Andy DeLaitsch

Thanks to all the Klein lab in Cologne and the many other collaborators who contributed to this work!

We then probed the mechanism(s): modeling intra-spike crosslinking on open Env conformations, and observing 007 IgG-crosslinked "trimer dimers" in solution, structures that could drive viral aggregation.

Ultimately, however, we could only speculate what was happening in neutralization assays. (4/5)

This led us to revisit neutralization assays.

Comparing bivalent 007 (IgG1, IgG3) with monovalent forms revealed a key insight:

bivalency plays a central role in 007's neutralization mechanism - surprising, given the HIV bNAbs by and large do not rely on avidity. (3/5)

Cryo-EM gave us the first clue that this bNAb Fab exhibited weak affinity for the BG505 Env trimer, despite being remarkably potent against BG505

SPR confirmed this: ~5uM affinity for the Fab

Confusing... given how potent 007 is 🤔 (2/5)

Identification of a potent V3 glycan site broadly neutralizing antibody targeting an N332gp120 glycan-independent epitope - Nature Immunology An anti-HIV-1 antibody that targets an N332gp120 glycan-independent V3 epitope, a site of Env vulnerability, can decline viremia in HIV-1-infected humanized mice while overcoming classical V3 escape m...

bNAb #007.

#HIV #antibody #V3 #avidity #cryo-EM

www.nature.com/articles/s41...

Cryo-EM revealed trimers with 0, 1, 2, or 3 Fabs bound -leading to some surprising insights into avidity and neutralization that make 007 stand out for more than just its name. (1/5)

Was such a great class last year! I’d highly recommend to ppl getting into tomography

Workflow Using a Cryogenic Coincident Fluorescence, Electron, and Ion Beam Microscope for Targeted Milling of Cells pubmed.ncbi.nlm.nih.gov/41182991/ #cryoEM

Thank you!

Huge thanks to Florian Klein's lab for this excellent collaboration and to the various lab members who provided so much help seeing this through!

Profiling of HIV-1 elite neutralizer cohort reveals a CD4bs bnAb for HIV-1 prevention and therapy - Nature Immunology Klein and colleagues characterize 04_A06, a new VH1-2-encoded broadly neutralizing antibody that has marked breadth and potency against extended multiclade HIV-1 pseudovirus panels and can maintain full viral suppression in HIV-1-infected humanized mice.

All these antibodies exhibit canonical gp120 interactions made by CD4 and CD4bs bNAbs. Interestingly, the VH1-2-encoded N58 is mutated to K58 in the best of these bNAbs, which mimics interactions made between K35 of CD4 and gp120. www.nature.com/articles/s41...

The third bNAb, 05_B08, does not have any insertions and does not contact the adjacent gp120. This antibody, exhibited just over 50% breadth, which is much lower than the others.

Another of the bNAbs, 01_D03, has two separate insertions and a 20-residue long CDRH3, which together allow it to contact conserved residues on the adjacent gp120. This antibody has a 4-residue long FWRH3 insertion in the same location as a 4-residue insertion in 3BNC60/3BNC117.

Interestingly, a crystal structure of this antibody alone revealed this protruding loop was pre-organized for binding, which is expected to lower the entropic cost for binding.

These bNAbs differ in the length and position of insertions. The best-in-class bNAb, 04_A06, has an 11-residue long FWRH1 insertion which manifests in a long CDRH1 that reaches over to contact highly conserved residues on the adjacent gp120.

a, Schematics illustrating the position and length of FWRH1 and/or FWRH3 insertions of 04_A06 (left), 01_D03 (middle) and 05_B08 (right; top), EM maps showing side views of 04_A06, 01_D03 and 05_B08 bnAb Fabs in complex with BG505SOSIP.664 Env trimers (middle) and insets illustrating a close-up of bnAb interactions with the adjacent gp120 protomer (gp1202; bottom); HC, heavy chain; LC, light chain. b, Canonical interactions of CD4 and bnAbs to the CD4bs (04_A06, IOMA and VRC01) with Env gp120 D368, the F43 pocket and gp120 N280/R456. c, Interactions between the CDRH1s of 04_A06 (blue cartoon representation) and 1-18 (red cartoon representation) with the secondary (gp1202) Env protomer, shown as a surface colored by percent conservation. The inset (top right) shows the Env trimer–04_A06 complex as a surface representation for orientation. d, Crystal structure of unbound 04_A06 Fab (bottom) and inset highlighting the 04_A06 CDRH1, with electron density contoured at 1.5σ (top). e, Molecular surface representation showing the surface area buried by VRC01-class bnAbs (04_A06, 01_D03, 05_08, 3BNC117 and VRC01) on primary (gp1201) or secondary (gp1202) Env protomers (top). Listing of Protein Data Bank (PDB) accession codes, breadth (%), heavy chain insertion length and position, buried surface area (BSA) on gp1201 and gp1202 as well as total BSA for VRC01-class bnAbs (bottom).

There's a new best-in-class HIV-1 antibody out today! Happy to have contributed to the structural characterization of this, and two other distinct VRC01-class bNAbs isolated from a single individual. www.nature.com/articles/s41...

I second this bet.

And then Shankar Balasubramanian for chemistry.

From what I gather, CXCR4 (previously called fusin) was identified as a co-receptor for HIV nearly 30 years ago (pubmed.ncbi.nlm.nih.gov/8629022/). Nice to see a structure, and interesting to see it was done with HIV-2 gp120.

I am excited to share our new preprint on the CAGE complex, a mysterious hollow protein complex that I first saw years ago while surveying Tetrahymena ciliary lysate www.biorxiv.org/content/10.1... #cilia #protistsonsky 🧬🧪

Super cool!

📣 New paper alert! Just out in Cell Reports! pubmed.ncbi.nlm.nih.gov/40644298/
Thrilled to share that we have discovered a brand-new anti-phage defense system! Bacteria have evolved various defense strategies (CRISPR etc) to counter phage attacks. We found a new one - fascinating and dramatic
⚔️🦠❄️🔬

“On Being The Right Size” is a true classic, highly recommend! www.phys.ufl.edu/courses/phy3...

If Management is the Only Way Up, We're All F'd - Rand Fishkin
sparktoro.com/blog/if-mana...

In-situ structures of the Legionella Dot/Icm T4SS identify the DotA-IcmX complex as the gatekeeper for effector translocation The Dot/Icm machine in Legionella pneumophila is one of the most versatile type IV secretion systems (T4SSs), with a remarkable capacity to translocate over 330 different effector proteins across the ...

In-situ SPA 🧨

www.biorxiv.org/content/10.1...

Latest preprint from the lab, many years in the making!

By combining #cryoEM with #AlphaFold3 modelling, we propose that norovirus NS3 forms a transmembrane RNA translocase.

This could have big implications for our understanding of viral replication & assembly (🧵)

www.biorxiv.org/content/10.1...

Cool structure!

Cool demo! Also, it’s nice to see your IgG binds bivalently!

Instant classic 🤯

My first project in the @elowitzlab.bsky.social is finally out in @cellpress.bsky.social! We explore how competitive, "many-to-many" dimerization allows complex, multi-input, and cell-type-specific biochemical computations🧵↓

doi.org/10.1016/j.ce...

MISO: Microfluidic protein isolation enables single particle cryo-EM structure determination from a single cell colony https://www.biorxiv.org/content/10.1101/2025.01.10.632437v1

Infant RSV Vaccination Trouble

RSV vaccination attempts in young children have a troubled history. Which seems to be continuing: