Biologist @Octantbio, coffee snob, injured runner-turned-cyclist
Bay Area
Joined July 2015
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Very cool, especially re: structure based drug design! Congrats Keedy lab, again proving RT is best 🔥🔥
TLDR: Many small-molecule fragments bind differently to proteins at room temperature (red) instead of the usual cryogenic temperature (blue): new binding poses, binding sites, solvation patterns, and even allosteric protein responses. (2/)
ALT Ligand with different pose at room temperature vs. cryogenic temperature
ALT Allosteric response from a fragment binding to the protein PTP1B only at room temperature
Have you ever wanted to make a library that includes indels? Well now you can! Super excited this is finally out, congrats @willowcoyote
Our 1st manuscript on DIMPLE from @ucsf @QBI_UCSF and my 1st senior author!
If interested in DMS, indels, high throughput assays, membrane proteins, and how we can combine these to explore protein evolution, disease, and structure function check it out!
biorxiv.org/content/10.1101/…
Erin Thompson retweeted
Happy to share the @biorxivpreprint for my first bit of work w/ @aliceyting. Together with @heegwangroh, we built a simple and versatile single-component luminescent biosensor for detecting the SARS-CoV-2 spike protein.
biorxiv.org/content/10.1101/…
Have to give a special shout out to my old labmate @willowcoyote, presenting on a library generation method, DIMPLE, to address the difficulty in making systematic indel libraries. He recently started as a Hannah Gray Fellow, go check out his work! #VariantEffect22
.@LindorffLarsen on disentangling stability-activity-folding contributions of variants that are important for fxn and using this data to predict effect mechanism for disease variants #VariantEffect22
Kresten Lindorf-Larsen on combining evolutionary sequence conservation and protein stability assay data to inform our understanding of protein function #VariantEffect22
On our way to to explore Toronto with our Canadian guide @fraser_lab #VariantEffect22
Ok fellow MAVE/DMS enthusiasts, I think the time has come that we standardize heat map coloring. Personally like blue for gain of function, red for loss of function (reasoning red = bad in my mind) but could be persuaded otherwise @varianteffects #VariantEffect22
Erin Thompson retweeted
🚨PREPRINT ALERT!!!🚨
I’m beyond excited to finally share this work, where we demonstrated the use of temperature-jump as a perturbation for time-resolved crystallography, specifically to study protein dynamics! 🔥💎
biorxiv.org/content/10.1101/…
🧵 1/32
.@Bennibolo using MAVEs to find Aß muts that accelerate amyloid formation & to show more comprehensive mutagenesis useful: many indels/truncations of Aß increase aggregation. Core muts strongly impact amyloid nucleation #VariantEffect22
Benedetta Bolognesi on deep indel mutagenesis reveals novel Amyloid beta mutations that acceleration amyloid formation and are likely pathogenic #varianteffect22
Latest from our amyloid factory with @mseumaar and @BenLehner : Deep Indel Mutagenesis reveals an Atlas of Amyloid Aggregation. Most frequent comment mumbled while writing this paper: "Oh my - It’s such a stunning dataset!".
biorxiv.org/cgi/content/shor…
.@JuliaDiumenge presents how to disentangle folding vs. binding contributions to variant effects. 2+ muts help, but libraries complex. Can constrain additional measured trait & do multidimensional mutagenesis. Fit thermodynamic models & mapped allostery,
nature.com/articles/s41586-0…
Talk by @JuliaDiumenge on global mapping of the energetic and allosteric landscapes of protein binding domains - searching for allosteric sites #varianteffect22
Excited to be here at #VariantEffect22 with my other @OctantBio colleagues. A great kickoff to the conference hearing about how clinical data + functional data can be used to improve variant interpretation @conor_j_howard @diane_dickel @srikosuri @n_s_abell
Conundrums and challenges of clinical variant interpretation @clare__turnbull gives opening keynote at #varianteffect22
Erin Thompson retweeted
Where are allosteric hotspots located in a protein? What properties differentiate such hotspots from other residues? We combine deep mutational scanning of four homologs with machine learning to reveal molecular rules governing allosteric hotspots.
biorxiv.org/content/10.1101/…
Erin Thompson retweeted
Very happy to announce the close of @OctantBio’s $80M Series B, led by Catalio, along with @a16z, @8vc, @bmsnews. Looking forward to working with @srikosuri, @rhomsany & their team to further develop Octant's innovative synthetic biology platform fiercebiotech.com/biotech/wi…
Erin Thompson retweeted
Lots of @OctantBio news to share today, including our Series B led by @CatalioCapital @georgecpetro. Immensely thankful for the support, including @a16z @bmsnews @fiftyyears @GaingelsVC @8vc Allen & Company LLC and many more amazing investors and angels, too long a list for here
Exciting news today on many fronts! Pumped to be going back to my DMS roots in collaboration with @bmsnews
Thrilled to finally share some significant Octant milestones today, including our $80 million Series B funding led by @CatalioCapital
bit.ly/37zxHFt
Having an in-house full plasmid sequencing service (aka Octopus) has been key to running our MPRAs, optimizing synbio designs, and more. Bryan Jiang & @willovvens have taken it to the next level, and we have made it open source! 🐙🧬🧑🔬
We open-sourced OCTOPUS, our scalable NGS-based method to verify plasmids, two years ago. Today,@willovvens and Bryan are sharing powerful new features and updates on how OCTOPUS has evolved since then. bit.ly/3wclXme