Novel targets in antibiotic development: Understanding the mechanisms of E. coli outer membrane protein folding and small-molecule transport
This project will involve folding and conductance studies on the E. coli β-barrel outer membrane protein, OmpX, in vivo, in vitro, in collaboration with partners in the U.S.A, in silico. Very importantly, the folding of outer membrane proteins is a high-interest target for novel antibiotics. This is well-funded project involving multiple collaboration partners, and it is expected that the MSc student will learn a large number of skills of high interest in both academic and pharmaceutical/industrial labs.
The prospective MSc student will study, at the single-molecule level using electrophysiology, the transport properties of OmpX and variants, and also perform in vivo and in vitro folding studies to better understand how it interacts with the so-called BAM Machinery (β-barrel assembly machinery). BAM is a highly conserved outer membrane protein complex that mediates the folding of nearly all OMPs in the outer membrane of Gram-negative bacteria, and its deletion is lethal. As such, it is a highly interesting target for antibiotics. While high resolution structures are now available, it is not yet understood mechanistically how BAM folds proteins into the membrane. We have methods by which to study this, both in vivo and in vitro. Importantly, we also have a close-collaboration with U.S. partners, who can perform in silico measurements.
Membrane insertion by BAM: Undetstanding how BAM folds and delivers membrane proteins into the outer membrane of Gram-negative bacteria will provide insight into how one can disrupt this process, potentially leading to the development of novel antibiotics.
This is a highly interdisciplinary and collaborative project. Methods and skills a student will learn include:
- Membrane protein expression and purification techniques (typically the most challenging and highly-sought after skills in structural and molecular biology labs)
- Single molecule conductance measurements using electrophysiology (a technique used often in the pharmaceutical industry to study receptors in drug screening studies)
- In vivo and in vitro functional assays
- Electron microscopy and 2D crystallization to study the structure of OmpX variants and also possibly their interactions with the BAM complex.
The student will be closely supervised by PhDs and Postdocs in the Linke lab, and will be trained in all methods necessary to complete the work. It is not expected that a student is familiar with all methods listed – simply that they have an eagerness to learn, and find the project interesting.