Chemical biology

Lipids on the move

Quantitative target profiling tools & applications (including advantages & limitations)

Flow of lipids

the first series of presentations

Paper discussion 7 and  8 to be discussed in week14:

Group 7: Kacem Youssef, Lang Victoire Jacqueline Françoise, Lopez Mejias Dulce Milagro, Mahfouz Maria

A covalently linked probe to monitor local membrane

properties surrounding plasma membrane proteins

Miwa Umebayashi,, Satoko Takemoto Luc Reymond, Mayya Sundukova, Ruud Hovius, Annalisa Bucci, Paul A. Heppenstall, Hideo Yokota, Kai Johnsson and Howard Riezman

DOI:10.1083/jcb.202206119

Abstract

Functional membrane proteins in the plasma membrane are suggested to have specific membrane environments that play important roles to maintain and regulate their function. However, the local membrane environments of membrane proteins remain largely unexplored due to the lack of available techniques. We have developed a method to probe the local membrane environment surrounding membrane proteins in the plasma membrane by covalently tethering a solvatochromic, environment-sensitive dye, Nile Red, to a GPI-anchored protein and the insulin receptor through a flexible linker. The fluidity of the membrane environment of the GPI-anchored protein depended upon the saturation of the acyl chains of the lipid anchor. The local environment of the insulin receptor was distinct from the average plasma membrane fluidity and was quite dynamic and heterogeneous. Upon addition of insulin, the local membrane environment surrounding the receptor specifically increased in fluidity in an insulin receptor-kinase dependent manner and on the distance between the dye and the receptor.

Group   8: Tambey Diane, Verhoeven Anthony David, , Roudaut Arthur Joël

A fluorogenic probe for SNAP-tagged plasma membrane proteins based on the solvatochromic

molecule Nile Red

Efthymia Prifti  1 , Luc Reymond, Miwa Umebayashi, Ruud Hovius, Howard Riezman, Kai Johnsson

ACS Chemical Biology

Abstract

A fluorogenic probe for plasma membrane proteins based on the dye Nile Red and SNAP-tag is introduced. It takes advantage of Nile Red, a solvatochromic molecule highly fluorescent in an apolar environment, such as cellular membranes, but almost dark in a polar aqueous environment. The probe possesses a tuned affinity for membranes allowing its Nile Red moiety to insert into the lipid bilayer of the plasma membrane, becoming fluorescent, only after its conjugation to a SNAP-tagged plasma membrane protein. The fluorogenic character of the probe was demonstrated for different SNAP-tag fusion proteins, including the human insulin receptor. This work introduces a new approach for generating a powerful turn-on probe for “no-wash” labeling of plasma membrane proteins with numerous applications in bioimaging.

DOI: 10.1021/cb400819c

Recap

Final exam will be a written exam (closed book) and will count 90% of the entire course grade. Questions will be largely targeted at real-world problem solving, just like what the students have seen in their biweekly practice problems. Exam will only test the know-how derived from the materials and concepts discussed during the course, and problem-solving abilities developed through active learning (interactive class discussions + problem sets).

Students are encouraged to reach out to the course instructor professor and PhD-student course teaching assistant, with any questions or concerns.

Location, date, time of final exam as seen in IS-Academia:

Saturday  20.01.2024 from 09h15 to 12h15 (CE1104)