Image: Magnus Andersson
Research project supported by the Swedish Research Council.
All life depends upon proteins that transport ions, such as zinc, calcium, and copper, in and out of cells. The transport is balanced by means of sensitive regulatory systems. If something goes wrong with the regulatory system, we can become ill, but it also gives us a tool to fight pathogenic bacteria. Using fast, intense X-ray pulses, combined with advanced computer calculations which harnesses the power of today’s supercomputers, we now want to visualise what these regulatory systems look like and how they behave over time.
The cell’s membrane – its “skin” – contains proteins, which are used to for example to spread nerve impulses and communicate with the environment. The transport of various chemical substances through the membranes of the cell is necessary to maintain basic cellular processes.
The proteins that carry out the membrane transport are extremely difficult to study since they are anchored to the lipids of the membrane. Even though today we know the structures of many membrane proteins, these are often trapped in conditions that do not correspond to their natural states in the cells. In addition, there is a lack of information available concerning how the protein and the surrounding membrane change their structures in order to perform their specific cellular task. The lipids in the membrane control the function of the protein, which further increase the potential benefit of studies close to the natural environment. In addition to the allosteric modulation by the membrane lipids, we will also investigate pH effects as well as regulatory systems built into the protein.
This project combines experimental and theoretical methods to describe the regulation of protein transport in its natural environment – with specfic lipids at room temperature. In particular, we will examine the regulatory systems governing the transport of calcium, zinc and copper.
We will record the membrane proteins under different regulatory conditions with ultra-fast X-ray pulses. The result will be a movie, which shows how these proteins change their structure during the transport process.
As the movie is coarse-grained, we supplement the experimental results with computer calculations to recreate the details. We do this by creating a model that contains the same lipids, pH, and built-in regulatory systems as in the experimental environment, and calculate the structural dynamics using supercomputers in a simulation. In this way, we obtain a detailed picture of the protein in its lipid environment which would be difficult, if not impossible, to achieve with experimental methods.
To make this resource-intensive computer calculations possible, some simplistic assumptions are required. Therefore it is important to anchor the simulation results in the experimental method. We solve this by allowing our experimental data to function as goals or targets, against which we drive the simulated system in so-called data-driven simulations. In this way, we can adjust the sharpness of our coarse-grained film recording and get a high-resolution description of the transport process, which helps us understand how the regulatory systems control the process under different conditions.
The proposed research enables a nuanced mapping of regulation of calcium, zinc and copper-transporting membrane proteins. Our research project is of medical relevance since pH regulation of calcium transport can be a general defence mechanism for bacteria, mutations in the copper transporter results in hereditary disease, and the zinc transporter is a target protein for the development of new antibiotics because the protein is commonly found in pathogenic bacteria, but not in humans.
In conclusion, our research will provide a unique insight into how membrane protein activity is regulated in its natural environment.
