Dr Annie Herbert

Profile

Currently a postdoctoral research associate in the biochemistry and biophysics of chaperone function, I work in the research groups Antonio Calebrese and Sheena Radford at the University of Leeds. In this role I am using biochemical and biophysical techniques alongside computational work to elucidate mechanistic details of the key bacterial chaperone SurA. This work is centred around understanding the complex rules of client binding to SurA, and how SurA binds to, chaperones and delivers unfolded outer membrane proteins to the BAM complex to enable folding and thus correct formation of the Gram-negative outer membrane.

In 2024, I completed my PhD; a my 3 year project developing novel therapeutics and diagnostic systems against Pseudomonas aeruginosa using Affimer technology. This is an important Gram-negative bacteria which causes 10% of deaths by hospital acquired infections. Here I identified attractive bacterial drug and diagnostic targets, used phage display to isolate high-affinity Affimer reagents, and developed diagnostic tools, as well as characterising the inhibition of my chosen drug targets; LptA and TolB. Prior to my PhD I completed an MRes MSc, also using Affimer technology to inhibit beta lactamase enzymes in bacteria.

Responsibilities

• Postdoctoral Research Associate in the Biochemistry and Biophysics of Chaperone Function

Research interests

Deciphering the Molecular Mechanism of Bacterial Chaperone SurA

The periplasmic chaperone SurA is the primary facilitator of outer membrane protein (OMP) biogenesis in E. coli, yet the molecular rules governing its client recognition remain unclear. One of the aims of this project is to understand the complex rules which govern OMP binding to SurA.

This work builds on previous work using small-scale in vitro studies of model OMPs, by extending our analysis across the entire E. coli OMPome (60 known/predicted OMPs) to identify sequence motifs that mediate SurA binding. Using high-throughput peptide arrays, we systematically map SurA binding sites in OMPs, revealing consensus motifs, with the utilisation of machine learning to refine these binding rules, enabling predictive models of SurA:OMP interactions.

Binding peptides identified in this first screen were used in high-throughput in silico docking methods using AlphaFold3, to refine the SurA binding site to residue-level detail, and to reveal site-specific preferences of the core and P1 domains. Critical residues in the SurA binding sites have been validated with in vitro and in vivo studies, concluding how SurA recognises clients and illuminating how SurA chaperones OMPs through the periplasm for delivery to BAM.

As well as defining the OMP motifs which contribute to binding, and mapping the SurA binding site, I have also been working on elucidating details of the SurA mechanism, specifically the role of the P1 domain in SurA OMP binding, chaperoning and delivery to BAM.

This study provides the first comprehensive organism-wide understanding of SurA client specificity, offering insights into OMP biogenesis and informing future strategies to target SurA:OMP binding as a novel antibacterial approach.

Qualifications

• PhD in Molecular and Cellular Biology
• MRes MSc in Molecular and Cellular Biology
• BSc (Hons) Biochemistry

Professional memberships

• The Biophysical Society