molecular dynamics (MD) simulations with the AMBER99SB force field and the TIP3P water model in GROMACS(Briones et al., 2018; Hornak et al., 2006). Atoms were centered in a dodecahedral water box with a buffer distance between the protein and the box edge of 3 nm. The protein was solvated to a neutral charge with water and 150 mM NaCl. A steepest descent minimization with a Verlet cutoff scheme was used to bring the protein to equilibrium. The solvent was equilibrated while restraining the protein atoms by NVT and NPT equilibration. For both NVT and NPT, the md integrator was selected and temperature coupling was performed with a modified Berendsen thermostat. For NPT equilibration Parrinello-Rahman pressure coupling was enforced. Production MD used the md integrator with a timestep of 2 fs and a total time of 1 ns or 50 ns. https://images.squarespace-cdn.com/content/v1/567a0c9bd8af105908588eb8/1555005817786-02YYC6PC1QYI0UZH2KIB/image-asset.jpeg Visualizing small proteins by single particle cryoEM - GFP:DARPin-aldolase monomer simulation 50 ns simulation of a GFP:DARPin-aldolase monomer. All atom molecular dynamics simulations All software was run through using SBGrid unless otherwise stated(Morin et al., 2013). The PDB model 6MWQ was used for molecular dynamics (MD) simulations with the AMBER99SB force field and the TIP3P water model in GROMACS(Briones et al., 2018; Hornak et al., 2006). Atoms were centered in a dodecahedral water box with a buffer distance between the protein and the box edge of 3 nm. The protein was solvated to a neutral charge with water and 150 mM NaCl. A steepest descent minimization with a Verlet cutoff scheme was used to bring the protein to equilibrium. The solvent was equilibrated while restraining the protein atoms by NVT and NPT equilibration. For both NVT and NPT, the md integrator was selected and temperature coupling was performed with a modified Berendsen thermostat. For NPT equilibration Parrinello-Rahman pressure coupling was enforced. Production MD used the md integrator with a timestep of 2 fs and a total time of 1 ns or 50 ns. https://images.squarespace-cdn.com/content/v1/567a0c9bd8af105908588eb8/1555038972567-ENEIA8QXJGQUP0LU39CT/image-asset.jpeg Visualizing small proteins by single particle cryoEM - Single Particle Tomography of GFP:DARPin-aldolase complex 25 nm scale bar http://www.sarajweaver.com/curriculumvitae daily 0.75 2022-09-09 http://www.sarajweaver.com/contact daily 0.75 2018-01-23 http://www.sarajweaver.com/about daily 1.0 2022-09-09 https://images.squarespace-cdn.com/content/v1/567a0c9bd8af105908588eb8/1516685737937-R6TMURP1BTFCL7KDE9P0/sjweaver.jpeg About http://www.sarajweaver.com/teaching daily 0.75 2019-05-11 https://images.squarespace-cdn.com/content/v1/567a0c9bd8af105908588eb8/1516689608121-A2YWKGAYVTE8WNAABT7O/poster.jpeg Teaching http://www.sarajweaver.com/research daily 0.75 2022-09-09 https://images.squarespace-cdn.com/content/v1/567a0c9bd8af105908588eb8/1557533932661-Y9W7TQC8JVXE4NNNARKC/structurepaper.png Research https://images.squarespace-cdn.com/content/v1/567a0c9bd8af105908588eb8/1603671860097-UPCN3EP3N6FESW9GY7FG/natcomm.jpg Research https://images.squarespace-cdn.com/content/v1/567a0c9bd8af105908588eb8/1583365753595-8ZFL5P36P4I1N74E3UKE/PilQ_bioRxiv Research https://images.squarespace-cdn.com/content/v1/567a0c9bd8af105908588eb8/1583306448247-MEPW1XR1ITGE0VNM4RC8/PilQ Research https://images.squarespace-cdn.com/content/v1/567a0c9bd8af105908588eb8/1555040679710-XJRP4CVS01TXJ5SDMY34/biorxivpaper.png Research https://images.squarespace-cdn.com/content/v1/567a0c9bd8af105908588eb8/1555040194329-HMI9KERLTMYK0BCX5DMO/sw2018-07-17-1_slicer19777.jpg Research This slice from a tomogram of a Vibrio cholerae cell demonstrates the presence of a chemoreceptor array (green) and a flagella motor (pink). The scale bar is 25 nm https://images.squarespace-cdn.com/content/v1/567a0c9bd8af105908588eb8/1516689477379-3JIWEUCM9HH2IK6HD26O/research.png Research http://www.sarajweaver.com/experience daily 0.75 2020-03-04 https://images.squarespace-cdn.com/content/v1/567a0c9bd8af105908588eb8/1523142503906-L6KZE1FLLAIMS2652BUF/ribosomeneg1.png Experience http://www.sarajweaver.com/em-tips daily 0.75 2022-04-21 http://www.sarajweaver.com/methods-development-for-cryoem daily 0.75 2018-04-07 https://images.squarespace-cdn.com/content/v1/567a0c9bd8af105908588eb8/1523142661132-RJGWCZR28FGKKOGAP9LQ/betagal1.png Methods development for cryoEM http://www.sarajweaver.com/single-particle-cryoem daily 0.75 2018-07-28 http://www.sarajweaver.com/interesting-images daily 0.75 2018-07-28 https://images.squarespace-cdn.com/content/v1/567a0c9bd8af105908588eb8/1532804377439-51YGSIFHGBLTQQSTAPUM/Screen+Shot+2018-06-28+at+10.33.10+AM.png Interesting Images Locket with a borzoi profile, or microbial membrane trash? https://images.squarespace-cdn.com/content/v1/567a0c9bd8af105908588eb8/1532804253929-1AQCFM5DDWUR48R57CYV/Screen+Shot+2018-05-23+at+1.51.24+PM.png Interesting Images Initial model or duck? https://images.squarespace-cdn.com/content/v1/567a0c9bd8af105908588eb8/1532804182102-Y5ZQ5FD7HG68C7DYR8GP/Screen+Shot+2018-07-28+at+11.55.09+AM.png Interesting Images Dog or protein complex? https://images.squarespace-cdn.com/content/v1/567a0c9bd8af105908588eb8/1532804548839-HN14EL2Q21X1BQHKKUUN/image-asset.png Interesting Images This ice is terrible for cryoEM, but looks cool! http://www.sarajweaver.com/aidslifecycle daily 0.75 2022-09-09 https://images.squarespace-cdn.com/content/v1/567a0c9bd8af105908588eb8/3dd0e6d4-c19b-4920-a824-42e6f09923af/ALC7.jpg AIDS/LifeCycle https://images.squarespace-cdn.com/content/v1/567a0c9bd8af105908588eb8/4890c45e-bdd2-44c9-a50b-facdfdeef431/ALC6.jpg AIDS/LifeCycle https://images.squarespace-cdn.com/content/v1/567a0c9bd8af105908588eb8/f4833463-4801-492a-8016-a127135f2985/2022-Route-Map-No-BG.png AIDS/LifeCycle - Make it stand out The 2022 AIDS/LifeCycle biking route from San Francisco to Los Angeles. Image credit to https://www.aidslifecycle.org https://images.squarespace-cdn.com/content/v1/567a0c9bd8af105908588eb8/2c8d9bdf-9e89-44cb-9f96-5634736ca565/ALC2.jpeg AIDS/LifeCycle - Make it stand out Whatever it is, the way you tell your story online can make all the difference.